Signatures of Domestication and Adaptation
Lead Research Organisation:
Earlham Institute
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
Uncovering genetic variation of natural and domesticated populations, quantifying gene flow between them and understanding diversification mechanisms operating in both environments is vital for sustainability of agriculture and aquaculture in the face of climate change, as well as increased vulnerability to diseases. We will apply our expertise in animal and plant genomics to identify domestication and adaptation diversification hotspots and bottlenecks in key systems: crops and wild relatives in Poaceae and Brassicaceae and aquaculture fish species (both farmed and wild Tilapia populations).
For each of these systems, we will scan genomes of domesticated and cultivated species, and those of their wild relatives, to assess genetic diversity in these populations and identify patterns of selection that are linked to environmental adaptation, speciation, and evolution under domestication. Using improved genome annotations, we will identify and characterise variants segregating at high frequency within protein coding sequences, their regulatory regions, and conserved noncoding elements in domesticated species in comparison to their wild relatives. We will compare the pattern of intraspecies diversity between wild and cultivated lines to assess the impact of artificial selection on the loss of heterozygosity and the fixation of weakly deleterious variants. We will assess the selective constraints acting on regulatory elements and gene regulation through evolutionary analyses to provide demographic and genetic data necessary to model interactions between farmed and wild species, and predict population character and abundance. This information will ultimately contribute to the improvement and expansion of breeding programs.
We will also utilise natural and synthetic hybrids to investigate the immediate and long-term effects of hybridisation and polyploidy on genome architecture and evolution. We will focus our investigations on Triticeae species (tetraploid: Triticum turgidum, T. dicoccum; diploid: T. urartu, T. monococcum) and their hybrids. We will apply sequence-based approaches to assay transcriptional activity (RNA-seq, smRNA-seq), and interrogate existing public data and data available through the Designing Future Wheat ISP WP4 (ATAC-Seq, ChIP-Seq, DNA methylation), to define the epigenome of natural and synthetic hybrids and the wild progenitors.
The widespread use and misuse of antimicrobials in our general environment has allowed bacteria to be frequently exposed to sub-inhibitory concentrations, favouring the evolution and spread of resistance to the most commonly used antimicrobial molecules. The effects of these low antibacterial concentrations on pathogenic bacteria leading to the selection of variants associated with resistance are currently not fully understood despite their implications for the effectiveness of antimicrobial drugs in the future. Using machine learning approaches to mine currently available data, we will investigate the genetic changes responsible for adaptation of Salmonella to certain hosts and environments as well as changes in virulence or drug resistance. We aim to characterise the fitness effects of resistance mutations and how they can be maintained in a population with and without antimicrobial selection. Using experimental selection (performed by QI collaborators) and genome sequencing (performed by EI), we will assess whether the trajectory of mutations and allele frequency changes at different antimicrobial concentrations can be predicted and modelled.
For each of these systems, we will scan genomes of domesticated and cultivated species, and those of their wild relatives, to assess genetic diversity in these populations and identify patterns of selection that are linked to environmental adaptation, speciation, and evolution under domestication. Using improved genome annotations, we will identify and characterise variants segregating at high frequency within protein coding sequences, their regulatory regions, and conserved noncoding elements in domesticated species in comparison to their wild relatives. We will compare the pattern of intraspecies diversity between wild and cultivated lines to assess the impact of artificial selection on the loss of heterozygosity and the fixation of weakly deleterious variants. We will assess the selective constraints acting on regulatory elements and gene regulation through evolutionary analyses to provide demographic and genetic data necessary to model interactions between farmed and wild species, and predict population character and abundance. This information will ultimately contribute to the improvement and expansion of breeding programs.
We will also utilise natural and synthetic hybrids to investigate the immediate and long-term effects of hybridisation and polyploidy on genome architecture and evolution. We will focus our investigations on Triticeae species (tetraploid: Triticum turgidum, T. dicoccum; diploid: T. urartu, T. monococcum) and their hybrids. We will apply sequence-based approaches to assay transcriptional activity (RNA-seq, smRNA-seq), and interrogate existing public data and data available through the Designing Future Wheat ISP WP4 (ATAC-Seq, ChIP-Seq, DNA methylation), to define the epigenome of natural and synthetic hybrids and the wild progenitors.
The widespread use and misuse of antimicrobials in our general environment has allowed bacteria to be frequently exposed to sub-inhibitory concentrations, favouring the evolution and spread of resistance to the most commonly used antimicrobial molecules. The effects of these low antibacterial concentrations on pathogenic bacteria leading to the selection of variants associated with resistance are currently not fully understood despite their implications for the effectiveness of antimicrobial drugs in the future. Using machine learning approaches to mine currently available data, we will investigate the genetic changes responsible for adaptation of Salmonella to certain hosts and environments as well as changes in virulence or drug resistance. We aim to characterise the fitness effects of resistance mutations and how they can be maintained in a population with and without antimicrobial selection. Using experimental selection (performed by QI collaborators) and genome sequencing (performed by EI), we will assess whether the trajectory of mutations and allele frequency changes at different antimicrobial concentrations can be predicted and modelled.
Planned Impact
unavailable
Organisations
- Earlham Institute (Lead Research Organisation)
- ROYAL BOTANIC GARDENS, KEW (Collaboration)
- IBM (Collaboration)
- University of Basel (Collaboration)
- University of the Andes (Collaboration)
- University of York (Collaboration)
- South Eastern Kenya University (Collaboration)
- National Research Center for Coffee (Collaboration)
- International Potato Center (Collaboration)
- Technology Partnership Plc (Collaboration)
- Broad Institute (Collaboration)
- University of Paris-Saclay (Collaboration)
- University of Dodoma (Collaboration)
- U.S. Department of Agriculture USDA (Collaboration)
- Cornell University (Collaboration)
- Centro de Investigación de la Caña de Azúcar de Colombia (Collaboration)
- Medicines Discovery Catapult (Collaboration)
- Elsoms Seeds (Collaboration)
- ECOspray Ltd (Collaboration)
- Kromek Group plc (Collaboration)
- Colombian Agricultural Research Corporation (Collaboration)
- University of Arizona (Collaboration)
- Quadram Institute Bioscience (Collaboration)
- University College London (Collaboration)
- KWS Group (Collaboration)
- National Biofilms Innovation Centre (Collaboration)
- University of Plymouth (Collaboration)
- University of Hull (Collaboration)
- Oxford Nanopore Technologies (Collaboration)
- Trinity College Dublin (Collaboration)
- IMPERIAL COLLEGE LONDON (Collaboration)
- Natural History Museum (Collaboration)
- University of California, Davis (Collaboration)
- University of Sussex (Collaboration)
- Google (Collaboration)
- Alan Turing Institute (Collaboration)
- George Mason University (Collaboration)
- Del Rosario University (Collaboration)
- WorldFish (Collaboration)
- BANGOR UNIVERSITY (Collaboration)
- Tropic Biosciences Ltd (Collaboration)
- CGIAR (Collaboration)
- King Abdullah University of Science and Technology (KAUST) (Collaboration)
- University of Dar es Salaam (Collaboration)
Publications
| Title | Additional file 13: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | REVIGO TreeMap representation of GO terms enrichment analysis associated with biological process GO terms found in the list of 204 differentially expressed transcripts down-regulated in transition from Day0 to Day5. (PNG 62â kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_13_of_Comprehensive_assembly_and_analys... |
| Title | Additional file 13: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | REVIGO TreeMap representation of GO terms enrichment analysis associated with biological process GO terms found in the list of 204 differentially expressed transcripts down-regulated in transition from Day0 to Day5. (PNG 62â kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_13_of_Comprehensive_assembly_and_analys... |
| Title | Additional file 14: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | REVIGO TreeMap representation of GO terms enrichment analysis associated with biological process GO terms found in the list of 594 differentially expressed transcripts up-regulated in transition from Day0 to Day5. (PNG 50â kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_14_of_Comprehensive_assembly_and_analys... |
| Title | Additional file 14: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | REVIGO TreeMap representation of GO terms enrichment analysis associated with biological process GO terms found in the list of 594 differentially expressed transcripts up-regulated in transition from Day0 to Day5. (PNG 50â kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_14_of_Comprehensive_assembly_and_analys... |
| Title | Additional file 15: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | REVIGO TreeMap representation of GO terms enrichment analysis associated with biological process GO terms found in the list of 344 differentially expressed transcripts down-regulated in transition from Day15 to Day25. (PNG 167â kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_15_of_Comprehensive_assembly_and_analys... |
| Title | Additional file 15: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | REVIGO TreeMap representation of GO terms enrichment analysis associated with biological process GO terms found in the list of 344 differentially expressed transcripts down-regulated in transition from Day15 to Day25. (PNG 167â kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_15_of_Comprehensive_assembly_and_analys... |
| Title | Additional file 16: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | REVIGO TreeMap representation of GO terms enrichment analysis associated with biological process GO terms found in the list of differentially expressed transcripts included in cluster 2. (PNG 53â kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_16_of_Comprehensive_assembly_and_analys... |
| Title | Additional file 16: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | REVIGO TreeMap representation of GO terms enrichment analysis associated with biological process GO terms found in the list of differentially expressed transcripts included in cluster 2. (PNG 53â kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_16_of_Comprehensive_assembly_and_analys... |
| Title | Additional file 17: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | REVIGO TreeMap representation of GO terms enrichment analysis associated with biological process GO terms found in the list of differentially expressed transcripts included in cluster 3. (PNG 75â kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_17_of_Comprehensive_assembly_and_analys... |
| Title | Additional file 17: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | REVIGO TreeMap representation of GO terms enrichment analysis associated with biological process GO terms found in the list of differentially expressed transcripts included in cluster 3. (PNG 75â kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_17_of_Comprehensive_assembly_and_analys... |
| Title | Additional file 3: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | E-value distribution of the BLAST hits resulting from the BLASTX alignment of the P. pinaster transcriptome to the NCBI non-redundant proteins database. (PNG 74â kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_3_of_Comprehensive_assembly_and_analysi... |
| Title | Additional file 3: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | E-value distribution of the BLAST hits resulting from the BLASTX alignment of the P. pinaster transcriptome to the NCBI non-redundant proteins database. (PNG 74â kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_3_of_Comprehensive_assembly_and_analysi... |
| Title | Additional file 5: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | Distribution of the sequence similarities (percentage) that were calculated for the BLAST hits. (PNG 79â kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_5_of_Comprehensive_assembly_and_analysi... |
| Title | Additional file 5: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | Distribution of the sequence similarities (percentage) that were calculated for the BLAST hits. (PNG 79â kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_5_of_Comprehensive_assembly_and_analysi... |
| Title | Additional file 6: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | Distribution of species to which most transcripts were aligned when only considering the Top-BLAST hits. (PNG 103â kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_6_of_Comprehensive_assembly_and_analysi... |
| Title | Additional file 6: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | Distribution of species to which most transcripts were aligned when only considering the Top-BLAST hits. (PNG 103â kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_6_of_Comprehensive_assembly_and_analysi... |
| Title | Additional file 7: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | InterProScan (IPS) results showing the number of transcripts with and without IPS as well as with GO terms retrieved by this annotation step. (PNG 45â kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_7_of_Comprehensive_assembly_and_analysi... |
| Title | Additional file 7: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | InterProScan (IPS) results showing the number of transcripts with and without IPS as well as with GO terms retrieved by this annotation step. (PNG 45â kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_7_of_Comprehensive_assembly_and_analysi... |
| Title | Additional file 8: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | Distribution of the number of GO terms, retrieved by the Blast2GO mapping step, per database resource. (PNG 24â kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_8_of_Comprehensive_assembly_and_analysi... |
| Title | Additional file 8: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | Distribution of the number of GO terms, retrieved by the Blast2GO mapping step, per database resource. (PNG 24â kb) |
| Type Of Art | Film/Video/Animation |
| Year Produced | 2018 |
| URL | https://springernature.figshare.com/articles/Additional_file_8_of_Comprehensive_assembly_and_analysi... |
| Description | Work Package 1. Analysing and Interpreting Genomes important in food security As part of the work package 1 of the Earlham Institute Core Strategic Programme (CSP) Genomics for Food Security, our objectives set in 2017 were to: 1) develop approaches to accurately reconstruct genomes and metagenomes; 2) develop and apply new methods for identifying and interpreting genetic variation; 3) characterise domestication bottlenecks in crop evolution and adaptation; 4) investigate natural diversity and adaptation in aquaculture; 5) identify the genetic determinants of foodborne pathogen virulence; 6) characterise the impact of polyploidy in plants on generation of new traits. We have now delivered all these objectives. The grant was awarded a 6th year as rollover funding, with three extended objectives, which were based on previous outputs and extend our interest in these specific areas: Ext1.1 Computational developments for rapid and accurate genome assembly from complex datasets; Ext1.2 Going beyond single nucleotide variants or single genome to associate genetic variation with traits of interest; Ext1.3 Characterisation of allele frequency and selective constraints in microbial populations and communities. In the following key findings, those pertaining specifically to the rollover funding are identified using the "Ext" identifier. We have either delivered the agreed objectives as part of the rollover or are on track for delivery within the agreed timeline. All together, as part of this work package work, we contributed to 329 publications, initiated 47 collaborations, and were involved in 360 engagement activities. Across the duration of the award our key findings are: Objective 1) develop approaches to accurately reconstruct genomes and metagenomes; and Objective 2) develop and apply new methods for identifying and interpreting genetic variation, objective Ext1.1 Computational developments for rapid and accurate genome assembly from complex datasets: 1. With the development of near real time sequencing, there is a need for software to be able to handle this new stream of data to enable real time identification of microbial species. Therefore, we further developed NanoOK into NanoOK RT and applied it to characterising preterm infant microbiota (doi: 10.1038/s41564-019-0626-z). We also applied similar approaches to allow culture free pathogen detection in Lower Respiratory Tract Infections enabling detection of resistance genes in patient samples within 6 hours. This enables practitioners to survey pathogens in an unbiased manner and rapidly identify potential resistant strains (doi: 10.1038/s41587-019-0156-5). 2. We developed Reverse Metagenomics, a low cost pipeline that allows semi-quantitative characterization of species composition in mixed-species eukaryote samples using a mix of long and short read sequencing. We successfully applied it to plant identification from mixed-pollen samples (doi: 10.1111/2041-210X.13265). We also contributed to a related review on pollen DNA metabarcoding (doi: 10.1111/mec.16689). 3. Whole genome sequencing is becoming the method of choice to investigate microbial community composition. However, accurate genome assemblies based on reads originating from a mixture of organisms remain a significant challenge. To provide accurate microbial genome assembly not only at the species level but also at the strain level, we developed MetaCortex, a metagenome assembler based on data structures from the Cortex de novo assembler. MetaCortex captures intra-species diversity by using signatures of local variation along assembled sequences in the assembly graph. Our tool produces accurate assemblies with higher genome coverage and contiguity than other popular metagenomic assemblers (doi: 10.1101/2021.07.23.453484, https://github.com/SR-Martin/metacortex). 4. As part of the rollover extension (Objective Ext1.1), we further improved our algorithms for the assembly and analyses of individual bacterial genomes sampled from complex microbial communities. Specifically to overcome the challenge presented by the low frequency of a given species among a community, we have generated a number of hybrid longitudinal microbiome data sets that combine PacBio HiFi sequencing of a small number of time points with a more extensive short read time series (from both anaerobic digesters and mice inoculated with resistant microbes prior to administration of antibiotics). To process these data sets, we have developed an entirely novel program, metaMDBG, for the assembly of HiFi PacBio metagenomes (https://github.com/GaetanBenoitDev/metaMDBG). This has both improved computational performance and generates more circularised genomes than the existing state-of-the-art. We are using this as the first step in a hybrid pipeline coupling with the short reads for almost complete assembly and binning of metagenome time series. It also provides a starting point for strain reconstruction within these circularised genomes. 5. A major challenge in studying microbial communities is the ability to accurately resolve its composition not just at the species level but within species at the strain level. Strains within a species can differ widely in their physiology and pathogenicity. To answer this challenge, we developed an entirely novel statistical framework for determining strain sequences from an algorithmic structure, assembly graphs. We use this to determine strains and their abundances in microbial time series, demonstrating that in anaerobic digestion reactors strain proportions are stable over time, with potential evidence of intra-species niche partitioning. Our algorithmic developments can easily be applied to other sequences and data types (doi: 10.1186/s13059-021-02419-7). 6. Not all sequences within a genomic pool might be of interest if we aim to detect specific species or traits such as antimicrobial resistance. Adaptive sampling is a method of software-controlled enrichment unique to nanopore sequencing platforms. We developed a model for the use of adaptive sampling in metagenomics in order to enrich low abundance organisms and showed how enrichment potential depends on species composition and molecule length. We validated the model using mock communities, as well as complex samples taken from garden compost. In the latter, we de-novo assembled a genome and used that as a reference to enrich for specific sequences from the same sample (doi: 10.1186/s13059-021-02582-x). 7. To enable the identification and quantification of genetics variation from raw reads and for organisms without reference genome, we developed an algorithm (Skip-mers, doi: 10.1101/179960) to efficiently identify conserved sequences across species.? ? 8. As part of a major effort from the Wheat community, we released updated algorithms enabling the assembly of complex genomes from short read sequencing, as well as algorithms for accurate genome annotation. The application of these novel developments led to the release of the first genome assembly and annotation of the bread wheat (doi: 10.1101/gr.217117.116.). 9. The advance of sequencing technologies and the development of long read sequencing allowed us to contribute to the generation of a long read assembly of the wheat genome further developing our assembly quality assessment tools (doi: 10.1093/gigascience/gix097). 10. We continued to develop genome assembly algorithms taking advantage of novel technologies to assemble complex genomes such as barley (doi: 10.1534/g3.119.401010) but we also explore combinations of sequencing technologies to deliver cost efficient genome assemblies for non-model species or difficult to collect samples (doi: 10.1093/gigascience/giaa045). 11. The reconstruction of genome assembly from highly heterozygous organisms is a significant challenge. Therefore we continued to develop algorithms and methods for low cost assembly of complex, highly heterozygous, or difficult to assemble genomes. We applied these developments to butterfly genomes as an example of an organism with extreme levels of heterozygosity (doi: 10.1126/science.aaw2090). We further applied these pipelines to generate draft assemblies of tilapia species, and a haplotype-resolved assembly of a heterozygous allotetraploid apomictic Urochloa grass accession. 12. We continued to develop algorithms and methods to generate high quality assemblies for complex genomes. We released Sequence Distance Graph (SDG, (doi: 10.12688/f1000research.20233.1) that enables the integration of short reads, linked reads, and long reads sequencing technologies and are applying it to generate the genome assemblies of the red clover, tilapia, wheat, and marigold. 13. We continued to develop our algorithms and pipelines for haplotype-specific assembly and karyotype-linkage analyses, using hybrid short-and-long read sequencing. These new tools (https://github.com/bioinfologics/sdg-assemblers) are tailored to conduct de novo full-karyotype analyses on complex karyotypes. We applied these algorithms to reconstruct the full karyotype for a cultured genotype of the diatom Fragilariopsis cylindrus. Our analyses showed that this diatom's genome is mostly triploid, with some degree of aneuploidy. We demonstrated that our newly developed algorithm can accurately identify highly complex structural variations within a single genome that would not be detected before, enabling novel insights on the underlying processes driving such events and their potential consequences. 14. We developed a novel algorithm (Alvis) for assembly and long read alignment visualisation and chimera detection contributing towards the improvement of long-read genome assemblies (doi: 10.1186/s12859-021-04056-0). Objective 3) characterise domestication bottlenecks in crop evolution and adaptation; objective 4) investigate natural diversity and adaptation in aquaculture; objective 6) characterise the impact of polyploidy in plants on generation of new traits; objective Ext. 1.2 Mining Genomes for Domestication and Adaptation: The genomes assemblies delivered through our technologies and algorithms development (Objectives 1 and 2) enable our researchers to apply population genomics approaches to quantify existing genetic diversity in species of interest, to assess the extent of gene flow between species and population but most importantly to identify genomic regions associated with environmental as well as artificial selection. 15. As part of the rollover extension (Objective Ext1.2), and building on the developments for genomes and metagenomes already completed, we are developing open access novel protocols, software and pipelines integrating sequencing technologies such as long reads (PacBio, Oxford Nanopore Technologies) and Hi-C for the accurate haplotype specific reconstruction of genomic sequences, resulting in improved genome assemblies. This enabled the reconstruction of the evolutionary history of haplotypes and their contributions to individual and population level traits. In collaboration with our National Capability in Genomics and Single Cell Analysis, we generated the most contiguous genomes to date for the Nile tilapia (10.1186/s12864-022-09065-8), and the Paragon wheat. The technologies used (PacBio, HiC) and the quality of the current assemblies will enable us to reconstruct haplotypes for these major species. We also completed the genome assembly of the Abassa elite strain from WorldFish, identifying genomic regions that have been introgressed from O. aureus during the breeding process. Furthermore our active collaboration with IBM Research towards the development of approaches for pan-genome reconstruction and analyses will further enable haplotype level characterisation of existing diversity. 16. Immune receptors are among the most dynamic gene families in plants. We investigated the diversity of immune receptors with integrated domains in grasses reporting large expansions and specific signatures of domain integrations (doi: 10.1186/s13059-018-1392-6.). 17. We used comparative genomics analyses to annotate immune genes across Eudicots and Monocots species. We identified a downstream immune signalling pathway conserved in all terrestrial monocots and eudicots plants that has been lost independently and repeatedly in species that have transitioned back to the water environment. This work highlighted sets of genes commonly lost among aquatic plants that are involved in broader immune response as well as in drought response (doi: 10.1105/tpc.19.00903). We publicly released our software for immune gene annotation (doi: 10.1104/pp.19.01273). 18. We developed a capture platform enabling genotype and methylation survey of selected sequences in wheat. We used this promoter exon capture to identify large amounts of variation in DNA methylation across wheat landraces and correlated some of this variation with changes in gene expression and phenotypic variation. We utilised the International Wheat Genome Sequencing Consortium assembly to further improve our capture design (doi: 10.1101/gr.233551.117, doi: 10.1093/gigascience/giz018). We made all our datasets publicly available. 19. We have worked with collaborators in Germany to annotate the Rye genome generating gene model using algorithms developed at the Earlham institute and combining iso-seq and RNA-seq data from a developmental time course (doi: 10.1038/s41588-021-00807-0). 20. As part of an international consortium EI researchers contributed to the sequencing and assembly of the D subgenome and to the analysis of genetic diversity across 262 accessions of Aegilops tauschii (doi: 10.1101/2021.01.31.428788). 21. Global warming poses a major threat to future food security and necessitates the development of crops that are more tolerant to heat stress while maintaining yields under favourable conditions. While multiple studies exist screening for heat tolerance in the lab, few have successfully made the transition to the field. In our study in collaboration with CIMMYT, we have identified three genetic loci which together increase yield by 56.7% under heat stress conditions and reduce canopy temperature by around 2 °C, with no penalty to yield under favourable field conditions. We use a novel strategy to pinpoint the region to an introgression of Aegilops tauschii (doi: 10.1038/s42003-022-04325-5). 22. Introgression from other triticeae species into the bread wheat genome have been widely used in breeding to improve strains. In collaboration with the University of Nottingham, we have developed markers to identify Amblyopyrum muticum introgressions with KASP assays (doi: 10.1002/tpg2.20193). We developed strategies to identify sites of introgression with single nucleotide resolution and associated introgression events with multiple large genome wide structural rearrangements (doi: 10.1111/pbi.13859). 23. To capture the existing variation in gene content and gene regulation between elite wheat cultivars, we have generated whole genome sequence data and RNA-seq data from 12 wheat wild relatives. We are investigating wild introgressions into landraces and identifying novel gene content. 24. Crop genetic diversity provides the reservoir of adaptive and resistant genes free of deleterious mutations used in genetic research on traits and crop improvement. Using low coverage genome sequencing, we have completed the genome wide association study of 612 Vietnamese rice accessions. We identified a strong population structure in Vietnamese-native rice landraces and identified regions in the rice genome under differential agricultural selection, which harboured candidate genes with non-synonymous substitutions and minor alleles. Using phenotypic measurements for 19 traits were scored, we identified 453 loci with significant trait-SNP associations comprising 21 QTLs including some associated with environmental adaptation but also QTLS for such as grains size, panicle length or heading date (doi: 10.1101/2020.07.07.191981, doi: 10.1186/s12284-021-00481-02021, doi: 10.1101/2021.08.04.455072). 25. As part of our rollover funding we aimed to go beyond single nucleotide variants or single genome to associate genetic variation with traits of interest (Ext1.2). We extended our investigations to tackle more challenging regions of the genome such as nucleotide repeats and transposable elements whose expansion/contraction or insertions are directly associated with changes in gene expression. We have completed a first set of experiments using nanopore Cas9-targeted sequencing (nCATS) to target sequencing to a genomic region of interest. In these experiments we have modified the original nCATS protocol so that, rather than flank the region of interest with cut sites to 'sequence in', we cut within a variable region of the genome and 'sequence out'. Therefore, these experiments demonstrate successful establishment of the nCATS protocol at EI and serve as proof-of-principle for our 'sequence out' strategy. In these experiments we successfully identified the site of integration of a plasmid that has randomly integrated into a single site in the genome of cultured human cells. We are now undertaking follow up experiments in which we will target more complex genome variation: transposable elements within the Wheat genome. 26. In collaboration with Ian and Julie King (University of Nottingham) we have generated Triticum timopheevii chromosome-specific KASP markers providing invaluable resources to wheat breeders for trait discovery to combat biotic and abiotic stress factors affecting wheat production due to climate change. 27. Our work on sequencing 17 hexaploid wheat/Ambylopyrum muticum introgression lines helped us to explore the genomic impact of introgression breeding and provides a schematic that can be followed to characterise introgression lines and identify segments and candidate genes underlying the phenotype. This will facilitate more effective utilisation of introgression pre-breeding material in wheat breeding programmes. 28. Within this rollover objective Ext1.2, we also aimed to quantify the impact of repeat instability on host fitness in an evolution experiment. We have established an experimental protocol for engineering short tandem repeats (STRs) within genomes. As proof of principle, we inserted ten CAG repeats (and a control scrambled sequence) into the yeast genome and have undertaken an evolution experiment. We are currently establishing a (new to EI) sequencing protocol, called Maximum Depth Sequencing, that can detect rare sequence variation (SNPs and STR expansion/collapse) by controlling for sequence variants introduced during library preparation. In a pilot sequencing experiment we were able to detect triplet repeat expansions and contractions in the yeast strain where ten CAG repeats were inserted (and not in the control strain). We are now scaling up this pilot experiment to test experimental replicates and additional time points from the evolution experiment. 29. Implementing a step-change we applied pangenomic diversity analysis, identifying genomic regions under selection or affecting regulatory network rewiring in aquaculture species, forage grasses and Triticeae (Ext 1.2) using the pipelines developed in Ext1.1. We have generated a new chromosome-scale assembly of a commercial red clover (Trifolium pratense) variety using HiFi long-reads and 10X linked-reads to overcome the challenge of its high heterozygosity (PRJEB57630). In parallel, we have completed short-read assemblies for over 50 accessions from a diversity panel from all around Europe. We are leveraging this pan-genome to understand gene present/absent variation at the species level. We are also using the genome to genotype a large nested population using a novel skim-seq approach. We completed during summer the resequencing of eight ryegrass (Lolium perenne) accessions representing a latitudinal and longitudinal gradient of its European natural range. We are assembling them in a new collaboration with a group at the University of Aberystwyth. Together with two public long-read assemblies, these will constitute the basis of a new ryegrass pan-proteome to study conserved synteny and homologous, and to identify genes associated to supernumerary B-chromosomes in ryegrass. 30. As part of Ext1.2. We generated HiFi assemblies and developmental RNA time courses through a new collaboration with the Durum wheat consortium allowing us to investigate network rewiring between Durum and bread wheat. We have generated a bread wheat Paragon assembly using HiFi reads. We will use this to unpick structural variants between Durum and bread wheat in collaboration with Italian and Canadian research groups. 31. We screened 191 Arabidopsis genotypes using deferred fluorescence imaging to demonstrate that natural variation at a single nucleotide in COR28 is associated with long period and late flowering phenotype (doi: 10.1111/pce.13941). 31. For red clover we applied the same approach to assess the population structure of 640 samples across Europe and Asia and identified 60 loci with signature of selection. Those include variants within a resistance gene as well as a variant within the homologue of the flowering time gene VEG2 in pea (doi: 10.1038/s41598-020-64989-z). 32. We identified genomic regions in a perennial ryegrass (Lolium perenne) associated with agriculturally important traits by integrating a BAC-based physical map with a genome-wide association study. This allowed us to identify a number of candidate genes for heading date, plant width, biomass, and water soluble carbohydrate accumulation (doi: 10.1093/aob/mcy230). 33. Through our long-established collaboration with IBERS on bioenergy crops, we published the reference genome for Miscanthus sacchariflorus (doi: 10.12688/f1000research.44714.1), and investigated adaptations and yielding between hybrids (doi: 10.1186/s13068-021-01948-4). 34. Many of the species of tilapia (Oreochromis sp), originate from East Africa. One of the major challenges for aquaculture development is associated with the difficulty to differentiate species, and with the associated risks of accidental release and stock contamination. We generated the genome assemblies of 11 Oreochromis species as well as the low coverage genome sequencing of 604 wild individuals we identified and quantified ongoing introgression between Oreochromis species Tanzania. This data set also enabled us to identified significant genetic divergence between isolated populations of several Oreochromis species. 35. We applied low coverage genome sequencing to assess the genetic diversity of farmed tilapia populations in Tanzania. This approach enables to also quantify the degree of ongoing gene flow between endogenous species and exotic species such as the Nile tilapia introduced for aquaculture purposes. We characterised a novel subspecies of tilapia but also identified and quantified ongoing hybridization with invasive species (doi: 10.1111/mec.15638). 36. Based on low coverage genome sequencing, we selected 96 single nucleotide variants that enable the discrimination of both endemic and invasive species in Tanzania. Based on this, we developed a SNP array enabling cost efficient genotyping. We demonstrated the power and sensitivity of the design in identifying species and hybrids compared to traditional approaches such as microsatellites as well as full genome sequencing (doi: 10.1016/j.aquaculture.2021.737637). 37. In collaboration with WorldFish and Genomics Pipelines at EI, we completed the genome assembly of a genetically improved strain of Nile tilapia, delivering a chromosome level genome assembly. This enabled us to identify genomic regions from other species introgressed during the breeding process. Those regions include genes of interest for the breeders, with genes associated with increased growth or improved resistance to pathogens (10.1186/s12864-022-09065-8). 38. We developed an evolutionary model to assess selective constraints acting on gene expression evolution in mammals (doi: 10.1101/gr.237636.118). We identified transposable elements to be enriched within the most diverge genomic regions between mouse strains (https://doi.org/10.1038/s41588-018-0223-8) and to drive lineage specific and species specific evolution through gene family expansion or cis-regulatory element expansion (doi: 10.1101/gr.234096.117). 39. EI researchers contributed to the assembly, annotations, and analysis of 242 Mammals genomes generating resources to better functionally characterise the impact of mutations in the human genome as well as in species of interest (domesticated, endangered). The genomes assemblies were for the first time made available to the community prior to analysis (doi: 10.1038/s41586-020-2876-6). Objective 5) identify the genetic determinants of foodborne pathogen virulence. As part of the rollover funding (objective Ext1.3) we aimed at initiating a step change through the application of novel sequencing technologies and algorithms developed in Objective 1 to characterise allele frequency and selective constraints in microbial populations and communities: 40. One of the major limitations in understanding antimicrobial resistance evolution is that we are relying on bulk sequencing of thousands of microbial organisms, losing the capacity to capture the dynamics of some alleles within the populations and often the ability to detect rare but potentially important variants. We adapted single cell isolation, library sequencing protocols to isolate and sequence the genome of single bacteria. We applied this novel protocol to the analysis of antimicrobial resistance evolution in Salmonella. Our single cell approach enabled us to identify subpopulations with polymorphisms in genes previously demonstrated to be associated with ciprofloxacin susceptibility. These subpopulations would not have been identified through bulk sequencing (doi: 10.1099/mgen.0.000871). 41. As part of our rollover extension (Ext.1.3), we aimed to characterise the allele frequency and selective constraints in microbial populations and communities. We specifically investigated how AMR evolves by detecting allele frequency variation and signatures of selection in a Salmonella population during experimental evolution. Identifying loci associated with resistance and characterising selection acting in those in healthy and treated communities (developments and results will directly feed into Ext2.2 and Ext3.1). 42. (Ext1.3) As above, we have completed our second evolution experiment, building on the results from our work which has been published in (10.1099/mgen.0.000871). We have developed sorting and DNA amplification protocols from cells obtained from the second experiment. This and the bulk sequence data is currently being analysed and has informed our single cell sequencing strategy. Our initial work has produced computational methods capable of resolving allelic variation within real-time evolutionary scenarios and we will further build on this in the analysis of this new data set, looking at differential variation within sub-populations. 43. We have developed a pipeline for low cost and rapid microbial genome sequencing that has enabled us to assemble and annotate over 7000 salmonella genomes from global collections of Salmonella. We have identified the first ST313 and monophasic ST34 isolates to be reported in Colombia (doi: 10.1101/588608). We have used DeltaBit Score to assess genes and gene-regions under strain-specific selection in the food-borne bacteria Salmonella. DeltaBit score is correlated with invasiveness of the pathogen and we are using metabolic pathways to investigate impact of this phenotype on the host for each serotype in our collection. This work is on track for publication in 2023. 44. To understand the dynamics between plant resistance and pathogen virulence evolution and the potential of wild populations to be a ground for the fungi pathogens/host co-evolution, we selected the sugar beet / beet rust system. We applied full genome low coverage sequencing to wild and agricultural pathogens and characterised signatures of domestication in crop pathogens highlighting candidate effectors important for pathogen adaptation on sugar beet (doi:10.1101/2021.08.12.456076). By screening wild polymorphism, breeders will be able to unlock the huge potential of wild/landrace breeding stock. We have our own germplasm collection and have tested it in three rounds of controlled resistance trials. Early trials have shown the same two resistance genes coming through from independent screens. With the potential success indicated, we will now increase the sequencing effort on these screens. 45. We extended our investigation of the genetic diversity of Hymenoscyphus fraxineus, a fungal pathogen leading to ash dieback. We report the pathogenicity of potential of two novel species of Hymenoscyphus of Asian origin (10.1101/2023.01.04.522732). 46. The poultry industry production in 2019 reached a value of £2.65 billion. The chicken microbiome not only contributes to health and productivity, it is also a potential source of human and animal pathogens. To understand the chicken microbiome, we have reconstructed genomes of bacteria commonly found in the chicken gut using metagenomics. We validated the species identified using culturing techniques. These genomes reported are important to industry and basic science alike. This is the first comprehensive study to investigate chicken gut genomes (doi:10.7717/peerj.10941). 47. In collaboration with the EMBL, we investigated the persistence and evolution of human gut bacteria in three continents, across all age groups, processing more than 5,000 metagenomic samples. We found a group of highly persistent, family associated bacteria, with a strong phylogeography, that are more adapted to the human host than other gut bacteria (doi: 10.1016/j.chom.2021.05.008). 48. Using longitudinal metagenomics we have constructed a collection of 2,240 microbial genomes from anaerobic digestion reactors, a key biotechnology for the production of biogas from organic and food waste. Furthermore, through time series analysis we identified the syntrophic interactions between methane producing archaea and bacteria that provide their substrates structuring these communities. This has the potential to lead to a better understanding of community function and hence engineering for improved performance (doi: 10.1101/2021.07.05.451125). 49. We used an integrated approach combining meta-proteomics of excreted proteins and metagenomics to identify proteins produced by the root associated microbiota of the rhizosphere in the presence of Brassica napus (oil seed rape) roots. This helps resolve the key microbial interactions underpinning plant growth (doi: 10.1101/2021.09.01.458574). 50. Microbial communities can vary widely depending on geographical locations. To provide an understanding of such variation on a global scale but also to identify and characterise co-occurring species, we analysed a set of pole-to-pole 16S/18S and metatranscriptome data. We showed that the geographic differentiation of co-occurring microbes in algal microbiomes can be explained by the latitudinal temperature gradient and associated break points in their beta diversity (doi: 10.1038/s41467-021-25646-9). In related work, we assembled MAGs from Arctic and Atlantic Oceans to provide a genomic context to complex phytoplankton microbiomes, showing that their community structure was likely driven by environmental conditions (doi: 10.1186/s40168-022-01254-7). We have also contributed metagenomic analyses as a member of the EcoOmics group, an international team of researchers who are part of the MOSAiC (Multidisciplinary drifting Observatory for the Study of Arctic Climate) expedition studying a year in the biological life of the central Arctic Ocean (doi: 10.1371/journal.pbio.3001835). 51. As a proof-of-principle, we applied low cost in field sequencing technologies to assess microbial diversity of 11 rivers across 3 continents and qualify river function. The study highlights our ability to detect local variation within a river due to anthropogenic activities (doi: 10.1093/gigascience/giaa053). 52. We created open-source protocols for single bacterial genome and transcriptome sequencing to capture and quantify genetic and expression heterogeneity associated with antimicrobial resistance across the microbial members of biofilms. We have developed approaches using combinations of stains to dissect mock communities and primary murine fecal microbiomes, and sequencing is underway to reveal the effectiveness of this enrichment. We will also submit an application for Wellcome Discovery funding to continue the development of these protocols towards real and more complex bacterial communities such as biofilms. |
| Exploitation Route | The outcomes of the work package Signatures of Domestication and Adaptation (CSP1) are taken forward through collaborations, partnerships, and training delivery. We have made all the data sets, protocols, pipelines developed as part of this award publicly and openly available either on public repositories or through the institutional github repository. We achieved academic impact through publishing 329 publications in open access journals providing for the scientific community a range of publicly available datasets, tools, and approaches allowing them to accurately reconstruct genomes and metagenomes, call and interpret genetic variation. 1. Tools and resources developed by the CSP1 were shared and discussed during our annual stakeholder engagement event EI innovate which is running since November 2019. EI Innovate provides an insight into the Earlham Institute's research, exploring opportunities for innovation and collaboration. We had between 70 and 200 attendees coming to these events each year (virtual during pandemic and face-to-face before and after the pandemic). The audience is a mixture of internal staff and other research organisations on the Norwich Research Park and external organisations. The external audience come from a range of sectors including agri-food, biotech, med-tech sectors, clinicians, developers of instrumentation, tools, products and services for genomics and bioinformatics, funders, investors, other academic organisations, and government departments. During these events we highlight areas where CSP1 research is generating impact, sharing tools that we develop, and highlighting opportunities for knowledge transfer and collaborations. An article about the event was produced by our Comms Team which enabled us to share more widely the discussions held at the event. EI Innovate events have gone on to foster exciting and valuable conversations between academia and industry. An example of an exciting collaboration that resulted from a previous EI Innovate is the Hybrid Wheat Initiative, which connects 25 breeding companies and research institutes worldwide, to resolve the critical challenge of hybrid wheat. 2. We continued our collaboration with large genome sequencing and assembly consortia such as the Darwin Tree of Life and the European Reference Genome Atlas. As part of these consortia, we are developing and applying our novel protocols for high quality genome production from very low input. We are applying our algorithm developments for accurate genome reconstruction, including for haplotype level assembly. 3. We have signed a partnership agreement with Eagle Genomics, to further translate our computational developments applied to metagenome reconstruction and microbial diversity analysis. This led Eagle Genomics to become a strategic partner in our future Institute Strategic Programmes, enabling us to share our data and tools with a wider community beyond academia through their platform E-DataScientist. As part of our collaboration with Eagle Genomics we successfully secured a MRC iCASE focussing on the effect of dietary fibre on the microbiome of Crohn's patients through the use of therapeutic diets in model colon systems. 4. Our collaboration with CIMMYT on the identification of QTLs in wheat associated with drought has immediate utility as these identified markers allow us to incorporate climate resilience traits into breeding programmes, and lay out the foundation of our collaborations with CIMMYT. This research attracted a lot of attention on social media and in news outlets including EDP and 20 other websites. 5. Our work on linking epigenetic variation with adaptation to local environments and contributing to increasing resilience, i.e. increased yield under heat stress, will be taken forward through the collaborative R&D as part of the Hybrid Wheat Initiative (HWI), a public-private-partnership including 25 breeding companies and research institutes worldwide, aiming to connect academia and the wheat industry to resolve the critical challenge of hybrid wheat and shape the future of crop research. Hybrid wheat has a significant potential impact on agricultural productivity, food chain resilience vs climate change and also benefits towards agriculture's carbon neutrality, and represents an attractive public investment opportunity. HWI identified a portfolio of R&D projects that will be undertaken as collaborative R&D addressing short, medium, and longer term challenges of making hybrid wheat a reality. 6. Within the agricultural sector, early detection and quantification of crop pathogens has the potential to reduce the use of pesticides, reduce crop losses due to the damage by pathogens, and, based on exact knowledge of pathogen levels and strain, improve crop spraying results thanks to better selection of agrochemicals. We are actively collaborating with beet breeding companies and informatics companies to model and forecast disease occurrence. Our partners will be able to take forward our work on identifying candidate effectors important for crop pathogen adaptation (doi:10.1101/2021.08.12.456076). We will be helping them implement our approaches into their practices, i.e. disease forecasting and breeding. Our developments will also be valuable information for disease epidemiologists and policy makers to enable prediction of wider crop disease outbreaks and leading better planning in breeding programmes for future disease threats. We are also planning to engage with agrochemical companies and agronomy companies developing prevention and treatment for future threats. 7. We are collaborating closely with aquaculture stakeholders delivering genomic resources. All previous work on tilapia was based on a reference genome with a markedly different composition relative to the high performance GIFT strain. The newly released genome of the GIFT Nile tilapia, will help accurately map QTLs associated with growth, immunity, feed efficiency, resilience and develop associated markers for WorldFish to apply genomic selection. The SNP design enabling species discrimination and hybrid identification will be of use for breeders in East Africa to survey existing stocks, prevent contamination and hybridization. The same design will be of interest to local authorities in East Africa in genotyping wild populations and stocks informing conservation actions and identifying potential stocks for aquaculture. We are collaborating with breeders in East Africa (Lake Victoria Fisheries Organization), CGIAR Research Center, WorldFish, and local authorities to build their capacity in managing and improving their aquaculture stocks. This collaboration led to successful grant applications and to financial commitments from WorldFish. As part of a European Development Fund award and in collaboration with WorldFish, the Lake Victoria Fisheries Organisation, the Kenya Marine and Fisheries Institute (KMFRI), the Tanzania Fisheries Research Institute (TAFIRI), and the National Fisheries Resources Research Institute (Uganda, NaFFIRI), the Earlham Institute is collaborating with WorldFish in assessing the genetic diversity of Tilapia stocks for the development of aquaculture industry in the Lake Victoria Basin. WorldFish also committed USD 50,000/year to EI as part of a collaboration to develop genomic resources and tools to enable the faster genetic improvement of cultured tilapia species, with a strong focus on improving resilience to pathogens and climate change. The work directly contributes to the goals of improving productivity, better livelihoods for fish farmers and greater food security and climate adaptation for their communities. In collaboration with the Roslin Institute and WorldFish as part of a BBSRC 2021 International Partnering Awards the Earlham Institute will provide training to fish breeders. Our successful outputs from our collaboration with WorldFish has laid the foundation for WorldFish becoming a partner on our future Institute Strategic Programme (ISP). 8. Training and skills development: Our outcomes in protocols and algorithms developments directly contributed to training of EI staff and early career researchers in genomics and bioinformatics. Our faculty contributed to training courses, organised by our National Capability in Advanced Training, including: Single Cell RNAseq; Microbial Communities Analysis; Nanopore Metagenomics. Our faculty hosted visiting scientists under our Immersive Visitor Training Programme (offering bespoke 1:1 training related to specific fields of research, and typically involving EI's in-house developed tools and resources), undergraduate students from the University of East Anglia (3rd year Biology) for 8 week research projects, training the students in bioinformatics and genomics. We also hosted students as part of Genetics Society Summer Studentships and Undergraduate Research Experience Placements. We engaged with the Nuffield Foundation to offer research placements to high school students from disadvantaged backgrounds. 9. In order to help life scientists to adopt data-intensive research, the Earlham Institute, together with Institutes on the Norwich Research Park initiated a collaboration with The Alan Turing Institute supported by a £600,000 award funding six research posts to expand the application of machine learning and artificial intelligence to several key areas, including one of the CSP1 areas, i.e. characterising the circadian rhythms of plants. Machine learning offers a promising route into not only exploring that data, but also helping us to find hidden patterns and new hypotheses that we had never previously considered. This aligns strongly with the mission of the Earlham Institute, to contribute to solving global challenges by applying data driven methods, and as a provider of a National Capability in computational infrastructure. 10. Our work on AMR evolution and single cell bacteria sequencing has also been increased and disseminated through invited presentations of this work at the University of Leeds and at the 2022 International Conference on Bioinformatics and Biomedicine hosted by the University of Hunan University of Technology, China. 11. Our protocols and algorithms developments for the application of long read sequencing and our engagement with technology providers (Oxford Nanopore Technology and Pacific Bioscience) led to ONT and PACBIO becoming partners as part of the upcoming ISP CELLGEN, committing in kind support. 12. Our close collaborations with Tropic Bioscience which is focusing on the genetic improvement of commercially important tropical plants led to the successful application for an iCASE fellowship, as well as Tropic Bioscience becoming a partner on the upcoming CELLGEN ISP, committing materials and in kind support. 13. Our computational developments to enable handling large data and complex sets led to a collaboration with Google Cloud to facilitate our data and software dissemination but also allow the deployment of our tools on Google Cloud. Google Cloud became a partner on the upcoming CELLGEN ISP committing in kind support. 14. Our work as part of WP1 led to engagement and collaboration with IBM Research, allowing a successful EPSRC iCASE is working in collaboration with IBM Research, using machine learning methods to understand the interaction between nutrition and the microbiome within the gut using the specific example of dietary treatment of Crohn's disease. Furthermore IBM is now a partner on both EI upcoming ISPs. |
| Sectors | Agriculture Food and Drink Digital/Communication/Information Technologies (including Software) Education Environment Healthcare Pharmaceuticals and Medical Biotechnology |
| Description | Within work package 1 of the Earlham Institute Genomics for Food Security strategic programme (CSP1), in 2017 we set to deliver six objectives focusing on algorithms developments for genomes and metagenome assembly. We have successfully delivered all these objectives making a significant impact in the area of food security. The grant was awarded a 6th year as rollover funding. This rollover funding allowed us to build on those objectives and deliver new developments in this important impact area. Our objectives as part of the rollover have either been delivered or will be delivered within the agreed timeframe. We used our computational developments for identification of the signatures of domestication in crops and aquaculture species and for identification of the genetic determinants of foodborne pathogen virulence. As evidenced by our recent socio economic impact report, the Earlham Institute is expected to contribute around £4 billion to the global economy over the next 10 years, and a return of nearly £13 for every £1 invested in the institute. We highlight below specific areas of research and their respective economic impact values. We engaged with our National Capabilities to offer our protocol developments. The UK research community can now benefit from our low cost library preparation (LITE) as fee for service (National Capability in Genomics and Single-cell). This new development enables the community to apply low coverage sequencing for hundreds of samples in a cost efficient manner. To empower end-users and researchers without command line expertise, advanced bioinformatic skills, or without HPC infrastructure, we made our algorithms (e.g. LOTUS2) available to the community on Galaxy and Cyverse UK through our e-Infrastructure National Capability. Our work on developing novel algorithms for genomes and metagenomes reconstruction and to identify signatures of domestication and adaptation has an impact on food security, below we list several emerging impacts based on the different models studied across the work package. Advancing wheat breeding A major area of impact is in wheat research where we have been an integral part of the international effort to deliver the first full bread wheat genome. In both the UK and globally, this work is supporting ongoing annual increases in wheat productivity and reducing the impact of disease outbreaks. In this area of research alone, the Earlham Institute's impact is estimated at £7.4m to the UK economy and £240m to the rest of the world over the next 10 years. The global impact is projected to rise to an estimated £1.5bn over 25 years (Socio-economic impact of the Earlham Institute, Brookdale Consulting, report 2022). As part of the CSP1, we developed markers for heat tolerance loci in wheat. We are collaborating with the International Maize and Wheat Improvement Center (CIMMYT) to use these markers to introgress the heat tolerance traits into elite CIMMYT material, which is used by the breeders worldwide in major wheat producing areas, and can help to generate commercial varieties which are better equipped to thrive in changing environmental conditions. The translation of this knowledge has continued as part of the Hybrid Wheat Initiative (HWI). The HWI was set up and led by the Earlham Institute. It is a public-private-partnership including 25 breeding companies and research institutes worldwide, aiming to connect academia and the wheat industry to resolve the critical challenge of hybrid wheat and shape the future of crop research. Hybrid wheat has a significant potential impact on agricultural productivity, food chain resilience vs climate change and also benefits towards agriculture's carbon neutrality, and represents an attractive public investment opportunity. HWI identified a portfolio of R&D projects that will be undertaken as collaborative R&D. To date this resulted in the submission of an sLOLA application "Understanding heterosis in hybrid wheat and its role in yield increase and climate resilience". Our work on wheat with related to the development of tools for genome assemblies and annotations is directly feeding into Designing Future Wheat, a flagship cross-institute programme funded by BBSRC, bringing together biologists, breeders, and informaticians spanning eight research institutes and universities. The programme aims to develop new wheat varieties containing the next generation of key traits and deliver them into the hands of academia and industry. As such we develop algorithms to deliver whole-wheat-genome assemblies that have been used for assembly of public and private wheat genomes, enabling the identification of families of agronomically important genes. We have generated a new HiFi PacBio assembly for a keystone wheat cultivar Paragon. Our work delivered not only genotyping platforms to the scientific and breeder community but also led to discoveries that can now be directly followed by breeders. Our work and associated publication highlighting genomic regions associated with phenotypic variation in wheat and with agronomic traits (e.g. biomass production, and water soluble carbohydrate accumulation) in ryegrass is of direct interest to breeders for improvement of existing strains. Our work on wheat genome assembly has been taken even further by industry, with a £340K hybrid short-and-long read project commissioned by BASF building on our previous £1M project sequencing 5 wheat lines for the same unit at Bayer. Our collaboration with Elsom Seeds continues. We delivered a KTN SPARKS award with Elsom Seeds to develop a low-cost marker discovery platform for orphan crops, and explored additional collaboration to help with the development of low-cost markers for a number of vegetable crops which will provide a significant boost to the development of the breeding tools for crops of UK significance. Our work on recombination in wheat and the identification of a QTL for altered crossover frequency enabled us to secure further funding and to demonstrate that the manipulation of this locus can increase recombination, thereby highlighting its potential for future breeding programmes. Improvement of vegetable crops protection: Building on the initial work to develop a low-cost marker discovery platform for orphan crops, we continue to collaborate with vegetable breeders Elsoms Seeds to help with the development of low-cost markers for a number of vegetable crops which will provide a significant boost to the development of the breeding tools for crops of UK significance. We have an iCASE with Elsoms "Applying next generation genetic approaches for trait discovery in the commercial vegetable industry" applying the approaches we developed in WP1". We are engaging with sugar beet breeders (KWS) to inform the development of pathogen resistant crops. A second iCASE with KWS has genome sequenced about 500 wild beets, representing new sources of pathogen resistance, garnering interest from industry (USDA). To further enable early detection of potential crop pathogens, we have developed Air-seq which allows near real time pathogen monitoring (10.1101/2022.12.13.520298). It comprises wet-lab techniques to Isolate DNA/RNA captured from air with bespoke software that can analyse data in real-time, as sequencing progresses, and highlight the presence of specific pathogens.The technology can also help to identify novel pathogens, new strains of known pathogens, and help develop better modelling of disease epidemiology. Two patent applications were filed to protect this intellectual asset and ensure maximum impact realisation via commercialisation in wide areas of application from agriculture to homeland security. Understanding rice genetic diversity: Plants adapt to a variety of environmental conditions, we investigate the effects of agricultural selection and other evolutionary processes in the genome and population structure of crop species to identify and mobilise new adaptive and resistance genes for traits under strong agricultural selection (so agronomically significant) in elite cultivars and breeding populations. We place ourselves as a bridge between gene banks (where crop natural diversity is preserved) and systematic pre-breeding and breeding that generates recombinant populations. In rice, we identified a strong population structure in Vietnamese-native rice landraces and identified regions in the rice genome differentially selected between them, which harboured candidate genes with non-synonymous substitutions and minor alleles (doi.org/10.1186/s12284-021-00481-0). Making genetic variation (held in collections) available for improvement is complex, agronomically valuable haplotypes are often unknown, and when known, they may be masked in complex interactions and underperform when introgressed in the breeding background in crosses. Better understanding of genetic resources, i.e. candidate genes, alleles and germplasm, allow to generate and evaluate new recombined populations in wild and elite crosses, and eventually to bring new adaptations and resistance into the commercial cultivars. Genomic resources for forage improvement: We are extending our analysis to new crops, particularly forage grasses (red clover, ryegrass, Urochloa grasses), and analysing population divergence and signatures of adaptation. We are also developing new pangenomes for ryegrass and red clover. Crop improvement and genetic research relies on the generation of large numbers of progenies from selected parents. Improved high-throughput methods to screen these populations allow to accelerate breeding programmes and reduce costs, ultimately reducing the time needed for new elite varieties to reach the farmers. The pangenomes provide us with a platform to genotype and impute the progeny using very low-coverage sequencing (so reducing cost), and also to easily assess the genetic variation and trace the introgression of new diversity into the elite genetic background. It showcases the benefits of moving away from single genome references in diversity research and to incorporate any gene absent in the reference into the analysis. Genes present/absent in the collections are often sources of new adaptation and resistance. Genomic resources for tilapia elite strains improvement: As farmed fish continues to overtake traditional line and net fishing practices, the need for breeders to improve yield, nutritional value, and resilience grows more important. Our work generating novel genomic resources (genome assemblies, SNP array) is of direct relevance to the aquaculture sector, and providing assistance to local communities aiming to develop sustained production of nutritious food and create opportunities for local employment. Our work on producing the genome of the GIFT Nile tilapia has emerging economic, environmental and societal impacts in East Africa, and beyond through transfer of associated knowledge and tools. The new genome is providing a framework for breeders to improve productivity and improve management of the local fish stocks contributing to food security, as well as to local development. It will also enable local authorities to improve their conservation strategies. These impacts will be enabled through our collaboration with breeders and local authorities in East Africa, and the CGIAR Research Center WorldFish, who initiated the breeding of the high performance strain. Based on the Institute continuing to help improve productivity in the future, the economic impact of this work is valued at more than £140m over the next decade (Socio-economic impact of the Earlham Institute, Brookdale Consulting, report 2022). Improving public health: Our work on the identification of pathways and genes associated with pathogenicity in pathogens of humans and along the food chain has potential significant impact on public health on disease management in food production. Our research on understanding the development of multidrug resistance in salmonella contributes towards tackling the rise of antimicrobial resistance (AMR) around the world, Bloodstream infections caused by nontyphoidal Salmonella are a major public health concern in Africa, causing ~49,600 deaths every year. With collaborators at the University of Liverpool, we analysed collections of Salmonella isolates from African patients with bloodstream infections, spanning 1966 to 2018. The resulting 680 genome sequences led to the discovery of a pan-susceptible ST313 lineage (ST313 L3), which emerged in Malawi in 2016 and is closely related to ST313 variants that cause gastrointestinal disease in the United Kingdom and Brazil. The protocol developments enabling the cost effective sequencing of large numbers of samples have been completed in collaboration with the National Capability in Genomics and Single Cell Analysis. This novel protocol is now offered as a fee for service by the sequencing facility at EI. This methodology has the potential for significant impact on improving public health by enabling LMICs to access genomic tools for epidemiology. The Earlham Institute's research also covers human health, with a major interest in tackling the rise of antimicrobial resistance around the world. As this science is applied, it could help reduce infections and deaths linked to AMR with an estimated global saving of close to £80m over the next 10 years (Socio-economic impact of the Earlham Institute, Brookdale Consulting, report 2022). Influence on Policy and Public Affairs There have been significant changes across Westminster and Whitehall. Earlham Institute has kept abreast of all these changes and anticipated their impact. We have maintained contact with ministerial offices and initiated policy advocacy opportunities and parliamentary engagement, both on our own and in collaboration with Norwich Research Park partners. Earlham Institute staff have played a leading role in the Norwich Research Park Public Affairs Group. We have worked successfully with the Norwich Research Park partners on a series of high level visits to the Park from senior policy makers and MPs: - Cabinet Office Officials (scouting for venue for Cabinet Meeting and Govt. Tech announcement aborted due to political developments) - Prof Paul Monks, BEIS Chief Scientific Adviser - Prof Robin May, Food Standards Agency Chief Scientific Adviser - Liz Truss's Chief of Staff - Genetic Technology (Precision Breeding) Bill team and DEFRA civil servants and policy officers - Food Standards Agency (FSA) personnel working on implementation strategy for Genetic Technology (Precision Breeding) Bill - James Wild MP - Chloe Smith MP - Jerome Mayhew MP - Paul Cracknell, Director of Strategy, Norfolk County Council - Clive Lewis MP - Professor Sir Patrick Vallance and officials from the Government Office for Science - Richard Bacon MP These visits have included representatives of the commercial organisations located on the Norwich Research Park to embrace the business voice and provide our visitors with a comprehensive, public and private sector innovation perspective. Since May 2022, when DEFRA's Genetic Technology (Precision Breeding) Bill was introduced to Parliament, Earlham Institute has engaged with Parliamentarians in both Houses to support the swift passage of the Bill. Earlham Institute has worked closely with Norwich Research Park colleagues to present a united front to Parliamentarians scrutinising the Bill. We have provided written material during the Committee stages and proactively sent parliamentary briefings to MPs and Peers. Our briefings have included case studies about our collective research, as well as advocacy about the potential for gene editing to contribute to tackling challenges such as climate change, food security and biodiversity loss. During the Sense About Science annual Evidence Week,representatives from the Norwich Research Park Public Affairs Group were in Parliament and met the following parliamentarians in person to present our scientific support for the Bill: - Greg Clarke MP, Chair of the Science & Technology Select Committee - Deirdre Brock MP - Sheryll Murray MP - Hilary Benn MP (former DEFRA Secretary) - Liz Twist MP - Alex Sobel MP - Olivia Blake MP - James Parton-Hughes on behalf of Richard Bacon MP - Baroness Bakewell of Hardington Mandeville - Nick Ross (former broadcaster and trustee of Sense About Science) - Lord Best Further online engagement took place with Lord Krebs, Chloe Smith MP, Lord Benyon, Lord Cameron. At every step of the Bill's parliamentary journey, Earlham Institute has engaged with the DEFRA and the Food Standards Agency Bill teams. As part of the Norwich Research Park Public Affairs Group, Earlham Institute has responded to various policy consultations (such as the Review of Research, Development and Innovation Landscape by Professor Sir Paul Nurse) and maintained ministerial correspondence (such as a letter to George Freeman MP, Minister for Science, Research and Technology requesting a meeting to discuss strategic science investment and Plan B (Horizon)). Earlham Institute has kept abreast of parliamentary committee work (such as contributing expertise to a Norwich Research Park submission to the EFRA Committee on Soil Health). |
| First Year Of Impact | 2017 |
| Sector | Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Environment,Healthcare |
| Impact Types | Cultural Societal Economic Policy & public services |
| Description | BBSRC ENWW panel membership |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Impact | The panel advises BBSRC exec and councillor how best to deliver BBSRC strategy. Impact is difficult to quantify |
| Description | Chair GCRF CABANA's advisory board |
| Geographic Reach | South America |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | Chair of the board (JDV). Advising CABANA's executive team on recommendations to accelerate the implementation of data-driven biology in the region by creating a sustainable capacity-building programme. CABANA is a capacity strengthening project for bioinformatics in Latin America by an international consortium of ten organisations. CABANA is funded by the Global Challenges Research Fund (GCRF). |
| URL | http://cabana.online |
| Description | Chair of BBSRC Institute Partnership |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Description | DEFRA's Expert Panel on Digital sequence information on genetic resources |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | Recommendation submitted to COP15 |
| Description | FNS cloud Advisory Board |
| Geographic Reach | Europe |
| Policy Influence Type | Influenced training of practitioners or researchers |
| URL | https://www.fns-cloud.eu/overview/advisory-board/ |
| Description | Input into "Balance and Effectiveness of Research and Innovation Spending" inquiry by the House of Commons Science and Technology Select Committee |
| Geographic Reach | National |
| Policy Influence Type | Citation in other policy documents |
| URL | https://publications.parliament.uk/pa/cm201719/cmselect/cmsctech/1453/145303.htm#_idTextAnchor000 |
| Description | Institutional Links ILECR Scheme (British Council and the Foreign Commonwealth and Development Office FCDO) |
| Geographic Reach | Asia |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | The UK-ASEAN Institutional Links Early Career Researchers (ILECR) Scheme is designed to provide small scale seed funding to senior researchers from UK and partner country's higher education institutions to lead a team of UK and partner country early career researchers for 12 months to work on emerging areas aligning to the Indo-Pacific Tilt and Sustainable Development Goals. the ILECR Scheme to stimulate new research impact by having senior researchers in UK and partner countries to lead a team of early career researchers (ECRs) in an interdisciplinary partnership on emerging areas while developing and broadening ECRs' professional knowledge, experience and skills in research and translation. |
| URL | https://www.britishcouncil.org/education/he-science/opportunities/uk-asean-institutional-links-early... |
| Description | Letter to Rt Hin Chris Skidmore to discuss science funding and science immigration post-brexit |
| Geographic Reach | National |
| Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
| Description | Meeting with Sir John Kingman to discuss UKRI strategy and the sustainability of Institutes |
| Geographic Reach | National |
| Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
| Description | Membership of BBSRC Transformative technology Panel |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Impact | The transformative technology strategy advisory panel have influence BBSRC policy on data intensive bioscience and big ideas pipeline |
| Description | Membership of Future Leaders Fellowship Panel |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Description | NERC 'Omics Review. I provided advice on the Environmental omics strategy as a memeber of the NERC Environmental omics steering committee |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Impact | The report generated has led to the NERC commissioning of an environmental omics facility to improve the delivery of the NERC strategy and to train the next generation of scientists. |
| URL | http://environmentalomics.org/steering-committee-and-editors/ |
| Description | 18-BTT: A PATHWAY TO THE EXPLOITATION OF EPIGENETIC VARIATION IN UK, US AND INTERNATIONAL BREEDING PROGRAMMES |
| Amount | £273,500 (GBP) |
| Funding ID | BB/S020942/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2019 |
| End | 03/2021 |
| Description | A proof of concept that RECQ 7 can be used as a tool to increase recombination |
| Amount | £137,389 (GBP) |
| Funding ID | BB/T011963/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2021 |
| End | 09/2022 |
| Description | Algebraic Invariants for Phylogenetic Network Inference |
| Amount | £64,068 (GBP) |
| Funding ID | EP/W007134/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2022 |
| End | 10/2023 |
| Description | AquaGenetics: Delivering gains from genetic improvements in farmed fish through public-private partnerships |
| Amount | £132,743 (GBP) |
| Organisation | Worldfish |
| Sector | Charity/Non Profit |
| Country | Malaysia |
| Start | 03/2022 |
| End | 01/2025 |
| Description | BBSRC BB/R019819/1 - Genomics-led improvement of biotic and abiotic stress tolerance in mustard rape for economic and environmental sustainability |
| Amount | £1,764,018 (GBP) |
| Funding ID | BB/R019819/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2018 |
| End | 08/2021 |
| Description | BBSRC NRPDTP Studentship - Global microbiome analysis of the desert adapted Acomys russatus and Acomys cahirinus. PhD Studentship |
| Amount | £20,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2018 |
| End | 09/2022 |
| Description | BBSRC NRPDTP iCASE Studentship - Applying next generation genetic approaches for trait discovery in the commercial vegetable industry |
| Amount | £28,000 (GBP) |
| Funding ID | HALLA_E22CASE |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2022 |
| End | 09/2026 |
| Description | BBSRC NRPDTP iCASE Studentship - Can we harness resistance by association directly in wild sea beet? |
| Amount | £28,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2019 |
| End | 09/2023 |
| Description | BBSRC NRPDTP iCASE Studentship - Safeguarding UK's best-loved fruit: immunity diversity in banana cultivar |
| Amount | £28,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2021 |
| End | 09/2025 |
| Description | BBSRC NRPDTP studentship - Data science to feed a changing world: superior drought tolerance in nutritious traditional beans |
| Amount | £20,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2021 |
| End | 09/2025 |
| Description | BBSRC NRPDTP studentship - The cost of domestication: Investigating hundreds of genomes to characterise deleterious mutations within noncoding regulatory regions |
| Amount | £20,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2021 |
| End | 09/2025 |
| Description | Biodiversity, wellbeing and colour: wildflower genomics to inform the creation of new habitat |
| Amount | £20,000 (GBP) |
| Funding ID | DEVEGA_E22DTP1A |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2022 |
| End | 09/2026 |
| Description | Boosting innovation in breeding for the next generation of legume crops for Europe |
| Amount | £319,250 (GBP) |
| Funding ID | 101081329-2 |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 03/2023 |
| End | 09/2027 |
| Description | Business Case for a Catalyst Partnership in Artificial Intelligence between the Alan Turing Institute and the Norwich Biosciences Institutes |
| Amount | £600,000 (GBP) |
| Funding ID | BB/V509267/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2020 |
| End | 06/2022 |
| Description | CGIAR Research Programme on Fish Agri-Food Systems (FISH) |
| Amount | £13,333 (GBP) |
| Organisation | Worldfish |
| Sector | Charity/Non Profit |
| Country | Malaysia |
| Start | 09/2020 |
| End | 12/2021 |
| Description | DNA sequencing for biological threat monitoring |
| Amount | $5,270,000 (USD) |
| Funding ID | HR001119C0031 |
| Organisation | Defense Advanced Research Projects Agency (DARPA) |
| Sector | Public |
| Country | United States |
| Start | 12/2018 |
| End | 12/2023 |
| Description | Darwin Tree of Life |
| Amount | £9,360,421 (GBP) |
| Funding ID | 218328/Z/19/Z |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 11/2019 |
| End | 05/2023 |
| Description | Darwin Tree of Life Extension Funding |
| Amount | £2,500,000 (GBP) |
| Funding ID | 226458/Z/22/Z |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 02/2023 |
| End | 01/2025 |
| Description | Developing capabilities in high performance digital infrastructure for data intensive scientific innovation in Colombia |
| Amount | £29,500 (GBP) |
| Funding ID | IAPP18-19\294 |
| Organisation | Royal Academy of Engineering |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 04/2019 |
| End | 12/2020 |
| Description | EU-EAC True Fish Farming Story in Lake Victoria Basin (TRUE-FISH) |
| Amount | € 1,278,237 (EUR) |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 02/2021 |
| End | 01/2025 |
| Description | FAecal microbiota transplantation in primaRy sclerosinG chOlangitis: The FARGO trial |
| Amount | £69,555 (GBP) |
| Organisation | LifeArc |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2022 |
| End | 09/2026 |
| Description | FTMA4 - Earlham Institute Flexible Talent Mobility Account |
| Amount | £107,000 (GBP) |
| Funding ID | BB/X017761/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2023 |
| End | 03/2023 |
| Description | GCRF Foundation Awards for Global Agriculture and Food Systems Research - Genetic improvement of rice seed vigour for dry direct-seeded conditions |
| Amount | £2,620 (GBP) |
| Funding ID | BB/P023428/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2017 |
| End | 04/2019 |
| Description | GCRF Growing Research Capability - Preserving, Restoring and Managing Colombian Biodiversity Through Responsible Innovation |
| Amount | £4,047,353 (GBP) |
| Funding ID | BB/P028098/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2017 |
| End | 12/2020 |
| Description | GCRF Impact Acceleration Account (IAA) |
| Amount | £217,594 (GBP) |
| Funding ID | BB/GCRF/IAA-05 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2016 |
| End | 03/2017 |
| Description | Grand Challenges Research Fund (GCRF) Data & Resources (EI) - extension |
| Amount | £160,963 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 11/2017 |
| End | 07/2018 |
| Description | H2020 ERC Starting Grant - Mechanisms of Immune Receptor Diversification in Cereals |
| Amount | £630,642 (GBP) |
| Funding ID | 716233 |
| Organisation | European Commission H2020 |
| Sector | Public |
| Country | Belgium |
| Start | 08/2017 |
| End | 10/2022 |
| Description | High-resolution genomics to reveal changes in microbial biodiversity across space and time in the warming Arctic Ocean |
| Amount | £471,632 (GBP) |
| Funding ID | NE/W005654/1 |
| Organisation | Natural Environment Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2022 |
| End | 07/2025 |
| Description | High-resolution genomics to reveal changes in microbial biodiversity across space and time in the warming Arctic Ocean |
| Amount | £32,737 (GBP) |
| Funding ID | NE/W005654/1 |
| Organisation | Natural Environment Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2022 |
| End | 06/2025 |
| Description | Industry-academia partnership - Colombia |
| Amount | £29,500 (GBP) |
| Funding ID | IAPP18\19-294 |
| Organisation | Royal Academy of Engineering |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2019 |
| End | 12/2021 |
| Description | Interactive real-time metagenomics algorithms for Nanopore sequencing (LEGGETT_E17DTP1) |
| Amount | £90,000 (GBP) |
| Funding ID | 1937486 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2017 |
| End | 09/2021 |
| Description | Investigation of the impact of mutations within cis regulatory regions on gene and transcript regulatory network topology using computational approaches |
| Amount | £18,400 (GBP) |
| Funding ID | HAERTY_E19SCB |
| Organisation | University of Bisha |
| Sector | Academic/University |
| Country | Saudi Arabia |
| Start | 09/2019 |
| End | 09/2023 |
| Description | John Innes Foundation internship in data-driven plant bioinformatics |
| Amount | £38,000 (GBP) |
| Organisation | John Innes Foundation |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 04/2021 |
| End | 08/2023 |
| Description | Leverage Yellow Common Bean Native Variety Liborino as a bioproduct for the sustainable and peaceful socioeconomic development of the rural communities in Colombia |
| Amount | £49,852 (GBP) |
| Funding ID | 527023146 |
| Organisation | British Council |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2020 |
| End | 10/2021 |
| Description | LongTREC: The Long-Reads Transcriptomics European Consortium. The next generation transcriptome biology revealed by single molecule seq. technologies |
| Amount | £265,251 (GBP) |
| Funding ID | EP/X035913/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2022 |
| End | 09/2026 |
| Description | Machine learning methods for the human microbiome |
| Amount | £118,513 (GBP) |
| Funding ID | QUINCE_E21EPSRC |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2022 |
| End | 09/2026 |
| Description | Mapping for Conservation of Native Tilapia Resources in East Africa |
| Amount | $264,100 (USD) |
| Organisation | JRS Biodiversity Foundation |
| Sector | Charity/Non Profit |
| Country | United States |
| Start | 03/2019 |
| End | 05/2022 |
| Description | Marsupial genomics: Antimicrobial peptides & endangered species conservation |
| Amount | $11,800 (AUD) |
| Funding ID | DP180102465 |
| Organisation | Australian Research Council |
| Sector | Public |
| Country | Australia |
| Start | 03/2019 |
| End | 03/2022 |
| Description | Meeting policy challenges for a responsible biodiversity based bio-economy in Colombia |
| Amount | £126,874 (GBP) |
| Funding ID | EP/T025026/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 05/2020 |
| End | 05/2020 |
| Description | Meeting policy challenges for a responsible biodiversity based bio-economy in Colombia |
| Amount | £126,874 (GBP) |
| Funding ID | EP/T025026/1 |
| Organisation | Engineering and Physical Sciences Research Council (EPSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 05/2020 |
| End | 05/2020 |
| Description | NERC ARIES Doctoral Training Partnership Studentship - Conservation genomics of the European Polecat |
| Amount | £7,015 (GBP) |
| Organisation | Natural Environment Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2020 |
| End | 09/2024 |
| Description | NRP Science Links Seed Corn funding |
| Amount | £14,000 (GBP) |
| Funding ID | R205991 |
| Organisation | Norwich Research Park |
| Sector | Private |
| Country | United Kingdom |
| Start | 12/2017 |
| End | 11/2018 |
| Description | New software for nanopore based diagnostics and surveillance |
| Amount | £151,570 (GBP) |
| Funding ID | BB/R022445/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2018 |
| End | 04/2020 |
| Description | Newton-Paulet Fund - Peru - Researcher Links 2018 |
| Amount | £36,725 (GBP) |
| Funding ID | 2018-RLWK10-10508 |
| Organisation | British Council |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2019 |
| End | 12/2019 |
| Description | Open call - Mapping for Conservation of Native Tilapia Resources in East Africa |
| Amount | £12,461 (GBP) |
| Organisation | JRS Biodiversity Foundation |
| Sector | Charity/Non Profit |
| Country | United States |
| Start | 09/2017 |
| End | 09/2020 |
| Description | Open plant fund - Single cell pollen meiosis screening in wheat |
| Amount | £4,000 (GBP) |
| Organisation | University of Cambridge |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 07/2017 |
| End | 07/2018 |
| Description | OpenPlant - Developing a frugal transcription factor relative affinity measurement pipeline (TRAMP) |
| Amount | £5,000 (GBP) |
| Organisation | University of Cambridge |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 08/2018 |
| End | 07/2019 |
| Description | Preserving, Restoring and Managing Colombian Biodiversity Through Responsible Innovation |
| Amount | £5,332,079 (GBP) |
| Funding ID | BB/P028098/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2017 |
| End | 12/2020 |
| Description | RCUK-CIAT Newton Fund: Exploiting biodiversity in Brachiaria/Panicum tropical forage grasses using genetics to improve livelihoods and sustainability |
| Amount | £150,692 (GBP) |
| Funding ID | BB/R022828/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2018 |
| End | 03/2019 |
| Description | Rapid nanopore metagenomic sequencing of preterm microbiota and proinflammatory mediators/biomarkers in infection mediated preterm labour |
| Amount | £48,661 (GBP) |
| Organisation | Norfolk and Norwich University Hospitals NHS Foundation Trust |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2023 |
| End | 03/2024 |
| Description | Research Enrichment - Public Engagement - Darwin Tree of Life |
| Amount | £399,123 (GBP) |
| Funding ID | 218328/Z/19/A |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 02/2021 |
| End | 12/2022 |
| Description | Resolving the impact of low-fibre therapeutic diets on the human microbiome through integrated 'omics |
| Amount | £25,600 (GBP) |
| Funding ID | QUINCE_E22MMBC |
| Organisation | Medical Research Council (MRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2022 |
| End | 09/2026 |
| Description | Responsive Mode - Ribosomal DNA variation in multi-locus systems |
| Amount | £28,268 (GBP) |
| Funding ID | BB/P022030/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2017 |
| End | 02/2020 |
| Description | Responsive Mode - Wheat Pan-Genomics |
| Amount | £1,084,628 (GBP) |
| Funding ID | BB/P010768/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2017 |
| End | 05/2020 |
| Description | Role of Senataxins in resolving transcription-replication conflicts |
| Amount | £387,880 (GBP) |
| Funding ID | BB/W01520X/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2022 |
| End | 08/2025 |
| Description | Singapore - Malaysia - UK Partnering Award: Genetic innovations to support sustainable tropical aquaculture |
| Amount | £30,489 (GBP) |
| Funding ID | BB/W018527/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2022 |
| End | 06/2025 |
| Description | Single molecule detection of DNA replication errors |
| Amount | £437,916 (GBP) |
| Funding ID | BB/W006014/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2022 |
| End | 06/2025 |
| Description | Single molecule detection of DNA replication errors |
| Amount | £437,915 (GBP) |
| Funding ID | BB/W006014/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2022 |
| End | 01/2025 |
| Description | Strategic Investment |
| Amount | £100,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2017 |
| End | 03/2018 |
| Description | Strategic Partnership Funding with Industry - Understanding the ecology of Listeria and its interactions with microbiomes in food processing facilities to inform biocontrol strategies |
| Amount | £25,520 (GBP) |
| Funding ID | BB/P017282/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 05/2017 |
| End | 06/2021 |
| Description | Studentship - Towards 'crop-pollinating' landscapes: quantifying pollensupply and demand to manage wild pollinators for their benefits to food production |
| Amount | £7,884 (GBP) |
| Organisation | University of Cambridge |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 09/2020 |
| End | 09/2021 |
| Description | The Earlham Institute 2021 Flexible Talent Mobility Account |
| Amount | £108,000 (GBP) |
| Funding ID | BB/W510890/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 12/2021 |
| End | 03/2022 |
| Description | True Fish Farming Story in Lake Victoria Basin (TRUE-FISH) |
| Amount | £281,284 (GBP) |
| Organisation | Worldfish |
| Sector | Charity/Non Profit |
| Country | Malaysia |
| Start | 06/2021 |
| End | 12/2023 |
| Description | UKRI - Earth Biogenome Project |
| Amount | £600,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2019 |
| End | 03/2022 |
| Description | Understanding the role of selection at the gametic level in adaptation to changing environments |
| Amount | £611,514 (GBP) |
| Funding ID | NE/S011188/1 |
| Organisation | Natural Environment Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2019 |
| End | 08/2022 |
| Title | Development of ChIP-Seq protocols in bread wheat |
| Description | The investigation of epigenetic marks enables deeper understanding of the gene expression regulation and the annotation of non coding functional sequences. Histone modifications (methylation, acetylation) are among the epigenetic marks most commonly assayed and specific modifications can be associated with biochemical activity (transcription, repression) and genomic elements (enhancers, promoters, coding regions). The protocols for chromatin immunoprecipation and sequencing have previously been developed for the model organism Arabidopsis thaliana, but never successfully applied to complex plant genomes such as the bread wheat. The protocols aimed to 1) improve the efficiency of chromatin extraction, 2) assay the antibodies, 3) evaluate yield and suitability of different tissues (leaves, root, spikelet, internode) fresh or frozen. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | The protocols will enable in depth understanding of gene expression regulation in bread wheat and relative crops. The protocols will directly be used to deliver objectives within the Designing Future Wheat (BBS/E/T/000PR9783), Signatures of Domestication and Adaptation (BBS/E/T/000PR9818), Regulatory interactions and Complex Phenotypes (BBS/E/T/000PR9819) awards. The protocols will be made available to the communities through the Supporting EI's ISPs and the UK Community with Genomics and Single Cell Analysis (BBS/E/T/000PR9816) award. |
| Title | Experimental Lab Technique Development - ATAC-Seq |
| Description | ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a technique used in molecular biology to study chromatin accessibility. Having first been described in 2013, it has not been extensively applied to teleost fish model systems, including cichlids. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2017 |
| Provided To Others? | No |
| Impact | We worked towards developing the technique to study chromatin accessibility in cichlid tissues, enabling an added angle of epigentic study contributing towards speciation/adaptation events in these fish. As such, collaborators are now interested in including the approach to study cichlids in future grants and we have also included in current Core-Strategic Programme grants. Also, we plan to roll the technique out as a service for sequencing platform users. |
| Title | Methyl-seq methods for wheat |
| Description | Background: Bread wheat has a large complex genome that makes whole genome resequencing costly. Therefore, genome complexity reduction techniques such as sequence capture make re-sequencing cost effective. With a high- quality draft wheat genome now available it is possible to design capture probe sets and to use them to accurately genotype and anchor SNPs to the genome. Furthermore, in addition to genetic variation, epigenetic variation provides a source of natural variation contributing to changes in gene expression and phenotype that can be profiled at the base pair level using sequence capture coupled with bisulphite treatment. Here, we present a new 12 Mbp wheat capture probe set, that allows both the profiling of genotype and methylation from the same DNA sample. Furthermore, we present a method, based on Agilent SureSelect Methyl-Seq, that will use a single capture assay as a starting point to allow both DNA sequencing and methyl-seq. Results: Our method uses a single capture assay that is sequentially split and used for both DNA sequencing and methyl-seq. The resultant genotype and epi-type data is highly comparable in terms of coverage and SNP/methylation site identification to that generated from separate captures for DNA sequencing and methyl-seq. Furthermore, by defining SNP frequencies in a diverse landrace from the Watkins collection we highlight the importance of having genotype data to prevent false positive methylation calls. Finally, we present the design of a new 12 Mbp wheat capture and demonstrate its successful application to re-sequence wheat. Conclusions: We present a cost-effective method for performing both DNA sequencing and methyl-seq from a single capture reaction thus reducing reagent costs, sample preparation time and DNA requirements for these complementary analyses. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | As yet not known |
| Title | promoter exon capture platform |
| Description | Whole genome shotgun re-sequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome making it difficult to unambiguously assign variation. Re-sequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. Previous studies have implemented cDNA/exon or gene-based probe sets where promoter and intron sequence is largely missing alongside newly characterized genes from the recent improved reference sequences. Results We present and validate two gold standard capture probe sets for hexaploid bread wheat, a gene and a putative promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high confidence genes and putative promoter regions that were identified in the genome alongside a large proportion of the low confidence genes and associated promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for SNP calling while significantly reducing cost per sample for gene and putative promoter capture. Conclusions We show that a capture design employing an 'island strategy' can enable analysis of the large gene/putative promoter space of wheat with only 2x160 Mb probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Currently being used by DFW, CIMMYT and US CAPS projects |
| Title | Additional file 1 of Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam |
| Description | Additional file 1: Table S1. Name and details of 672 rice varieties. Detailing read number, mapping statistics, Vietnamese National Genebank number, local name, location, characteristic, subtype and subpopulation. Table S2. Name and details of 3635 rice varieties. Detailing the new subpopulation and PCO analysis. Table S3. Phenotypic measurements for 20 traits for 672 samples. Detailing individual measurements for each sample, description of phenotypes, statistics for all samples and individually for the Indica and Japonica subtypes. Phenotypes are available for around 75% of the samples. Table S4. Phenotype abbreviations and details. Table S5. Phenotype statistics (mean and coefficient of variation) and population comparisons (t-test). Table S6. Diversity (p) of each subpopulation. Table S7. GWAS results. List of the 21 QTL and the positions of the individual QTLs for each panel. Table S8. Gene lists for the 21 QTL. Table S9 List of 107 IRRI rice samples. Detailing IRRI accession, country on origin, K9 and K15 group and Vietnamese subpopulation. Table S10. List of 14 SNP sets used for analysis. Detailing filtering parameters, sample and SNP numbers for each SNP set. Table S11. Summary count of SNPs with effects on the genome. Detailing SnpEff annotation of the full set of 3,750,621 SNPs using the Oryza sativa MSU release 7 rice annotation. Six tables detailing number of effects by impact, functional class, type, region, base changes and Ts/Tv ratio. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_1_of_Resequencing_of_672_Native... |
| Title | Additional file 1 of Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in Vietnam |
| Description | Additional file 1: Table S1. Name and details of 672 rice varieties. Detailing read number, mapping statistics, Vietnamese National Genebank number, local name, location, characteristic, subtype and subpopulation. Table S2. Name and details of 3635 rice varieties. Detailing the new subpopulation and PCO analysis. Table S3. Phenotypic measurements for 20 traits for 672 samples. Detailing individual measurements for each sample, description of phenotypes, statistics for all samples and individually for the Indica and Japonica subtypes. Phenotypes are available for around 75% of the samples. Table S4. Phenotype abbreviations and details. Table S5. Phenotype statistics (mean and coefficient of variation) and population comparisons (t-test). Table S6. Diversity (p) of each subpopulation. Table S7. GWAS results. List of the 21 QTL and the positions of the individual QTLs for each panel. Table S8. Gene lists for the 21 QTL. Table S9 List of 107 IRRI rice samples. Detailing IRRI accession, country on origin, K9 and K15 group and Vietnamese subpopulation. Table S10. List of 14 SNP sets used for analysis. Detailing filtering parameters, sample and SNP numbers for each SNP set. Table S11. Summary count of SNPs with effects on the genome. Detailing SnpEff annotation of the full set of 3,750,621 SNPs using the Oryza sativa MSU release 7 rice annotation. Six tables detailing number of effects by impact, functional class, type, region, base changes and Ts/Tv ratio. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_1_of_Resequencing_of_672_Native... |
| Title | Additional file 10: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | Number of proteins from P. pinaster, P. taeda and P. lambertiana clustered together according to the eggNOG group of their respective best orthologous sequenced in EMBL's eggNOG database of functionally annotated proteins. Information on each eggNOG group is complemented by a general category and its description. (XLSX 844 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_10_of_Comprehensive_assembly_and_analys... |
| Title | Additional file 10: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | Number of proteins from P. pinaster, P. taeda and P. lambertiana clustered together according to the eggNOG group of their respective best orthologous sequenced in EMBL's eggNOG database of functionally annotated proteins. Information on each eggNOG group is complemented by a general category and its description. (XLSX 844 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_10_of_Comprehensive_assembly_and_analys... |
| Title | Additional file 11: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | Transcripts abundance per developmental time point (0D_eff_counts to 25D_eff_counts). (XLSX 4407â kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_11_of_Comprehensive_assembly_and_analys... |
| Title | Additional file 11: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | Transcripts abundance per developmental time point (0D_eff_counts to 25D_eff_counts). (XLSX 4407â kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_11_of_Comprehensive_assembly_and_analys... |
| Title | Additional file 11: of Identification of functional long non-coding RNAs in C. elegans |
| Description | Raw brood size measurement data (CSV 7 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_11_of_Identification_of_functional_long... |
| Title | Additional file 11: of Identification of functional long non-coding RNAs in C. elegans |
| Description | Raw brood size measurement data (CSV 7 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_11_of_Identification_of_functional_long... |
| Title | Additional file 12: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | Results from the edgeR analysis for the identification of differentially expressed transcripts between each pair of consecutive stages at FDR |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_12_of_Comprehensive_assembly_and_analys... |
| Title | Additional file 12: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | Results from the edgeR analysis for the identification of differentially expressed transcripts between each pair of consecutive stages at FDR |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_12_of_Comprehensive_assembly_and_analys... |
| Title | Additional file 12: of Identification of functional long non-coding RNAs in C. elegans |
| Description | Raw data of growth rate measurements (CSV 10 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_12_of_Identification_of_functional_long... |
| Title | Additional file 12: of Identification of functional long non-coding RNAs in C. elegans |
| Description | Raw data of growth rate measurements (CSV 10 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_12_of_Identification_of_functional_long... |
| Title | Additional file 13: of Identification of functional long non-coding RNAs in C. elegans |
| Description | Raw data of length measurements (CSV 4 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_13_of_Identification_of_functional_long... |
| Title | Additional file 13: of Identification of functional long non-coding RNAs in C. elegans |
| Description | Raw data of length measurements (CSV 4 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_13_of_Identification_of_functional_long... |
| Title | Additional file 1: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | List of all sequences of proteins in the final proteome encoded by the reference transcriptome of P. pinaster zygotic embryogenesis. Only the longest ORF possibility per transcript was translated into protein sequence to generate the final proteome. (FASTA 14164â kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_1_of_Comprehensive_assembly_and_analysi... |
| Title | Additional file 1: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | List of all sequences of proteins in the final proteome encoded by the reference transcriptome of P. pinaster zygotic embryogenesis. Only the longest ORF possibility per transcript was translated into protein sequence to generate the final proteome. (FASTA 14164â kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_1_of_Comprehensive_assembly_and_analysi... |
| Title | Additional file 1: of Identification of functional long non-coding RNAs in C. elegans |
| Description | List of the RNA-Seq libraries used to annotate lncRNAs (XLSX 20 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_1_of_Identification_of_functional_long_... |
| Title | Additional file 1: of Identification of functional long non-coding RNAs in C. elegans |
| Description | List of the RNA-Seq libraries used to annotate lncRNAs (XLSX 20 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_1_of_Identification_of_functional_long_... |
| Title | Additional file 2: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | Reference transcriptome of P. pinaster zygotic embryogenesis with annotations from BRH to the proteomes of P. taeda, P. lambertiana and A. thaliana, and from homology to proteins in NCBI databases. Table S1: List of assembled transcripts, longest ORFs, and corresponding predicted proteins. Table S2: Annotation information for the predicted proteins derived from the longest ORFs. Table S3: List of short non-coding transcripts without an ORF that were excluded. (XLSX 11164â kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_2_of_Comprehensive_assembly_and_analysi... |
| Title | Additional file 2: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | Reference transcriptome of P. pinaster zygotic embryogenesis with annotations from BRH to the proteomes of P. taeda, P. lambertiana and A. thaliana, and from homology to proteins in NCBI databases. Table S1: List of assembled transcripts, longest ORFs, and corresponding predicted proteins. Table S2: Annotation information for the predicted proteins derived from the longest ORFs. Table S3: List of short non-coding transcripts without an ORF that were excluded. (XLSX 11164â kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_2_of_Comprehensive_assembly_and_analysi... |
| Title | Additional file 2: of Identification of functional long non-coding RNAs in C. elegans |
| Description | Annotation of the novel lncRNAs in C. elegans (GTF 878 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_2_of_Identification_of_functional_long_... |
| Title | Additional file 2: of Identification of functional long non-coding RNAs in C. elegans |
| Description | Annotation of the novel lncRNAs in C. elegans (GTF 878 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_2_of_Identification_of_functional_long_... |
| Title | Additional file 3: of Identification of functional long non-coding RNAs in C. elegans |
| Description | a Annotation of the lncRNAs in C. elegans, including genomic position, multi-exonic or mono-exonic nature, distance to CAGE peak, distance to closest locus, overlap with previously annotated lncRNA, overlap with epigenomic marks and miRNA binding sites, GC proportion, nucleotide conservation, number of libraries in which the locus is expressed, median and mean expression (FPKM), stage of highest expression, closest upstream and downstream protein-coding genes, correlation of expression and associated P value, reported phenotype for the protein. b Reported phenotypes for upstream and downstream protein-coding genes of knockout and knock-down lncRNAs (XLSX 810 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_3_of_Identification_of_functional_long_... |
| Title | Additional file 3: of Identification of functional long non-coding RNAs in C. elegans |
| Description | a Annotation of the lncRNAs in C. elegans, including genomic position, multi-exonic or mono-exonic nature, distance to CAGE peak, distance to closest locus, overlap with previously annotated lncRNA, overlap with epigenomic marks and miRNA binding sites, GC proportion, nucleotide conservation, number of libraries in which the locus is expressed, median and mean expression (FPKM), stage of highest expression, closest upstream and downstream protein-coding genes, correlation of expression and associated P value, reported phenotype for the protein. b Reported phenotypes for upstream and downstream protein-coding genes of knockout and knock-down lncRNAs (XLSX 810 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_3_of_Identification_of_functional_long_... |
| Title | Additional file 6 of Differential expression of starch and sucrose metabolic genes linked to varying biomass yield in Miscanthus hybrids |
| Description | Additional file 6: Table S1. Individual trait scores and Person correlation between traits. Table S2. Traits significantly different (T-test) between the sequenced samples. Table S3. Normalised counts, expression fold-change and P-values for all the genes in roots, stem and leaf tissue between groups of hybrids. Table S4. Normalised counts, expression fold-change and P-values for all the genes in roots, stem and leaf tissue between hybrids and parents. Table S5. Functional annotation, GO and enzyme codes for all the genes in the reference genome. Table S6. Enriched GO terms among DEG between groups of hybrids. Table S7. Enriched GO terms among DEG between hybrids and parents. Table S8. Detailed functional annotation of 88 DEG within the enriched "carbohydrate metabolism" GO term. Table S9. Detailed functional annotation of 29 DEG within the enriched "generation of precursor metabolites and energy" GO term. Table S10. Detailed functional annotation of 72 DEG within the enriched "response to stress" GO term. Table S11. Detailed functional annotation of 31 DEG within the enriched "secondary metabolism" GO term. Table S12. Transcription factor and target genes contained in each regulon in the TRN. Table S13. Enrichment analysis of differential expression genes for each regulon in the TRN. Table S14. Enrichment analysis of GO terms in each regulon for the TRN. Table S15. Annotation of the twenty-eight regulons were enriched with the "carbohydrate metabolism", "generation of precursor metabolites and energy", or "secondary metabolism" GO terms; and were also enriched in DEGs, or where the TF was DE. Table S16. Annotation of the target genes in the twenty-eight highlighted regulons. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_6_of_Differential_expression_of... |
| Title | Additional file 6 of Differential expression of starch and sucrose metabolic genes linked to varying biomass yield in Miscanthus hybrids |
| Description | Additional file 6: Table S1. Individual trait scores and Person correlation between traits. Table S2. Traits significantly different (T-test) between the sequenced samples. Table S3. Normalised counts, expression fold-change and P-values for all the genes in roots, stem and leaf tissue between groups of hybrids. Table S4. Normalised counts, expression fold-change and P-values for all the genes in roots, stem and leaf tissue between hybrids and parents. Table S5. Functional annotation, GO and enzyme codes for all the genes in the reference genome. Table S6. Enriched GO terms among DEG between groups of hybrids. Table S7. Enriched GO terms among DEG between hybrids and parents. Table S8. Detailed functional annotation of 88 DEG within the enriched "carbohydrate metabolism" GO term. Table S9. Detailed functional annotation of 29 DEG within the enriched "generation of precursor metabolites and energy" GO term. Table S10. Detailed functional annotation of 72 DEG within the enriched "response to stress" GO term. Table S11. Detailed functional annotation of 31 DEG within the enriched "secondary metabolism" GO term. Table S12. Transcription factor and target genes contained in each regulon in the TRN. Table S13. Enrichment analysis of differential expression genes for each regulon in the TRN. Table S14. Enrichment analysis of GO terms in each regulon for the TRN. Table S15. Annotation of the twenty-eight regulons were enriched with the "carbohydrate metabolism", "generation of precursor metabolites and energy", or "secondary metabolism" GO terms; and were also enriched in DEGs, or where the TF was DE. Table S16. Annotation of the target genes in the twenty-eight highlighted regulons. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_6_of_Differential_expression_of... |
| Title | Additional file 6: of Identification of functional long non-coding RNAs in C. elegans |
| Description | Primers and gRNAs used in this study. The strain name (SX), allele name for deletions (mj), lincRNA loci (XLOC), CRISPR guide RNA sequences (CRISPR gRNA), genotyping primers and RT-PCR primers are shown. Oligos are named with a prefix "M" followed by a number identifying their location in the local laboratory database. Similarly plasmids are identified by a prefix "pEM" followed by a number (XLSX 13 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_6_of_Identification_of_functional_long_... |
| Title | Additional file 6: of Identification of functional long non-coding RNAs in C. elegans |
| Description | Primers and gRNAs used in this study. The strain name (SX), allele name for deletions (mj), lincRNA loci (XLOC), CRISPR guide RNA sequences (CRISPR gRNA), genotyping primers and RT-PCR primers are shown. Oligos are named with a prefix "M" followed by a number identifying their location in the local laboratory database. Similarly plasmids are identified by a prefix "pEM" followed by a number (XLSX 13 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_6_of_Identification_of_functional_long_... |
| Title | Additional file 8: of Identification of functional long non-coding RNAs in C. elegans |
| Description | Sequence of 10 lncRNAs and deletions. Full sequence information of the lincRNAs and their deletions. The legend is within the file (RTF 46 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_8_of_Identification_of_functional_long_... |
| Title | Additional file 8: of Identification of functional long non-coding RNAs in C. elegans |
| Description | Sequence of 10 lncRNAs and deletions. Full sequence information of the lincRNAs and their deletions. The legend is within the file (RTF 46 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_8_of_Identification_of_functional_long_... |
| Title | Additional file 9: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | List of proteins from P. pinaster, P. taeda and P. lambertiana clustered together according to the eggNOG group of their respective best orthologous sequenced in EMBL's eggNOG database of functionally annotated proteins. (TXT 3127 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_9_of_Comprehensive_assembly_and_analysi... |
| Title | Additional file 9: of Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos |
| Description | List of proteins from P. pinaster, P. taeda and P. lambertiana clustered together according to the eggNOG group of their respective best orthologous sequenced in EMBL's eggNOG database of functionally annotated proteins. (TXT 3127 kb) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/Additional_file_9_of_Comprehensive_assembly_and_analysi... |
| Title | Brachiaria ruziziensis genome reference |
| Description | A reference assembly and annotation of the Brachiaria ruziziensis genome. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | The first draft version of the reference has been shared with Brachiaria breeders in two CGIAR centres, CIAT in Colombia and ILRI in Kenya, for validation. |
| Title | British European polecat introgression |
| Description | The European polecat (Mustela putorius) is a mammalian predator which breeds across much of Europe east to central Asia. In Great Britain, following years of persecution the European polecat has recently undergone a population increase due to legal protection and its range now overlaps that of feral domestic ferrets (Mustela putorius furo). During this range expansion, European polecats hybridised with feral domestic ferrets producing viable offspring. Here we carry out population-level whole genome sequencing on domestic ferrets, British European polecats, and European polecats from the European mainland and find high degrees of genome introgression in British polecats outside their previous stronghold, even in those individuals phenotyped as 'pure' polecats. We quantify this introgression and find introgressed genes under selection that may assist in sight or load-bearing. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | These datasets enabled us to develop and apply approaches to identify introgressed regions in a reference species |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB48359?show=reads |
| Title | Chromium linked-read_Nicotiana benthamiana_PRJEB37026 |
| Description | Chromium linked-read: PRJEB37026 (accession number ERR3972084 and ERR3972085) and ERX10379414 |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | Nicotiana benthamiana is a widely used model organism for plant-pathogen interactions as well as a a platform for rapid gene expression using transient expression. Multiple genes can be transiently expressed by co-infiltrating multiple Agrobacterium strains enabling the reconstruction of complex metabolic pathways. There is established interest for using N. benthamiana as a commercial-scale biotechnology platform for the production of proteins and small molecules. |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB37026 |
| Title | Epigenomic variation across a polyploid wheat diversity collection |
| Description | We survey genotype and DNA methylation across the core Watkins bread wheat landrace collection. We observe high transposable element variability and expansion, most frequently in retrotransposons, alongside high epigenomic diversity; while there is an association between methylation and genotype, methylation is a standalone source of variation between closely related accessions. Both methylation and genotype are influenced by geographic origin. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Lead to an EAGER grant to translate the research |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB23320 |
| Title | Long-read assembly of the admixed Japonica x Indica rice Vietnamese-native landrace |
| Description | Long-read assembly of the admixed Japonica x Indica rice Vietnamese-native landrace CHIEM TONG NHAT 1 (IRGC 47496-1) (IRGC 127275) (IRIS 313-11384).Sequel II sequencing |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | Oryza sativa Indica Group x Oryza sativa Japonica Group |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB60047 |
| Title | Nile Tilapia GIFT genome assembly |
| Description | We used PacBio HiFi, PacBio CLR, and 10x Genomics linked-reads to assemble the genome of the Genetically Improved Farmed Tilapia (GIFT) and then scaffolded the assembly against the GIFT linkage map. LG0 contains unplaced scaffolds |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | Our work on producing the genome of the GIFT Nile tilapia has emerging economic, environmental and societal impacts in East Africa, and beyond through transfer of associated knowledge and tools. The new genome is providing a framework for breeders to improve productivity and improve management of the local fish stocks contributing to food security, as well as to local development. It will also enable local authorities to improve their conservation strategies. These impacts will be enabled through our collaboration with breeders and local authorities in East Africa, and the CGIAR Research Center WorldFish, who initiated the breeding of the high performance strain. |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB48957?show=reads |
| Title | Oreochromis mossambicus cell line mapping |
| Description | Mapping of O. mossambicus Illumina reads from cell line to farmed/wild reference genome to asses cell-line specific mutations |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | To enable the assessment of the functional implications of variants of interest in a tilapia cell lines, we generated low coverage genome sequencing of a Oreochromis mossambicus cell line. This work ensured the genetic integrity of the cell line and enabled the selection of regions for mutagenesis |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB51165 |
| Title | PRJEB31845 - Comparison of 3L and 3DL in wheat |
| Description | Comparison of 3L and 3DL in wheat |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Comparison of 3L and 3DL in wheat has led to a publication in Biorxiv; doi: https://doi.org/10.1101/571133 |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB31845 |
| Title | PRJEB32549 - A carbohydrate-binding protein, FLOURY ENDOSPERM 6 influences the initiation of A- and B-type starch granules in wheat. |
| Description | A carbohydrate-binding protein, FLOURY ENDOSPERM 6 influences the initiation of A- and B-type starch granules in wheat. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | A carbohydrate-binding protein, FLOURY ENDOSPERM 6 influences the initiation of A- and B-type starch granules in wheat. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB32549 |
| Title | PRJEB33767 - European Polecat Genome project |
| Description | In contrast to research in human biomedical sciences, sample quality of non-model vertebrates is often low, with the DNA being quite degraded. We used PCR-free Illumina paired-end reads, Bionano optical maps, Long mate pairs, and 10x Genomics data at 60x coverage (for de novo assembly) and at 30x coverage (for scaffolding only) from the European Polecat (Mustela putorius) to examine how different combinations of these datatypes can be used most effectively in de novo assembly, whilst providing value for money. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The research resulted in a bioRxiv paper which has been submitted to GigaScience, as well as a valuable reference for smaller research groups aiming to carry out genome assemblies to answer specific biological questions. The data was further used for preliminary research that resulted in a successful application of an ARIES-funded PhD studentship. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB33767 |
| Title | PRJEB33948 - Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB34003 - Red clover Trifolium pratense high-quality genome |
| Description | Red clover Trifolium pratense high-quality genome assembly USING OUR PIPELINE DEVELOPED IN WP1 |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Used as the reference for a new dataset for a GCRF funded project. |
| Title | PRJEB34119 - European Polecat Genome project |
| Description | In contrast to research in human biomedical sciences, sample quality of non-model vertebrates is often low, with the DNA being quite degraded. We used PCR-free Illumina paired-end reads, Bionano optical maps, Long mate pairs, and 10x Genomics data at 60x coverage (for de novo assembly) and at 30x coverage (for scaffolding only) from the European Polecat (Mustela putorius) to examine how different combinations of these datatypes can be used most effectively in de novo assembly, whilst providing value for money. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The research resulted in a bioRxiv paper which has been submitted to GigaScience, as well as a valuable reference for smaller research groups aiming to carry out genome assemblies to answer specific biological questions. The data was further used for preliminary research that resulted in a successful application of an ARIES-funded PhD studentship. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34119 |
| Title | PRJEB34120 - European Polecat Genome project |
| Description | In contrast to research in human biomedical sciences, sample quality of non-model vertebrates is often low, with the DNA being quite degraded. We used PCR-free Illumina paired-end reads, Bionano optical maps, Long mate pairs, and 10x Genomics data at 60x coverage (for de novo assembly) and at 30x coverage (for scaffolding only) from the European Polecat (Mustela putorius) to examine how different combinations of these datatypes can be used most effectively in de novo assembly, whilst providing value for money. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | The research resulted in a bioRxiv paper which has been submitted to GigaScience, as well as a valuable reference for smaller research groups aiming to carry out genome assemblies to answer specific biological questions. The data was further used for preliminary research that resulted in a successful application of an ARIES-funded PhD studentship. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34120 |
| Title | PRJEB34121 - European Polecat Genome project |
| Description | In contrast to research in human biomedical sciences, sample quality of non-model vertebrates is often low, with the DNA being quite degraded. We used PCR-free Illumina paired-end reads, Bionano optical maps, Long mate pairs, and 10x Genomics data at 60x coverage (for de novo assembly) and at 30x coverage (for scaffolding only) from the European Polecat (Mustela putorius) to examine how different combinations of these datatypes can be used most effectively in de novo assembly, whilst providing value for money. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The research resulted in a bioRxiv paper which has been submitted to GigaScience, as well as a valuable reference for smaller research groups aiming to carry out genome assemblies to answer specific biological questions. The data was further used for preliminary research that resulted in a successful application of an ARIES-funded PhD studentship. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34121 |
| Title | PRJEB34122 - European Polecat Genome project |
| Description | In contrast to research in human biomedical sciences, sample quality of non-model vertebrates is often low, with the DNA being quite degraded. We used PCR-free Illumina paired-end reads, Bionano optical maps, Long mate pairs, and 10x Genomics data at 60x coverage (for de novo assembly) and at 30x coverage (for scaffolding only) from the European Polecat (Mustela putorius) to examine how different combinations of these datatypes can be used most effectively in de novo assembly, whilst providing value for money. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The research resulted in a bioRxiv paper which has been submitted to GigaScience, as well as a valuable reference for smaller research groups aiming to carry out genome assemblies to answer specific biological questions. The data was further used for preliminary research that resulted in a successful application of an ARIES-funded PhD studentship. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34122 |
| Title | PRJEB34123 - European Polecat Genome project |
| Description | In contrast to research in human biomedical sciences, sample quality of non-model vertebrates is often low, with the DNA being quite degraded. We used PCR-free Illumina paired-end reads, Bionano optical maps, Long mate pairs, and 10x Genomics data at 60x coverage (for de novo assembly) and at 30x coverage (for scaffolding only) from the European Polecat (Mustela putorius) to examine how different combinations of these datatypes can be used most effectively in de novo assembly, whilst providing value for money. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The research resulted in a bioRxiv paper which has been submitted to GigaScience, as well as a valuable reference for smaller research groups aiming to carry out genome assemblies to answer specific biological questions. The data was further used for preliminary research that resulted in a successful application of an ARIES-funded PhD studentship. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34123 |
| Title | PRJEB34124 - European Polecat Genome project |
| Description | In contrast to research in human biomedical sciences, sample quality of non-model vertebrates is often low, with the DNA being quite degraded. We used PCR-free Illumina paired-end reads, Bionano optical maps, Long mate pairs, and 10x Genomics data at 60x coverage (for de novo assembly) and at 30x coverage (for scaffolding only) from the European Polecat (Mustela putorius) to examine how different combinations of these datatypes can be used most effectively in de novo assembly, whilst providing value for money. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The research resulted in a bioRxiv paper which has been submitted to GigaScience, as well as a valuable reference for smaller research groups aiming to carry out genome assemblies to answer specific biological questions. The data was further used for preliminary research that resulted in a successful application of an ARIES-funded PhD studentship. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34124 |
| Title | PRJEB34125 - European Polecat Genome project |
| Description | In contrast to research in human biomedical sciences, sample quality of non-model vertebrates is often low, with the DNA being quite degraded. We used PCR-free Illumina paired-end reads, Bionano optical maps, Long mate pairs, and 10x Genomics data at 60x coverage (for de novo assembly) and at 30x coverage (for scaffolding only) from the European Polecat (Mustela putorius) to examine how different combinations of these datatypes can be used most effectively in de novo assembly, whilst providing value for money. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The research resulted in a bioRxiv paper which has been submitted to GigaScience, as well as a valuable reference for smaller research groups aiming to carry out genome assemblies to answer specific biological questions. The data was further used for preliminary research that resulted in a successful application of an ARIES-funded PhD studentship. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34125 |
| Title | PRJEB34126 - European Polecat Genome project |
| Description | In contrast to research in human biomedical sciences, sample quality of non-model vertebrates is often low, with the DNA being quite degraded. We used PCR-free Illumina paired-end reads, Bionano optical maps, Long mate pairs, and 10x Genomics data at 60x coverage (for de novo assembly) and at 30x coverage (for scaffolding only) from the European Polecat (Mustela putorius) to examine how different combinations of these datatypes can be used most effectively in de novo assembly, whilst providing value for money. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The research resulted in a bioRxiv paper which has been submitted to GigaScience, as well as a valuable reference for smaller research groups aiming to carry out genome assemblies to answer specific biological questions. The data was further used for preliminary research that resulted in a successful application of an ARIES-funded PhD studentship. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34126 |
| Title | PRJEB34127 - European Polecat Genome project |
| Description | In contrast to research in human biomedical sciences, sample quality of non-model vertebrates is often low, with the DNA being quite degraded. We used PCR-free Illumina paired-end reads, Bionano optical maps, Long mate pairs, and 10x Genomics data at 60x coverage (for de novo assembly) and at 30x coverage (for scaffolding only) from the European Polecat (Mustela putorius) to examine how different combinations of these datatypes can be used most effectively in de novo assembly, whilst providing value for money. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The research resulted in a bioRxiv paper which has been submitted to GigaScience, as well as a valuable reference for smaller research groups aiming to carry out genome assemblies to answer specific biological questions. The data was further used for preliminary research that resulted in a successful application of an ARIES-funded PhD studentship. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34127 |
| Title | PRJEB34131 - European Polecat Genome project |
| Description | In contrast to research in human biomedical sciences, sample quality of non-model vertebrates is often low, with the DNA being quite degraded. We used PCR-free Illumina paired-end reads, Bionano optical maps, Long mate pairs, and 10x Genomics data at 60x coverage (for de novo assembly) and at 30x coverage (for scaffolding only) from the European Polecat (Mustela putorius) to examine how different combinations of these datatypes can be used most effectively in de novo assembly, whilst providing value for money. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The research resulted in a bioRxiv paper which has been submitted to GigaScience, as well as a valuable reference for smaller research groups aiming to carry out genome assemblies to answer specific biological questions. The data was further used for preliminary research that resulted in a successful application of an ARIES-funded PhD studentship. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34131 |
| Title | PRJEB34357 - Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB34358 - Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB34359 - Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB34373 - Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB34375 - Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB34385 - Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB34386 - Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB34387 - Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB34388 -Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB34594 - Genotypic Diversity of Salmonella Typhimurium |
| Description | Long-read (Pacbio) genome assemblies generated by EI for the QIB of diverse Salmonella Typhimurium strains. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The dataset has resulted in a bioRxiv pre print. It also provides a resource for the population structure of Salmonella enterica serotype Typhimurium. It also a resource for the research and public health community and can be used to inform decisions. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34594 |
| Title | PRJEB34595 - Genotypic Diversity of Salmonella Typhimurium |
| Description | Long-read (Pacbio) genome assemblies generated by EI for the QIB of diverse Salmonella Typhimurium strains. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The dataset has resulted in a bioRxiv pre print. It also provides a resource for the population structure of Salmonella enterica serotype Typhimurium. It also a resource for the research and public health community and can be used to inform decisions. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34595 |
| Title | PRJEB34596 - Genotypic Diversity of Salmonella Typhimurium |
| Description | Long-read (Pacbio) genome assemblies generated by EI for the QIB of diverse Salmonella Typhimurium strains. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The dataset has resulted in a bioRxiv pre print. It also provides a resource for the population structure of Salmonella enterica serotype Typhimurium. It also a resource for the research and public health community and can be used to inform decisions. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34596 |
| Title | PRJEB34597 - Genotypic Diversity of Salmonella Typhimurium |
| Description | Long-read (Pacbio) genome assemblies generated by EI for the QIB of diverse Salmonella Typhimurium strains. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The dataset has resulted in a bioRxiv pre print. It also provides a resource for the population structure of Salmonella enterica serotype Typhimurium. It also a resource for the research and public health community and can be used to inform decisions. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34597 |
| Title | PRJEB34598 - Genotypic Diversity of Salmonella Typhimurium |
| Description | Long-read (Pacbio) genome assemblies generated by EI for the QIB of diverse Salmonella Typhimurium strains |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The dataset has resulted in a bioRxiv pre print. It also provides a resource for the population structure of Salmonella enterica serotype Typhimurium. It also a resource for the research and public health community and can be used to inform decisions. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34598 |
| Title | PRJEB34599 - Genotypic Diversity of Salmonella Typhimurium |
| Description | Long-read (Pacbio) genome assemblies generated by EI for the QIB of diverse Salmonella Typhimurium strains. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | The dataset has resulted in a bioRxiv pre print. It also provides a resource for the population structure of Salmonella enterica serotype Typhimurium. It also a resource for the research and public health community and can be used to inform decisions. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB34599 |
| Title | PRJEB35182 - 10k Salmonella Project |
| Description | 10k Salmonella Project sequencing - A worldwide effort to understand the epidemiology, transmission and virulence of invasive non-Typhoidal Salmonellosis |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | This dataset has resulted in one publication. The data has been made public so it will form a genomic resource for the Salmonella community. |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB35182 |
| Title | PRJEB35709 - Sequencing and assembly of 5 wheat lines |
| Description | Sequencing and assembly of Claire, Paragon, Robigus, Cadenza and Weebil hexaploid wheat lines |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Impact | Contribute to understanding of wheat lines. Part of an international collaboration with 10+ wheat genome project. Data being used by UK wheat breeders and researchers across the UK. Uploaded into EMSEML plants. http://www.10wheatgenomes.com/ |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB35709 |
| Title | PRJEB36511 - Tilapia genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB36512 - Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB36513 - Tilapia Genomes |
| Description | sequencing data to assemble Tilapia genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | Assembly of tilapia genomes to identify signatures of domestication and adaptation |
| Title | PRJEB36631: Whole-genome resequencing of 612 varieties of Vietnamese rice |
| Description | These lines have been selected from the Vietnamese National Genebank to show diversity within the phenotypes of interest. There are currently ~8000 accessions in the Vietnamese National Genebank, 616 of which have been selected by AGI for additional phenotyping focusing on traits of interest such as biotic and abiotic stresses and root phenotypes. From these 616, we have sequenced 508 at a coverage between 3X and 5X as part of this project. Deposit at NCBI's SRA under accession number PRJEB36631. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | No |
| Impact | Contributing to identify markers suitable for Vietnamese materials and traits of agronomic importance. |
| Title | PRJEB36772 - Population genomics of Oreochromis korogwe |
| Description | Whole-genome sequencing project of four Oreochromis tilapia species. One of these species, Oreochromis korogwe has recently been discovered to have a separate population in the south Tanzania; previously it was only known from the North. We were investigating gene flow between an invasive species, Oreochromis niloticus, and this newly discovered southern population of Oreochromis korogwe. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | We have a publication published in Molecular Ecology https://onlinelibrary.wiley.com/doi/full/10.1111/mec.15638 with this data we hope it will influence the management of fish translocations, as we have shown that species introduced for fish farming can hybridise with native species. This may likely have conservation implications. |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB36772 |
| Title | PRJEB37024 - Nicotiana benthamiana |
| Description | Raw sequencing reads for the high-quality assembly of Solanaceous allotetraploid, Nicotiana benthamiana |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | High-quality assembly of Solanaceous allotetraploid, Nicotiana benthamiana will provide a community resource for researchers in terms of the sequence data and also providing methods for the accurate reconstruction of genomes and metagenomes |
| Title | PRJEB37024_Nicotiana benthamiana |
| Description | Paired end: ERR3971933: Illumina HiSeq 2500, ERR3971934 Secondary study accession ERP120313 |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | Nicotiana benthamiana is a widely used model organism for plant-pathogen interactions as well as a a platform for rapid gene expression using transient expression. Multiple genes can be transiently expressed by co-infiltrating multiple Agrobacterium strains enabling the reconstruction of complex metabolic pathways. There is established interest for using N. benthamiana as a commercial-scale biotechnology platform for the production of proteins and small molecules. |
| URL | https://www.ebi.ac.uk/ena/browser/text-search?query=PRJEB37024 |
| Title | PRJEB37025 - Nicotiana benthamiana |
| Description | Raw sequencing reads for the high-quality assembly of Solanaceous allotetraploid, Nicotiana benthamiana |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | High-quality assembly of Solanaceous allotetraploid, Nicotiana benthamiana will provide a community resource for researchers in terms of the sequence data and also providing methods for the accurate reconstruction of genomes and metagenomes |
| Title | PRJEB37025_Nicotiana Benthamiana |
| Description | ONT: accession numbers ERR3971506-509 and ERR3972081-83 |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | Nicotiana benthamiana is a widely used model organism for plant-pathogen interactions as well as a a platform for rapid gene expression using transient expression. Multiple genes can be transiently expressed by co-infiltrating multiple Agrobacterium strains enabling the reconstruction of complex metabolic pathways. There is established interest for using N. benthamiana as a commercial-scale biotechnology platform for the production of proteins and small molecules. |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB37025 |
| Title | PRJEB37026 - Nicotiana benthamiana |
| Description | Raw sequencing reads for the high-quality assembly of Solanaceous allotetraploid, Nicotiana benthamiana |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | High-quality assembly of Solanaceous allotetraploid, Nicotiana benthamiana will provide a community resource for researchers in terms of the sequence data and also providing methods for the accurate reconstruction of genomes and metagenomes |
| Title | PRJEB39723 - 10k Salmonella Project |
| Description | This data was produced as part of the 10k Salmonella genomes project which is a a worldwide effort to understand the epidemiology, transmission and virulence of invasive non-Typhoidal Salmonellosis. GP have used a new library preparation method to sequence these genomes (lite pipeline) and we have an in-house bioinformatics pipeline which was also created for this dataset (Bgrrl). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | Parts of this data have already been published here doi: 10.1093/cid/ciab051 (Epub ahead of print). |
| Title | PRJEB39749 - 10k Salmonella Project |
| Description | This data was produced as part of the 10k Salmonella genomes project which is a a worldwide effort to understand the epidemiology, transmission and virulence of invasive non-Typhoidal Salmonellosis. GP have used a new library preparation method to sequence these genomes (lite pipeline) and we have an in-house bioinformatics pipeline which was also created for this dataset (Bgrrl). |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | Parts of this data have already been published here doi: 10.1093/cid/ciab051 (Epub ahead of print) |
| Title | PRJEB40189 - IN VITRO EVOLUTION OF BACTERIAL POPULATIONS WITH SINGLE CELL SEQUENCING |
| Description | Single-cell DNA sequencing has the potential to reveal detailed hierarchical structures in evolving populations of cells. Here, we present an approach for single-cell bacterial sequencing of in vitro experiments to study bacterial evolution. Using populations of a hypermutator strain of Salmonella grown under antibiotic stress for 150 generations, we identified the presence and prevalence of sub-populations within a community that was not resolvable from bulk sequence data. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| Impact | Our results show the applicability of high-throughput single-cell sequencing to experimental evolution experiments that allows population dynamics to be studied in unprecedented detail. |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB40189 |
| Title | PRJEB57630: Haplotype-resolved assembly and annotation of Trifolium pratense cv. Milvus using HiFi long-reads and 10X linked-reads |
| Description | We assembled the complete 18 chromosomes of a heterozygous genotype of the outcrossed species Trifolium pratense |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | Enhancing red clover's role in sustainable agriculture requires genetic improvement of persistency, disease resistance, and tolerance to grazing. To help address these challenges, we assembled a chromosome-scale reference genome for red clover. We observed large blocks of conserved synteny with the model legume Medicago truncatula and estimated that the two species diverged ~23 million years ago. Among the 40,868 annotated genes in red clover, we identified gene clusters involved in biochemical pathways of importance for forage quality and livestock nutrition. |
| Title | PRJEB62882: WGS from the 190 banana cultivars in the genebank used by the Colombian breeding programme |
| Description | Bananas and plantains (Musa spp.) are one of the most important crops worldwide. The cultivated varieties are vegetatively propagated, and their diversity is essentially fixed over time. Nevertheless, millennia of diversification and selection have led to hundreds of edible varieties. We aimed to characterise chromosomal exchanges and structural variation among lineages to understand shared foundational events and identify sources of allelic diversity in introgressed loci for genetic improvement. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | =Two publications in collaboration with the group =PhD project to explore PAV of NLR genes in this dataset =Discussion with another lab using a different technique to assess introgressions in the same species |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB62882 |
| Title | Polyfun annotations with Zoonomia genome conservation |
| Description | Dataset from: "Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease" Abstract: Although thousands of genomic regions have been associated with heritable human diseases, attempts to elucidate biological mechanisms are impeded by a general inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function that is agnostic to cell type or disease mechanism. Here, single base phyloP scores from the whole genome alignment of 240 placental mammals identified 3.5% of bases in the human genome as significantly constrained and very likely functional. We compared these scores to large-scale genome annotation, genome-wide association studies (GWAS), copy number variation, clinical genetics findings, and cancer data sets. Evolutionary constrained positions are enriched for variants explaining common disease heritability more than any other functional annotation. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease. Dataset description: functional annotations of the human common genetic variants including conservation metrics across 240 mammals and subset of primates. These annotations are to be used in conjunction with the polyfun method. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://kilthub.cmu.edu/articles/dataset/Polyfun_annotations_with_Zoonomia_genome_conservation/19380... |
| Title | Polyfun annotations with Zoonomia genome conservation |
| Description | Dataset from: "Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease" Abstract: Although thousands of genomic regions have been associated with heritable human diseases, attempts to elucidate biological mechanisms are impeded by a general inability to discern which genomic positions are functionally important. Evolutionary constraint is a powerful predictor of function that is agnostic to cell type or disease mechanism. Here, single base phyloP scores from the whole genome alignment of 240 placental mammals identified 3.5% of bases in the human genome as significantly constrained and very likely functional. We compared these scores to large-scale genome annotation, genome-wide association studies (GWAS), copy number variation, clinical genetics findings, and cancer data sets. Evolutionary constrained positions are enriched for variants explaining common disease heritability more than any other functional annotation. Our results improve variant annotation but also highlight that the regulatory landscape of the human genome still needs to be further explored and linked to disease. Dataset description: functional annotations of the human common genetic variants including conservation metrics across 240 mammals and subset of primates. These annotations are to be used in conjunction with the polyfun method. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| URL | https://kilthub.cmu.edu/articles/dataset/Polyfun_annotations_with_Zoonomia_genome_conservation/19380... |
| Title | Supplementary dataset to "Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus" |
| Description | Miscanthus sacchariflorus (Maxim.) Hack. is a C4 perennial rhizomatous biofuel grass crop. M. sacchariflorus is among the most widely distributed species within the genus, particularly at cold northern latitudes, and one of the progenitor species of the main biomass commercial crop M. × giganteus. We generated a 2.54 Gbps whole-genome assembly of the diploid M. sacchariflorus "Robustus 297" genotype, which represented ~59% of the expected genome size. We later anchored this assembly in the chromosomal-scale M. sinensis genome to improve its contiguity. We annotated 86,767 and 69,049 protein-coding genes in the unanchored and anchored, respectively. We estimated our assemblies include ~85% of the M. sacchariflorus genes based on homology, core markers and RNA-seq alignments stats. Raw data and further metadata are available under Bioproject PRJNA435476. Msac_v2.fasta: Unanchored whole-genome assembly (WGA) of M. sacchariflorus in FASTA format. Msac_v3.fasta: The previous WGA re-scaffolded with the M. sinensis public reference. Msac_v3.agp: Chromosomal position in the M. sinensis reference of the previous scaffolds in Msac_v3.fasta Msac_v2.gff3: Gene annotation of the unanchored WGA in GFF3 format, which contains 86,767 coding genes Msac_v3.gff3: Gene annotation of the anchored WGA in GFF3 format, which contains 69,049 coding genes Msac_v2.func_annot.tsv: Text table containing the functional annotation of the 86,767 coding genes in Msac_v2.gff3 Msac_v2.repeats_annotation.gff3: Repeats annotation (Repeatmasker) of the unanchored reference. Msac_v2.masked.fasta.gz: Repeats-masked version (Repeatmasker) of Msac_v2.fasta all.satsuma.blocks_Msac_v2-vs-Msin.gz: Every alignment from scaffolds in Msac_v3.fasta into M. sinensis reference Msac_v2.orthology_Msin.tsv: Ortologous between Msac_v2 and M. sinensis Msac_v3-vs-Msin.tsv: Ortologous between Msac_v3 and M. sinensis |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/record/4270235 |
| Title | Supplementary dataset to "Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus" |
| Description | Miscanthus sacchariflorus (Maxim.) Hack. is a C4 perennial rhizomatous biofuel grass crop. M. sacchariflorus is among the most widely distributed species within the genus, particularly at cold northern latitudes, and one of the progenitor species of the main biomass commercial crop M. × giganteus. We generated a 2.54 Gbps whole-genome assembly of the diploid M. sacchariflorus "Robustus 297" genotype, which represented ~59% of the expected genome size. We later anchored this assembly in the chromosomal-scale M. sinensis genome to improve its contiguity. We annotated 86,767 and 69,049 protein-coding genes in the unanchored and anchored, respectively. We estimated our assemblies include ~85% of the M. sacchariflorus genes based on homology, core markers and RNA-seq alignments stats. Raw data and further metadata are available under Bioproject PRJNA435476. Msac_v2.fasta: Unanchored whole-genome assembly (WGA) of M. sacchariflorus in FASTA format. Msac_v3.fasta: The previous WGA re-scaffolded with the M. sinensis public reference. Msac_v3.agp: Chromosomal position in the M. sinensis reference of the previous scaffolds in Msac_v3.fasta Msac_v2.gff3: Gene annotation of the unanchored WGA in GFF3 format, which contains 86,767 coding genes Msac_v3.gff3: Gene annotation of the anchored WGA in GFF3 format, which contains 69,049 coding genes Msac_v2.func_annot.tsv: Text table containing the functional annotation of the 86,767 coding genes in Msac_v2.gff3 Msac_v2.repeats_annotation.gff3: Repeats annotation (Repeatmasker) of the unanchored reference. Msac_v2.masked.fasta.gz: Repeats-masked version (Repeatmasker) of Msac_v2.fasta all.satsuma.blocks_Msac_v2-vs-Msin.gz: Every alignment from scaffolds in Msac_v3.fasta into M. sinensis reference Msac_v2.orthology_Msin.tsv: Ortologous between Msac_v2 and M. sinensis Msac_v3-vs-Msin.tsv: Ortologous between Msac_v3 and M. sinensis |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/record/4270234 |
| Title | Supporting data for "A Galaxy-based training resource for single-cell RNA-seq quality control and analyses" |
| Description | It is not a trivial step to move from single-cell RNA-seq (scRNA-seq) data production to data analysis. There is a lack of intuitive training materials and easy-to-use analysis tools, and researchers can find it difficult to master the basics of scRNA-seq quality control and the later analysis.
We have developed a range of practical scripts, together with their corresponding Galaxy wrappers, that make scRNA-seq training and quality-control accessible to researchers previously daunted by the prospect of scRNA-seq analysis. We implement a 'visualise-filter-visualise' paradigm through simple command-line tools that use the Loom format to exchange data between the tools. The point-and-click nature of Galaxy makes it easy to assess, visualise, and filter scRNA-seq data from short-read sequencing data. We have developed a suite of scRNA-seq tools that can be used for both training and more in-depth analyses. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Title | Tilapia genomic reads (various technologies) and assemblies |
| Description | Genomic data produce to enable the genome reconstruction of Oreochromis leucostictus |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | These resources enable the identification of the extent of wild population diversity |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB34359 |
| Title | Tilapia genomic reads (various technologies) and assemblies - Alcolapia grahami |
| Description | Genomic resources for the reconstruction of the genome of Alcolapia grahami |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | These resources enable the identification of the extent of wild population diversity |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB34375 |
| Title | Tilapia genomic reads (various technologies) and assemblies - Oreochromis esculentus |
| Description | Genomic data for the reconstruction of the genome of Oreochromis esculentus |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | These resources enable the identification of the extent of wild population diversity |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB33948 |
| Title | Tilapia genomic reads (various technologies) and assemblies - Oreochromis mossambicus |
| Description | Genomic sequencing data for the genome reconstruction of Oreochromis mossambicus |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | These resources enable the identification of the extent of wild population diversity |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB36511 |
| Title | Tilapia genomic reads (various technologies) and assemblies - Oreochromis rukwaensis |
| Description | Genomic resources for the reconstruction of the genome of Oreochromis rukwaensis |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | These resources enable the identification of the extent of wild population diversity |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB36513 |
| Title | Tilapia genomic reads (various technologies) and assemblies - Oreochromis urolepis |
| Description | Genomic resources for the assembly of the Oreochromis urolepis genome |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | These resources enable the identification of the extent of wild population diversity |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB34373 |
| Title | Tilapia genomic reads (various technologies) and assemblies - Oreochromis urolepis |
| Description | PRJEB34386 Illumina HiSeq 4000 paired end sequencing; Tilapia Genome |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | Tilapia breeding |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB34386 |
| Title | Tilapia genomic reads Oreochromis rukwaensis PRJEB36512 |
| Description | PRJEB36512 Illumina NovaSeq 6000 paired end sequencing; Tilapia Genomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | Tilapia breeding |
| URL | https://www.ebi.ac.uk/ena/browser/text-search?query=PRJEB36512 |
| Title | Tilapia genomic reads: Oreochromis mossambicus |
| Description | PRJEB34388 |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | Tilapia genomic resources |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB34388 |
| Title | Tilapia genomic resources Oreochromis urolepis |
| Description | Oreochromis urolepis: 10x Chromium |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | Tilapia breeding |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB34385 |
| Title | Trifolium pratense reference |
| Description | We assembled 309 Mb of the red clover genome in 39,904 scaffolds. Half of the assembly was contained in 353 scaffolds (N50 = 223 Kb), while 1054 scaffolds longer than 50 Kbp contained another 25%. We annotated 40,868 genes and 42,223 transcripts. Of those, 22,042 genes were anchored onto the seven chromosomes. The reference is available through ensEMBL (https://plants.ensembl.org/Trifolium_pratense/Info/Index), Phytozome (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Tpratense) and Legumebase (https://legumeinfo.org/genomes/gbrowse/Tp2.0) |
| Type Of Material | Database/Collection of data |
| Year Produced | 2015 |
| Provided To Others? | Yes |
| Impact | Enhancing red clover's role in sustainable agriculture requires genetic improvement of persistency, disease resistance, and tolerance to grazing. To help address these challenges, we assembled a chromosome-scale reference genome for red clover. We observed large blocks of conserved synteny with the model legume Medicago truncatula and estimated that the two species diverged ~23 million years ago. Among the 40,868 annotated genes in red clover, we identified gene clusters involved in biochemical pathways of importance for forage quality and livestock nutrition. |
| URL | https://plants.ensembl.org/Trifolium_pratense/Info/Index |
| Title | Watkins core collection re-sequencing data |
| Description | Re-sequence data for the Watkins collection |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | International collabration |
| URL | https://grassroots.tools/data/under_license/toronto/ |
| Title | Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes |
| Description | Cichlid fish of the genus Oreochromis form the basis of the global tilapia aquaculture and fisheries industries. Broodstocks for aquaculture are often collected from wild populations, which in Africa may be from locations containing multiple Oreochromis species. However, many species are difficult to distinguish morphologically, hampering efforts to maintain good quality farmed strains. Additionally, non-native farmed tilapia populations are known to be widely distributed across Africa and to hybridize with native Oreochromis species, which themselves are important for capture fisheries. The morphological identification of these hybrids is particularly unreliable. Here, we describe the development of a single nucleotide polymorphism (SNP) genotyping panel from whole-genome resequencing data that enables targeted species identification in Tanzania. We demonstrate that an optimized panel of 96 genome-wide SNPs based on FST outliers performs comparably to whole genome resequencing in distinguishing species and identifying hybrids. We also show this panel outperforms microsatellite-based and phenotype-based classification methods. Case studies indicate several locations where introduced aquaculture species have become established in the wild, threatening native Oreochromis species. The novel SNP markers identified here represent an important resource for assessing broodstock purity in hatcheries and helping to conserve unique endemic biodiversity. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| Impact | The SNP design enabling species discrimination and hybrid identification will be of use for breeders in East Africa to survey existing stocks, prevent contamination and hybridization. The same design will be of interest to local authorities in East Africa in genotyping wild populations and stocks informing conservation actions and identifying potential stocks for aquaculture. We are collaborating with breeders in East Africa (Lake Victoria Fisheries Organization), CGIAR Research Center, WorldFish, and local authorities to build their capacity in managing and improving their aquaculture stocks. |
| URL | http://datadryad.org/stash/dataset/doi:10.5061/dryad.h44j0zpmg |
| Title | Whole genome sequencing of 150 common bean landraces from South America |
| Description | 150 common bean landraces were obtained from international genebanks, grow and DNA extracted. Samples were sequenced using Illumina short-read technology to a coverage of approx. 20X per sample. Data is being deposited in genomic repositories, namely EBI's nt archive. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | No |
| Impact | This dataset is being analysed by both teams in the UK and Colombia using different approaches (diversity analysis, phenotype-genotype association and genotype-environment association) to clarify several hypothesis regarding the adaptation of common bean to future climatic scenarios. |
| Title | genome and transcriptome of Oreochromis mossambicus |
| Description | Genome and transcriptome for Oreochromis mossambicus |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | This data set enable the generation of the tilapia elite strain (GIFT) genome completion and analysis |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB49245 |
| Title | promoter exon capture data |
| Description | The data contain the design space for the promoter and exon used in our capture |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Whole genome shotgun re-sequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome making it difficult to unambiguously assign variation. Re-sequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. We present two gold standard capture probe sets for hexaploid bread wheat, a gene and a promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. The capture probe sets effectively enrich the high confidence genes and promoters that were identified in the genome alongside a large proportion of the low confidence genes and promoters. We use a capture design employing an 'island strategy' to enable analysis of the large gene/promoter space of wheat with only 2x160 Mb NimbelGen probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations. Here, we release the targeted sequence of the capture probe sets on the wheat RefSeqv1, the design space that was used to tile our capture probes across and finally the positions of the probes themselves across this design space for both the gene and promoter capture probe sets. |
| URL | https://opendata.earlham.ac.uk/wheat/under_license/toronto/Gardiner_2018-07-04_Wheat-gene-promoter-c... |
| Description | Agrosavia-Earlham Institute MoU |
| Organisation | Colombian Agricultural Research Corporation |
| Country | Colombia |
| Sector | Charity/Non Profit |
| PI Contribution | Genomic approaches to access the crop diversity at the Colombian National Germplasm collection hosted by Agrosavia/Corpoica |
| Collaborator Contribution | Making available genetic resources and evaluation trials |
| Impact | Two pilot projects on Musa accessions and legume forages to identify genome-wide trait-SNP associations for molecular breeding. |
| Start Year | 2019 |
| Description | Analysing Tilapia species diversity and salinity adaptation in Lake Rukwa, Tanzania. |
| Organisation | Bangor University |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Full organisation and expenses for Lake Rukwa, Tanzania sampling expedition to collect Oreochromis esculentus and Oreochromis rukwaensis tissue samples. This includes sampling equipment/reagents, travel, accomodation and subsistance. This also included species handling and tissue dissection training for University of Dar Es Salaam and University of Dodoma collaborators. |
| Collaborator Contribution | Levinus Leonard and Edward A. Moto (University of Dar Es Salaam and University of Dodoma) aided 1. Organisation and permits for sampling in Lake Rukwa upon dealing directly with the lake fisheries officers 2. Private boat hire 3. Transport hire and accomodation 4. Species identification, tissue sampling and dissection Alexandra Tyers (Bangor University) aided in tissue sampling and dissection. |
| Impact | Tissue samples from O. rukwaensis and O. esculentus have been sequenced to include: 1. Genotyping several individuals including variant analyses for species identification, admixture and phylogenetics 2. RNA-Seq of gill, liver and kidney for genome annotation and gene expression analyses Both will be published. |
| Start Year | 2017 |
| Description | Analysing Tilapia species diversity and salinity adaptation in Lake Rukwa, Tanzania. |
| Organisation | University of Dar es Salaam |
| Country | Tanzania, United Republic of |
| Sector | Academic/University |
| PI Contribution | Full organisation and expenses for Lake Rukwa, Tanzania sampling expedition to collect Oreochromis esculentus and Oreochromis rukwaensis tissue samples. This includes sampling equipment/reagents, travel, accomodation and subsistance. This also included species handling and tissue dissection training for University of Dar Es Salaam and University of Dodoma collaborators. |
| Collaborator Contribution | Levinus Leonard and Edward A. Moto (University of Dar Es Salaam and University of Dodoma) aided 1. Organisation and permits for sampling in Lake Rukwa upon dealing directly with the lake fisheries officers 2. Private boat hire 3. Transport hire and accomodation 4. Species identification, tissue sampling and dissection Alexandra Tyers (Bangor University) aided in tissue sampling and dissection. |
| Impact | Tissue samples from O. rukwaensis and O. esculentus have been sequenced to include: 1. Genotyping several individuals including variant analyses for species identification, admixture and phylogenetics 2. RNA-Seq of gill, liver and kidney for genome annotation and gene expression analyses Both will be published. |
| Start Year | 2017 |
| Description | Analysing Tilapia species diversity and salinity adaptation in Lake Rukwa, Tanzania. |
| Organisation | University of Dodoma |
| Country | Tanzania, United Republic of |
| Sector | Academic/University |
| PI Contribution | Full organisation and expenses for Lake Rukwa, Tanzania sampling expedition to collect Oreochromis esculentus and Oreochromis rukwaensis tissue samples. This includes sampling equipment/reagents, travel, accomodation and subsistance. This also included species handling and tissue dissection training for University of Dar Es Salaam and University of Dodoma collaborators. |
| Collaborator Contribution | Levinus Leonard and Edward A. Moto (University of Dar Es Salaam and University of Dodoma) aided 1. Organisation and permits for sampling in Lake Rukwa upon dealing directly with the lake fisheries officers 2. Private boat hire 3. Transport hire and accomodation 4. Species identification, tissue sampling and dissection Alexandra Tyers (Bangor University) aided in tissue sampling and dissection. |
| Impact | Tissue samples from O. rukwaensis and O. esculentus have been sequenced to include: 1. Genotyping several individuals including variant analyses for species identification, admixture and phylogenetics 2. RNA-Seq of gill, liver and kidney for genome annotation and gene expression analyses Both will be published. |
| Start Year | 2017 |
| Description | CGIAR Excellence in Breeding (EiB) |
| Organisation | CGIAR |
| Department | CGIAR Excellence in Breeding (EiB) |
| Country | France |
| Sector | Charity/Non Profit |
| PI Contribution | Coordinating our genotyping projects on heterozygous allotetraploids with their work in autotetraploids |
| Collaborator Contribution | Working group that offers expert guidance, resources, shared service platforms, and access to data on cutting edge technologies and practices. |
| Impact | EiB is generating new data in species of our interest |
| Start Year | 2021 |
| Description | Collaboration - WorldFish |
| Organisation | Worldfish |
| Country | Malaysia |
| Sector | Charity/Non Profit |
| PI Contribution | As part of this collaboration we have been generating genomic resources and identifying the genetic bases of traits of interest |
| Collaborator Contribution | WorldFish has been providing samples for sequencing, genetic data |
| Impact | 10.1186/s12864-022-09065-8 |
| Start Year | 2020 |
| Description | Collaboration on AI for bioscience with the Alan Turing Institute |
| Organisation | Alan Turing Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Our team have identified areas of Bioscience research that can be investigated using AI techniques. We have hired fellows supported by this award that will have 12 months training in AI from our collaborative partner |
| Collaborator Contribution | Advice and mentorship in the application of AI. A training programme is to be provided to the hired fellows. |
| Impact | This is a very new award |
| Start Year | 2020 |
| Description | Collaboration with Cornell University, George Mason University - Graham Etherington |
| Organisation | Cornell University |
| Department | Weill Cornell Medicine |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The group is developing computational pipelines to identify and characterise deleterious variants, including copy number variants, associated with inbreeding. |
| Collaborator Contribution | The collaborators are providing samples from endangered black footed ferrets as well as sequencing data from those samples |
| Impact | Oral presentation: Conservation Genomics of the Black-footed ferret Conservation Genomics at the Population Level Conference 2022 |
| Start Year | 2022 |
| Description | Collaboration with Cornell University, George Mason University - Graham Etherington |
| Organisation | George Mason University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The group is developing computational pipelines to identify and characterise deleterious variants, including copy number variants, associated with inbreeding. |
| Collaborator Contribution | The collaborators are providing samples from endangered black footed ferrets as well as sequencing data from those samples |
| Impact | Oral presentation: Conservation Genomics of the Black-footed ferret Conservation Genomics at the Population Level Conference 2022 |
| Start Year | 2022 |
| Description | Collaboration with Natural History Museum and Trinity College Dublin |
| Organisation | Imperial College London |
| Department | Department of Life Sciences |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | As part of the collaboration myself and Will Nash have been contributing computational analyses of contemporary and museum samples genetic data. We contributed sequencing for contemporary populations |
| Collaborator Contribution | The partners (Trinity College Dublin, Imperial College London, and Natural History Museum London) have contributed the sequences of museum specimens dating from the late 1800s |
| Impact | Publication: First large-scale quantification study of DNA preservation in insects from natural history collections using genome-wide sequencing. https://doi.org/10.1111/2041-210X.13945 |
| Start Year | 2019 |
| Description | Collaboration with Natural History Museum and Trinity College Dublin |
| Organisation | Natural History Museum |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | As part of the collaboration myself and Will Nash have been contributing computational analyses of contemporary and museum samples genetic data. We contributed sequencing for contemporary populations |
| Collaborator Contribution | The partners (Trinity College Dublin, Imperial College London, and Natural History Museum London) have contributed the sequences of museum specimens dating from the late 1800s |
| Impact | Publication: First large-scale quantification study of DNA preservation in insects from natural history collections using genome-wide sequencing. https://doi.org/10.1111/2041-210X.13945 |
| Start Year | 2019 |
| Description | Collaboration with Natural History Museum and Trinity College Dublin |
| Organisation | Trinity College Dublin |
| Department | Smurfit Institute of Genetics |
| Country | Ireland |
| Sector | Academic/University |
| PI Contribution | As part of the collaboration myself and Will Nash have been contributing computational analyses of contemporary and museum samples genetic data. We contributed sequencing for contemporary populations |
| Collaborator Contribution | The partners (Trinity College Dublin, Imperial College London, and Natural History Museum London) have contributed the sequences of museum specimens dating from the late 1800s |
| Impact | Publication: First large-scale quantification study of DNA preservation in insects from natural history collections using genome-wide sequencing. https://doi.org/10.1111/2041-210X.13945 |
| Start Year | 2019 |
| Description | Collaboration with Oxford Nanopore Technologies |
| Organisation | Oxford Nanopore Technologies |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | As part of the upcoming EI strategic programme we will be producing novel protocols for single cell long read RNA and DNA sequencing as well as novel approaches to detect DNA replication through base modification |
| Collaborator Contribution | ONT will contribute through providing expertise in machine learning models applications (base modification), technology solutions and protocols developments for single cell RNA / DNA seq |
| Impact | Engagement with ONT on March 7th to develop the collaboration as part of the upcoming ISPs |
| Start Year | 2022 |
| Description | Collaboration with University of Arizona - Ryan GutenKunst |
| Organisation | University of Arizona |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Collaboration with Ryan GutenKunst to further apply demographic modelling to pollinator populations |
| Collaborator Contribution | The partner provided help and guidance in the application of a method they developed for demographic modelling (dadi) |
| Impact | manuscript preparation |
| Start Year | 2022 |
| Description | Developing a concept for a prototype Air-seq device |
| Organisation | Technology Partnership Plc |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Earlham developed the Air-seq workflow for detection of biological material from air using bespoke sequencing and bioinofmratics pipeline. Earlham is looking to develop commercial solutions based on this technology and commercialise via a spin-out. The prototype development will inform the business plan and investment needed. |
| Collaborator Contribution | Expertise in engineering of diagnostic and detection devices for the life science applications. |
| Impact | Technical products |
| Start Year | 2022 |
| Description | EI-QIB collaboration in microbial genomics |
| Organisation | Quadram Institute Bioscience |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | There is a joint PDRA post in this area and now a joint PI group. EI is undertaking bioinformatics development and single cell and genomic analysis. We also provide HPC capability. |
| Collaborator Contribution | The team at QIB are undertaking the evolutionary experiments, providing samples and data. We work closely with the Webber and Kingsley groups in this area. |
| Impact | The collaboration involved microbiology and bioinformatics. |
| Start Year | 2015 |
| Description | Earlham-GDSC collaboration |
| Organisation | University of Sussex |
| Department | School of Life Sciences Sussex |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We are contributing single-molecule expertise in DNA replication to our joint collaborative project to determine the role of Senataxins in protecting genome stability. This work is funded by a joint BBSRC grant. |
| Collaborator Contribution | The collaborators bring expertise in genome stability research and preliminary data on the role that Senataxins may play. |
| Impact | Ongoing collaboration. |
| Start Year | 2022 |
| Description | EcoSpray |
| Organisation | Ecospray Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Use of genomics and bioinformatics to analyse soil microbiome |
| Collaborator Contribution | Knowledge and expertise in developing nematicides |
| Impact | Engagement activities |
| Start Year | 2022 |
| Description | Ecospray collaboration on soil health |
| Organisation | Ecospray Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | We are providing method development and tools for this joint project on soil health |
| Collaborator Contribution | Ecospray are providing the sampling for this joint project on soil health |
| Impact | No outputs or outcomes, this project is in the set-up phase. |
| Start Year | 2019 |
| Description | Elsom seeds collaboration - a low-cost marker discovery platform to unlock the breeding potential of orphan crops. |
| Organisation | Elsoms Seeds |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Scientific understanding and technical expertise from EI |
| Collaborator Contribution | Elsom provided material, biological question and commercial application |
| Impact | Tis collaboration has led to a KTN SPARKS award |
| Start Year | 2019 |
| Description | Evolution of cis-regulatory activity associated with rapid phenotypic diversity |
| Organisation | University of Basel |
| Country | Switzerland |
| Sector | Academic/University |
| PI Contribution | To further analyse gene regulatory network evolution associated with traits of cichlid phenotypic diversity, we 1. developed and optimised the assay for transposable active chromatin sequencing (ATAC-seq) protocol for cichlid fish tissues, and 2. characterised and compared the tissue-specific activity of regulatory regions in representative species of the great lake radiations. This can then be carried over |
| Collaborator Contribution | Our collaborators include Domino Joyce (University of Hull) and Walter Salzburger (University of Basel) that provided live fish and tissues to isolate cells for ATAC-Seq. |
| Impact | We have: 1. Developed and optimised the assay for transposable active chromatin sequencing (ATAC-seq) protocol for cichlid fish tissues, and 2. Carried out a single lane of Hi-Seq sequencing of 20 ATAC and genomic DNA control libraries to test the protocol Since the protocol has been largely optimised, we are now preparing libraries for more tissue samples and species for higher-coverage sequencing. |
| Start Year | 2017 |
| Description | Evolution of cis-regulatory activity associated with rapid phenotypic diversity |
| Organisation | University of Hull |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | To further analyse gene regulatory network evolution associated with traits of cichlid phenotypic diversity, we 1. developed and optimised the assay for transposable active chromatin sequencing (ATAC-seq) protocol for cichlid fish tissues, and 2. characterised and compared the tissue-specific activity of regulatory regions in representative species of the great lake radiations. This can then be carried over |
| Collaborator Contribution | Our collaborators include Domino Joyce (University of Hull) and Walter Salzburger (University of Basel) that provided live fish and tissues to isolate cells for ATAC-Seq. |
| Impact | We have: 1. Developed and optimised the assay for transposable active chromatin sequencing (ATAC-seq) protocol for cichlid fish tissues, and 2. Carried out a single lane of Hi-Seq sequencing of 20 ATAC and genomic DNA control libraries to test the protocol Since the protocol has been largely optimised, we are now preparing libraries for more tissue samples and species for higher-coverage sequencing. |
| Start Year | 2017 |
| Description | Genetic basis of adaptation to extreme environments: insights from the genome of Alcolapia grahami |
| Organisation | University College London |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Sequencing of A. grahami genome with short and long read technology and transcriptome sequencing |
| Collaborator Contribution | Our collaborators Julia Day and Kanchon Dasmahapatra are able to source live Alcolapia and preserved fish samples for sequencing. As such we have used O. amphimelas for whole genome and transcriptome sequencing. |
| Impact | O. amphimelas DNA/RNA is currently being extracted for genome and transcriptome sequencing. For the purpose of this collaboration, we are also improving the Alcolapia genome assembly for chromosome level contiguity. Our collaborators are interested in carrying out functional testing of interesting candidate genes in Alcolapia that may be important in their adaptations. Julia Day and Lewis White recently travelled to Tanzania, bringing back live Alcolapia to the UK to set up experimental stocks for functional testing. As such, Lewis White has succcesfully carried out gene knock-outs and rescue in Alcolapia that will be useful for future functional validations. |
| Start Year | 2017 |
| Description | Genetic basis of adaptation to extreme environments: insights from the genome of Alcolapia grahami |
| Organisation | University of York |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Sequencing of A. grahami genome with short and long read technology and transcriptome sequencing |
| Collaborator Contribution | Our collaborators Julia Day and Kanchon Dasmahapatra are able to source live Alcolapia and preserved fish samples for sequencing. As such we have used O. amphimelas for whole genome and transcriptome sequencing. |
| Impact | O. amphimelas DNA/RNA is currently being extracted for genome and transcriptome sequencing. For the purpose of this collaboration, we are also improving the Alcolapia genome assembly for chromosome level contiguity. Our collaborators are interested in carrying out functional testing of interesting candidate genes in Alcolapia that may be important in their adaptations. Julia Day and Lewis White recently travelled to Tanzania, bringing back live Alcolapia to the UK to set up experimental stocks for functional testing. As such, Lewis White has succcesfully carried out gene knock-outs and rescue in Alcolapia that will be useful for future functional validations. |
| Start Year | 2017 |
| Description | Genetic basis of adaptation to extreme environments: insights from the genome of the soda tilapia (Alcolapia grahami) |
| Organisation | South Eastern Kenya University |
| Country | Kenya |
| Sector | Academic/University |
| PI Contribution | Full expenses for Geraldine Kavembe (SEKU) to sample Alcolapia tissue samples from Lake Magadi, Kenya. This included sampling equipment/reagents, travel, accomodation and subsistance. |
| Collaborator Contribution | Dr Geraldine Kavembe (SEKU) contributed in the: 1. Organisation and permits for sampling in Lake Magadi by dealing with the appropriate fisherie officers 2. Private boat hire 3. Transport hire and accomodation 4. Species identification, tissue sampling and dissection 5. Sample shipping |
| Impact | Tissue samples from A. grahami have been sequenced to include: 1. Whole genome sequencing using short Illumina and Nanopore reads (10x Chromium pending). We currently have a whole genome assembly based on the short reads that is currently being supplemented with the long read data. 2. RNA-Seq of gill and liver for genome annotation and gene expression analyses. Both will be published. Also, Tarang Mehta hosted a year in industry student (Nicole Forrester) at the Earlham Institute where she extracted RNA, prepared cDNA libraries and sequenced the trnascriptomes of Alcolapia and other tilapia tissue samples. |
| Start Year | 2017 |
| Description | Genome 10K Consortium |
| Organisation | University of California, Davis |
| Department | UC Davis Genome Cente |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The G10K consortium is an international consortium of tissue curators, biologists, conservationists, genome scientists, computer scientists, outreach educators, and more. Federica Di Palma is a council member of the Consortium and has provided advice to the current ongoing projects. Organised meetings and contributed talks to several workshops and meetings. |
| Collaborator Contribution | The G10K leadership and community of scientists built an infrastructure from sample collection to genome sequencing, assembly, annotation, alignments, public data releases, and analyses for publications. |
| Impact | Collaboration is multidisciplinaryand includes tissue curators, biologists, conservationists, genome scientists, computer scientists, outreach educators, and more from different countries. Outputs include press releases, workshops, meetings, publications. |
| Start Year | 2011 |
| Description | Google Cloud |
| Organisation | |
| Department | Google UK |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | As part of this collaboration we will make available high dimension data sets and pipelines for analyses |
| Collaborator Contribution | As part of the collaboration Google Cloud will facilitate access to data sets and online analyses |
| Impact | This collaboration contributed to the submission of the CELLGEN ISP |
| Start Year | 2022 |
| Description | IBM |
| Organisation | IBM |
| Department | IBM Research in the UK |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | As part of this collaboration the Earlham Institute is providing data, genomic expertise to the collaborator |
| Collaborator Contribution | IBM is providing expertise in machine learning application, and software development |
| Impact | no output yet |
| Start Year | 2022 |
| Description | IBM |
| Organisation | IBM |
| Department | IBM UK Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | This project aims to leverage these new resources together with large gene expression data sets to reconstruct regulatory networks controlling important traits. With outputs feeding directly into UK and International wheat research and UK wheat breeding programmes. The collaboration focuses around two large data sets: the first, a high resolution time series data set for wheat and the second, a developmental time course for 16 international elite cultivars. The project aims to: 1. Develop normalisation methods for the transcriptome data sets (RNA-seq data), specific for dealing with the complexities of time course data and a complex polyploid genome. Benchmark these new approaches against existing tools. 2. Develop AI pattern matching algorithms to identify gene-expression modules and correlate these with biological processes. Use pattern matching algorithms to interrogate the high resolution data sets and to identify differences between regulatory networks in elite cultivars 3. Correlate changes in temporal or developmental expression patterns with changes in promoter architecture 4. Use network inference, co-expression and gene modules to reconstruct regulatory networks. Identify how network structure changes over time and between cultivars. This project will have impact for scientists as it will address fundamental questions about temporal regulation of processes in wheat and how a complex networks work across multiple genomes within a polyploid. By comparing networks across elite cultivars it will also have an impact for UK and international wheat breeders, identification of how breeding programmes have changed the architure of regulatory networks. This will have important impact for the selection of future networks for breeders to target or for assessing the selection of breeding material. It will allow breeders to make full use of the new resources and technologies. To ensure the impact to the UK industry is realised we aim to present this work a UK networking meeting and to visit and involve three private UK breeding companies RAGT, KWS and Elsoms seeds in early output from the project. |
| Collaborator Contribution | IBM have are involved in applying ML and AI approaches to analyse gene expression data in wheat and reconstruct gene networks. |
| Impact | https://github.com/AHallLab/PredictingCircadianTime Joint grant with the Alan Turing Institute https://doi.org/10.1101/2021.02.04.429826 |
| Start Year | 2017 |
| Description | International Center for Tropical Agriculture (CIAT), Cali, Colombia |
| Organisation | CGIAR |
| Department | International Center for Tropical Agriculture |
| Country | Colombia |
| Sector | Charity/Non Profit |
| PI Contribution | Organisation of a workshop hosted at Aberystwyth University with attendants from CIAT to explore future projects and funding opportunities. Training of a MSc student at Earlham Institute (Formerly, TGAC) during 3 months. Visit of Jose De Vega (Earlham), and Leif Skot and Charlotte Jones (IBERS) to CIAT. |
| Collaborator Contribution | Hosting Jose De Vega (Earlham), Sita Ghimere (ILRI), and Leif Skot and Charlotte Jones (IBERS) for 1 week in CIAT HQ in Cali, Colombia. Designated and support Alex Silva stay in UK. |
| Impact | We are applying together for several funding, including the former Newton Fund, in progress RCUK's Grow RC, and planning for the next BBSRC's GCRF. |
| Start Year | 2014 |
| Description | KAUST |
| Organisation | King Abdullah University of Science and Technology (KAUST) |
| Department | Biological and Environmental Science and Engineering Division |
| Country | Saudi Arabia |
| Sector | Academic/University |
| PI Contribution | Co-supervision KAUST's PhD candidate Saule Mussurova |
| Collaborator Contribution | Expertise on salinity tolerance |
| Impact | Supervision of the bioinformatics pipelines for PhD project; Coordination meeting during PAG XXVII; |
| Start Year | 2019 |
| Description | KWS Harnessing wild sugar beet diversiy |
| Organisation | KWS Group |
| Country | Germany |
| Sector | Private |
| PI Contribution | Knowledge of the wild and agricultural beet rust pathosystem combined with NGS expertise meant that we could put together PhD proposal which offered an opportunity to be able to develop new methods which could help identify novel pathogen resistance directly in wild hosts. |
| Collaborator Contribution | KWS provided input to the project design have promised significant resource (cost and in kind) to allow controlled trials and sequencing to take place. KWS have also granted access to the use of their labs for cloning and other biotechnology. |
| Impact | This collaboration resulted in a successful PhD iCASE application which will begin later 2019. |
| Start Year | 2018 |
| Description | Kromek |
| Organisation | Kromek Group plc |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Kromek approached us about applying for DARPA funding for a project to sequence airborne DNA for threat monitoring (see separate grant). We supplied expertise in sequencing, bioinformatics and molecular biology and helped to write a grant proposal. |
| Collaborator Contribution | Kromek have engineering expertise and have previously delivered a DARPA radiation detector contract. |
| Impact | Successful application of funding to DARPA. Continued discussions on future work. |
| Start Year | 2018 |
| Description | Molecular Medicine Catapult - Psychiatry Consortium |
| Organisation | Medicines Discovery Catapult |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | As part of the Psychaitry Consortium my group will be leading on all the bioinformatic analyses for the project aiming to identfy transcripts with tissue specific expression for a primary candidate in neuropsychaitric disorder. The aim it be able to identify proteins with brain specific expressions that can be used as targets for frug development |
| Collaborator Contribution | The University of Oxford leads on the molecular work, generating the data that are analysed by my group. As industrial partners, lead scientists at Boehringer Ingelheim and Biogen provide feedback on their needs, the selection of transcripts to pursue, further analyses. |
| Impact | The project started n December 1st 2020, it is too early to list outputs. The major outcome is the funding to support the work as part of the project (£120,000). The collaboation is highly disciplinary inculding molecular biology, neurobiology and bioinformatics. |
| Start Year | 2020 |
| Description | Moussa Benhamed |
| Organisation | University of Paris-Saclay |
| Country | France |
| Sector | Academic/University |
| PI Contribution | WE are collaborating with Moussa Benhamed to develop Next generation sequencing technology to explore the 3D structural organisation in the wheat nucleus and epigenetic regulation in wheat. |
| Collaborator Contribution | The have built sequencing libraries for design future wheat and are providing staff training |
| Impact | Production of sequencing libraries analysis of histone modification, 3D genome structural organisation and Chromatin accessibility. |
| Start Year | 2018 |
| Description | National Biofilms Innovation Centre |
| Organisation | National Biofilms Innovation Centre |
| Sector | Private |
| PI Contribution | Information about researchers working on biofilms |
| Collaborator Contribution | Establish a network of research and innovation capacity catalysing collaboration with industry in the study of biofilms to achieve breakthrough innovation |
| Impact | No outcomes or outputs |
| Start Year | 2020 |
| Description | National Research Center for Coffee CENICAFE MoU |
| Organisation | National Research Center for Coffee |
| Country | Colombia |
| Sector | Public |
| PI Contribution | We analysed dataset facilitated by the the National Research Center for Cofee as part of our project to to characterize the genomic architecture of the causal agent of the American Leaf Spot in coffee, Mycena citricolor. |
| Collaborator Contribution | The National Research Center for Coffee provided Pacbio sequencing for our project. They also developed an infection assay coffee-Mycena to provide samples for our projects. |
| Impact | Characterization of infection and candidate virulence factors involved in the coffee-Mycena that can be exploited for the marker-assisted selection of coffee varieties. |
| Start Year | 2020 |
| Description | Plymouth Dental School collaboration |
| Organisation | University of Plymouth |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Richard Leggett has been asked to be on a PhD supervisory team for a project looking at using the MinION for oral screening in dentistry. Richard has also been named as a collaborator on a grant looking at metagenomics of the oral microbiome. This work came as a result of our work on MinION sequencing of preterm babies. |
| Collaborator Contribution | Applied for PhD studentship and grant. |
| Impact | Grant application. |
| Start Year | 2019 |
| Description | RBG Kew |
| Organisation | Royal Botanic Gardens, Kew |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | Joint PhD studentship |
| Collaborator Contribution | Joint PhD studentship |
| Impact | Joint PhD studentship |
| Start Year | 2021 |
| Description | The 200 mammals project: sequencing genomes by a novel cost-effective method, yielding a high resolution annotation of the human genome. |
| Organisation | Broad Institute |
| Country | United States |
| Sector | Charity/Non Profit |
| PI Contribution | Part of the consortium which is analysing the data. |
| Collaborator Contribution | Proposal submitted to NHGRI and funded |
| Impact | In combination with the ~50 already existing high quality placental mammalian assemblies, the project produced the sequence of one placental mammal per family for a total of 150 species. The new assembly method: DISCOVAR de novo, was used to allow the production of a good quality novel genome assembly using only a single sequencing library type. |
| Start Year | 2016 |
| Description | Tilapia for sustainable fish production while maintaining Biodiversity |
| Organisation | Worldfish |
| Country | Malaysia |
| Sector | Charity/Non Profit |
| PI Contribution | F. Di Palma is a research partner in the new CGIAR research program on fish agri-food systems. |
| Collaborator Contribution | J. Benzie from WorldFish is a research partner on Earlham BBSRC Core Strategic programme "Genomics for Food Security" for the Natural diversity and adaptation in aquaculture research activities. |
| Impact | Partnership yielded activities in Core strategic programmes and training workshops and further partnerships.I t is multidisciplinary including genomics, informatics, breeding expertise, Fisheries officers from tanzania, Ministry of aquaculture and Life stocks in Tanzania, further academic institutions in Tanzania Uk and Sweden, ecology, and environmental policy as well as disease resistance. |
| Start Year | 2016 |
| Description | Tropic Biosciences |
| Organisation | Tropic Biosciences Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Our iCASE PhD project to answer fundamental questions on the diversity of immunity receptors in the Musa genus, and the relation of this diversity with genome composition and TR4 response. To contribute to developing resistant varieties, the project will build on genomic resources to identify candidate genes and alleles to facilitate future endeavours. |
| Collaborator Contribution | Tropic Biosciences is an NRP-based biotechnology company developing improved commercial varieties of banana and other tropical crops using CRISPR gene editing technologies. Tropic Biosciences has been developing novel Cavendish banana mutants that show resistance to TR4 or longer shelf lives. In addition to domain knowledge on banana and R genes, Tropic Biosciences will contribute their expertise on how to establish and propagate banana plantlets in CER control conditions, and how to perform fungal infection bioassays in banana plants. |
| Impact | One joint PhD studenship |
| Start Year | 2021 |
| Description | Tropic Biosciences |
| Organisation | Tropic Biosciences Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | As part of this collaboration we will be sequencing materials from Tropic Bioscience to identify variants segregating in their stocks, we will develop novel protocols for early assessment of plant embryos |
| Collaborator Contribution | As part of the collaboration Tropic Bioscience is providing material (tissues, DNA) and expertise |
| Impact | The collaboration contributed to the submission of the CELLGEN ISP |
| Start Year | 2022 |
| Description | University of Los Andes, Universy del Rosario and Earlham Institute (RAEng partnership) |
| Organisation | Del Rosario University |
| Country | Colombia |
| Sector | Academic/University |
| PI Contribution | This is a consortium to promote capacity building in data science in Colombia. Funding was awarded by the Newton Fund - Royal Academy of Eng. |
| Collaborator Contribution | This is a consortium to promote capacity building in data science in Colombia. Funding was awarded by the Newton Fund - Royal Academy of Eng. |
| Impact | two training workshops held at Uniandes campus in 2019 one Data Science summer school in 2020 |
| Start Year | 2020 |
| Description | University of Los Andes, Universy del Rosario and Earlham Institute (RAEng partnership) |
| Organisation | University of the Andes |
| Country | Colombia |
| Sector | Academic/University |
| PI Contribution | This is a consortium to promote capacity building in data science in Colombia. Funding was awarded by the Newton Fund - Royal Academy of Eng. |
| Collaborator Contribution | This is a consortium to promote capacity building in data science in Colombia. Funding was awarded by the Newton Fund - Royal Academy of Eng. |
| Impact | two training workshops held at Uniandes campus in 2019 one Data Science summer school in 2020 |
| Start Year | 2020 |
| Description | Visiting researcher Dr Hannele Lindqvist from the International Potato Centre (CIP, Lima). |
| Organisation | International Potato Center |
| Country | Peru |
| Sector | Charity/Non Profit |
| PI Contribution | Know-how potato GWAS computational analysis |
| Collaborator Contribution | Visiting researcher to analysed own data |
| Impact | Preprint in Biorxiv on the analysis in tetraploid potato |
| Start Year | 2019 |
| Description | Visiting researcher at Cenicaña (Dr Nasmille L Larke-Mejia) |
| Organisation | Centro de Investigación de la Caña de Azúcar de Colombia |
| Country | Colombia |
| Sector | Charity/Non Profit |
| PI Contribution | As a postdoctoral researcher for the GROW Colombia project, I will be analysing the sequence data of the experiment. This collaboration began in 2019 with the planning of the experiment, the fieldwork was done in 2020 and we will analyse the sequence in 2021. |
| Collaborator Contribution | Our Colombian collaborators have engaged and contributed to the experimental plan, search for the appropriate sampling sites, search of other national collaborators to work with to achieve the objectives of the project. Because of COVID we were not able to travel to Colombia to do some of the field work in April and September 2020. Our collaborators have been proactive in looking for solutions, looking for people inside the organization that could do all the sampling and doing the essential lab work and DNA extractions. |
| Impact | Application for further funding with the Newton Fund (unsuccessful) |
| Start Year | 2019 |
| Description | Wild beet host-pathogen genomic surveillance |
| Organisation | U.S. Department of Agriculture USDA |
| Country | United States |
| Sector | Public |
| PI Contribution | Knowledge exchange to summarise our advances in using wild beet pathogen (rust) genomic diversity to identify virulence important for pathogen success on the sugar beet crop. We also outlined our wild beet sequencing project in which, in collaboration with KWS, we have sequenced hundreds of wild beets and are assembling wild beet genomes. Our aims there are to identify novel resistance genes. |
| Collaborator Contribution | Our partners summarised their work on numerous sugar beet and pathogen work streams. We focussed primarily on their cercospora work which we identified was a key area for collaboration. This related to USDA expertise in pathogen wild and wet lab biology, their culture collection and understanding of the population genomics and pathology on sugar beet in the USA. |
| Impact | This collaboration has resulted in a proof of concept experimental proposal being submitted (and taken on) for the one year Earlham Institute Year in Industry program. Promising early results have inspired talks for funding a two year PDRA. |
| Start Year | 2022 |
| Description | Worldfish Tilapia MTA |
| Organisation | Worldfish |
| Country | Malaysia |
| Sector | Charity/Non Profit |
| PI Contribution | Sequencing and analysis of WorldFish GIFT strains |
| Collaborator Contribution | Sampling of WorldFish GIFT strains |
| Impact | None yet, project at early stage |
| Start Year | 2019 |
| Title | Air-seq IP |
| Description | Methods for DNA extraction, sequencing and analysis of aerosol samples. |
| IP Reference | |
| Protection | Protection not required |
| Year Protection Granted | 2018 |
| Licensed | Yes |
| Impact | As part of the DARPA funding (see funding), we are licensing our Air-seq technology to Kromek to build devices for biological threat monitoring. |
| Title | METHOD AND APPARATUS FOR DETECTING PATHOGENS |
| Description | We describe a method and system for detecting pathogens in a sample, particularly an air sample. The method is designed to run in real-time alongside sequencing processing of the sample so that results are quickly available to a user. Each input sequence read in the plurality of sequence reads is compared using a first classification algorithm and assigned to a taxon. An input sequence is classified as potentially pathogenic when the taxon to which the input sequence read is assigned corresponds to a pathogen taxon. Each input sequence read classified as potentially pathogenic is compared using a second classification algorithm to a plurality of target sequences in a second database which is selected based on the pathogen taxon. A confidence score is used as part of the decision-making process to decide if an individual read represents a genuine match to a pathogen. |
| IP Reference | WO2023131795 |
| Protection | Patent / Patent application |
| Year Protection Granted | 2023 |
| Licensed | No |
| Impact | We are in the process of developing a spinout company that will license this IP and realise impact. |
| Title | Adaptive Sequencing Enrichment model - hosting on the CyVerse UK e-infrastructure |
| Description | A shiny web application that provides an interactive implementation of a nanopore adaptive sequencing model. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | Enables users to plan their own adaptive sequencing experiments. |
| URL | https://readuntil.cyverseuk.org |
| Title | Alvis |
| Description | Tool to produce a range of production quality alignment diagrams based on the output of common aligner tools. Will also spot chimeric contigs/reads. |
| Type Of Technology | Software |
| Year Produced | 2019 |
| Open Source License? | Yes |
| Impact | An earlier version was used to create diagrams for the RenSeq paper. The tool is currently being used for analysis of genome assembly quality within EI. A paper on the tool will be submitted during 2019. |
| Title | Legopore |
| Description | Software to control the Lego DNA sequencer model built for public engagement. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | Hundreds of members of the public, adults and children, have used the software at one of our engagement events. |
| Title | MARTi demonstration server - hosting on the CyVerse UK e-infrastructure |
| Description | MARTi is software for real-time analysis of metagenomic sequence data. Cyverse UK hosts two instances of MARTi - one is a demonstration server for potential users to try out, one is a development server for sharing analysis with key collaborators. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | Requests for access to the software. |
| URL | http://marti.cyverseuk.org |
| Title | NanoOK RT software tool |
| Description | A real-time analysis tool for metagenomic classification and identification of antimicrobial resistances form nanopore sequence data. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | The software was developed for and initially used in our work with pre-term babies suffering from Necrotizing Enterocolitis. We are now working to apply it to a wide range of other application areas and have had discussions with a number of interested parties at national and international institutes. |
| Title | Pipeline for long non coding RNA identification |
| Description | Pipeline enabling long non coding identification taking as input RNA-Seq data, genome sequence, and annotation. The pipeline handle the read mapping, de noo transcript assembly, comparison with existing annotations to identify novel intergenic transcript, assess the coding potential of the noevl transcripts report those identified as non coding and at least 200 nt long. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2021 |
| Open Source License? | Yes |
| Impact | Long non codig RNAs are generally associated with gene expression regulation and previouly identified to have major roles in both animals and plant biology. The pipeline is organism agnostic, enabling the identification of lon non coding RNAs in any eukaryotic species. The aim is to make the pipeline available on Galaxy for the community to use. |
| URL | https://github.com/TGAC/lncRNA-analysis |
| Title | SDG |
| Description | SDG is a framework to analyse sequence graphs such as those generated by various genome assemblers. It provides a workspace that can contains a graph and datastores for paired, linked and long reads. These reads can be mapped to the graph, and can be used to untangle or scaffold the graph. A SWIG API enables SDG to be used as a Python module, and there is experimental Julia and R support. |
| Type Of Technology | Software |
| Year Produced | 2018 |
| Open Source License? | Yes |
| Impact | We are currently producing genome assemblies of: multiple wheat cultivars, multiple strawberry cultivars, and more. |
| URL | https://f1000research.com/articles/8-1490 |
| Title | SKM-tools |
| Description | These are a series of tools to compare skip-mers (cyclic spaced-seeds) spectra between different datasets. It can be used to study conservation of sequence across evelotuonary distant organisms. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | We are using skm-tools to study conservation in the context of EI's CSP and BBSRC's DFW projects. |
| URL | https://github.com/bioinfologics/skm-tools |
| Title | TAQLORE - annotation and quantification of transcripts from long read sequencing |
| Description | The pipeline uses long read RNA amplicon sequencing to annotate and quantify transcripts. The pipeline mappes the reads to a genome, identify novel exons and splice sites, reconstruct transcripts, quantify and normalise transcript expression for visualisation. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2020 |
| Open Source License? | Yes |
| Impact | The application of this pipeline is the basis of a publication (Clark et al 2020 Mol Psychiatry) and the developments as part of this research lead to further funding as a partnership between academia and industry (Medicine Discovery Catapult, Psychiatry Consortium). |
| URL | https://taqlore.readthedocs.io/en/latest/ |
| Title | w2rap |
| Description | w2rap is a genome assembly pipeline for complex genomes from short reads. |
| Type Of Technology | Software |
| Year Produced | 2017 |
| Open Source License? | Yes |
| Impact | W2rap has enabled wheat genomics to jump into a new era of high-quality genomes from short reads. While there are some alternative tools from private companies, w2rap remains the standard for quality reconstruction across the genome. W2rap has already been used to assemble 5 wheat genomes in the public domain, putting the UK at the forefront of wheat genomics. With tens of genomes being assembled now, new modules veing developed for new data types, and 5 wheat lines assembled in a £1M private project, w2rap is one of the flagship projects for Earlham Institute. |
| URL | https://github.com/bioinfologics/w2rap/ |
| Company Name | TraitSeq |
| Description | TraitSeq develops a platform for the agricultural industry, which uses AI to identify and predict complex traits and breed optimised crops. |
| Year Established | 2023 |
| Impact | We are currently in the start up stage and wait for UKRI follow on funding, the company was developed as part of the iCURE process. |
| Website | https://traitseq.com/ |
| Company Name | TraitSeq |
| Description | TraitSeq develops a platform for the agricultural industry, which uses AI to identify and predict complex traits and breed optimised crops. |
| Year Established | 2023 |
| Impact | TraitSeq will be the vehicle to commercialise Earlham research. The impacts have not been realised yet. The company is still raising funding. |
| Website | https://traitseq.com/ |
| Description | 'New' rice varieties offer potential for greater crop resilience |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | https://www.agri-tech-e.co.uk/new-rice-varieties-offer-potential-for-greater-crop-resilience/ |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.agri-tech-e.co.uk/new-rice-varieties-offer-potential-for-greater-crop-resilience/ |
| Description | 10 plus wheat genome project workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The meeting was to provide a consortium update on the 10 plus wheat genome project |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.10wheatgenomes.com |
| Description | 17-21 July 2017_2nd Interdisciplinary Signaling Workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | In this interdisciplinary workshop advanced science was combined with informal summer activities to solve multi-disciplinary scientific questions, by bringing early career scientists together with more established researchers in a relaxing and beautiful location. Invited speakers presented talks on the topics of cell regulation, network modelling, genomics, systems biology, bioinformatics, structural biology, biochemistry, and cheminformatics. Then, selected talks from other participants will be followed by multi-disciplinary teamwork sessions in the afternoon, followed by cultural and social activities, such as medieval team building and handicraft activities in the Visegrad Castle. Poster sessions and plenty of informal opportunities allowed the participants to discuss complex and exciting questions as well as develop new collaborations. The renaissance surroundings of the venue nicely matched with the interdisciplinary nature of the workshop. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://signalingworkshop.org/ |
| Description | 2nd Beet Resources Conference talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A talk on the application of population genetics to the sugar beet rust pathogen to identify genes important to crop pathogen success. The workshop was attended by the global beet researchers as well as a number of beet breeding companies. |
| Year(s) Of Engagement Activity | 2022 |
| Description | 5 ways EI is improving global food security |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | 5 ways EI is improving global food security |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/5-ways-earlham-institute-improving-global-food-security |
| Description | 600k machine learning collaboration to supercharge data driven science |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | 600k machine learning collaboration to supercharge data driven science |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/newsroom/%C2%A3600k-machine-learning-collaboration-supercharge-data-driven... |
| Description | A PhD, is it worth it? Just ask our students |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | A PhD, is it worth it? Just ask our students |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/phd-it-worth-it-just-ask-our-students |
| Description | A framework for the sequencing and assembly of rodent genome at the chromosome level |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | I presented a framework to assemble rodent genome at the chromosome level using using comparative analysis and chromosome painting data. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/genome-technologies-and-innovation-workshop#Programme-2 |
| Description | A talk or presentation - Oral presentation - Genome wide signatures of range expansion in a key UK pollinator |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation at the PopGroup55 Norwich |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.populationgeneticsgroup.org.uk |
| Description | A talk or presentation - Poster presentation - lncRNA identification and characterisation in wheat pan-transcriptome |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation at the ISMBECCB 2021 - BOSC 2021 |
| Year(s) Of Engagement Activity | 2021 |
| Description | Activity - DNA sequencer at Great Hockham Primary School |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Activity at the Great Hockham Primary School |
| Year(s) Of Engagement Activity | 2019 |
| Description | Activity - Pink Pigeon Trail at the Norfolk Show |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Activity Pink Pigeon Trail at the Norfolk Show |
| Year(s) Of Engagement Activity | 2019 |
| Description | Activity - Where have you BEEn? |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Activity at the Norwich Science Festival |
| Year(s) Of Engagement Activity | 2019 |
| Description | Affordable genome sequencing for pathogen analysis to help tackle global epidemics |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Blog post for the publication of the development of an affordable sequencing protocol applied to the sequencing of over 10,000 Salmonella isolates |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/newsroom/affordable-genome-sequencing-pathogen-analysis-help-tackle-global... |
| Description | Agri-tech East industrial engagement 2019 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | Presented ideas on wild agricultural pathogen evolution to regional industry in order to inform on methods of crop protection. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.agri-tech-e.co.uk/ |
| Description | Agritech East Week |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | In order to stimulate a dialogue and discussion between scientists, farmers, breeders and more, we organised an interactive, show-and-tell style workshop for members of AgriTech East, who came to EI for three hours on a Tuesday evening. The event showcased the latest advances in genome sequencing and bioinformatics, while then allowing groups to explore themes relevant to modern agriculture and research together. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Antibiotic resistance: people will die when antibiotics fail - 09/03/2010 |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Audio interview to highlight work on antibiotic resistance in salmonella, combining big data and computational biology with single cell analysis to understand the rapid evolution going on at the fine scale, which draws out work carried out through the CSP. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/articles/antibiotic-resistance-people-will-die-when-antibiotics-fail |
| Description | Article - Why is genome annotation important? |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Article EI website - Why is genome annotation important? Highlighting annotation tool developed and training activities |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/articles/why-genome-annotation-important |
| Description | BBSRC Pool of experts |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | As a member of the Pool of Experts in the area of Bioinformatics I play a key role in delivering our mission through participation in the assessment of research grant applications, and identification of the highest quality research for investment. Serving on a Research Committee provides useful insight into the grant funding process, offers an opportunity to be involved in the support of cutting edge research and will be beneficial in the preparation of future grant applications. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.bbsrc.ac.uk/about/governance-structure/committees/committee-pool-membership/ |
| Description | BROADCAST: Federica Di Palma, Genome 10K |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | BBC Look East |
| Year(s) Of Engagement Activity | 2017 |
| Description | Biodiversity bites - Podcast |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Podcast discussing the importance of Biodiversity - supportive material for our work with Colombia. SOCIAL MEDIA Engagement 62 Impressions 122963 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/articles/biodiversity-bites |
| Description | Bread and butter: decoding wheat - 12/08/2019 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Website article outlining the key contributions from the Earlham Institute in the sequencing, assembly, annotation and analysis of the wheat genome including work led through the CSP. This article highlights the coordinated and integrated efforts led through EIs CSP, DFW and research grants to improve our knowledge and understanding of this economically critical crop. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/articles/bread-and-butter-decoding-wheat |
| Description | Breeding crop with a higher resilience to climate change: finding novel rice diversity in Vietnam to help breeding resistant varieties |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Agri Tech East. 2021. Webminar. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Cataloging genetic diversity in the Black-footed Ferret Black-footed Ferret Genetics Symposium, Fort Collins, Colorado, USA. 19-20 Jan 15. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation of EI's work on Black-footed Ferret. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Cheap and robust genomes using the PDABS pipeline Advances in Genome Biology and Technology |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Advances in next-generation sequencing (NGS) technologies and the subsequent reduction in cost have enabled the research community to sequence the genomes of many non-model organisms. Genome assemblies using next generation technologies such as Illumina show high quality nucleotide level information, but are fragmented due to the inability to retain contiguity. The absence of low-cost methods for creating high quality genome sequences from a wide range of organisms currently hampers the generation of de novo genomes for comparative genomic studies, and new methodologies and data types need to be tested to achieve this goal. We have integrated NGS with nano-channel genome mapping and developed the PCR-free Discovar Assembly BioNano Scaffolding (PDABS) pipeline to assemble cheap, contiguous and robust genomes. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Circadian clock insights could be key to increased wheat yields |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Article about a new publication focused on research into the circadian clock in wheat. Primary objectives were to promote the paper and raise awareness of the Institute's expertise in wheat genomics, as part of the CSP work programme. This article led to the author being invited to speak on a podcast and contacted about an event on the Norwich Research Park. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/news/circadian-clock-insights-could-be-key-increased-wheat-yields |
| Description | Clive Lewis - Member of Parliment for Norwich South - 08/03/2019 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Visit from local MP to discuss Institute research activity and input into policy |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://twitter.com/EarlhamInst/status/1104040111401066496 |
| Description | Colombia BRIDGE Overview - Video |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Video to support the work of the BRIDGE Colombia project - interviewing members and showing the importance of working in Colombia. Youtube views |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.youtube.com/watch?v=xOPL2OKM6dc |
| Description | Conference Oral Presentation - Mark McMulla PopGroup |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | presentation at the annual PopGroup meeting: Beet rust Wild-Agricultural population genetics |
| Year(s) Of Engagement Activity | 2021 |
| Description | Conference Oral Presentation: Genomic regions and candidate genes selected during the breeding of rice in Vietnam |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Monogram 2022, Leeds. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Conference Poster - Genome 10K and Genome Science |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Conference poster on Evolution of tissue-specific regulatory programs in cichlids - this research will soon lead to a publication and as such, we had a wide interest from relevant publishers |
| Year(s) Of Engagement Activity | 2017 |
| Description | Conference Poster Presentation: Discovery and visualisation of homologous genes and gene families using Galaxy |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The poster presented at the International Plant and Animal Genomes Conference (San Diego, USA) conference was selected on abstract submission. The poster was presented in front of industry participants, donors, university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of Anil Thanki, Nicola Soranzo, Wilfried Haerty, Robert Davey and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | Conference Presentation - Genomics in Aquaculture - Evolutionn of chromatin accessibility in Nile tilapia |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Genomics in Aquaculture |
| Year(s) Of Engagement Activity | 2022 |
| Description | Conference oral presentation - Monogram 2020 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation of the results from hyperspectral reflectance and GWAS analysis in spring Wheat |
| Year(s) Of Engagement Activity | 2020 |
| Description | Conference poster: IIRB77 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Presented poster on resistance gene identification directly in wild beets to industry leaders and seed companies |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.iirb.org/congresses/77th-iirb-congress |
| Description | Conference poster: PAG XVII |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the Plant and Animal Genomes conference in San Diego. This was done to bring my research to a wider audience. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Conference poster: PopGroup53 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Conference poster presentation on methods of resistance gene identification directly in wild plant hosts |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.populationgeneticsgroup.org.uk/ |
| Description | Conference presentation at PopGroup52, Oxford, Jan 3-6 2019 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Title: Don't throw the baby out with the bathwater: a RADiKal new solution to processing RAD data. Lots of positive feedback and email contact afterwards with offers to collaborate. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://populationgeneticsgroup.org.uk/ |
| Description | Conference talk - Air-seq: using DNA sequencing to provide early warning of airborne crop disease (REAP 2020) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Agri-TechE REAP Conference 2020: From micro-scape to landscape - Innovating at the frontier |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.agri-tech-e.co.uk/event/reap-conference-2020/ |
| Description | Contribution to EI - DToL stand at the Norwich Science Festival - Will Nash, Sofia Kudasheva, Rebecca Shaw, Kamil Hepak |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Contribution to the EI stand at the Norwich Science Festival, engagement with the general public to provide a better understanding of the importance of biodiversity and of the large activities around monitoring, characterizing, and preserving diversity. |
| Year(s) Of Engagement Activity | 2023 |
| Description | DNA deck shuffled in rapid cichlid evolution |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Press release for a manuscript focusing on the importance of genome rearrangements in cichlids |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/newsroom/dna-deck-shuffled-rapid-cichlid-evolution |
| Description | Darwin Tree of Life Project (UK) |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Press release detailing the institutes involvement (partner) in the project which will create a new foundation for biology to drive solutions for preserving biodiversity and sustaining human societies. The institute is likely to be involved in the sampling and sequencing of protists (single-celled eukaryotes - organisms with a nucleus) and the analysis of vertebrate genomes. |
| Year(s) Of Engagement Activity | 2018 |
| Description | De Novo Assembly - 13-16 March 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This training course attracted 22 international delegates with approximately one-third PhD students and one-half Post-Doctoral scientists. Taking delegates through from sequencing technology, introduction to k-mers and assembly pipeline parameters 100% of delegates said that they would recommend the course and over 80% rated the trainers as excellent, the remainder as very good. The proof in the accessibility of this course, is that an attendee from our condensed course as part of the Genome 10K and Genome Science 2017 conference, applied and returned to the 2018 full course, demonstrating real value in the knowledge and expertise imparted by the trainers. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/de-novo-assembly-2018 |
| Description | De Novo Assembly 11-14 February 2019 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Of the 18 attendees, ~78% were researchers based in the UK with the remaining delegates coming from Spain, South Africa and Australia. Two-thirds of the delegates were PhD and PostDocs, other research scientists including those with or wishing to create collaborations or connections with the institute, and one attendee from a company based in the region and who is interested in follow-on support from the group beyond the extent of the course. Significant progress was made through the outline syllabus during this iteration of the course and when compared with previous years. This may be, at least in part, down to the significant effort put in by the lead trainer to produce an online post (GitHub) to introduce some tricky but essential concepts and which was made available as essential pre-reading - "Introduction to k-mers". As a result of the success and delegates' abilities to solve the group working problems during the course, there are plans to create further posts that will introduce other, related concepts. |
| Year(s) Of Engagement Activity | 2017,2018,2019 |
| URL | http://www.earlham.ac.uk/de-novo-assembly-2019 |
| Description | De novo Assembly Training (Genome 10K and Genome Science Conferences) - 1 September 2017 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Organised as one in a series of workshops to encourage and support early career researchers attending the Genome 10K and Genome Science 2017 conferences, this one-day training workshop was a condensed version of our 3.5 day de novo assembly training, followed the formal conference programme closure and ran in parallel with the Genome 10K working groups meetings. This training was oversubscribed and a selection process ensured that the 'best fit' of delegates were given priority places on the course. This intense course immersed a varied delegation in the concepts of assembly whilst giving hands-on opportunities to run assemblies and interpret the metrics to identify good quality data sets and assemblies that were the closest approximation to the original genomes. Over 85% of delegates providing feedback for this course rated the trainers as very good to excellent and said that there was suitable opportunities for discussions amongst trainees and with trainers. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/genome-10k-and-genome-science-conference#Day4-4 |
| Description | De novo assembly 2018-12 Argentina |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | De novo assembly training, delivering the same content from the annual EI training. We provided access to the computing resources ad EI. This training was co-founded by CONICET. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Decoding Life on Earth - The Earth BioGenome Project (EBP) |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Press release detailing the institutes involvement (partner) in the project which is a global effort to sequence the genetic code of all 1.5 million known animal, plant, protozoan and fungal species on Earth. The project will create a new foundation for biology to drive solutions for preserving biodiversity and sustaining human societies. The aim is to sequence, catalogue and categorise the genomes of all of Earth's eukaryotic biodiversity over a period of ten years. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Developing NERC's 'Omic's strategy: invitation to join a working group |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | To be part of a working group looking at developing a new Omic's strategy for NERC. The review group is a small group of invited experts to input into a future strategy for environmental omics.The group are/will be asked to: 1. Provide advice to NERC on strategic need of environmental 'omics including shaping a community town meeting consultation 2. Reviewing the output of the consultation, help draft a strategy document and advise NERC on future strategy and capability |
| Year(s) Of Engagement Activity | 2018 |
| Description | Dialogue: food and health, what matters to you? - 24/10/2019 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Dialogue: food and health, what matters to you? was a new event at the Norwich Science Festival supported by Professor Neil Hall and Dr Nicola Patron. The event was an invitation to the public to join Norwich Research Park scientists and work together with them to solve the problems that you see, and inspire the science of the future. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://docs.google.com/document/d/13yGwFkzh-9YDVUYMBzkhm7i_E4NnytZt74LBFrmjhNU/edit?usp=sharing |
| Description | Dr Paul Kersey - Royal Botanic Gardens Kew - 14/12/2018 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Meeting to discuss collaborative project |
| Year(s) Of Engagement Activity | 2018 |
| Description | EI Innovate - 09/01/2019 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Website article highlighting the importance of knowledge exchange, reflecting on the success of the first EI Innovate KEC focussed event which including showcasing the CSP. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/articles/ei-innovate-why-knowledge-exchange-important |
| Description | EI Innovate 17 November 2022 (In-Person) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | In its fourth year, EI Innovate is an annual engagement event that explores opportunities for innovation and collaboration among attendees from agri-food, biotech and med-tech sectors. The theme of EI Innovate 2022 was 'tackling urgent global challenges through pioneering research' and served to highlight specific areas where EI's research is generating impact, driven by a targeted programme delivered by Group Leaders, members of faculty and departmental heads. This year was held purely in an in-person format, and on a single day to maximise accessibility for attendees. Three key themes were represented across the programme of talks: Food Security and Environment Sustainability (the impact of genomes on crop breeding, and improving aquaculture with genomic resources for tilapia breeding); Enabling others to advance research and innovate (advancing and enabling data-intensive bioscience, and sharing expertise through training); and Improving Human Health (Genomic approaches to understand the emergence of virulence and AMR in Salmonella, and preventative lifestyle modifications). A registration fee of £50 covered refreshments and lunch for delegates. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/events/ei-innovate-2022#programme |
| Description | EI Innovate 17-18 November 2021 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | In its third year, EI Innovate aimed to explore opportunities for collaboration and innovation with external organisations. This year the event was delivered as an online-only format, spread across two days, with each half-day session focusing on one of the three themes: 1) Natural products & biomanufacturing - exploring how synthetic biology and data-driven approaches can facilitate the discovery of new bioactive compounds and develop biomanufacturing platforms based on plants 2) AI in plant science - exploring how AI and ML tools and techniques can help with the understanding of many biological functions in plants that underline important economic traits such as resistance to pathogens, nutrient utilisation and structural development 3) Omics approaches to study the human gut microbiome - exploring how bioinformatics, systems biology and machine learning approaches can be used for advanced microbiome analysis and to facilitate personalised microbiome treatments, identification of novel biomarkers and pathogens, and antimicrobial resistant features of our microbiota. Sharing examples of existing collaborations, this event was a chance to explore new opportunities. The two sessions on day 1 were structured with three talks, one from EI faculty and two from external collaborators, a Q&A panel discussion, and group networking on Spatial. The second session on AI also included flash talks from the Alan Turing Institute Fellows. The third session on the morning of day 2 took the format of several short talks from groups leaders and PhD students, followed by a Q&A panel discussion and further networking opportunities in spatial in the afternoon. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.earlham.ac.uk/ei-innovate-2021-linking-datasets-and-bioscience |
| Description | EI Innovate 17-19 November 2020 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | In its second year, EI Innovate aimed to explore opportunities for collaboration and innovation with external organisations. This year the event was converted to an online only format, spread across three days, with each day focussing on one of the three themes: 1) Disease identification and monitoring - how genomics and bioinformatics are used for disease identification and monitoring, from COVID-19, to AMR to agricultural pathogens. 2) Finding a needle in a haystack - Identifying specific targets in health and disease with long read RNA and single cell sequencing. 3) Accelerating plant breeding with next generation genetics, genomics and epigenetics. Sharing examples of existing collaborations, this event was a chance to explore new opportunities. Each day was structured with two talks, one from EI faculty and one from an external collaborator, a Q&A panel discussion, facilitated break out discussions and then slots to arrange one-to-one meetings with other participants in the afternoon (event times 09:30-15:30), arranged using the software Meeting Mojo. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/ei-innovate-2020 |
| Description | EI Innovate Day 3: Accelerating plant breeding with next generation genetics, genomics, and epigenetics. |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Assessing crop diversity and metagenomics as a resource for breeders - crop diversity; how we link genebanks with crop improvement |
| Year(s) Of Engagement Activity | 2020 |
| Description | EI Innovate event - 13/11/2019 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | The inaugural EI innovate event showcased EIs capabilities and expertise in genomics, bioinformatics, synthetic biology, crop phenotyping, and high-performance computing including the CSP. This event aimed to help industry, academics, charity and voluntary organisations fully understand the opportunities for collaboration with EI, and how engaging with EI science and services can be of benefit. EI Innovate: genomics data to advance bioscience, held on 13th November 2019, was a success. It was attended by 82 people, 26 EI staff who delivered talks, tours and discussion sessions, prepared posters and came to network, 31 representatives from industry (across agri-food, biotech and life sciences sectors), 2 BBSRC staff, 2 representatives from Food Standards Agency, representatives from KTN, NALEP, National Biofilms Centre and Centre for Process Innovation, and 14 representatives from (9 from UEA) academic institutions. We attracted 3 high profile external speakers from: Natural History Museum (Director of Research); Royal Botanic Gardens Kew (Director of Science); and Oxford Nanopore Technologies (Vice President for Applications). We delivered 5 talks, prepared 11 posters, led 2 tours of Genomics Pipelines and Bio-Foundry to showcase EI expertise and capabilities. The afternoon programme had 3 breakout sessions, aiming to explore opportunities for collaborative projects: 1. New Frontiers in Next-Generation Sequencing 2. Data Mining of the UK Tree of Life to Understand and Utilise Biodiversity of British Species 3. A guided discussion about the value of data for driving research, innovation and commercialisation This was EI's first externally-facing KEC event, bringing together various stakeholders to learn about EI expertise and how it can add value to their projects. We received a lot of informal positive feedback and following upon the interactions that this event enabled. A date has already been secured for November 2020. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/innovate2019-0 |
| Description | EI Innovate: a platform for collaboration and new ideas |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | EI Innovate: a platform for collaboration and new ideas |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/ei-innovate-platform-collaboration-and-new-ideas |
| Description | EI Long Read RNA Symposium 15-17 June 2021 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | In this inaugural symposium focusing on Long Read RNA technologies and applications, we combined use cases of long read RNAseq, sample processing hints and tips from experts in sequencing facilities at Earlham Institute and SciLifeLab National Genomics Infrastructure, plus technology developments from leading long read technology companies with break out groups to discuss particular challenges faced in use of long read technology for: Genome Annotation; Differential Expression (gene and transcript) and Networks; and Sample processing and Low input single cell applications. We accepted abstract submissions, which were all offered as lightning talks, encouraging PhD students and ECRs to present their research. The majority of attendees were PostDoctoral researchers (52%), with significant attendance from PhD and Postgraduate students (35%) and 10% PI/group leaders, with the remainder identifying as undergraduate or 'Other' categories, demonstrating the relevance of this event to those at varying stages of their career due to the rapid development of this technology. Furthermore, 59% of attendees were from the UK, with the remainder spread across a further 9 countries, expanding the reach of EI's expertise. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.earlham.ac.uk/ei-long-read-rna-symposium-2021 |
| Description | EI Socioeconomic impact report 2022 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | News story to publicise a socioeconomic impact report undertaken on the Institute's research. In forecasting future impact, the report was designed to demonstrate the quality and breadth of our work to our funders, stakeholders, and the wider public. Figures from the report have since been used in presentations and at other events. Feedback has been positive and demonstrates an increased awareness of EI impact and the areas of research we're engaged in. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/news/earlham-institute-economic-impact |
| Description | EI helps to crack wheat code - 16/08/2018 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. Collectively, our international reach as of March 2019 has extended across the globe, with highlight pieces in the Guardian, the BBC World Service, the Washington Post and more, as well as local TV and radio. In 2018, the estimated readership of news stories we shared was well in excess of 1 million. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/newsroom/earlham-institute-helps-finally-crack-wheat-code |
| Description | EI innovation day |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Engagement with industry to introduce the breadth of research going at the Earlham Institute |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/innovate2019-0 |
| Description | Earlham Institute at the Royal Norfolk Show |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Using our work in robotics and artificial intelligence as a launch pad, we were able to engage with a large swathe of the general public in the Innovation Zone at the Royal Norfolk Show. The aim: to promote awareness of the important work that Earlham Institute does across all of its CSPs and NCs, particularly emphasising our computational, data-driven approach. The outcome: hundreds of members of the public, as well as certain interested stakeholders, engaged in the work that we do. The setting was perfect to have a dialogue with particular groups of interest, including breeders and farmers, while opening the discussion about the role of genomics research and associated projects in influencing and advancing UK agriculture now and in the future. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Emma's Antarctic Diary - 15/04/2019 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Website blog article highlighting the work of Emma Langan, a PhD student in EI's Leggett group who has been on a six-week expedition to Antarctica to analyse the effects of climate change on coccolithophores with real-time DNA sequencing algorithms. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media and showcase the work of our staff. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/articles/emma-langan-antarctic-adventure-algae-climate-change |
| Description | Engagement - European Researchers Night - LATES at Natural History Museum |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Activity at the European Researchers Night - LATES at Natural History Museum |
| Year(s) Of Engagement Activity | 2019 |
| Description | Engagement with General Public: Royal Norfolk Show 2022 - Will Nash |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Engagement activities with the general public as part of the Royal Norfolk Show 2022, demonstrating our activities focusing on the application of new technologies to characterise biodiversity |
| Year(s) Of Engagement Activity | 2022 |
| Description | Engagement with Government - Welcomed Clive Lewis (MP) to EI and discussed current work on Pollinator Biodiversity in the UK |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Visit of Clive Lewis (MP) to EI |
| Year(s) Of Engagement Activity | 2022 |
| Description | Engagement with the Master student of bioinformatic in Rennes France |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Undergraduate students |
| Results and Impact | The goal of this activity was to present to French student the job of a principal investigator in a UK academic institution and presenting the work carried out at the Earlham institute and my research group. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Engineering day at the Norwich Science Festival |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Through a series of talks and activities, we highlighted Earlham Institute's important work in aquaculture and synthetic biology, among other things. Disseminating this sort of research is of vital importance, as is collecting feedback from both participants and volunteers alike, in order that we can better stimulate conversations around complex science and increase understanding of the taxpayer funded research that we do. In depth feedback showed that people were more aware of the important research that we do, and how it influences how we understand and conserve important ecosystems and increase sustainable food production. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Epic Genetic: The Hidden Story of Wheat - 09/08/2018 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. Collectively, our international reach as of March 2019 has extended across the globe, with highlight pieces in the Guardian, the BBC World Service, the Washington Post and more, as well as local TV and radio. In 2018, the estimated readership of news stories we shared was well in excess of 1 million. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/newsroom/epic-genetic-hidden-story-wheat |
| Description | Event - DNA Detectives |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Activity at the Eden project |
| Year(s) Of Engagement Activity | 2019 |
| Description | Event - Pink Pigeon Trail |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Public engagement activity as part of the Norwich Science Festival |
| Year(s) Of Engagement Activity | 2018 |
| Description | Evolutionary History and Domestication of the Ferret (Mustela putorius furo). Genome Science 2016 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The domestic ferret (Mustela putorius furo) models biological processes that are highly relevant to human disease and health research such as influenza, cystic fibrosis and asthma. The recently completed draft of the ferret genome and associated annotation project (Peng et al 2014) allows us to extend research and examine the domestication of the ferret. Most domestic animals were domesticated ~10,000 years ago, but the history of the ferret's domestication is uncertain. It is likely that ferrets have been domesticated for at least 2,000 years, a similar time to the domestication of the rabbit, of which the ferret was domesticated to hunt. We have sequenced the genomes of a further eight domestic ferrets along with 12 European Polecats (M. putorius), 2 Steppe Polecats (M. eversmanii) and 4 Black-footed Ferrets (M. nigripes). In order to examine the genetics underpinning ferret domestication and compare the genomes of domestic and wild ancestor, we first need to identify the ancestral species of the domestic ferret, the identification of which is not fully resolved. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Exotic Wheat DNA news story |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | News story to highlight new publication from an EI researcher, with the aim of generating media coverage to engage with industry, professional practitioners, and the general public. National, local, and trade media covered the story, which saw an increase in visitors to the website, strong engagement on social media, and queries directed at the authors. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/news/exotic-wheat-dna-could-help-breed-climate-proof-crops |
| Description | Exotic wheat press interview 2023 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Media interview given by research author based at the Earlham Institute regarding new research on climate resilient wheat, leading to heightened awareness of the paper, its potential impact, and the Earlham Institute. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.thetimes.co.uk/article/climate-proof-wheat-developed-by-british-researchers-m8bw6g0pl |
| Description | Extreme environments: genome sequencing & space |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | EI website article on our fieldwork in Iceland |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/extreme-environments-genome-sequencing-space |
| Description | FTMA visit of WorldFish at EI and training of partners from the Lake Victoria Fisheries Organisation |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Meeting at the Earlham Institute with WorldFish researchers to develop the report for the Lake Victoria Fisheries Organization to inform policy development for the sustainable exploitation of tilapia. Training of representatives from Uganda, Kenya, and Tanzania on the bioinformatics for population genetics |
| Year(s) Of Engagement Activity | 2023 |
| Description | FTMA3 - Eagle Genomics Workshop for ECRs on engagement with industry and exploratory meetings to identify new collaborations - 23-24 March 2022 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | A 2-day workshop with Eagle Genomics' Director of Microbiome Solutions and Director of Bioinformatics. The workshop consisted of short sessions and networking lunch to facilitate ECR identification of transferrable skills for industry to improve employability within this sector, plus networking and engagement with industry skills. Further to this several 1:1 meetings and a networking dinner were facilitated with group leaders to explore potential longer-term collaborations between EI and Eagle Genomics. This includes identification of potential involvement in one of EI's future ISPs plus the opportunity to apply for joint CASE studentship funding. |
| Year(s) Of Engagement Activity | 2022 |
| Description | FTMA3 -Beet genetic diversity and, wild and agricultural pathogens (Cornell & USDA Fargo) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Engagement with the USA beet research and industry linked breeding community. I was there to share new ideas on the impact of wild pathogens on agricultural beets as well as the power of utilising wild beet genetic diversity. While there I learned about how epidemiology might aid our understanding of pathogen spread and also how breeders are delivering their latest resistances. There is a lot of further work that can be developed via a collaboration. I also subsequently gave a lecture to Cornell postgraduate students on plant pathogen evolution. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Farm week, page 19, 22/04/2021 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Farm Week magazine |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://internationalprintmonitoringservice.vuelio.co.uk/file/displaypdf?articleid=793089&clientname... |
| Description | Focus on the future at EI Innovate |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Write-up of the EI Innovate event held at the Earlham Institute in November 2022, designed to provide an overview of the topics discussed to those who were unable to attend or may want to follow up with speakers having been here. The piece received some positive engagement and comments on social and will be a valuable tool for encouraging registration for the 2023 event. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/articles/focus-future-ei-innovate |
| Description | Forward Genetics Identification of Genes Responsible for Differential Carbohydrate Metabolic Profiles in Miscanthus |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Conference Oral Presentation in the "Bioenergy Grasses" workshop at PAG XXVII |
| Year(s) Of Engagement Activity | 2019 |
| Description | Genetic Diversity of the Mustelidae: Implications for understanding Evolution, Domestication and Conservation. Genome 10K |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The ferret (Mustela putorius furo) models biological processes that are highly relevant to human disease and health research such as influenza, cystic fibrosis (CF) and asthma. Since CF is a multi-organ disorder, research using CF ferrets span a range of organs, thus the impact of research in this model is broad and allows for the analysis of early stages of the diseases. The recently completed draft of the ferret genome has allowed us to look more closely into ferret domestication and examine the underpinning processes of domestication from the ancestral European Polecat (M. putorius). We have sequenced eight domestic ferrets genomes and will sequence samples from European Polecat. Beneficial genetic variants increase in frequency due to positive selection together with linked neutral variants resulting in genomic islands of reduced heterozygosity between populations. By examining fixation indexes and heterozygosity between wild and domestic ferrets we can find genomic regions that have undergone selective sweeps. Using whole genome sequencing also allows us to leverage the ferret genome sequence to look into the genetic diversity and evolution of other species of wild Mustelidae. The current population of the endangered Black-footed Ferret (M. nigripes) from North America stems from only seven individuals. Using whole genome sequencing of Black-footed Ferrets from both before and after the population crash we will identify genetic diversity not present in the current population with a view to reintroducing it via genome editing technology. About two million years ago, the ancestral species of modern day Steppe Polecats (M. eversmanni) from Asia entered North America via the Bering Land Bridge and speciated into what is now Black-footed Ferret. Using a reference-free unbiased kmer approach, we will examine how closely-related Steppe Polecat is to both Black-footed Ferret and its sister species the European Polecat. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Genetics Unzipped podcast - Tarang Mehta |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Two researchers appeared in the Genetics Unzipped podcast to talk about their science and share it with the listenership. The primary aim was to raise awareness of the Institute and its science among those with an interest in genetics, which this podcast is able to do. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://geneticsunzipped.com/blog/2022/10/6/bread-and-fishes?utm_campaign=Oktopost-General+Notices+&... |
| Description | Genetics Unzipped podcast Sept 2022 |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Two researchers appeared in the Genetics Unzipped podcast to talk about their science and share it with the listenership. The primary aim was to raise awareness of the Institute and its science among those with an interest in genetics, which this podcast is able to do. The producers have asked about future contributors to the podcast who they could feature. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://geneticsunzipped.com/blog/2022/10/6/bread-and-fishes?utm_campaign=Oktopost-General+Notices+&... |
| Description | Genome 10K - vertebrate 'genomic zoo' to help protect our planet |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Press release to promote the Genome 10K conference to be held at EI 2017.The Genome 10K initiative, led by the University of California, Santa Cruz Genomics Institute, aims to understand how complex animal life evolved through changes in DNA and use this knowledge to become better stewards of the planet. SOCIAL MEDIA Engagement 169 Impressions 171,000 |
| Year(s) Of Engagement Activity | 2016 |
| URL | http://www.earlham.ac.uk/newsroom/genome-10k-vertebrate-%E2%80%98genomic-zoo%E2%80%99-help-protect-o... |
| Description | Genome 10K and Genome Science Conference - Video |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Follow up video of the Genome 10k Genome Science conference held at NRP. View son Youtube - 70 |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.youtube.com/watch?v=25Dtu6ay7Is |
| Description | Genome 10K and Genome Science social media engagement |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Social media campaign and press releases to promote the Genome10K and Genome Science event at NRP August 2017. We ran several campaigns from January to August to help promote registration for the event and gain interest from industry. SOCIAL MEDIA - Engagement 1920 Impressions 2084245. This has been our biggest campaign to date garnering engagement with International delegates in science and industry. The comms team also supported with design for promotional material such as posters, sponsor brochures and conference programmes. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/genome-10k-and-genome-science-conference |
| Description | Genome-resolved metagenomics bioinformatics course, 31 Oct - 4 Nov 2022, EBI (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Acted as trainer, teaching on long-read metagenomics, including on our MARTi software. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.ebi.ac.uk/training/events/metagenomics-bioinformatics-2022 |
| Description | Genomic characterisation of wild tilapia populations |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The presentation took place as part of a workshop organised in Bogota (Colombia) between UK and Colombia scientific Institutions. The audience was composed of UK and Colombia university lecturers, Colombian industry partners. The presentation helped raising the international profile of Wilfried Haerty, Federica Di Palma and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | George Freeman MP, Minister for Transport visit - 20/09/2019 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Policymakers/politicians |
| Results and Impact | In September 2019, George Freeman MP, Transport Minister, visited EI and address NRP staff. EI and CSP researchers lobbied him on our priorities and policy asks and staff were able to question him on the Government's Brexit policy as well as its wider science strategy |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.georgefreeman.co.uk/content/earlham-institute-visit |
| Description | Guest Lecture Cornell |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | I was invited to give a guest lecture at Cornell University after a visit. The lecture was on the population genetics of fungal invasions with reference to the ash dieback pathogen and crop pathogen emergence. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Hosting undergraduate summer student, Giorgio Koufous for work experience in lab. |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Undergraduate students |
| Results and Impact | We hosted Giorgio Koufous, an international student for one month to gain experience in wet lab research - he thorougly enjoyed the research project on characterising polymorphisms associated with fin egg spot diversity in cichlid fish. |
| Year(s) Of Engagement Activity | 2019 |
| Description | How does this "orphan crop" tolerate toxic aluminium? |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Blog post for the general public about our research in Brachiaria in general, and focused one of our recent projects. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/newsroom/how-does-orphan-crop-tolerate-toxic-aluminium |
| Description | How does this 'orphan crop' tolerate toxic aluminium? |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | How does this 'orphan crop' tolerate toxic aluminium? |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/newsroom/how-does-orphan-crop-tolerate-toxic-aluminium |
| Description | How to communicate science on climate change? ¿Cómo comunicar la ciencia del cambio climático? |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | De Vega J,Arango J,Fog L,Calzadilla L; Virtual Press Conference. British Council Colombia. Bogota, 2021. |
| Year(s) Of Engagement Activity | 2021 |
| Description | Improving the diet of livestock for healthier herds in Sub Saharan Africa |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Improving the diet of livestock for healthier herds in Sub Saharan Africa |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/newsroom/improving-diet-livestock-healthier-herds-sub-saharan-africa |
| Description | Industry Seminar - Chris Burt, RAGT 'Bridging the valley of death: Molecular breeding in cereals'. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Second of our Industry seminar series. Chris Burt of the RAGT group spoke about the challenges associated with molecular breeding in cereals. A meeting with the Senior Management Team was organised along with a networking lunch with students. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Industry Seminar - Ed Byrne, KWS. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Third of our Industry Seminar series. Ed Byrne, Cereal genomics Scientist at KWS gave a talk entitled 'Breeding Technology: Bridging the gap between research and applied breeding'. Breeding and releasing cereal varieties is a long term and high-risk endeavour. Cereal breeding relies on the principles of quantitative genetics, the skills and craft of the breeder, and the support of scientific and technology expertise and this talk provided an overview of what is meant by applied breeding and explored why we see a lag and the role that breeding technology has in this process. A meeting with the Senior Management team took place along with a networking lunch with students. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Industry Seminar - R&D Facilitator, AB Agri |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Firts of the EI Industry Seminars programme, provides an opportunity for companies to visit EI and discuss the challenges they face in industry and how EI's research could help. Mike Salter (AB Agri) was the first speaker and delivered a talk on challenges on monetising the microbiome. In addition to the talk, Mike met with members of the Senior Management Team, joined a networking lunch with students, post-docs and other EI staff and had met with researchers and EI director. Key Figures: Talk attendance= ~45 Networking Lunch attendance = 7 Meetings = 3 (members of SMT, Ji Zhou, Neil Hall) |
| Year(s) Of Engagement Activity | 2017 |
| Description | Inside EI - 21/05/2019 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Inside EI is an open day when the public are invited to learn more about the work at the Earlham Institute, meet our team and engage with our research and understand its relevance and impact. There were talks and posters based on CSP-led research. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://earlhaminstitute.coveragebook.com/b/0ee62ba7 |
| Description | Inside EI - Open Day 2019 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | One day in May 2019 EI opened its doors to the public and schools from the region. Offering an overview of the Tree of Life with the branches of our tree culminating in posters displaying colourful imagery of our research, visitors were able to talk to researchers about their projects and why the research is important. There were hands on activities providing insight into de novo genome assembly, nanopore sequencing technology, synthetic biology and high performance/cloud computing. In addition to the activities, there were talks and tours of the laboratories, which were fully subscribed. We were joined by schools from across the region in the morning, and opened our doors to the general public for the afternoon, with a total of over 400 visitors, media coverage (TV and radio) reaching an estimated 500+. The feedback was incredibly positive and we achieved an unbelievably successful set of outcomes. Comparison of pre- and post Open Day attitudes demonstrated that: Participants reported very high increases in understanding of a range of topics, while overwhelmingly agreed that research at EI should be funded by the government. The majority of people left with an increased appreciation of the importance of bioinformatics, genomics, etc. for their every day life, the environment, and more. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/articles/inside-ei-public-engagement-science-impact |
| Description | Inside EI 2019: Diving into cichlid diversity (Oral Presentation) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Around 100 people attended the 'Inside EI' open day; there were several talks and informal discussions based on this. As a result, there was increased interest in several of the research areas, including our work on fish. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/open-day-2019#Programme-7 |
| Description | Inside EI 2019: Preserving Tilapia biodiversity (poster) |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Around 100 people attended the 'Inside EI' open day; there were several talks and informal discussions on our work at poster sessions. As a result, there was increased interest in several of the research areas, including our work on fish. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/open-day-2019#Programme-7 |
| Description | Inside EI: Public engagement with impact - 06/08/2019 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Website highlighting the Inside EI event for the public to explore our fascinating and diverse range of important scientific research projects including talks and posters on our CSP work and the importance and impact of public engagement in research |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/articles/inside-ei-public-engagement-science-impact |
| Description | Integrating omic-based technologies for the valorisation of Peruvian crop biodiversity |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This three-day workshop aimed to understand the potential application of high-throughput "omics-technologies" for the characterization and valuation of the genetic biodiversity of Peruvian crop in a more holistic and integrated approach. The workshop convened UK and Peruvian leading researchers and early-career researchers, with the aim of outlining the best strategies to integrate omic approaches in the research of Peruvian crop biodiversity. This contributed to developing resilience in local agriculture under the context of climate change and the current demand for healthier foods and natural compounds. Developed in collaboration with Universidad Catolica de Santa María, this workshop has been granted by the Newton-Paulet fund under the program "Researcher Links - Workshop Grants - Talleres 2018-01". This grant is the result of an agreement between the British Council and the Consejo Nacional de Ciencia Tecnologia e Innovacion (CONCYTEC) from Peru. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Internal Seminar on 'Evolution of regulatory networks associated with traits of cichlid phenotypic diversity' |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | Earlham Institute Internal Seminar (also open to NBI colleagues) on the 'Evolution of regulatory networks associated with traits of cichlid phenotypic diversity'. There was a round of questions and discussion afterwards. |
| Year(s) Of Engagement Activity | 2020 |
| Description | International Conference Oral Presentation: Discovery and visualisation of homologous genes and gene families using Galaxy |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The oral presentation at the International Plant and Animal Genomes Conference (San Diego, USA) conference was selected on abstract submission. The presentation was delivered in front of industry participants, donors, university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of Anil Thanki, Nicola Soranzo, Wilfried Haerty, Robert Davey and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | International Conference Poster Presentation: Evolution of tissue-specific regulatory programs in cichlids. |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The poster presented at the Cold Spring Harbour Biology of Genomes conference was selected on abstract submission. The poster was presented in front of university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of Tarang Metha, Luca Penso Dolfin, Tomasz Wrzesinski, Will Nash, Padhmanand Sudhakar, Wilfried Haerty, Tamas Korcsmaros, Federica Di Palma and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | International Conference Poster: Binding sites within long non-coding RNAs discriminate between RNA- and transcription mediated mechanism. |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The poster presented at the Cold Spring Harbour Biology of Genomes conference was selected on abstract submission. The poster was presented in front of university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of Tomasz Wrzesinski, Wilfried Haerty and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | International Conference poster presentation: Discovery and visualisation of homologous genes and gene families using Galaxy |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The poster presentation at the 18th The Bioinformatics Open Source Conference (BOSC), 25th Intelligent Systems for Molecular Biology (ISMB) and 16th European Conference on Computational Biology - ISMB/ECCB conference was selected on abstract submission. The poster was presented in front of industry participants, donors, university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of Anil Thanki, Nicola Soranzo, Wilfried Haerty, Robert Davey and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | Interviewed for a BBC news feature on the Darwin Tree of LIFE project - shown worldwide on BBC world news |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | The feature covered the Darwin Tree of Life project and the involvement of EI. Particularly focussing on Protists |
| Year(s) Of Engagement Activity | 2019 |
| Description | Intro to EI: Genomics, High Performance Computing, and Rebranding an Institute |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Undergraduate students |
| Results and Impact | 9.15 - Arrival 9.30 - Intro to EI and platforms technology - Stuart Catchpole & Dave Baker 9.45 - Tours. Lab and Data Centre. 3 groups 10.45 - Rebranding an Institute - Stuart Catchpole 11.15 - High Performance and Optical Computing (Optalysys case study) - Tim Stitt |
| Year(s) Of Engagement Activity | 2017 |
| Description | Invaders from the Far East: Ash dieback |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Article on disease |
| Year(s) Of Engagement Activity | 2018 |
| Description | Invasive species threat to native tilapia biodiversity |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Invasive species threat to native tilapia biodiversity |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/newsroom/invasive-species-threat-newly-discovered-native-tilapia-biodivers... |
| Description | Invited seminar - Swedish University of Agricultural Sciences, Uppsala, Faculty of Veterinary Medicine and Animal Sciences - Complex evolutionary history of tilapia |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited presentation at the Swedish University of Agricultural Sciences, Uppsala, Faculty of Veterinary Medicine and Animal Sciences |
| Year(s) Of Engagement Activity | 2023 |
| Description | Invited seminar: Characterization of transcriptional complexity of Voltage Gated Calcium Channels in the human brain using Nanopore long read sequencing |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited seminar at the Division of Evolution & Genomic Sciences, University of Manchester. The audience was composed of group leaders, University lecturers, postdoctoral researchers, graduates and undergraduates students interested in RNA biology. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Invited seminar: Comparative genomics of Australian marsupials: Expansion of gene families and signatures of selection following an ancient divergence |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited seminar at University College Dublin presented by Will Nash. The audience was composed of University professors and Lecturers, postdoctoral researchers, graduates and undergraduates students. Outcomes: Increased the international profile of Will Nash and Wilfried Haerty and increased the international profile of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | Invited seminar: Nanopore cDNA sequencing reveals transcriptional complexity of CACNA1C gene in human brain |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited seminar in the satellite meeting of The Americal Society for Human Genetics organised by Oxford Nanopore. The audience of the seminar was composed of industrial professionals, group leaders, university professors and lecturers, postdoctoral researchers, graduates and undergraduate students. The seminar allowed to raise the personal profile of Wilfried Haerty and to raise the profile of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | Invited seminar: Nanopore cDNA sequencing reveals transcriptional complexity of CACNA1C gene in human brain |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited seminar at the MRC Institute of Genetics and Molecular Medicine. The audience consisted group leaders, University professors, University Lectures, postdoctoral researchers, graduates and undergraduates students. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Invited talk - Automating sample preparation for nanopore real-time sequencing applications (Miroculus Science Simplified, 24 Mar 2022) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Richard Leggett and Darren Heavens spoke at the Miroculus Science Simplified virtual symposium. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://miroculus.com/videos/nanopore-real-time-sequencing-applications/ |
| Description | Invited talk - Improving nanopore sequencing outputs using the femto pulse (Agilent User Group) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Darren Heavens was asked to present at the Agilent UK Genomics user group meeting in London. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://twitter.com/EarlhamInst/status/1227529033539313664 |
| Description | Invited talk - In situ sequencing, automated sample prep, and real-time analysis using MARTi and Miro (Extreme Microbiome Group, 3 May 2022) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Richard Leggett invited to present at the Extreme Microbiome Group virtual meeting, 3rd May 2022. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Invited talk - Real-time gut microbiome diagnostics using nanopore sequencing (Cambridge Nanopore Day, 22 Nov 2022) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Richard Leggett invited speaker at Oxford Nanopore Technologies' Nanopore Day Cambridge, CRUK Cambridge Institute, 22 November 2022 |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://nanoporetech.com/nanopore-day-cambridge |
| Description | Invited talk - Real-time sequencing and analysis of microbial communities with nanopores |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Research day on microbe research attended by approx. 200. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://microbesinnorwich.org/ |
| Description | Invited talk - Semi-quantitative characterisation of mixed pollen samples using nanopore sequencing and Reverse Metagenomics (RevMet) (NHM workshop) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited speaker at Natural History Museum Next Generation Sequencing and Molecular Workshop, 13th February 2020. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Invited talk - Unbiased detection of airborne pathogens with Air-seq (Agri-TechE Farmer First Innovation Group, 18 Oct 2022) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | Invited to present Air-seq work to the Agri-TechE Farmer First Innovation Group |
| Year(s) Of Engagement Activity | 2022 |
| Description | Invited talk -Crop pathogen invasion and adaptation |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | An invited talk with USDA Fargo beet researchers to consider the population genetics signals associated with crop pathogen invasion and adaptation. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Jim Hasseloff - Department of Plant Sciences, Cambridge - 27/08/2018 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Other audiences |
| Results and Impact | Meeting to discuss collaborative project |
| Year(s) Of Engagement Activity | 2018 |
| Description | Just one more Ash Dieback spore could push European ash trees to the brink |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | News article on disease |
| Year(s) Of Engagement Activity | 2018 |
| Description | KTN Agri-tech mission in Colombia |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Attended and contributed to Agri-tech Catalyst Colombia organised by the agri tech KTN and innovate UK. Talked and participated in workshops across Colombia |
| Year(s) Of Engagement Activity | 2018 |
| Description | KWS seed company workshop on Genetic Resources of the Genus Beta |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Industry led workshop designed to bring industry and scientists together to consider resources available for sharing and to identify areas of future research of the greatest benefit to the community. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Kew-JIC Crop Wild Relatives and Domestication Genomics Workshop |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation and participation at a workshop designed to integrate researchers in wild and crop systems in order to drive novel ideas associated with wild plant resistance integration. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Key tilapia genome offers boost to global food security |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | News story to highlight a new publication from EI researchers on reference genome for a key aquaculture species, designed to reach breeders, industry, and academics working in this space. Positive trade media coverage, as well as promotion from project collaborators, helped this news to reach a wide audience and enhance EI's reputation. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/news/key-tilapia-genome-offers-boost-global-food-security |
| Description | Key tilapia genome offers boost to global food security - Tarang Mehta, Graham Etherington, Will Nash, Adam Ciezarek |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | News story to highlight a new publication from EI researchers on reference genome for a key aquaculture species, designed to reach breeders, industry, and academics working in this space. Positive trade media coverage, as well as promotion from project collaborators, helped this news to reach a wide audience and enhance EI's reputation. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/news/key-tilapia-genome-offers-boost-global-food-security |
| Description | Koala Genome Cracked Down Under to help save species - 02/07/2018 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. Collectively, our international reach as of March 2019 has extended across the globe, with highlight pieces in the Guardian, the BBC World Service, the Washington Post and more, as well as local TV and radio. In 2018, the estimated readership of news stories we shared was well in excess of 1 million. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.eurekalert.org/pub_releases/2018-07/ei-kgc070218.php |
| Description | Lecture - Foundation Biological Sciences: Exploring Genomes |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Undergraduate students |
| Results and Impact | Lecture delivered at UEA to undergraduate students |
| Year(s) Of Engagement Activity | 2019 |
| Description | Lecture Will Nash - Introduction to Bioinformatics Workshops |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Undergraduate students |
| Results and Impact | Lecture at UEA for undergraduates and graduate students |
| Year(s) Of Engagement Activity | 2018 |
| Description | Lectures - Vertebrate Biodiversity |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Undergraduate students |
| Results and Impact | Lectures at UEA - Vertebrate Biodiversity |
| Year(s) Of Engagement Activity | 2019 |
| Description | Lectures delivered Will Nash - Vertebrate Biodiveristy |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Undergraduate students |
| Results and Impact | Lectures (6) delivered at UEA to undergraduate students |
| Year(s) Of Engagement Activity | 2018 |
| Description | Leszek Wysocki (Department for International Trade ) 10/06/2019 - visit to EI |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Leszek Wysocki (Department for International Trade) visited EI and met with CSP researchers to discuss their work in relation to International Trade |
| Year(s) Of Engagement Activity | 2019 |
| Description | Linkage is a drag - 15/04/2019 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Website article on the data-driven approached used to identify and understand more about genes that control genome-wide gene conversion or the high level of gene conversion in wheat. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. The article has estimated coverage views of 34.3K. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/newsroom/linkage-drag-first-wheat-gene-rapidly-convert-defective-traits-new |
| Description | Local Rice Varieties in Vietnam Could be Used to Breed Improved Climate-Resilient Crops |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | https://www.azocleantech.com/news.aspx?newsID=29646 |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.azocleantech.com/news.aspx?newsID=29646 |
| Description | Local rice varieties in Vietnam could be used to help breed improved crops with a higher resilience to climate change, according to a new study published in Rice. |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | https://www.seedquest.com/news.php?type=news&id_article=129197 |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.seedquest.com/news.php?type=news&id_article=129197 |
| Description | Local rice varieties in Vietnam could be used to help breed improved crops with higher resilience to climate change, according to a new study. Researchers are aiming to identify varieties that can survive an increasingly unpredictable climate. |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | https://www.sciencedaily.com/releases/2021/06/210615132132.htm |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.sciencedaily.com/releases/2021/06/210615132132.htm |
| Description | Long non-codes in nematodes - 21/02/2019 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. Collectively, our international reach as of March 2019 has extended across the globe, with highlight pieces in the Guardian, the BBC World Service, the Washington Post and more, as well as local TV and radio. In 2018, the estimated readership of news stories we shared was well in excess of 1 million. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/newsroom/long-non-codes-nematodes |
| Description | Media Article - Genome Biology: Fostering Partnerships and Advancing Research |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Technology Networks interview with Prof Federica DiPalma, raising awareness of the G10k/Genome Sciences Conference and partnerships. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.technologynetworks.com/TN/blog/genome-biology-fostering-partnerships-and-advancing-resea... |
| Description | Metagenomics: Data Analysis and Interpretation 16-19 September 2019 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Attended by approximately equal numbers of PhD students to PostDoctoral and Academic researchers (combined), this course provided an overview of metagenomic data analysis, including ample time spent on hands-on activities using example data sets and relevant tools and resources, taking delegates through to production of publication-ready figures. As a newly redeveloped course with new teaching staff, this course still received positive feedback with over 75% recommendation of the course and 70% rating trainers as Very Good or Excellent. There are some lessons learned and the training team are reviewing the course programme and structure, including leadership of the course by an individual research group to address the areas for improvement. Attendees were predominantly from the UK, with some from Europe and one from South America. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/metagenomics-data-analysis-and-interpretation |
| Description | Microbial Community Analysis Workshop 29 - 31 March 2022 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | This was a three-day course covering microbiome analysis - going from samples, to sequencing, to numerical ecology analysis. It provided an overview from raw sequencing reads to publication ready analysis and figures. Lecture materials comprised the theory of DNA extraction, sample storage and existing pipelines for amplicon sequencing. Use of the LotuS2 pipeline was applied to an example dataset via a Galaxy interface. R was also used to explore abundance data from producing diversity measures to visualisation of taxonomic differences. We had 25 participants comprising PhD students (~53%), Postdocs (~30%), Professors/PIs (12%) and other representatives from research organisations in attendance. The overall quality of the course was rated as 'Very Good' or 'Excellent' (92%) and there are plans to host this again in Q4 2023. Participants reported this allowed them unique hands-on experience with 16S/amplicon sequencing data, and that after attending the course it allowed them to present papers in the field of bioinformatics. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/events/microbial-community-analysis-workshop-2022 |
| Description | Museum collections reveal century of growing stress on bees |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | News story to publicise paper on insights gained from sequencing museum collections, with the aim of raising awareness of the plight of pollinators, influencing policy makers, and engaging audiences in the science of genomics. The story was a joint release with collaborators and generated interest on social media and some coverage, while also strengthening relationships between partners involved. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/news/museum-collections-reveal-century-growing-stress-bees |
| Description | Museum collections reveal century of growing stress on bees - Will Nash |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | News story to publicise paper on insights gained from sequencing museum collections, with the aim of raising awareness of the plight of pollinators, influencing policy makers, and engaging audiences in the science of genomics. The story generated interest on social media and some coverage, while also strengthening relationships between collaborators. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/news/museum-collections-reveal-century-growing-stress-bees |
| Description | NanoOK of the North and South |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | EI website article about our work developing the nanopore analysis software NanoOK |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/articles/nanook-north-south-life-in-antarctic |
| Description | Nanopore Metagenomics: from sample to analysis 26-28 April 2022 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The first iteration of this 3-day course covered Nanopore Metagenomics and provided an overview of in-field, real-time nanopore sequencing using the Oxford Nanopore Technologies (ONT) platform. It covered experimental considerations, sample collection and preparation theory, plus data analysis and visualisation. Hands-on opportunities for data analysis of metagenomic data covered the use of EI's in-house software MARTi via virtual machines, accessed remotely by the participants. Participants also had the opportunity to discuss and apply lessons to their own projects with EI's experts and a representative from Oxford Nanopore Technologies during an optional Q&A session. Attendees were predominantly from the UK (65%) with remaining participants from Sweden, Norway, Germany and Hong Kong. The majority were Postdoctoral researchers (~33%), and PhD students (~27%), while the remainder comprised Undergraduates (~7%), Professor/PIs (~7%) and 'other' job functions. These included a research scientist, senior engineer (food technologist) and laboratory technician. Delegates rated the course overall as "Very Good" or "Excellent" (40% and 60% respectively), while 67% rated the trainers "Excellent". 100% would recommend the course. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/events/nanopore-metagenomics-sample-analysis-2022 |
| Description | Nature Day at Norwich Science Festival |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Through a series of engaging, innovative activities, we showcased the valuable research we are doing into understanding genomes and bottlenecks. We had a hugely popular "Pink Pigeon Trail", which allowed us to engage with children and adults simultaneously in an interactive, exploratory activity that allowed participants to understand the concepts around genetic bottlenecks and how they affect species. Feedback from the event suggested that the public came away with a better understanding of the issues surrounding conservation and genetic diversity, while thinking more about the role of Institutes such as EI in tackling global issues from protecting biodiversity through to improving food security. Over the whole week of Norwich Science Festival, the activities and talks we put on in relation to genetic bottlenecks and genetic diversity reached well over 20 000 people. Importantly, feedback from the organisers suggested that our public engagement activities have "set the standard" and "raised the bar" for future Science Festivals, which was a fantastic achievement for the Institute and the communications team. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/celebration-science-norwich |
| Description | New Scientist coverage of polecat research 2022 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Interview with New Scientist for a piece on our polecat research, highlighting an issue and the Institute's specific expertise in genome analysis. The piece received a lot of interest on social media and helped our research to reach broad scientific audience |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.newscientist.com/article/2334445-uk-polecats-numbers-are-rising-as-they-interbreed-with-... |
| Description | New bioinformatics tool spots hybrid fish that threaten the survival of natural tilapia populations in aquaculture |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | News letter describing the development of a cost effective genotyping platform enabling tilapia species discrimination and species identification |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.earlham.ac.uk/newsroom/new-bioinformatics-tool-spots-hybrid-fish-threaten-survival-natur... |
| Description | New method and model address blindspot towards uncommon species in mixed samples |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Website article about paper |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/newsroom/new-method-and-model-address-blindspot-towards-uncommon-species-m... |
| Description | Newsletter - Developing a frugal and medium throughput method for assessing protein-DNA binding affinity |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | News Letter for Open Plant |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.openplant.org/blog/2019/4/4/developing-a-frugal-and-medium-throughput-method-for-assessi... |
| Description | Norwich Research Park Day at the Norwich Science Festival |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | This, a celebration of science from across the NRP, was a fantastic chance for us to showcase the work across our collective CSPs and NCs. All in all, we had dozens of staff involved from across the institute who helped us to deliver a set of multiple activities, workshops and talks on the day. Activities included a live LEGO sequencer with BLAST analysis of genomes and a live DNA sequencing experiment. Additionally, there were talks on the Institute and how it applies big data and computational approaches to understanding life on earth, the interactions underpinning ecosystems and communities, as well as how we can better understand evolution to drive trait improvement. The event was a spectacular success, with desired outcomes being a greater awareness of the important research undertaken by EI, as well as the value of applying computational approaches to tackling a swathe of biological questions. The specific feedback showed that this event had definitely increased understanding among participants, who numbered more than 8000, of the role that EI and its core programmes play at the cutting edge of science. Social media coverage ensured that the activities we put on reached many thousands more people than just those who attended the event on the day. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.youtube.com/watch?v=Uf0h8Q8PVxI |
| Description | Norwich Science Festival |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Earlham Institute put on a well received stand in the Forum, as well as putting on several talks and presentations, which were incredibly well received by members of the general public and organisers alike. The event really sparked an interest in the sheer range of science undertaken at Earlham Institute, as well as the myriad applications of genome sequencing and bioinformatics. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Norwich Science Festival - 22/10/2019 to 24/10/2019 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Norwich Science Festival is a wonderful showcase of science from Norwich and beyond for learning and excellent public engagement. This year, EI presented 11 talks and poems covering a fascinating range of science topics, from Salmonella and guts through to sequencing algae in the Antarctic, covering the whole tree of life in the process, bringing an innovative Bee Trail, LEGO sequencer, robots and more. Researchers from the CSP participated, presented their work and engaged with the public. Coverage on TV, radio and media with estimated coverage views of 698K |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://earlhaminstitute.coveragebook.com/b/02819684cc7da5de |
| Description | Norwich Science Festival - Lego DNA sequencer |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | We created a working Lego Mindstorms model of a DNA sequencer, along with software to run it. We arranged activities around it during the Norwich Science Festival and engaged lots of adults and children. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://twitter.com/brickopore/status/1055043270999465985 |
| Description | Norwich Science Festival - The Nedome |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | During Norwich Science Festival, we ran live demonstrations of nanopore sequencing in which we sequenced the "Ned-ome" (DNA kindly provided by Ned, a PhD student). |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://twitter.com/hashtag/nedome?lang=en |
| Description | Norwich Science Festival Ops Note |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. Collectively, our international reach as of March 2019 has extended across the globe, with highlight pieces in the Guardian, the BBC World Service, the Washington Post and more, as well as local TV and radio. In 2018, the estimated readership of news stories we shared was well in excess of 1 million. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/newsroom/first-ei-lego-sequencer-human-dna-and-endangered-species-earlham-i... |
| Description | Norwich Science Park Open Day |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Presented poster on work linked to Big Data Bioinformatics |
| Year(s) Of Engagement Activity | 2016 |
| Description | Nuffield Research Experience Placements Summer 2020 (Virtual) |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Schools |
| Results and Impact | Nuffield reported a dramatic loss of placements due to the COVID-19 pandemic and the need to move these placements online. Earlham Institute were able to host 6 students, 5 to completion, through a four week research programme. Students worked in pairs, with each pair being assigned a different supervisor and organism to study, however, the cohort was combined in twice-weekly meetings to go over the tools and resources that were relevant to each project on a weekly basis so that they could see the data analysis approaches were similar across the different projects, and in a final presentation to all of the project supervisors and the training team at the end of their placement. The presentations at completion of the placements demonstrated just how much the students had each learned and achieved in such a short time, despite the difficulties in having to host these placements entirely remotely. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Oceans Day at Norwich Science Festival |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Tarang Mehta gave a well-received talk on how he delves into cichlid fish diversity for the Norwich Science Festival. He had given a similar talk the year before, and this was an update due to its roaring success the first time around. The talk helped to promote an awareness of the importance of understanding the evolution of interesting groups of organisms such as cichlid fish, and how this can be applied to a number of interesting research projects, from better understanding human disease through to improving aquaculture practice in East Africa. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Octoseq Workshop 18-19 December 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Project leaders and researchers engaged in the grant came together to report on the development of the project plus a short training activity relating to the grant output - a browser developed to explore the data. 14 people attended. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Old for new: using ancient genetic variation to supercharge wheat - 26/04/2019 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | A media interview and website articles on a global, collaborative effort led by the Earlham Institute, UK and CIMMYT, Mexico which sheds light on the genetic basis of biomass accumulation and efficiency in use of light, both of which are bottlenecks in yield improvement in wheat. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. This story has an estimated coverage views of 32.9K. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/newsroom/old-new-using-ancient-genetic-variation-supercharge-wheat |
| Description | On the beet: into the wild! |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Article on disease |
| Year(s) Of Engagement Activity | 2019 |
| Description | One day in New York: bioinformatics and family life |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Article on work life balance and career journey/progression |
| Year(s) Of Engagement Activity | 2018 |
| Description | Opportunities and challenges in Tanzanian tilapia fisheries and aquaculture programme |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Workshop 1: Biodiversity, species identification, and stocking of non-native tilapiines, Sokoine University of Agriculture, Morogoro, Tanzania, 16-17 Jan 2017. This workshop raised awareness of potential threats to native Tanzanian Tilapia species by breeding and stocking non-native species in Tanzanian water bodies. We included practical training in the identification of tilapia species, both in the field and from captive breeding facilities, through introduction of the new smartphone app 'TilapiaMap', and featured research seminars addressing issues of hybridisation, and the problems that mixed stocks may present to aquaculture. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Oral Presentation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Oral presentation as part of the annual PopGroup meeting |
| Year(s) Of Engagement Activity | 2021 |
| Description | Oral Presentation - Genomics in Aquaculture (GIA) 6th, Granada, Spain - EXAMINING GENETIC DIVERSITY AND CHROMATIN ACCESSIBILITY IN AQUACULTURE-RELEVANT TILAPIA SPECIES - Tarang Mehta |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Oral presentation as part of the Genomics in Aquaculture (GIA) 6th, Granada, Spain |
| Year(s) Of Engagement Activity | 2022 |
| Description | Oral Presentation - 34th European Mustelid Colloquium - Extensive genome introgression between domestic ferret and European polecat during population recovery in Great Britain - Graham Etherington |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Oral presentation as part of the 34th European Mustelid Colloquium |
| Year(s) Of Engagement Activity | 2022 |
| URL | http://www.european-mustelid-colloquium.org/ |
| Description | Oral Presentation - Characterization of noncoding expression and splicing diversity in the human brain |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Seminar at the Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden |
| Year(s) Of Engagement Activity | 2019 |
| Description | Oral Presentation - EI Innovate - Generating high-quality genomes for agriculturally relevant insects - Will Nash |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Presentation as part of EI Innovate |
| Year(s) Of Engagement Activity | 2022 |
| Description | Oral Presentation - Natural History Museum - Using DToL Data to study UK pollinating insects |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Supporters |
| Results and Impact | Oral presentation at the Natural History Museum London in front of UKRI officers |
| Year(s) Of Engagement Activity | 2022 |
| Description | Oral Presentation - Norwich Science Festival - Bee Biobiodiversity Bonanza - Will Nash |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Oral presentation as part of the Norwich Science Festival |
| Year(s) Of Engagement Activity | 2023 |
| Description | Oral Presentation - Post-bottleneck European polecat populations show high degrees of genome introgression |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Oral presentation at the 33rd European Mustelid Colloquium, Lisbon, Portugal |
| Year(s) Of Engagement Activity | 2019 |
| Description | Oral Presentation - Regulatory networks evolution underlying the rapid diversification of cichlids fishes in the Great African Lakes - Tarang Mehta |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited presentation at the Society for Molecular Biology and Evolution Annual Meeting (Ferrara Italy) |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.smbe2023.org/ |
| Description | Oral Presentation - Royal Entomolgical Society Conference 'Ento2022' Lincoln UK - Genome Wide Signatures of Range Expansion in A Key UK Pollinator - Will Nash |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Oral presentation as part of the Royal Entomolgical Society Conference 'Ento2022' Lincoln UK |
| Year(s) Of Engagement Activity | 2022 |
| Description | Oral presentation - Non-human genomes, why bother? |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Oral presentation at the EI Open Day |
| Year(s) Of Engagement Activity | 2019 |
| Description | Oral presentation - Characterization of splicing diversity and gene fusions through Nanopore sequencing |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Oral presentation at the Long Read Sequencing Meeting, SciLifeLab Uppsala, Sweden |
| Year(s) Of Engagement Activity | 2019 |
| Description | Oral presentation - Characterization of splicing diversity in bulk samples and single cells using long read technologies |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Seminar at the Maurice Wohl Clinical Neuroscience Institute King's College London |
| Year(s) Of Engagement Activity | 2019 |
| Description | Oral presentation - Detection of differential isoform expression and usage during cellular differentiation using long read RNA sequencing |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation at the London Calling 2021 meeting |
| Year(s) Of Engagement Activity | 2021 |
| Description | Oral presentation - Disruptive omics technologies in Molecular Medicine |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Oral presentation and panel discussion as part of the Disruptive omics technologies in Molecular Medicine workshop organised by the University ofYork |
| Year(s) Of Engagement Activity | 2021 |
| Description | Oral presentation - Enter the Nanoporium |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Oral presentation as part of the Pint of Science |
| Year(s) Of Engagement Activity | 2019 |
| Description | Oral presentation - How well do you know your family tree? |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Oral presentation at the Norwich Science Festival |
| Year(s) Of Engagement Activity | 2019 |
| Description | Oral presentation - Pint of Science - Pollinating the tree of life - Will Nash |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Presentation as part of the Pint of Science Event |
| Year(s) Of Engagement Activity | 2022 |
| Description | Oral presentation - Population level cis-regulatory variation highlights the importance of DNA shape to transcription factor binding affinity |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Oral presentation at the SMBE Annual Meeting 2019, Manchester, UK 21-25 July 2019 |
| Year(s) Of Engagement Activity | 2019 |
| Description | Oral presentation - Saving the Spectacled Bear of Deepest, Darkest Colombia |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Oral presentation at the Norwich Science Festival |
| Year(s) Of Engagement Activity | 2019 |
| Description | Oral presentation - Silent orchards: The importance of pollinators |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | Oral presentation at the Norwich Science Festival |
| Year(s) Of Engagement Activity | 2019 |
| Description | Oral presentation - Taking the long (read) view of alternative splicing during cell differentiation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Presentation at the EI Long Read Symposium, Earlham Institute (virtual) 15 - 17th June 2021 |
| Year(s) Of Engagement Activity | 2021 |
| Description | Oral presentation - What Can We Learn from a High Koala-ty Genome?' |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Orap presentation as part of the EI Open Days |
| Year(s) Of Engagement Activity | 2019 |
| Description | Oral presentation - Whole genome sequencing of tilapia species and improved strains WorldFish |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Oral presentation at the WorldFish Genetic Improvement Program (GIP) Meeting, Edinburgh UK |
| Year(s) Of Engagement Activity | 2019 |
| Description | Oral presentation at international conference: Characterization of functional long non-coding RNAs in human |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The presentation at the Genome 10K / Genome Science conference was selected on abstract submission. The presentation was delivered in front of industry participants, university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The presentation helped raising the international profile of Wilfried Haerty and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | Organising and hosting: Genome 10K and Genome Science Parallel Conferences 2017 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Earlham Institute hosted two conferences in parallel - The biannual Genome 10K conference and the annual Genome Science meeting from 29 August - 1 September 2017 (http://www.earlham.ac.uk/genome-10k-and-genome-science-conference). The conference attracted over 350 delegates, including sponsors and local council representatives in addition to the target attendees of PhD students, Postdocs and PIs from around the World. We received fantastic support from Greater Norwich Partnership, which comprises several local councils, including fantastic opportunities to showcase the city as well as entertain delegates with an exclusive tour of the castle. A joint press release was made with the councils, which was picked up by local media, resulting in a news article, and a lengthy (~15 minute) in-studio interview with our Director of Science, Federica Di Palma, raising awareness of the institute, our research and the wider goals of projects associated to the conference e.g. Genome 10K Project. Feedback from the delegates was fantastic with many delegates providing verbal feedback at the conference itself, including praise around gender balance of speakers, logistics and organisation of the conference, catering and entertainment. As part of our commitment to supporting early career researchers, we offered, at no additional registration cost, limited spaces on training and careers development workshops (de novo assembly course, RNAseq using Galaxy course, science communication workshop, CV skills workshops, and a session on career paths). Delegates enjoyed the location of the conference, for many it was their first visit to the area, and hosting these two conferences not only raised the profile of the institute and it's location, but also the fantastic research that we are engaged in, and elicited promises of return visits through anticipated collaborations, plus an appreciation for our skills in wider activities such as training and events. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/articles/genome-10k-and-genome-science-conference-2017-gallery |
| Description | Orphan Crops: the neglected side of food security & climate change |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Blog interview to PI and PD working on this project about their work on orphan crops, and the importance of research about orphan crops. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/orphan-crops-neglected-side-food-security-climate-change |
| Description | Orphan crops, the neglected side of food security and climate change |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Orphan crops, the neglected side of food security and climate change |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/orphan-crops-neglected-side-food-security-climate-change |
| Description | PAG 2019 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Gave talk at the Plant and Animal genome conference: Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency Sequence exchange between homologous chromosomes through crossing over and gene conversion is highly conserved among eukaryotes, contributing to genome stability and genetic diversity. Lack of recombination limits breeding efforts in crops, therefore increasing recombination rates can reduce linkage-drag and generate new genetic combinations. We use computational analysis of 13 recombinant inbred mapping populations to assess crossover and gene conversion frequency in the hexaploid genome of wheat (Triticum aestivum). We observe that high frequency crossover sites are shared between populations and that closely related parental founders lead to populations with more similar crossover patterns. We demonstrate that gene conversion is more prevalent and covers more of the genome in wheat than in other plants, making it a critical process in the generation of new haplotypes, particularly in centromeric regions where crossovers are rare. We have identified QTL for altered gene conversion and crossover frequency and confirm functionality for a novel RecQ helicase gene that belongs to an ancient clade that is missing in some plant lineages including Arabidopsis. This is the first gene to be demonstrated to be involved in gene conversion in wheat. Harnessing the RecQ helicase has the potential to break linkage-drag utilizing widespread gene conversions. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Participation in I'm A Scientist |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Schools |
| Results and Impact | I'm a Scientist is an online activity where school students connect with scientists. It's an X Factor-style competition between scientists, where students are the judges. Students challenge the scientists over fast-paced online text-based live CHATs. They ASK the scientists anything they want, and VOTE for their favourite scientist to win a prize of £500 to communicate their work with the public. I was a pannel member for the Genes zone, whose pages reached around 400 students and had nearly 20000 page views |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://imascientist.org.uk/ |
| Description | Paul Bailey talk at PAG at Cyverse workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | As more genomes are sequenced it is becoming apparent that gene duplication and deletion are important drivers in evolution, with rapidly expanding gene families often a signature of their role in an organism's adaptation to the environment. To identify these events, we are building a gene family analysis toolkit which will be deployed on the Cyverse cloud infrastructure for use by the scientific community. Central to its purpose will be the ability to distinguish evolutionary relationships between genes within gene families for currently and newly sequenced species, both at the intra- and inter-species level. As a pilot study, we are using a collection of landrace bread wheats (the Watkins collection) which have been sequenced by exome capture to explore the diversity of the large Nucleotide Binding Leucine Rich Repeat (NLR) family of plant resistance genes in the collection. Illumina read data from each wheat line have been assembled using various tools. The resulting contigs have been aligned to their corresponding subgroups within the NLR family. Looking at subgroups that are expanded relative to other monocot species, we can demonstrate that further novel gene duplication events have occurred in specific lines of the Watkins collection. The next step will be to understand whether specific genes in the family are under positive selection and therefore which genes have particular functional significance. The assembly and downstream procedures will be placed into a Docker container for use on Cyverse as a tool for exploring the diversity of any gene family in any species with sequence data. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://pag.confex.com/pag/xxvi/meetingapp.cgi/Paper/29841 |
| Description | Pint of Science |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Will Nash gave a well-received talk about his work understanding the koala genome, and what we can learn from understanding it - particularly how koalas can somehow withstand a toxic diet of eucalyptus. Pint of Science is a great occasion to share information with the public in an informal setting, which stimulates and encourages debate and discussion, therefore the opportunity for a dialogue - which is a valuable outcome for any public engagement event. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Pint of Science 2022 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Two of our researchers took part in a Pint of Science event to discuss plants and pollinators. The talks are designed to engage an adult audience with an interest in science, inviting questions and discussion on the topics in an informal way. Feedback from the event indicated a strong interest in the subject matter with new things learned and potential follow-up - particularly in relation to the bees. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://pintofscience.co.uk/event/pollinators-plants-and-pints |
| Description | Plants can be larks or night owls just like us |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Plants can be larks or night owls just like us |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.telegraph.co.uk/news/2020/12/18/plants-night-owls-early-birds-just-like-humans-scientist... |
| Description | Podcast - Genetics Unzipped Podcast by the Genetics Society - S5.20 Bread and fishes: the future of food in a changing climate - Tarang Mehta |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Podcast to highlight activities focusing on building genomic resources for aquaculture |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://geneticsunzipped.com/blog/2022/10/6/bread-and-fishes |
| Description | Pole to Pole: breaking point for ocean's microbial biodiversity most likely to affect UK |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Article linked to a publication |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.earlham.ac.uk/newsroom/pole-pole-breaking-point-oceans-microbial-biodiversity-most-likel... |
| Description | PopGroup56 conference talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Approximately 100 scientists attended this conference presentation on the development of methodologies to study and understand the evolutionary processes involved in adaptation of pathogens to crops. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.populationgeneticsgroup.org.uk/ |
| Description | Poster Presentation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation as part of the Biodiversity Genomics conference |
| Year(s) Of Engagement Activity | 2020 |
| Description | Poster Presentation - Intelligent Systems for Molecular Biology - Scaling up GeneSeqToFamily to handle pan transcriptomes and million of genes |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation as part of the Intelligent Systems for Molecular Biology 2022 conference |
| Year(s) Of Engagement Activity | 2022 |
| Description | Poster Presentation - 200 Genomes EI Open Days |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Poster Presentation EI Open Days |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster Presentation - Brain Isoforms EI Open Days |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Poster Presentation as part of EI Open Days |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster Presentation - Cambridge Stem Cell Symposium - Characterization of splicing in the haematopoietic landscape using combined short and long read single-cell sequencing |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the Cambridge Stem Cell Symposium |
| Year(s) Of Engagement Activity | 2018 |
| Description | Poster Presentation - Characterisation of long non coding RNAs in T. aestivum strains |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the Plant and Animal Genome (PAG2020) Conference |
| Year(s) Of Engagement Activity | 2020 |
| Description | Poster Presentation - Cichlid Science 2022 - Ongoing and ancient introgression in Oreochromis tilapias - Adam Ciezarek |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation as part of the Cichlid Science 2022, Cambridge UK |
| Year(s) Of Engagement Activity | 2022 |
| Description | Poster Presentation - Cichlid Science 2022, Cambridge - Evolution of regulatory networks associated with traits of cichlid phenotypic diversity - Tarang Mehta |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation as part of the Cichlid Science 2022 conference |
| Year(s) Of Engagement Activity | 2022 |
| Description | Poster presentation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation as part of the Biodiversity Genomics Conference |
| Year(s) Of Engagement Activity | 2020 |
| Description | Poster presentation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the annual PopGroup meeting |
| Year(s) Of Engagement Activity | 2021 |
| Description | Poster presentation - Examining genetic diversity and traits under selection in several aquaculture-relevant tilapia species |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the Genome Science Conference, Nottingham, UK . The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Poster presentation - The evolution of mammalian microRNAs |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the Biology of Genomes, Cold Spring Harbor Laboratory. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Poster presentation - Acomys EI Open Days |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Poster presentation as part of the EI Open Days |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster presentation - BIOINFORMATICS IN THE ERA OF GENOMICS IN AFRICA |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the First Nigerian Bioinformatics Conference (FNBC) 2019 |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster presentation - Characterisation of structural variants in the adaptive radiation of East African Lake cichlids |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the SMBE Annual Meeting 2019, Manchester, UK 21-25 July 2019 |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster presentation - Characterising and visualising gene families within Galaxy using GeneSeqToFamily and Aequatus |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the SMBE Annual Meeting 2019, Manchester, UK 21-25 July 2019 |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster presentation - Evolution of chromatin accessibility associated with traits of cichlid phenotypic diversity |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the SMBE Annual Meeting 2019, Manchester, UK 21-25 July 2019 |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster presentation - Evolution of chromatin accessibility associated with traits of cichlid phenotypic diversity |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the Evolutionary Systems Biology 2020 , Wellcome Genome Campus Conference Centre UK |
| Year(s) Of Engagement Activity | 2020 |
| Description | Poster presentation - Gene regulatory network evolution in East African lake cichlids |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation as part of the PopGroup 52, Oxford. The audience included group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster presentation - Generating and visualizing assemblies of Arabidopsis thaliana Col-0 using nanopore data and Alvis |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation given by Sam Martin at London Calling 2019 |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster presentation - Genomic introgression in Oreochromis tilapias |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the PopGroup53 , Leicester UK |
| Year(s) Of Engagement Activity | 2020 |
| Description | Poster presentation - Koala EI Open Days |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Poster presentation as part of the EI Open Days |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster presentation - Nanopore sequencing reveals the transcriptional complexity of neuropsychiatric disease genes in human brain |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation Biology of Genomes, Cold Spring Harbor Laboratory. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Poster presentation - Post-bottleneck European polecat populations show high degrees of genome introgression |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the SMBE Annual Meeting 2019, Manchester, UK 21-25 July 2019 |
| Year(s) Of Engagement Activity | 2019 |
| Description | Poster presentation - Real-time metagenomic analysis with MARTi (AGBT 2021) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at AGBT 2021 conference. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.agbt.org |
| Description | Poster presentation - Real-time surveillance and diagnostics with NanoOK RT |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the London Calling conference, May 2018 |
| Year(s) Of Engagement Activity | 2018 |
| Description | Poster presentation - The long and the short of eukaryotic metagenomics: Identification and quantification of plant species in bee pollen |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the Advances in Genome Biology and Technology (AGBT) conference in Marco Island, Florida. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.agbt.org |
| Description | Poster presentation : Resistant Escherichia coli Interactome identifies putative novel drug combinations to break antimicrobial resistance 2nd Interdisciplinary Signaling Workshop 2017 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Modos D., Bulusu K., Afzal A., Sudhakar P., Korcsmaros T., Cokol M., Bender A. (2017) Resistant Escherichia coli Interactome identifies putative novel drug combinations to break antimicrobial resistance 2nd Interdisciplinary Signaling Workshop 2017 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://signalingworkshop.org/ |
| Description | Poster presentation : SalmoNet: an integrated multi-layered network for Salmonella 2nd Interdisciplinary Signaling Workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Study participants or study members |
| Results and Impact | Olbei M. L. O., Metris A. M., Sudhakar P. S., Fazekas D. F., Demeter A. D., Ari E. A., Branchu P. B., Kingsley R. K., Baranyi J. B., Korcsmaros T. K. (2017) SalmoNet: an integrated multi-layered network for Salmonella 2nd Interdisciplinary Signaling Workshop |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://signalingworkshop.org/ |
| Description | Poster presentation : SalmoNet: an integrated multi-layered network for Salmonella Genome 10K and Genome Science Conference. Genome 10K and Genome Science Conference 2017 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Study participants or study members |
| Results and Impact | Olbei M. L. O., Metris A. M., Sudhakar P. S., Fazekas D. F., Demeter A. D., Ari E. A., Branchu P. B., Kingsley R. K., Baranyi J. B., Korcsmaros T. K. (2017) SalmoNet: an integrated multi-layered network for Salmonella Genome 10K and Genome Science Conference |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://genome10k.soe.ucsc.edu/node/130 |
| Description | Poster presentation at National Conference: Expansion of gene families and signatures of selection in the Australian marsupials |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | The poster presented at the 50th Population Genetics Group meeting (Cambridge UK) was selected on abstract submission. The poster was presented in front of iuniversity professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of AWill Nash, Wilfried Haerty, and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | Poster presentation at international conference: Binding sites within long non-coding RNAs discriminate between RNA- and transcription-mediated mechanism |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The poster presented at the Genome 10K / Genome Science conference was selected on abstract submission. The poster was presented in front of industry participants, university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of Tomasz Wrzesinski, Wilfried Haerty and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | Poster presentation: Tackling microbial diseases of the preterm infant gut using MinION diagnostics and NanoOK |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at AGBT 2018 conference, Florida, USA, February 2018. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation - Characterization of functional noncoding RNAs: From prediction to experimental validation. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation at the Evolution in the 21st Century: The Inaugural Conference of the Milner Centre for Evolution. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation - Convergent evolution of immunity in aquatic plants |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Presentation at The Sainsbury Laboratory retreat. The audience included group leaders, postdoctoral researchers and graduate students |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation - Evolution of regulatory networks controlling adaptive traits in cichlids Network Biology CSHL, NY, USA Mar 19-23 2019 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation at the Network Biology meeting Cold Spring Harbor Laboratory. The audience included group leaders, university lecturers, postdoctoral researchers, graduate students and industry representatives. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Presentation - The role of structural variants in the adaptive radiation of African Cichlids |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentatio at the Genome Informatics 2018 Conference, Hinxton, Cambridge. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation - Characterization of noncoding expression and splicing diversity in the human brain |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited seminar at the Institute of Ophthalmology, University College London. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Presentation - Characterization of splicing diversity and gene fusions through Nanopore sequencing |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Selected presentation at AGBT2019, Marco Island Florida. The audience consisted of group leaders, postdoctoral researchers, graduate students, industry representatives. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Presentation - Festival of Genomics 2023 - Long Read RNA Seq Applications for Targets Identification |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Presentation at the Festival of Genomics |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.festivalofgenomics.com/ |
| Description | Presentation - Genomics applications for conservation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Presentation as part of a training course for the use of genomic resources for species identification delivered to law enforcement officers in Cali, Colombia. The audience included university lecturers, graduate and undergraduate students, conservation organizations, law officers, representatives of the ministry of environment, ministry of justice, |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation - Lego sequencer at the Women of the Fututre event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Activity at the Women of the Fututre event |
| Year(s) Of Engagement Activity | 2019 |
| Description | Presentation - Long Read Sequencing Uppsala - Comprehensive human brain transcriptome characterisation using long-read CaptureSeq |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation as part of the Annual Long Read Sequencing Uppsala meeting |
| Year(s) Of Engagement Activity | 2022 |
| Description | Presentation - Natural History Museum Lates - Seven Worlds, One Planet |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Presentation at the Natural History Museum Lates - Seven Worlds, One Planet |
| Year(s) Of Engagement Activity | 2019 |
| Description | Presentation - Poster - Characterization of Functional ncRNA in Plants |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the Bioinformatics for Plant Biology Course, EMBL-EBI Hinxton |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation - RCUK GROW Colombia Natural Diversity |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Presentation as part of FIMA 2018 in Bogota, Colombia. The audience included general public, conservation organization, schools, law officers |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation - What can we learn form a high Koala-ty genome? |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Presentation as part of the Norwich Science Festival. The audience included general public and schools |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation - What can we learn from a high Koala-ty genome |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Public/other audiences |
| Results and Impact | Presentation as part of the Pint of Science. The audience included general public and graduate students |
| Year(s) Of Engagement Activity | 2018 |
| Description | Presentation - Winter Conference on Brain Research - Characterisation of Transcript and Protein Diversity in Major Candidates for Neuropsychiatric Disorders |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation at the Winter Conference on Brain Research |
| Year(s) Of Engagement Activity | 2023 |
| Description | Presentation - Working with sequences |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Lecture delivered to BBSRC DTP graduate students as part of the Computational & Systems Biology DTP course |
| Year(s) Of Engagement Activity | 2019 |
| Description | Presentation as part of Agri-tech week |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | Scientist from Norwich Research Park came together to discuss the research surrounding crop/soil health studies. The event was advertised in the Eastern Daily press and the audience included people from the general public, researchers and farmers/industry around East Anglia. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.edp24.co.uk/news/business/agri-tech-week-norwich-research-park-6415196 |
| Description | Preserving and Restoring Colombian Biodiversity - Bogota Workshop |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Video to highlight the workshop that took place in Bogota in October 2017. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://www.youtube.com/watch?v=aKqQLOFW4HA |
| Description | Press Release - 'Better barley is on the way' |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Press release to illustrate our role in an international consortium, led in the UK by the James Hutton Institute, which published the first high-quality genome sequence of barley in the journal Nature. -SOCIAL MEDIA- Engagement x155, Impressions x144617 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/better-barley-way-crop-genome-unravelled |
| Description | Press Release - 'New era for nature in colombia' |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Press Release to highlight the Colombia project and formation of the BRIDGE consortia. -SOCIAL MEDIA- Engagement x164, Impressions x117000 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/new-era-nature-colombia |
| Description | Press Release - 'a practitioners perspective at the 'Doing Science with Colombia' event '. |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Press release to Highlight Federica Di Palmas role as panellist at the 'doing Science with Colombia' event, Natural History Museum, 7th December 2017. -SOCIAL MEDIA- Engagement x55, Impressions x57826 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/newsroom/federica-di-palma-provides-practitioners-perspective-%E2%80%98doin... |
| Description | Press Release - Core funding announcement |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Core funding announcement via Press Release. -SOCIAL MEDIA- Engagement x94, Impressions x24888 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://earlham.ac.uk/statement-in-response-to-bbsrc-319m-investment-announcement |
| Description | Press Release - Network science unravels the secrets of the evolution of Salmonella's disease adaptations |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Press release to introduce SalmoNet, a systems biology approach that uses network biology and bioinformatic techniques to collate molecular interactions within Salmonella, and to link information on how genes and metabolic pathways are regulated in Salmonella, and how proteins interact with each other. -SOCIAL MEDIA- Engagement x45, Impressions x54800 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/newsroom/network-science-unravels-secrets-evolution-salmonella%E2%80%99s-di... |
| Description | Press Release - Sat nav for bread wheat uncovers hidden genes |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Press release on the publication of the world's most complete picture of the wheat genome. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/sat-nav-bread-wheat-uncovers-hidden-genes |
| Description | Press Release - Spectre 'catch of the day: a net full of trees' |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Press release on SPECTRE, a new open-source software package that simplifies the complex business of creating phylogenetic networks and trees. Sarah Bastkowski and Dan Mapleson. -SOCIAL MEDIA- Engagenments x 135, Impressions x78755 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/newsroom/catch-day-net-full-trees |
| Description | Press article - Improved strain of tilapia genome sequencing highlighted by UKRI and BBSRC Impact Showcase of 2022 - Tarang Mehta, Will Nash, Adam Ciezarek, Graham Etherington |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Article as part of BBSRC Impact showcase 2022 |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://preview.shorthand.com/uG7dbZH9ZkAyeO0M#group-section-Collaboration-Tv0V86lglL |
| Description | Press article - UK polecats numbers are rising as they interbreed with ferrets |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Press article in New Scientist associated with a publication |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.newscientist.com/article/2334445-uk-polecats-numbers-are-rising-as-they-interbreed-with-... |
| Description | Press article - UKRI BBSRC Strategic Delivery Plan 2022 - Cichlid GRNs work 'A role for non-coding DNA in biodiversity' - Tarang Mehta |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Article highlighting activities to characterise regulatory networks in cichlids published in UKRI BBSRC Strategic Delivery Plan 2022 |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.ukri.org/wp-content/uploads/2022/09/BBSRC-010922-StrategicDeliveryPlan2022.pdf |
| Description | Press release - Crowning the "King of the Crops": Sequencing the White Guinea Yam Genome |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Press Release on an international collaboration involving the Earlham Institute, Norwich, UK, and the Iwate Biotechnology Research Centre, Japan. The project has, for the first time, provided a genome sequence for the white Guinea yam, a staple crop with huge economic and cultural significance on the African continent and a lifeline for millions of people. -SOCIAL MEDIA- Engagement 207, Impressions 93116 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/newsroom/crowning-the-king-of-the-crops-sequencing-the-white-guinea-yam-gen... |
| Description | Press release - Improving aquaculture with genomics resources for breeders - Tarang Mehta |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Press release for publication of the GIFT genome |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/impact-story-improving-aquaculture-genomics-resources-breeders |
| Description | Press release - The miRNA driving the Weddell Seal's incredible deep diving ability |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | The miRNA driving the Weddell Seal's incredible deep diving ability |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/mirna-driving-weddell-seal%E2%80%99s-incredible-deep-diving-abili... |
| Description | Press release - regulatory networks in cichlids |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Press release for the publication of the article describing regulatory network rewiring in cichlids |
| Year(s) Of Engagement Activity | 2021 |
| Description | Prof. Tracey Chapman & Dr Emily Fowler - UEA - 28/11/2018 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Other audiences |
| Results and Impact | Meeting to discuss collaborative project |
| Year(s) Of Engagement Activity | 2018 |
| Description | Professor Ian Boyd - Chief Scientific Adviser to DEFRA - 04/02/2019 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Meeting to discuss Institute influence and impact into government policy and input into Select Committees |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://data.parliament.uk/writtenevidence/committeeevidence.svc/evidencedocument/science-and-technol... |
| Description | Real time sequencing solutions: taking the lab to the sample and beyond |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Article on the EI website about our work with real-time nanopore sequencing |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/real-time-sequencing-solutions-taking-lab-sample-and-beyond |
| Description | Researchers Report Resequenced Vietnamese Rice Genome |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | https://www.isaaa.org/kc/cropbiotechupdate/article/default.asp?ID=18856 |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.isaaa.org/kc/cropbiotechupdate/article/default.asp?ID=18856 |
| Description | Rice varieties could sustain crop supplies facing climate change |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | https://phys.org/news/2021-06-rice-varieties-sustain-crop-climate.html |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://phys.org/news/2021-06-rice-varieties-sustain-crop-climate.html |
| Description | Salmonella - how the body fights back - 14/11/2019 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Website article highlighting collaborative research from the University of East Anglia, supported by Earlham Institute (EI) which shows how the human body powers its emergency response to salmonella infection. Contributions from the Macaulay and Di Palma groups. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/newsroom/salmonella-how-body-fights-back |
| Description | Salmonella, who gives a faeces? - 23/04/2019 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Website article showcasing the CSPs work on a number of different aspects of Salmonella Researchers through understanding its invasiveness, pathogenicity, genetics and evolution, especially with regard to the growing threat of multidrug resistance and alarmingly devastating new strains arising in sub-Saharan Africa. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/articles/salmonella-who-gives-a-faeces |
| Description | School visit - Great Hockham Students, Parents, and Teachers - Will Nash |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | School visit: Great Hockham Students, Parents, and Teachers |
| Year(s) Of Engagement Activity | 2022 |
| Description | Science Camp |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Schools |
| Results and Impact | Graham Etherington put on a a workshop on how to use bioinformatics tools, namely Galaxy, in the life sciences. This is a very valuable introduction to the work undertaken at EI, and a chance to show the next generation of budding scientists the important role of computational-driven approaches to understanding life, evolution, and how we can improve crops through better understanding genetic diversity and variation. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Scientists develop a test for sepsis in premature babies which works by analysing bacteria in their NAPPIES (Mail Online) |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Article about our work in Daily Mail Online website, 16 December 2019. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.dailymail.co.uk/health/article-7797493/Scientists-develop-test-sepsis-premature-babies.h... |
| Description | Seedquest.com |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | https://www.seedquest.com/news.php?type=news&id_article=126658 |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.seedquest.com/news.php?type=news&id_article=126658 |
| Description | Selective sweeps during domestication and adaptation of rice subpopulations within a diverse collection of Vietnamese Rice (3rd UK Plant Evolution Meeting ) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented by Janet Higgins at the 3rd UK Plant Evolution Meeting on 4th Apr 2019 |
| Year(s) Of Engagement Activity | 2019 |
| Description | Sequencing and chromosome level assembly of rodent genomes : Understading the mechanisms of lineage-specific genome evolution in mammals. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I presented work on chromosome level assembly of mammalian genomes and the comparison of these genomes in order to understand the mechanisms driving lineage-specific evolution in mammals. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Shropshire Star, p17. 16/04/2021 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Farming talk |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.shropshirestar.com/news/farming/2021/04/15/the-biofuel-that-could-help-us-achieve-net-ze... |
| Description | Single-Cell RNAseq 1-4 November 2021 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Aimed at researchers who were in the experimental planning stages of a Single-Cell genomics project, the course required no previous experience in bioinformatics approaches with the najority of hands-on analysis delivered through the web-based, user-friendly interface - Galaxy. The course provided an introduction to single-cell genomics for researchers who are new to bioinformatics and covered: assessing the quality of sequence data, data visualisation, differential expression analyses and identifying Copy Number Variations at the single-cell level. It consisted of a mixture of conceptual and methodological lectures and hands-on sessions, including best practices and tips as learned first-hand by Earlham Institute's faculty. The course was redeveloped from the course delivered in 2020 focusing on bioinformatics only, spread over 4, shorter days (10:00-15:00) and involved a number of new teaching faculty. The majority of attendees were national and outside of the Norwich Research park (50%), and from academia (94%). They rated the training overall as very good or excellent (91%) and the trainers very good or excellent (91%), with 91% saying that they would recommend the course. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.earlham.ac.uk/single-cell-rnaseq-training-course-2021 |
| Description | Single-Cell RNAseq 19-22 October 2020 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Aimed at researchers who were in the experimental planning stages of a Single-Cell genomics project, the course required no previous experience in bioinformatics approaches with the najority of hands-on analysis delivered through the web-based, user-friendly interface - Galaxy. The course provided an introduction to single-cell genomics for researchers who are new to bioinformatics and covered: assessing the quality of sequence data, data visualisation, differential expression analyses and identifying Copy Number Variations at the single-cell level. It consisted of a mixture of conceptual and methodological lectures and hands-on sessions, including best practices and tips as learned first-hand by Earlham Institute's faculty. The course was converted from a 5-day course that was previously split 3 days of lab work and 2 days of bioinformatics into a bioinformatics only course, spread over 4, shorter days (10:00-15:00) and involved a number of new teaching faculty. The majority of attendees were national and outside of the Norwich Research park, and from academia (88%). They rated the training overall as very good or excellent (100%) and the trainers very good or excellent (100%), with 100% saying that they would recommend the course. Despite the virtual nature of the course, there were plenty of opportunities to to discuss matters with both trainers and discuss with other delegates and there were many requests during our introductory delegate 'flash' presentations where individuals wished to reach out to each other for longer-term collaborations and/or to discuss new techniques/approaches that were presented. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/single-cell-rnaseq-2020 |
| Description | Single-Cell RNAseq Data Analysis 7 - 10 November 2022 (Hybrid) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | The Single-Cell RNAseq workshop is now in its fourth year, although this was the first iteration to be conducted in hybrid format. It is aimed at students and early-career researchers in the early stages of a single-cell project and provides an introduction to single-cell genomics via a combination of lectures, hands-on bioinformatics sessions (using Smartseq and 10X protocols) and case studies from EIs own PhD cohort. Familiarity with Unix Shell and R was required. Registration was on an application basis, to establish the relevance/suitability of the course for each applicant in accordance with their project, experience, or studies. Access to virtual machines (via Cyverse UK) allowed students to access data and software required for the hands-on sessions, with access continuing to be provided for a short time after the course to allow optimal use for the attendees. All sessions were recorded and distributed to attendees. The hybrid format allowed international attendance, and while the majority were based in parts of the UK (53%) there were attendees from America (11%), Italy, Scandinavia, Spain and New Zealand. Of the 19 registrants, 4 were based at the Norwich Research Park. The majority opted for virtual attendance (74%). In terms of job function, the majority were Post Doctoral researchers and PhD students (58%), the remainder comprising Professors, bioinformaticians and data analysts. 100% rated the overall quality of the course as very good/excellent and all would recommend the course. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/events/single-cell-rnaseq-data-analysis-2022#about-the-event |
| Description | Single-cell RNAseq Training Course Delivered 3-7 Dec 2018 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was the first iteration of this course, demonstrating EI's both introducing Single Cell Genomics and demonstrating EI's capability. It covered several aspects such as: the experimental design, cell sorting and processing for production of quality samples for sequencing, in the three-days of laboratory hands-on sessions; generation of sequencing data, assessing the quality of sequence data, data visualisation, differential expression analyses and identifying Copy Number Variants at the single cell level in the following two-days of theory and computational hands-on sessions. A total of twelve (12) delegates attended this course, with ten (10) attending the full five days. Also included was a short half-day session with practical elements on single molecule FISH, delivered by EI faculty, and an overview of 10X Genomics' data analysis platform, presented by one of their Field Application Specialists. Delegates were predominantly UK-based (~83%) and PostDocs (two-thirds), with a couple of attendees responsible for similar laboratory facilities in their home institutions. All attendees rated the trainers as "Very Good" to "Excellent", and a survey of the ten laboratory sessions attendees suggested that, having followed the course, many hoped to engage with a Single-Cell RNAseq service for their research (53% very likely and 40% likely), with 53% wishing to provide cells. Following the unprecedented success of delegates producing high quality data to analyse, course organisers wish to review the programme. The proposal for the second iteration is to run the course as 3 or 4 days in the laboratory, with sequencing running over a weekend, and then extending the bioinformatics from 2 days to 4 days, running this on the following week. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/single-cell-rnaseq-training-course |
| Description | Sleep, wake, repeat: how do plants work on different time zones? - 03/06/2019 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Website article on a new method developed by Anthony Hall's group to reliably measure plant circadian clocks and understand how different plants respond to day and night, which has revealed that these circadian rhythms change as they age. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/newsroom/sleep-wake-repeat-how-do-plants-work-different-time-zones |
| Description | Soil health case study submitted to the Microbiology society |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | The soil health case study was presented to the '75th Anniversary: A Sustainable Future' of the Microbiology Society that looks into 'The role of microbiology in achieving the United Nations Sustainable Development Goals'. The article showcases the work that is being done by the GROW-Colombia project to undestrand the role of microbial diversity in sustaining ecosystem services derived from agricultural/managed soils. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://microbiologysociety.org/our-work/75th-anniversary-a-sustainable-future/soil-health/soil-heal... |
| Description | Space-inspired speed breeding for crop improvement - 16/11/2018 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. Collectively, our international reach as of March 2019 has extended across the globe, with highlight pieces in the Guardian, the BBC World Service, the Washington Post and more, as well as local TV and radio. In 2018, the estimated readership of news stories we shared was well in excess of 1 million. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/newsroom/space-inspired-speed-breeding-crop-improvement |
| Description | Students need to up their bioinformatics game |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Undergraduate students |
| Results and Impact | Interview of an undergraduate student doing a research placement at EI on the importance of developing bioinformatic skills |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/students-need-their-bioinformatics-game-why-i-am-learning-code-py... |
| Description | Sustainable Tropical Agricultural Systems Programme Project Scoping Workshop at CIAT Headquarters in Cali |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Sustainable Tropical Agricultural Systems Programme Project Scoping Workshop at CIAT Headquarters in Cali focused on tropical agricultural systems containing pulses and/or forages that are relevant to, and part of, the livelihood of communities in Colombia. Applications were invited from individual researchers who could contribute to the project scoping workshop and the resulting research projects. Up to 40 participants in total (around 20 from the UK and 20 from CIAT) were identified to take part. |
| Year(s) Of Engagement Activity | 2017 |
| URL | https://bbsrc.ukri.org/funding/filter/2017-sustainable-tropical-agricultural-systems-programme/ |
| Description | Talk - Developing a Streamlined Field Protocol for In Situ Sequencing and Analysis of Extremophiles |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk at American Geophysical Union Fall Meeting, Washington DC, 10-14 December 2018 |
| Year(s) Of Engagement Activity | 2018 |
| Description | Talk - In-field and real-time metagenomics using nanopore sequencing (ELSA Workshop 2020) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Policymakers/politicians |
| Results and Impact | ELSA Workshop: Metagenomics, Norwich Research Park, 2nd Dec 2020 |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.norwichresearchpark.com/event/elsa-workshop-metagenomics |
| Description | Talk - Rapid sequencing diagnostics for plant and animal pathogens (EI Innovate 2020) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Delivered talk and participated in workshop at EI Innovate 2020. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/ei-innovate-2020 |
| Description | Talk - Real-time pathogen identification and AMR profiling with nanopore sequencing (EI Innovate 2021) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Talk at EI Innovate 2021 event |
| Year(s) Of Engagement Activity | 2021 |
| Description | Talk and discussion with Elsoms seeds |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | The talk was to breeders and crop scientist work at Elsoms seed, The aim was to raise awareness of the work that Design future wheat and my group were doing. This lead to a letter of support for our BBSRC grant and a line of communication with their wheat and brassica breeders. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Talk and poster presentation - Taking the lab to the sample: enabling new ways of working with nanopore sequencing |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster and flash talk at the Advances in Genome Biology and Technology (AGBT) conference in Marco Island, Florida. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.agbt.org |
| Description | Talk at Visegrad Interdisciplinary Signaling workshop, Hungary |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Federica Di Palma gave a talk on "Evolution of tissue-specific regulatory programs in cichlids". In vertebrates, the East African cichlid radiations represent arguably the most dramatic examples of adaptive speciation. In the great lakes Victoria, Malawi and Tanganyika and within the last few million years, one or a few ancestral lineages of haplochromine cichlid fish have given rise to over 1500 species exhibiting an unprecedented diversity of morphological and ecological adaptations. Such explosive phenotypic diversification of East African cichlids is unparalleled among vertebrates and the low protein divergence between species implies the rapid evolution of regulatory regions and networks underlying the traits under selection. Comparative functional genomics, transcriptomics and epigenomics are powerful tools to study the evolution of tissue and species divergence. We recently developed Arboretum, an algorithm to identify modules of co-expressed genes across multiple species in a phylogeny. By integrating inferred modules with nucleotide variation, predicted cis regulatory elements and miRNA profiles from five East African Cichlids, we investigated the evolution of tissue-specific gene regulation. Our analyses identified modules with tissue-specific patterns for which we reconstructed the evolutionary gene regulatory networks across the five cichlids species. We report striking cases of rapid network rewiring for genes known to be involved in traits under natural and/or sexual selection such as the visual systems, and more specifically a cone opsin (sws2a) responsible for colour vison of selected cichlid fishes. Furthermore, in-depth analyses of regulons (transcription factor - target interactions, e.g. Egr3) show similar rapid species-specific rewiring. Investigation of these novel interactions in Astatotilapia burtoni, a model species for behaviour evolution, reveal significant enrichment for genes involved in neuronal and brain function. Our unique integrative approach that interrogates the evolution of regulatory networks allowed us to identify the rapid regulatory changes associated with certain traits under selection in cichlids. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Teaching - BIO4001A UEA - Will Nash |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Undergraduate students |
| Results and Impact | Teaching at UEA |
| Year(s) Of Engagement Activity | 2022 |
| Description | Techology Day at Norwich Science Festival |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | 7500 members of the general public attended Nature Day at Norwich Science Festival. A number of activities were available to engage the general public with the work of the institute. A number of talks/presentations were scheduled also. |
| Year(s) Of Engagement Activity | 2018 |
| Description | The Earlham Institute LEGO sequencer |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Article on EI website about our engagement project in which we built a LEGO DNA sequencer |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/earlham-institute-lego-sequencer |
| Description | The genetic machinery that drives biodiversity |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Article to explore research into a key species for aquaculture and how genomics approaches can inform breeding programmes. The article was used in helping to secure a podcast interview for one of the researchers. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/articles/genetic-machinery-drives-biodiversity |
| Description | The genetic machinery that drives biodiversity - Graham Etherington |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Article to explore research into a key species for aquaculture and how genomics approaches can inform breeding programmes. The article was used in helping to secure a podcast interview for one of the researchers. |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/articles/genetic-machinery-drives-biodiversity |
| Description | The role of Structural variants in the adaptive radiation of African Cichlids |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Our study on the evolution of Structural variants in African Cichlids was presented at the Genome Informatics Conference (Genome campus, Hinxton,Cambridge). The audience was engaged and a few questions were asked to further clarify some important aspects of the study. |
| Year(s) Of Engagement Activity | 2018 |
| Description | The taming of the dog, cow, horse, pig and rabbit - 19/11/2018 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. Collectively, our international reach as of March 2019 has extended across the globe, with highlight pieces in the Guardian, the BBC World Service, the Washington Post and more, as well as local TV and radio. In 2018, the estimated readership of news stories we shared was well in excess of 1 million. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.sciencedaily.com/releases/2018/11/181120125840.htm |
| Description | Thought for Food - Podcast |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Podcast - Discussion on the Thought for Food conference attended by Ben White and other researchers. SOCIAL MEDIA Engagement 61 Impressions 97047 The Thought For Food Global Summit 2017 was held in the vibrant Dutch city of Amsterdam, bringing together the brightest minds in food security, agriculture, technology, health and life science. On the agenda is making the world a better place by making sure people have enough food to eat for themselves and their families. This year, one of our researchers, Ben White, went to experience this rather unconventional conference first hand - renowned for its bright lights, energetic events and passionate speakers from all across the world and all walks of life. Pete Bickerton went along too, both a regular contributor to our science communications and an ambassador for Thought for Food himself. We had a special reason for attending this year. Ben and his colleagues have developed an app - called PatchIt App - as part of the TFF Challenge to tackle the issue of food security. PatchIt App looks to connect city-dwellers with growing their own food through the technology they carry around every day, the smartphone. Ben and the team were also able to bring back the things they learned from the conference and apply it in their own research, for a truly interdisciplinary approach. Shouldn't this be the best outcome of any conference worth it's salt? |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/articles/thought-food-take-it-farmer |
| Description | Three Ways EI is helping bees |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Three Ways EI is helping bees |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/three-ways-ei-helping-bees |
| Description | Training - Single-Cell RNAseq Training Course |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Training delivered as part of the Single-Cell RNAseq Training Course at EI. The audience included postdoctoral researchers and graduate students |
| Year(s) Of Engagement Activity | 2018 |
| Description | Training delivered - Single Cell RNA-Seq data analysis 2022 - Graham Etherington, David Wright, Yuxuan Lan, Wilfried Haerty, Iain Macaulay |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Training delivered as part of the Single Cell RNA-Seq data analysis 2022 |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/events/single-cell-rnaseq-data-analysis-2022 |
| Description | Transformed: the plant whose sex life fascinated Charles Darwin - 11/12/2018 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. Collectively, our international reach as of March 2019 has extended across the globe, with highlight pieces in the Guardian, the BBC World Service, the Washington Post and more, as well as local TV and radio. In 2018, the estimated readership of news stories we shared was well in excess of 1 million. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.sciencedaily.com/releases/2018/12/181211113015.htm |
| Description | UK CBCB: an ELIXIR for cross-disciplinary collaboration in bioinformatics |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | UK CBCB: an ELIXIR for cross-disciplinary collaboration in bioinformatics |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/uk-cbcb-elixir-cross-disciplinary-collaboration-bioinformatics |
| Description | UK project underpins global effort to map genomes of all life on earth |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Blog post on the contributions of EI to the Earth Biogenome Project |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/newsroom/uk-project-underpins-global-effort-map-genomes-all-life-earth |
| Description | UK-Conference of Bioinformatics and Computational Biology (UK-CBCB) 27-29 September 2022 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was the third iteration of the UK Conference of Bioinformatics and Computational Biology (UK-CBCB), organised in conjunction with ELIXIR-UK. The conference was designed to bring together biologists, bioinformaticians, computer scientists, software engineers and data scientists across the life sciences to discuss and present on how to manage biological data and use computational methods to power life science research. The 3-day programme combined a keynote lecture with presentations of use cases from researchers working at the cutting edge, plus breakout discussion groups at the end of each session. The breakout groups were intended for participants to exchange expertise and challenges with one another, in order to develop multidisciplinary solutions to complex problems together. Discussions and themes as a result of these breakout groups were then summarised by the facilitator at the end of each session. To maximise engagement across multiple disciplines we opted for a streamlined programme (no parallel sessions), and short introductory talks to support each session to encourage focus on the theme in question. Research facilitators also headed up each session to reinforce key themes, and encourage or stimulate conversation. The sessions covered: Metagenomics and Microbial Bioinformatics; Bioimaging and Artificial Intelligence; Sex and Gender Bias in Computational Disciplines; Federated Analytics/Learning; Structural Bioinformatics; Open Science and Spatial Transcriptomics. Over 130 delegates registered to attend the conference, the majority from the United Kingdom (~86%) however registrants were also based in the US and Europe, Asia, the Middle East and South Africa. Approximately half of these virtual attendees were Postdoctoral Researchers (52%) while other significant groups comprised PhD Students (19%) and Professor/PIs (11%). |
| Year(s) Of Engagement Activity | 2022 |
| URL | https://www.earlham.ac.uk/uk-cbcb-2022#about-the-event |
| Description | UK-Conference of Bioinformatics and Computational Biology (UK-CBCB) 28-30 September 2021 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was the second iteration of the UK Conference of Bioinformatics and Computational Biology (UK-CBCB), organised in conjunction with ELIXIR-UK. The conference was designed to bring together biologists, bioinformaticians, computer scientists, software engineers and data scientists across the life sciences to share innovations, applications and best practice in their fields. Applicable to bioinformatics researchers working on core services or in research teams as well as computer scientists or bioinformaticians developing tools or maintaining data resources. Originally planned as an in-person event, as the pandemic progressed the decision was made to convert this to virtual only format. With all speakers happy to present for the event in this format, we continued with the planned 3-day event, and took abstract submissions for selected speakers for each of the sessions. We opted here for a nominal registration fee of £15 to cover the additional use of the Spatial chat platform for networking and poster sessions. Sessions included: Research Data Management; Metagenomics and Microbial Genomics; Computational Proteomics and Metabolomics; Bridging Genotype to Phenotype; Structural Bioinformatics; and Artificial Intelligence. The event also included a workshop session for the UKRI Innovation Scholars - Data Science Training in Health and Bioscience, to allow engagement across the various planned activities from this scheme, plus a short funder's perspective session on Data-intensive bioscience and artificial intelligence (UKRI-BBSRC). The sessions saw an even spread of attendees with similar numbers across all sessions. Three themes emerged from the conference: Theme 1: FAIR data Theme 2: COVID-19 response Theme 3: AI and Machine Learning. Attendees were predominantly national (non-Norwich Research Park) (85%) with some international (~17%) and from academia (92%) with the remainder (8%) from industry. |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.earlham.ac.uk/uk-conference-bioinformatics-and-computational-biology-21 |
| Description | UK-Conference of Bioinformatics and Computational Biology (UK-CBCB) 29-30 September 2020 (Virtual) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was the inaugural UK Conference of Bioinformatics and Computational Biology (UK-CBCB), organised in conjunction with ELIXIR -UK. The conference was designed to bring together biologists, bioinformaticians, computer scientists, software engineers and data scientists across the life sciences to share innovations, applications and best practice in their fields. Applicable to bioinformatics researchers working on core services or in research teams as well as computer scientists or bioinformaticians developing tools or maintaining data resources. Converting this to an online format, we reduced the number of presentations, namely by including only invited speakers for this iteration, and ran this as a shorter two-day programme of talks. In contrast to the Single Cell Symposium, we opted here for a nominal registration fee of £10 and this saw our attendance rates from those registered reach 90%. Sessions included: Data Management; Metagenomics and Microbial Genomics; Computational Proteomics and Metabolomics; Bridging Genotype to Phenotype; Structutral Bioinformatics; and Single Cell Genomics. These sessions saw an even spread of attendees with similar numbers across all sessions. Three themes emerged from the conference: Theme 1: FAIR data Theme 2: COVID-19 response Theme 3: AI and Machine Learning Attendees were predominantly national (non-Norwich Research Park) (60%) with some international (~20%) and from academia (88%) with the remainder (12%) from industry. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/uk-conference-bioinformatics-and-computational-biology-2020 |
| Description | Uniqueness amongst the Indica and Japonica subpopulations within a diverse collection of Vietnamese Rice |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation and discussion with rice breeding and researchers during the quadrennial Rice International Congress in Singapore. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Unravelling the Diversity of Native Rice in Vietnam for Future Climatic Scenarios |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Talk and discussion with the members of the International Rice Informatics Consortium (IRIC-IRRI) during PAG XXVII |
| Year(s) Of Engagement Activity | 2019 |
| Description | Untapped rice varieties could sustain crop supplies in face of climate change |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | https://scienmag.com/untapped-rice-varieties-could-sustain-crop-supplies-in-face-of-climate-change/ |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://scienmag.com/untapped-rice-varieties-could-sustain-crop-supplies-in-face-of-climate-change/ |
| Description | Untapped rice varieties could sustain crop supplies in face of climate change |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | https://www.eurekalert.org/news-releases/484861 |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.eurekalert.org/news-releases/484861 |
| Description | Using local knowledge to guide bean breeding programmes |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Article on a visit to Colombia designed to help showcase PhD researchers and their projects to potential applicants in the future, as well as to highlight our international relationships. Positive engagement will hopefully mean the article is part of a wider campaign to encourage applications for future PhD projects at EI, as well as giving our students recognition and visibility internally. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/articles/using-local-knowledge-guide-bean-breeding-programmes |
| Description | Visit from Poulton group UEA to Richard Leggett 01/08/2019 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | To observe and receive training using nanopore technologies |
| Year(s) Of Engagement Activity | 2019 |
| Description | We're ten years old, leading the field in decoding complex, non-human genomes - 21/09/2019 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Website article highlighting contributions of EI, including work delivered through the CSP in decoding complex, non-human genomes. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.earlham.ac.uk/articles/ten-years-leading-decoding-complex-genomes |
| Description | Web Article - 'Doing Science in Colombia'. |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | In December 2017, the Colombian Embassy to the UK hosted a diplomatic event at the Natural History Museum to celebrate the UK's support for "Doing Science with Colombia". Scientists, academics, NGOs and policy makers from both countries spoke to an audience of nearly 300 people. All of them welcomed the emerging and strengthening partnership between the UK and Colombia to grow scientific research collaboration. This Web article covers the key points with Earlham Institute's work in Colombia celebrated at this science and diplomatic event. -SOCIAL MEDIA- Engagement x29, Impressions 55419. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/articles/doing-science-colombia |
| Description | Web Article - Day in the life of... a wheat bioinformatician on her own research path - 18.07.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. This is part of our women in computing to promote this as a career addressing the skill shortage and lack of gender balance in the UK |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/day-life-%E2%80%A6-wheat-bioinformatician-her-own-research-path |
| Description | Web Article - Helping to save the Koala: a conservation genome blueprint - 02.07.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. This artice focuses on our part in a multidisciplinary team using molecular biology and population genetics to help protect the Koala, the Earlham Institute was instrumental in assembling and analysing the first complete genome sequence of the Koala. EI researchers used their bioinformatics expertise to uncover novel insights into Marsupial evolution and biology, including dietary and immune adaptations. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/helping-save-koala-conservation-genome-blueprint |
| Description | Web Article - How our tools can help you: MIKADO - 23.05.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. This article promotes Mikado is a novel algorithm that lets you integrate multiple RNA-Seq assemblies into a coherent transcript annotation. The performance of genomics RNA-Seq aligners and assemblers varies greatly across different organisms and experiments and the accuracy of the transcript reconstruction is boosted by combining multiple approaches. The open-source bioinformatics tool can remove redundancies and select the best transcript models according to user-specific metrics while solving common genetic artefacts. Lead developer Luca Venturini explains how Mikado leverages multiple transcriptome assembly methods for improved gene structure annotation. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/how-our-tools-can-help-you-mikado |
| Description | Web Article - Thought for food - what's nexxxt? |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Learning article on the Thought for Food competition and conference, including EI's participation. -SOCIAL MEDIA- Engagement x 147, Impressions x 115250 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/articles/thought-food-what%E2%80%99s-nexxxt |
| Description | Web Article - What is bioinformatics? - 16.10.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. Bioinformatics is a growing field of research, existing at the cutting-edge of the biological sciences. But what is it? Biology is going large. With the advent of next generation (and third generation) genome sequencing and along with it an explosion in the amount of biological data being produced daily, scientists are now playing with terabytes or even petabytes (lots and lots of zeros) of data at a time. It would take infinite infinities for a single person to analyse this digital abundance. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/what-is-bioinformatics |
| Description | Web Article - Women in computing: a journey into bioinformatics with Erin Baggs - 08.05.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. This is part of our women in computing to promote this as a career addressing the skill shortage and lack of gender balance in the UK For many in the bioinformatics world, coding is a leap into the unknown. This was the case for Erin Baggs, who has learned from scratch how to apply computational science to biology while doing her PhD with Ksenia Krasileva. She gives us an insight into what life is like for a PhD student, and how to negotiate the intrepid plunge into the choppy sea of coding. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/women-computing-journey-bioinformatics-erin-baggs |
| Description | Web Special feature: 'Keeping Colombia megadiverse' |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Earlham Institute is at the heart of an international network aiming to preserve, maintain and enrich the biodiversity of this fascinatingly diverse country. This article sought to be an informative and engaging piece to reach a general audience. It is packed with interesting content and vibrant images. -SOCIAL MEDIA- Engagement x176, Impressions x169000 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/keeping-colombia-megadiverse |
| Description | Web article - 'Ageless and timeless: the lords of the rings |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | The oldest trees have seen it all over millennia, and though their rings tell us their age, their meristems hold the secret to eternal youth. Web article focused on a public audience. -SOCIAL MEDIA- Engagement x63, Impressions x105000. |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/articles/ageless-and-timeless-lords-rings |
| Description | Web article - A celebration of science in Norwich - 27.08.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. Promoting our engagement in the Noriwch Science festival beyond our region. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/celebration-science-norwich |
| Description | Web article - Aquaculture and tilapia: a fish that may tip the balance. |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Web article to support the WorldFish Press Release 'Genetics roadmap to develop more resilient farmed fish. -SOCIAL MEDIA - Engagement 30, Impressions 9676 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/articles/aquaculture-and-tilapia-fish-may-tip-balance |
| Description | Web article - Decoding Living Systems: from cell to ecosystem - 28.03.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/decoding-living-systems-cell-ecosystem |
| Description | Web article - Fostering symbiosis in the biosciences through multiscale modelling |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | News article to highlight the "Multiscale analysis of host-microbe interactions in plants, animals & humans" workshop and it's outcomes. -SOCIAL MEDIA- Engagement x102, Impressions x113433 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/articles/fostering-symbiosis-biosciences-through-multiscale-modelling |
| Description | Web article - Orchestrating life: miRNA - 19.11.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. Article describing how Prof Federica Di Palma's Group, are using computer-based bioinformatics methods that are helping us to understand miRNA's role in the evolution of different characteristics. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/orchestrating-life-micro-rna |
| Description | Web article - There's more to a belch than meets the eye. |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Web article focused on the organisms that lie behind a bovine belch, and what can methane tell us about the complex lives of microbial communities. -SOCIAL MEDIA- Engagement x65, Impressions x215108 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/articles/there%E2%80%99s-more-belch-meets-eye |
| Description | Web article - What is biohacking? |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Web article to raise awareness of biohacking: a grassroots movement promoting open science & open minds. -SOCIAL MEDIA_- Engagement x 152, Impressions x 107633 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/articles/what-is-biohacking-how-and-why |
| Description | Web article - What's in a gene? - 10.12.2018 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. Article describing a shift in our understanding of what a gene is revealed by improvements to sequencing technology. |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.earlham.ac.uk/articles/whats-in-a-gene |
| Description | Web article - Year of the pig: Flu, you swine! - 05.02.2019 |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. This Chinese New Year sees the pig come around again after twelve years, an important animal for the country: of the 2 billion pigs on earth, half live in China. Not only are they an important food source, they provide an incredibly diverse range of products, from violin strings to hearts for human transplantation. However, for all of their tastiness and usefulness, farming pigs comes with several downsides - an obvious one being that such abundant numbers living in closely confined spaces provides a fertile breeding ground for some very deadly viruses, including Swine Flu. Prof Federica Di Palma Group, describe their work to understand the evolution of this disease. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://www.earlham.ac.uk/articles/chinese-year-of-the-pig-flu-you-swine |
| Description | Web article - why should you care about biodiversity? |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Information piece to support the Colombian project. Interview with Jose De Vega. -SOCIAL MEDIA- Engagement 107, Impressions 100738 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/articles/why-you-should-care-about-biodiversity |
| Description | Web article for Public Engagement - What's in a genome? |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | 'Learning' Article to explain what's in agenome. -SOCIAL MEDIA- Engagement x 285, Impressions x 138027 |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.earlham.ac.uk/articles/whats-genome |
| Description | Website article: Why do a Year in Industry? |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Undergraduate students |
| Results and Impact | Web article outlining the experience of two year ins industry students undertaking a placement between September 2019 and August 2020. Focus on the research and transferrable skills, in particular the benefits of bioinformatics, that they were able to develop through their placements and how this is impacting the next steps in their careers. Demonstrates the supportive and engaging environment offered whilst learning valuable skills at EI. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/why-do-year-industry |
| Description | What doesn't kill you makes you stronger? Cracking Salmonella and antibiotic resistance |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Article on tackling Salmonella by exploring a highly mutable, evolved strain to help answer why antibiotics are becoming less effective and improve our bodies' antimicrobial armour. |
| Year(s) Of Engagement Activity | 2018 |
| Description | What makes a plant killer? Meet the scientists hot on the trail of invading pathogens |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | What makes a plant killer? Meet the scientists hot on the trail of invading pathogens |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/what-makes-plant-killer |
| Description | What's living in the River Yare? |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Metagenomic analysis of the water of the River Yare: What's living in the River Yare? |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/newsroom/whats-living-river-yare |
| Description | When one become two: separating DNA for more accurate nanopore analysis |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Article about tool and paper |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.earlham.ac.uk/newsroom/when-one-become-two-separating-dna-more-accurate-nanopore-analysi... |
| Description | Why bioinformatics is important |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Blog post on the importance of bioinformatics |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/why-bioinformatics-important |
| Description | Why statistics is important in a world of big data |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Why statistics is important in a world of big data |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.earlham.ac.uk/articles/why-statistics-important-world-big-data |
| Description | Workshop Oral Presentation: Gene families dynamics associated with lineage specific adaptations in Vertebrates |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | Invited presentation to the students of the Earth and Life Systems Alliance (Norwich Research Park). The audience of the seminar was mainly composed of graduate and undergraduate students as well as University Professors and Lecturers. The presentation helped raising the profile of Wilfried Haerty and of the Earlham Institute |
| Year(s) Of Engagement Activity | 2017 |
| Description | Workshop on Genomic Selection in WorldFish Breeding Programs |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The workshop was held to determine strategy and focus with respect to the introduction of genomic selection to the WorldFish breeding programs, and in particular the development of key to tolls to enable this (specifically discussed to date a SNP chip for marker assay). The agenda included: Discussion of WorldFish breeding programs and their goals; of the best strategy to introduce genomic selection to WorldFish breeding programs; on introduction of genomic selection to WorldFish breeding programs focused on selection of specific targets and of next steps and development of a strategy, including specifically that of SNP chip development including a draft workplan. |
| Year(s) Of Engagement Activity | 2017 |
| Description | World Federation of Science Journalists (WFSJ) workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Workshop objectives: Acquire basic knowledge about food security innovation and what is exportable to LMIC. Sharing experiences amongst participants. Workshop themes included: -How crop technology is transforming agriculture around the world -How farmers from developing countries are challenged by these changes, affecting livelihoods, food security and environment -How researchers can better understand the complex human dynamics in agro-ecosystems and design more equitable and sustainable solutions -What is the essential message you want journalists to remember from your talk? Federica Di Palma was asked to concentrate on: -Meat from livestock is the main source of world protein and also source of GHG. What are the challenges for scientists to provide enough protein from livestock while coping with climate change? -The latest livestock (and fisheries) research innovations that suitable to LMICs -How LMICs can feed themselves? -Do we have enough sources to provide protein for the world? |
| Year(s) Of Engagement Activity | 2017 |
| Description | WorldFish Genetic Improvement Program (GIP) Meeting |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Around 50 people attended the WorldFish Genetic Improvement Program (GIP) Meeting, this involved discussions and outlook towards genetic improvement programmes of aquaculture-relevant species. |
| Year(s) Of Engagement Activity | 2019 |
| Description | azocleantech.com |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | https://www.azocleantech.com/news.aspx?newsID=29140 |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.azocleantech.com/news.aspx?newsID=29140 |
| Description | biofuelsdigest.com |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | https://www.biofuelsdigest.com/bdigest/2021/04/04/keep-off-the-grass-the-biofuel-that-could-help-us-achieve-net-zero/ |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.biofuelsdigest.com/bdigest/2021/04/04/keep-off-the-grass-the-biofuel-that-could-help-us-... |
| Description | bioindustry.org |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | UK bioindustry association https://www.bioindustry.org/news-listing/guest-blog-keep-off-the-grass-the-biofuel-that-could-help-us-achieve-net-zero.html |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.bioindustry.org/news-listing/guest-blog-keep-off-the-grass-the-biofuel-that-could-help-u... |
| Description | brickopore.co.uk |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | Created a website to provide information on our Lego DNA sequencer, details of events and instructions to build. Designed to promote the institute's engagement and to encourage it elsewhere. |
| Year(s) Of Engagement Activity | 2019 |
| URL | http://brickopore.co.uk |
| Description | dpaonthenet.net |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | http://www.dpaonthenet.net/article/184208/Grass-could-help-us-achieve-net-zero--say-researchers.aspx |
| Year(s) Of Engagement Activity | 2021 |
| URL | http://www.dpaonthenet.net/article/184208/Grass-could-help-us-achieve-net-zero--say-researchers.aspx |
| Description | enn.com |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | https://www.enn.com/articles/67413-keep-off-the-grass-the-biofuel-that-could-help-us-achieve-net-zero |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.enn.com/articles/67413-keep-off-the-grass-the-biofuel-that-could-help-us-achieve-net-zer... |
| Description | eurekalert.org |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | https://eurekalert.org/pub_releases/2021-03/ei-ot032521.php |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://eurekalert.org/pub_releases/2021-03/ei-ot032521.php |
| Description | nanowerk.com |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | https://www.nanowerk.com/news2/green/newsid=57632.php |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.nanowerk.com/news2/green/newsid=57632.php |
| Description | newenergyandfuel.com |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | https://newenergyandfuel.com/http:/newenergyandfuel/com/2021/04/01/miscanthus-grass-may-be-used-in-poor-growing-regions/ |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://newenergyandfuel.com/http:/newenergyandfuel/com/2021/04/01/miscanthus-grass-may-be-used-in-p... |
| Description | poster presentation - Characterising and visualising 10 plus wheat gene families within Galaxy using GeneSeqToFamily |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation at the Monogram 2021 meeting |
| Year(s) Of Engagement Activity | 2021 |
| Description | sciencedaily.com |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | https://www.sciencedaily.com/releases/2021/03/210325115319.htm |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.sciencedaily.com/releases/2021/03/210325115319.htm |
| Description | solarify.eu (DE) |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | In german: https://www.solarify.eu/2021/04/22/815-miscanthus-nachhaltige-energiequellen-auf-grenzertragsflaechen/ |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.solarify.eu/2021/04/22/815-miscanthus-nachhaltige-energiequellen-auf-grenzertragsflaeche... |
| Description | techxplore.com |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | https://techxplore.com/news/2021-03-grass-biofuel-net.html |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://techxplore.com/news/2021-03-grass-biofuel-net.html |