Signatures of Domestication and Adaptation

Lead Research Organisation: Earlham Institute
Department Name: UNLISTED

Abstract

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.

Organisations

Publications

10 25 50
 
Description As part of the work package 1 of the Earlham Institute Core Strategic Programme (CSP), 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 contributing to 306 publications, initiating 31 collaborations, being involved in 312 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:

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 (doi: 10.1038/s41564-019-0626-z).

2. We developed 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. It was extended to allow culture free pathogen detection in Lower Respiratory Infection 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: 10.1111/2041-210X.13265, doi: 10.1038/s41587-019-0156-50).

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. 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).

5. 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).

6. 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.? ?

7. 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.).

8. 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).

9. 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).
10. 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.

11. 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.

12. 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 its 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.

13. We developed a novel algorithm (Alvis) for assembly and long read alignment visualisation and chimaera 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 on generation of new traits:

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.
14. 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.).

15. 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).

16. 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 took advantage of the newly released IWGSC 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.

17. 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).

18. 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).
19. 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: 10.1101/2022.02.09.479695). This is an important study with immediate utility as these identified markers will allow to incorporate climate resilience traits into breeding programmes.

20. 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: 10.1101/2021.11.16.468825).

21. 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.

22. 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).

23. 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).
24. 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).
25. 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).

26. 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).

27. 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 9 Oreochromis species as well as the low coverage genome sequencing of 604 wild individuals we identified and quantified ongoing introgression between Oreochromis species Tanzania.

28. 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).

29. 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).

30. 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.

31. 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).

32. 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:

33. 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: 10.1101/2020.08.25.266213).

34. 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).

35. 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).

36. 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).

37. 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).

38. 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).

39. 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).

40. 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).

41. 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).
Exploitation Route The outcomes of the 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 308 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.

Tools and resources developed by the CSP were shared and discussed during our annual stakeholder engagement event EI innovate. In 2020 the event attracted 170 attendees including 115 external participants from 73 different organisations. Including breeding and agrochemical companies, and the farming sector. The 2021 edition attracted 211 attendees, among 85 external organisations, representing agricultural industry, funders, government departments, and other academic organisations, helping to develop new collaborations and facilitate realisation of impact from CSP1. This is the 3rd year we are delivering this event and have seen a number of collaborations described below arising as an outcome of this event.

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.

We have signed a partnership agreement with Eagle Genomics, to further translate our computational developments applied to metagenome reconstruction and microbial diversity analysis.

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.

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.

To further enable early detection of potential crop pathogens, we have developed AirSeq which allows near real time pathogen monitoring. It comprises wet-lab techniques to analyse 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. A patent application to protect our developments was filed to protect this intellectual asset and ensure maxim impact realisation via commercialisation in wide areas of application from agriculture to homeland security.

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 mapping accurately 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.

Training and skills development: Our outcomes in protocols and algorithms developments directly contribute to training of EI staff and early career researchers in genomics and bioinformatics. Our faculty hosts 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. Our faculty contributes to training courses organised by our National Capability (Single Cell Bioinformatics).

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
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Education,Environment,Healthcare,Pharmaceuticals and Medical Biotechnology

 
Description As part of the work package 1 of the Earlham Institute CSP, 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. 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. 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. Influence on Policy and Public Affairs Researchers at EI have been involved in informing Gene Editing policies through interactions with DEFRA and BEIS officials to inform R&D Place Strategy and the Life Science Vision, both of which were BEIS policy papers. EI researchers also engaged with the Parliamentary Office of Science and Technology for the preparation of a new POSTnote on gene editing in agriculture. EI researchers were involved in 8 events which included a round table with 15 members of DEFRA policy team, the visit of DEFRA officials at EI, the visit of George Freeman MP to present the findings from his task force for Innovation, Growth and Regulatory Reform, commissioned by the Prime Minister. Researchers at EI engaged with BEIS officials to inform the Levelling Up White Paper and the Innovation Strategy. EI researchers also contributed to the RDI Organisational Review led by Sir Paul Nurse. 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 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. 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 are engaging with sugar beet breeders (KWS) to inform the development of pathogen resistant crops. 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: Our work generating novel genomic resources (genome assemblies, SNP array) is of direct relevance to the aquaculture sector. 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. 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. 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.
First Year Of Impact 2018
Sector Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Environment,Healthcare
Impact Types Cultural,Societal,Economic

 
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 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 Contribution to the National Food Strategy Public Consultation
Geographic Reach National 
Policy Influence Type Participation in a national consultation
URL https://consult.defra.gov.uk/agri-food-chain-directorate/national-food-strategy-call-for-evidence/
 
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 GCRF CABANA's advisory board
Geographic Reach South America 
Policy Influence Type Participation in a advisory committee
Impact 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 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 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 Oral Evidence to House of Commons Science and Technology Committee enquiry on Balance and effectiveness of research and innovation spending
Geographic Reach National 
Policy Influence Type Gave evidence to a government review
URL https://parliamentlive.tv/Event/Index/4bdf3ff7-d1a6-4605-8b73-aca355bf9f89
 
Description Particapited in parliamentary debate on CRISPR CAS and post-BREXIT genetic engineering in crops -APPG Science & Technology in Agriculture
Geographic Reach National 
Policy Influence Type Gave evidence to a government review
 
Description Wilfried Haerty - meeting with French Embassy representatives to provide evidence to French Government review, gain visibility of research park and potential source of funding between France and UK
Geographic Reach Europe 
Policy Influence Type Gave evidence to a government review
 
Description submission to UKRI infrastructure review
Geographic Reach National 
Policy Influence Type Participation in a national consultation
URL https://www.ukri.org/files/infrastructure/progress-report-summary-document-final-march-2019-pdf/
 
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 03/2020 
End 09/2021
 
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 11/2021 
End 10/2022
 
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 Business Case for a Catalyst Partnership in Artificial Intelligence between the Alan Turing Institute and the Norwich Biosciences Institutes
Amount £300,000 (GBP)
Funding ID BB/V509267/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 06/2020 
End 06/2021
 
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 05/2022
 
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 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 £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 08/2017 
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 Iness Foundation internship in data-driven plant bioinformatics
Amount £17,500 (GBP)
Organisation John Innes Foundation 
Sector Charity/Non Profit
Country United Kingdom
Start 04/2021 
End 05/2022
 
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 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 05/2021
 
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 08/2017 
End 12/2021
 
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 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 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 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 02/2022 
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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/
 
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 '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 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 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 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 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 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 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 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 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 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 17-18 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 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 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 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 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 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 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 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 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: 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 - 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 - 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 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 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 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 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 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 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 - 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 - 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 - 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 - 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 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 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 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 - 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 
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 - Eukaryotic metagenomics: Identification and quantification of bee collected 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 London Calling conference, May 2018
Year(s) Of Engagement Activity 2018
 
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 - 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 - 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