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.
 
Description 1. 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. Both studies are available as preprints on biorXiv (https://doi.org/10.1101/551960; https://doi.org/10.1101/387548).
2. We continued to develop algorithms and methods for low cost assembly of complex, highly heterozygous, or difficult to assemble genomes. We applied these development to butterfly genomes and published as a preprint in biorXiv (https://doi.org/10.1101/466292). We further applied this pipelines to generate draft assemblies of 6 tilapia species and one closely related species showing adaptation to extreme salinity.
3. We developed a new graph-based framework to assemble and analyse genome sequences, projecting and mapping long (Nanopore and Pacbio), linked (10x genomics), and short (illumina PE and LMP) reads. This BSG (https://github.com/bioinfologics/bsg) framework is being used to assemble multiple species with challenging karyotype characteristics, such as ploidy and heterozygosity. It already enables better reconstruction of challenging genomes such as Strawberry (Octoploid and highly heterozygous), and Bread Wheat (hexaploid, large and repetitive), and we expect it to be of further use in sequencing the tree of life.
4. We used 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 release IWGSC assembly to further improve our capture design. Both studies are available in Genome Research (http://doi.org/10.1101/gr.233551.117) and GigaScience (http://doi.org/10.1093/gigascience/giz018) and all data sets are publicly available.
5. 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 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 (https://doi.org/10.1101/572560).
6. 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 (https://doi.org/10.1093/aob/mcy230).
7. We developed an evolutionary model to assess selective constraints acting on gene expression evolution in mammals (https://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 (https://doi.org/10.1101/gr.234096.117).
8. We successfully sorted and sequenced bacterial single cells to detect point mutations and derive single genome haplotypes from cells growing in planktonic cultures.
9. We have developed methods for high throughput, low input, cheap sequencing of Salmonella and have now generated sequence for over 10,000 isolates and assembled over 8000 isolates with high quality metadata associations. We demonstrated that hypermutator strains can adapt to low concentrations of antimicrobials faster than wild type and reach higher levels of resistance.
Exploitation Route All our data, protocols and algorithms have been made publicly available for the community to use either through the Institute website, or public repositories (github, ENA, NCBI). The release of the wheat genome assembly and annotation has open new areas of research in wheat, allowing the community to develop better genotyping platforms (capture-sequencing) to survey population diversity and analyse gene regulation. The assembly and raw data generated for the bread wheat genome sequencing project are now contributed toward an international effort to sequence elite strains.
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Education,Environment,Healthcare,Pharmaceuticals and Medical Biotechnology

 
Description Our continuous research developments for emerging sequencing technologies, genome assembly and comparative genomic analyses are of direct interest for a wide range of stakeholders. We also continued to actively engage with the public through social media, web articles and news letters on our website, presentations al local engagements (Pint of Science) and activities at science festivals (Norwich Science Festival). Our protocols and analysis pipelines development for emerging long read technologies and their application in species identification from mixed samples enable rapid, reproducible and semi quantitative environmental surveys. The ability to rapidly characterize the inherent biodiversity of a selected site is of direct interest to ecologists, but also environmental and governmental agencies as reflected by the recently secured award (Defense Advanced Research Projects Agency). Following our previous work on the characterisation of the microbiome of preterm babies, we demonstrated the impact of near real time sequencing technologies to identify antibiotic resistant genes from uncultured patient samples with lower respiratory tract infections. These new developments enabling faster pathogen identification and diagnosis are of direct interest to medical and veterinary communities. We finalised a Memorandum of Understanding with WorldFish (CGIAR) giving us access to samples from the two genetically improved tilapia strains (GIFT - worldwide, Abbassa - Egypt). Our work on crops and grasses genomics delivered not only genotyping platforms to the scientific and breeder community but also led to discovery 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 is being taken even further by Industry, with a new £340K hybrid short-and-long read project commisioned by BASF building on our previous £1M project sequencing 5 wheat lines for the same unit at Bayer. 16 commercially important Strawberry lines are being delivered to breeders in the context of our OctoSeq project to further advance the breeding of this UK key crop. Most of the microbial diversity is still unknown as we are unable to culture the vast majority of bacteria. Our recent application of single cell technologies for single bacteria sequencing opens new opportunities for both academic and industrial communities in understanding and exploiting the bacterial diversity enabling comprehensive environmental and surveys for instance. We surveyed the genomic diversity of an unprecedented well curated Salmonella isolates that will be of direct interest of the academic and industrial communities but also governmental agencies in tracking transmission and infections, as well as identifying pathogenicity factors and antibiotic resistance.
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 of BBSRC Institute Partnership
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
 
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 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 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 09/2018 
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 10/2018 
End 09/2022
 
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 10/2019 
End 09/2023
 
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 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 05/2017 
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 10/2017 
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 09/2016 
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 09/2017 
End 10/2022
 
Description Interactive real-time metagenomics algorithms for Nanopore sequencing (LEGGETT_E17DTP1)
Amount £90,000 (GBP)
Funding ID 1937486 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2017 
End 09/2021
 
Description Mapping for Conservation of Native Tilapia Resources in East Africa
Amount $264,100 (USD)
Organisation JRS Biodiversity Foundation 
Start 04/2019 
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 04/2019 
End 03/2022
 
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 10/2018 
End 04/2020
 
Description Newton-Paulet Fund - 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 
Start 10/2017 
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 08/2017 
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 09/2018 
End 07/2019
 
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 05/2017 
End 05/2020
 
Description Strategic Investment
Amount £100,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2017 
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 06/2017 
End 06/2021
 
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 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 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 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 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
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 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 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
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 No outputs to data
Start Year 2017
 
Description KAUST 
Organisation King Abdullah University of Science and Technology (KAUST)
Department Biological and Environmental Science and Engineering Division
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 Moussa Benhamed 
Organisation University of Paris-Saclay
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 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
 
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 - 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 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 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 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 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 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 - 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 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 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 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 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 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 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 - 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 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 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 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 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 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 - 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 - 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 - 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 - 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 - Real-time surveillance and diagnostics with NanoOK RT 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation at the London Calling conference, May 2018
Year(s) Of Engagement Activity 2018
 
Description Poster presentation - The long and the short of eukaryotic metagenomics: Identification and quantification of plant species in bee pollen 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation at the Advances in Genome Biology and Technology (AGBT) conference in Marco Island, Florida.
Year(s) Of Engagement Activity 2019
URL https://www.agbt.org
 
Description Poster presentation : Resistant Escherichia coli Interactome identifies putative novel drug combinations to break antimicrobial resistance 2nd Interdisciplinary Signaling Workshop 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Modos D., Bulusu K., Afzal A., Sudhakar P., Korcsmaros T., Cokol M., Bender A. (2017) Resistant Escherichia coli Interactome identifies putative novel drug combinations to break antimicrobial resistance 2nd Interdisciplinary Signaling Workshop 2017
Year(s) Of Engagement Activity 2017
URL http://signalingworkshop.org/
 
Description Poster presentation : SalmoNet: an integrated multi-layered network for Salmonella 2nd Interdisciplinary Signaling Workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact Olbei M. L. O., Metris A. M., Sudhakar P. S., Fazekas D. F., Demeter A. D., Ari E. A., Branchu P. B., Kingsley R. K., Baranyi J. B., Korcsmaros T. K. (2017) SalmoNet: an integrated multi-layered network for Salmonella 2nd Interdisciplinary Signaling Workshop
Year(s) Of Engagement Activity 2017
URL http://signalingworkshop.org/
 
Description Poster presentation : SalmoNet: an integrated multi-layered network for Salmonella Genome 10K and Genome Science Conference. Genome 10K and Genome Science Conference 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact Olbei M. L. O., Metris A. M., Sudhakar P. S., Fazekas D. F., Demeter A. D., Ari E. A., Branchu P. B., Kingsley R. K., Baranyi J. B., Korcsmaros T. K. (2017)
SalmoNet: an integrated multi-layered network for Salmonella Genome 10K and Genome Science Conference
Year(s) Of Engagement Activity 2017
URL https://genome10k.soe.ucsc.edu/node/130
 
Description Poster presentation at National Conference: Expansion of gene families and signatures of selection in the Australian marsupials 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact The poster presented at the 50th Population Genetics Group meeting (Cambridge UK) was selected on abstract submission. The poster was presented in front of iuniversity professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of AWill Nash, Wilfried Haerty, and of the Earlham Institute
Year(s) Of Engagement Activity 2017
 
Description Poster presentation at international conference: Binding sites within long non-coding RNAs discriminate between RNA- and transcription-mediated mechanism 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The poster presented at the Genome 10K / Genome Science conference was selected on abstract submission. The poster was presented in front of industry participants, university professors and lecturers, postdoctoral researchers, graduates and undergraduates students. The poster presentation helped raising the international profile of Tomasz Wrzesinski, Wilfried Haerty and of the Earlham Institute
Year(s) Of Engagement Activity 2017
 
Description Poster presentation: Tackling microbial diseases of the preterm infant gut using MinION diagnostics and NanoOK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation at AGBT 2018 conference, Florida, USA, February 2018.
Year(s) Of Engagement Activity 2018
 
Description Presentation - Characterization of functional noncoding RNAs: From prediction to experimental validation. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation at the Evolution in the 21st Century: The Inaugural Conference of the Milner Centre for Evolution. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 2018
 
Description Presentation - Convergent evolution of immunity in aquatic plants 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Presentation at The Sainsbury Laboratory retreat. The audience included group leaders, postdoctoral researchers and graduate students
Year(s) Of Engagement Activity 2018
 
Description Presentation - Evolution of regulatory networks controlling adaptive traits in cichlids Network Biology CSHL, NY, USA Mar 19-23 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation at the Network Biology meeting Cold Spring Harbor Laboratory. The audience included group leaders, university lecturers, postdoctoral researchers, graduate students and industry representatives.
Year(s) Of Engagement Activity 2019
 
Description Presentation - The role of structural variants in the adaptive radiation of African Cichlids 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentatio at the Genome Informatics 2018 Conference, Hinxton, Cambridge. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 2018
 
Description Presentation - Characterization of noncoding expression and splicing diversity in the human brain 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Invited seminar at the Institute of Ophthalmology, University College London. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 2019
 
Description Presentation - Characterization of splicing diversity and gene fusions through Nanopore sequencing 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Selected presentation at AGBT2019, Marco Island Florida. The audience consisted of group leaders, postdoctoral researchers, graduate students, industry representatives.
Year(s) Of Engagement Activity 2019
 
Description Presentation - Genomics applications for conservation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Presentation as part of a training course for the use of genomic resources for species identification delivered to law enforcement officers in Cali, Colombia. The audience included university lecturers, graduate and undergraduate students, conservation organizations, law officers, representatives of the ministry of environment, ministry of justice,
Year(s) Of Engagement Activity 2018
 
Description Presentation - Poster - Characterization of Functional ncRNA in Plants 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Poster presentation at the Bioinformatics for Plant Biology Course, EMBL-EBI Hinxton
Year(s) Of Engagement Activity 2018
 
Description Presentation - RCUK GROW Colombia Natural Diversity 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Presentation as part of FIMA 2018 in Bogota, Colombia. The audience included general public, conservation organization, schools, law officers
Year(s) Of Engagement Activity 2018
 
Description Presentation - What can we learn form a high Koala-ty genome? 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Presentation as part of the Norwich Science Festival. The audience included general public and schools
Year(s) Of Engagement Activity 2018
 
Description Presentation - What can we learn from a high Koala-ty genome 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Presentation as part of the Pint of Science. The audience included general public and graduate students
Year(s) Of Engagement Activity 2018
 
Description Presentation - Working with sequences 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Lecture delivered to BBSRC DTP graduate students as part of the Computational & Systems Biology DTP course
Year(s) Of Engagement Activity 2019
 
Description Preserving and Restoring Colombian Biodiversity - Bogota Workshop 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Video to highlight the workshop that took place in Bogota in October 2017.
Year(s) Of Engagement Activity 2017
URL https://www.youtube.com/watch?v=aKqQLOFW4HA
 
Description Press Release - 'Better barley is on the way' 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Press release to illustrate our role in an international consortium, led in the UK by the James Hutton Institute, which published the first high-quality genome sequence of barley in the journal Nature. -SOCIAL MEDIA- Engagement x155, Impressions x144617
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/better-barley-way-crop-genome-unravelled
 
Description Press Release - 'New era for nature in colombia' 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Press Release to highlight the Colombia project and formation of the BRIDGE consortia. -SOCIAL MEDIA- Engagement x164, Impressions x117000
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/new-era-nature-colombia
 
Description Press Release - 'a practitioners perspective at the 'Doing Science with Colombia' event '. 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Press release to Highlight Federica Di Palmas role as panellist at the 'doing Science with Colombia' event, Natural History Museum, 7th December 2017. -SOCIAL MEDIA- Engagement x55, Impressions x57826
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/newsroom/federica-di-palma-provides-practitioners-perspective-%E2%80%98doin...
 
Description Press Release - Core funding announcement 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Core funding announcement via Press Release. -SOCIAL MEDIA- Engagement x94, Impressions x24888
Year(s) Of Engagement Activity 2017
URL http://earlham.ac.uk/statement-in-response-to-bbsrc-319m-investment-announcement
 
Description Press Release - Network science unravels the secrets of the evolution of Salmonella's disease adaptations 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Press release to introduce SalmoNet, a systems biology approach that uses network biology and bioinformatic techniques to collate molecular interactions within Salmonella, and to link information on how genes and metabolic pathways are regulated in Salmonella, and how proteins interact with each other. -SOCIAL MEDIA- Engagement x45, Impressions x54800
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/newsroom/network-science-unravels-secrets-evolution-salmonella%E2%80%99s-di...
 
Description Press Release - Sat nav for bread wheat uncovers hidden genes 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Press release on the publication of the world's most complete picture of the wheat genome.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/sat-nav-bread-wheat-uncovers-hidden-genes
 
Description Press Release - Spectre 'catch of the day: a net full of trees' 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Press release on SPECTRE, a new open-source software package that simplifies the complex business of creating phylogenetic networks and trees. Sarah Bastkowski and Dan Mapleson. -SOCIAL MEDIA- Engagenments x 135, Impressions x78755
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/newsroom/catch-day-net-full-trees
 
Description Press release - Crowning the "King of the Crops": Sequencing the White Guinea Yam Genome 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Press Release on an international collaboration involving the Earlham Institute, Norwich, UK, and the Iwate Biotechnology Research Centre, Japan. The project has, for the first time, provided a genome sequence for the white Guinea yam, a staple crop with huge economic and cultural significance on the African continent and a lifeline for millions of people. -SOCIAL MEDIA- Engagement 207, Impressions 93116
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/newsroom/crowning-the-king-of-the-crops-sequencing-the-white-guinea-yam-gen...
 
Description Prof. Tracey Chapman & Dr Emily Fowler - UEA - 28/11/2018 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact Meeting to discuss collaborative project
Year(s) Of Engagement Activity 2018
 
Description Professor Ian Boyd - Chief Scientific Adviser to DEFRA - 04/02/2019 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Meeting to discuss Institute influence and impact into government policy and input into Select Committees
Year(s) Of Engagement Activity 2019
URL http://data.parliament.uk/writtenevidence/committeeevidence.svc/evidencedocument/science-and-technol...
 
Description Real time sequencing solutions: taking the lab to the sample and beyond 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Article on the EI website about our work with real-time nanopore sequencing
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/real-time-sequencing-solutions-taking-lab-sample-and-beyond
 
Description Science Camp 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Graham Etherington put on a a workshop on how to use bioinformatics tools, namely Galaxy, in the life sciences.

This is a very valuable introduction to the work undertaken at EI, and a chance to show the next generation of budding scientists the important role of computational-driven approaches to understanding life, evolution, and how we can improve crops through better understanding genetic diversity and variation.
Year(s) Of Engagement Activity 2018
 
Description Sequencing and chromosome level assembly of rodent genomes : Understading the mechanisms of lineage-specific genome evolution in mammals. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I presented work on chromosome level assembly of mammalian genomes and the comparison of these genomes in order to understand the mechanisms driving lineage-specific evolution in mammals.
Year(s) Of Engagement Activity 2018
 
Description Single-cell RNAseq Training Course Delivered 3-7 Dec 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This was the first iteration of this course, demonstrating EI's both introducing Single Cell Genomics and demonstrating EI's capability. It covered several aspects such as: the experimental design, cell sorting and processing for production of quality samples for sequencing, in the three-days of laboratory hands-on sessions; generation of sequencing data, assessing the quality of sequence data, data visualisation, differential expression analyses and identifying Copy Number Variants at the single cell level in the following two-days of theory and computational hands-on sessions. A total of twelve (12) delegates attended this course, with ten (10) attending the full five days. Also included was a short half-day session with practical elements on single molecule FISH, delivered by EI faculty, and an overview of 10X Genomics' data analysis platform, presented by one of their Field Application Specialists.

Delegates were predominantly UK-based (~83%) and PostDocs (two-thirds), with a couple of attendees responsible for similar laboratory facilities in their home institutions. All attendees rated the trainers as "Very Good" to "Excellent", and a survey of the ten laboratory sessions attendees suggested that, having followed the course, many hoped to engage with a Single-Cell RNAseq service for their research (53% very likely and 40% likely), with 53% wishing to provide cells.

Following the unprecedented success of delegates producing high quality data to analyse, course organisers wish to review the programme. The proposal for the second iteration is to run the course as 3 or 4 days in the laboratory, with sequencing running over a weekend, and then extending the bioinformatics from 2 days to 4 days, running this on the following week.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/single-cell-rnaseq-training-course
 
Description Space-inspired speed breeding for crop improvement - 16/11/2018 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. Collectively, our international reach as of March 2019 has extended across the globe, with highlight pieces in the Guardian, the BBC World Service, the Washington Post and more, as well as local TV and radio. In 2018, the estimated readership of news stories we shared was well in excess of 1 million.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/newsroom/space-inspired-speed-breeding-crop-improvement
 
Description Sustainable Tropical Agricultural Systems Programme Project Scoping Workshop at CIAT Headquarters in Cali 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Sustainable Tropical Agricultural Systems Programme Project Scoping Workshop at CIAT Headquarters in Cali focused on tropical agricultural systems containing pulses and/or forages that are relevant to, and part of, the livelihood of communities in Colombia. Applications were invited from individual researchers who could contribute to the project scoping workshop and the resulting research projects. Up to 40 participants in total (around 20 from the UK and 20 from CIAT) were identified to take part.
Year(s) Of Engagement Activity 2017
URL https://bbsrc.ukri.org/funding/filter/2017-sustainable-tropical-agricultural-systems-programme/
 
Description Talk - Developing a Streamlined Field Protocol for In Situ Sequencing and Analysis of Extremophiles 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk at American Geophysical Union Fall Meeting, Washington DC, 10-14 December 2018
Year(s) Of Engagement Activity 2018
 
Description Talk and discussion with Elsoms seeds 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact The talk was to breeders and crop scientist work at Elsoms seed, The aim was to raise awareness of the work that Design future wheat and my group were doing. This lead to a letter of support for our BBSRC grant and a line of communication with their wheat and brassica breeders.
Year(s) Of Engagement Activity 2018
 
Description Talk and poster presentation - Taking the lab to the sample: enabling new ways of working with nanopore sequencing 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster and flash talk at the Advances in Genome Biology and Technology (AGBT) conference in Marco Island, Florida.
Year(s) Of Engagement Activity 2019
URL https://www.agbt.org
 
Description Talk at Visegrad Interdisciplinary Signaling workshop, Hungary 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Federica Di Palma gave a talk on "Evolution of tissue-specific regulatory programs in cichlids". In vertebrates, the East African cichlid radiations represent arguably the most dramatic examples of adaptive speciation. In the great lakes Victoria, Malawi and Tanganyika and within the last few million years, one or a few ancestral lineages of haplochromine cichlid fish have given rise to over 1500 species exhibiting an unprecedented diversity of morphological and ecological adaptations. Such explosive phenotypic diversification of East African cichlids is unparalleled among vertebrates and the low protein divergence between species implies the rapid evolution of regulatory regions and networks underlying the traits under selection.

Comparative functional genomics, transcriptomics and epigenomics are powerful tools to study the evolution of tissue and species divergence. We recently developed Arboretum, an algorithm to identify modules of co-expressed genes across multiple species in a phylogeny. By integrating inferred modules with nucleotide variation, predicted cis regulatory elements and miRNA profiles from five East African Cichlids, we investigated the evolution of tissue-specific gene regulation. Our analyses identified modules with tissue-specific patterns for which we reconstructed the evolutionary gene regulatory networks across the five cichlids species. We report striking cases of rapid network rewiring for genes known to be involved in traits under natural and/or sexual selection such as the visual systems, and more specifically a cone opsin (sws2a) responsible for colour vison of selected cichlid fishes. Furthermore, in-depth analyses of regulons (transcription factor - target interactions, e.g. Egr3) show similar rapid species-specific rewiring. Investigation of these novel interactions in Astatotilapia burtoni, a model species for behaviour evolution, reveal significant enrichment for genes involved in neuronal and brain function. Our unique integrative approach that interrogates the evolution of regulatory networks allowed us to identify the rapid regulatory changes associated with certain traits under selection in cichlids.
Year(s) Of Engagement Activity 2017
 
Description Techology Day at Norwich Science Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact 7500 members of the general public attended Nature Day at Norwich Science Festival. A number of activities were available to engage the general public with the work of the institute. A number of talks/presentations were scheduled also.
Year(s) Of Engagement Activity 2018
 
Description The Earlham Institute LEGO sequencer 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Article on EI website about our engagement project in which we built a LEGO DNA sequencer
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/earlham-institute-lego-sequencer
 
Description The role of Structural variants in the adaptive radiation of African Cichlids 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Our study on the evolution of Structural variants in African Cichlids was presented at the Genome Informatics Conference (Genome campus, Hinxton,Cambridge). The audience was engaged and a few questions were asked to further clarify some important aspects of the study.
Year(s) Of Engagement Activity 2018
 
Description The taming of the dog, cow, horse, pig and rabbit - 19/11/2018 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. Collectively, our international reach as of March 2019 has extended across the globe, with highlight pieces in the Guardian, the BBC World Service, the Washington Post and more, as well as local TV and radio. In 2018, the estimated readership of news stories we shared was well in excess of 1 million.
Year(s) Of Engagement Activity 2018
URL https://www.sciencedaily.com/releases/2018/11/181120125840.htm
 
Description Thought for Food - Podcast 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Podcast - Discussion on the Thought for Food conference attended by Ben White and other researchers. SOCIAL MEDIA Engagement 61 Impressions 97047
The Thought For Food Global Summit 2017 was held in the vibrant Dutch city of Amsterdam, bringing together the brightest minds in food security, agriculture, technology, health and life science. On the agenda is making the world a better place by making sure people have enough food to eat for themselves and their families.

This year, one of our researchers, Ben White, went to experience this rather unconventional conference first hand - renowned for its bright lights, energetic events and passionate speakers from all across the world and all walks of life.

Pete Bickerton went along too, both a regular contributor to our science communications and an ambassador for Thought for Food himself.

We had a special reason for attending this year. Ben and his colleagues have developed an app - called PatchIt App - as part of the TFF Challenge to tackle the issue of food security.

PatchIt App looks to connect city-dwellers with growing their own food through the technology they carry around every day, the smartphone.

Ben and the team were also able to bring back the things they learned from the conference and apply it in their own research, for a truly interdisciplinary approach. Shouldn't this be the best outcome of any conference worth it's salt?
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/articles/thought-food-take-it-farmer
 
Description Training - Single-Cell RNAseq Training Course 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Training delivered as part of the Single-Cell RNAseq Training Course at EI. The audience included postdoctoral researchers and graduate students
Year(s) Of Engagement Activity 2018
 
Description Transformed: the plant whose sex life fascinated Charles Darwin - 11/12/2018 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. Collectively, our international reach as of March 2019 has extended across the globe, with highlight pieces in the Guardian, the BBC World Service, the Washington Post and more, as well as local TV and radio. In 2018, the estimated readership of news stories we shared was well in excess of 1 million.
Year(s) Of Engagement Activity 2018
URL https://www.sciencedaily.com/releases/2018/12/181211113015.htm
 
Description Uniqueness amongst the Indica and Japonica subpopulations within a diverse collection of Vietnamese Rice 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation and discussion with rice breeding and researchers during the quadrennial Rice International Congress in Singapore.
Year(s) Of Engagement Activity 2018
 
Description Unravelling the Diversity of Native Rice in Vietnam for Future Climatic Scenarios 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Talk and discussion with the members of the International Rice Informatics Consortium (IRIC-IRRI) during PAG XXVII
Year(s) Of Engagement Activity 2019
 
Description Web Article - 'Doing Science in Colombia'. 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact In December 2017, the Colombian Embassy to the UK hosted a diplomatic event at the Natural History Museum to celebrate the UK's support for "Doing Science with Colombia". Scientists, academics, NGOs and policy makers from both countries spoke to an audience of nearly 300 people. All of them welcomed the emerging and strengthening partnership between the UK and Colombia to grow scientific research collaboration. This Web article covers the key points with Earlham Institute's work in Colombia celebrated at this science and diplomatic event. -SOCIAL MEDIA- Engagement x29, Impressions 55419.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/articles/doing-science-colombia
 
Description Web Article - Day in the life of... a wheat bioinformatician on her own research path - 18.07.2018 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge.
This is part of our women in computing to promote this as a career addressing the skill shortage and lack of gender balance in the UK
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/day-life-%E2%80%A6-wheat-bioinformatician-her-own-research-path
 
Description Web Article - Helping to save the Koala: a conservation genome blueprint - 02.07.2018 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge.

This artice focuses on our part in a multidisciplinary team using molecular biology and population genetics to help protect the Koala, the Earlham Institute was instrumental in assembling and analysing the first complete genome sequence of the Koala. EI researchers used their bioinformatics expertise to uncover novel insights into Marsupial evolution and biology, including dietary and immune adaptations.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/helping-save-koala-conservation-genome-blueprint
 
Description Web Article - How our tools can help you: MIKADO - 23.05.2018 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge.

This article promotes Mikado is a novel algorithm that lets you integrate multiple RNA-Seq assemblies into a coherent transcript annotation. The performance of genomics RNA-Seq aligners and assemblers varies greatly across different organisms and experiments and the accuracy of the transcript reconstruction is boosted by combining multiple approaches.

The open-source bioinformatics tool can remove redundancies and select the best transcript models according to user-specific metrics while solving common genetic artefacts. Lead developer Luca Venturini explains how Mikado leverages multiple transcriptome assembly methods for improved gene structure annotation.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/how-our-tools-can-help-you-mikado
 
Description Web Article - Thought for food - what's nexxxt? 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Learning article on the Thought for Food competition and conference, including EI's participation. -SOCIAL MEDIA- Engagement x 147, Impressions x 115250
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/articles/thought-food-what%E2%80%99s-nexxxt
 
Description Web Article - What is bioinformatics? - 16.10.2018 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge.

Bioinformatics is a growing field of research, existing at the cutting-edge of the biological sciences. But what is it?
Biology is going large. With the advent of next generation (and third generation) genome sequencing and along with it an explosion in the amount of biological data being produced daily, scientists are now playing with terabytes or even petabytes (lots and lots of zeros) of data at a time. It would take infinite infinities for a single person to analyse this digital abundance.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/what-is-bioinformatics
 
Description Web Article - Women in computing: a journey into bioinformatics with Erin Baggs - 08.05.2018 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. This is part of our women in computing to promote this as a career addressing the skill shortage and lack of gender balance in the UK
For many in the bioinformatics world, coding is a leap into the unknown. This was the case for Erin Baggs, who has learned from scratch how to apply computational science to biology while doing her PhD with Ksenia Krasileva. She gives us an insight into what life is like for a PhD student, and how to negotiate the intrepid plunge into the choppy sea of coding.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/women-computing-journey-bioinformatics-erin-baggs
 
Description Web Special feature: 'Keeping Colombia megadiverse' 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Earlham Institute is at the heart of an international network aiming to preserve, maintain and enrich the biodiversity of this fascinatingly diverse country. This article sought to be an informative and engaging piece to reach a general audience. It is packed with interesting content and vibrant images. -SOCIAL MEDIA- Engagement x176, Impressions x169000
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/keeping-colombia-megadiverse
 
Description Web article - 'Ageless and timeless: the lords of the rings 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact The oldest trees have seen it all over millennia, and though their rings tell us their age, their meristems hold the secret to eternal youth. Web article focused on a public audience. -SOCIAL MEDIA- Engagement x63, Impressions x105000.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/articles/ageless-and-timeless-lords-rings
 
Description Web article - A celebration of science in Norwich - 27.08.2018 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge.

Promoting our engagement in the Noriwch Science festival beyond our region.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/celebration-science-norwich
 
Description Web article - Aquaculture and tilapia: a fish that may tip the balance. 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Web article to support the WorldFish Press Release 'Genetics roadmap to develop more resilient farmed fish. -SOCIAL MEDIA - Engagement 30, Impressions 9676
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/articles/aquaculture-and-tilapia-fish-may-tip-balance
 
Description Web article - Decoding Living Systems: from cell to ecosystem - 28.03.2018 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/decoding-living-systems-cell-ecosystem
 
Description Web article - Fostering symbiosis in the biosciences through multiscale modelling 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact News article to highlight the "Multiscale analysis of host-microbe interactions in plants, animals & humans" workshop and it's outcomes. -SOCIAL MEDIA- Engagement x102, Impressions x113433
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/articles/fostering-symbiosis-biosciences-through-multiscale-modelling
 
Description Web article - Orchestrating life: miRNA - 19.11.2018 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge.
Article describing how Prof Federica Di Palma's Group, are using computer-based bioinformatics methods that are helping us to understand miRNA's role in the evolution of different characteristics.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/orchestrating-life-micro-rna
 
Description Web article - There's more to a belch than meets the eye. 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Web article focused on the organisms that lie behind a bovine belch, and what can methane tell us about the complex lives of microbial communities. -SOCIAL MEDIA- Engagement x65, Impressions x215108
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/articles/there%E2%80%99s-more-belch-meets-eye
 
Description Web article - What is biohacking? 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Web article to raise awareness of biohacking: a grassroots movement promoting open science & open minds. -SOCIAL MEDIA_- Engagement x 152, Impressions x 107633
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/articles/what-is-biohacking-how-and-why
 
Description Web article - What's in a gene? - 10.12.2018 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge.
Article describing a shift in our understanding of what a gene is revealed by improvements to sequencing technology.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/whats-in-a-gene
 
Description Web article - Year of the pig: Flu, you swine! - 05.02.2019 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge.

This Chinese New Year sees the pig come around again after twelve years, an important animal for the country: of the 2 billion pigs on earth, half live in China. Not only are they an important food source, they provide an incredibly diverse range of products, from violin strings to hearts for human transplantation.

However, for all of their tastiness and usefulness, farming pigs comes with several downsides - an obvious one being that such abundant numbers living in closely confined spaces provides a fertile breeding ground for some very deadly viruses, including Swine Flu.

Prof Federica Di Palma Group, describe their work to understand the evolution of this disease.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/articles/chinese-year-of-the-pig-flu-you-swine
 
Description Web article - why should you care about biodiversity? 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Information piece to support the Colombian project. Interview with Jose De Vega. -SOCIAL MEDIA- Engagement 107, Impressions 100738
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/articles/why-you-should-care-about-biodiversity
 
Description Web article for Public Engagement - What's in a genome? 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact 'Learning' Article to explain what's in agenome. -SOCIAL MEDIA- Engagement x 285, Impressions x 138027
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/articles/whats-genome
 
Description What doesn't kill you makes you stronger? Cracking Salmonella and antibiotic resistance 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Article on tackling Salmonella by exploring a highly mutable, evolved strain to help answer why antibiotics are becoming less effective and improve our bodies' antimicrobial armour.
Year(s) Of Engagement Activity 2018
 
Description Workshop Oral Presentation: Gene families dynamics associated with lineage specific adaptations in Vertebrates 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Postgraduate students
Results and Impact Invited presentation to the students of the Earth and Life Systems Alliance (Norwich Research Park). The audience of the seminar was mainly composed of graduate and undergraduate students as well as University Professors and Lecturers. The presentation helped raising the profile of Wilfried Haerty and of the Earlham Institute
Year(s) Of Engagement Activity 2017
 
Description Workshop on Genomic Selection in WorldFish Breeding Programs 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The workshop was held to determine strategy and focus with respect to the introduction of genomic selection to the WorldFish breeding programs, and in particular the development of key to tolls to enable this (specifically discussed to date a SNP chip for marker assay). The agenda included: Discussion of WorldFish breeding programs and their goals; of the best strategy to introduce genomic selection to WorldFish breeding programs; on introduction of genomic selection to WorldFish breeding programs focused on selection of specific targets and of next steps and development of a strategy, including specifically that of SNP chip development including a draft workplan.
Year(s) Of Engagement Activity 2017
 
Description World Federation of Science Journalists (WFSJ) workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Workshop objectives:
Acquire basic knowledge about food security innovation and what is exportable to LMIC.
Sharing experiences amongst participants.
Workshop themes included:
-How crop technology is transforming agriculture around the world
-How farmers from developing countries are challenged by these changes, affecting livelihoods, food security and environment
-How researchers can better understand the complex human dynamics in agro-ecosystems and design more equitable and sustainable solutions
-What is the essential message you want journalists to remember from your talk?
Federica Di Palma was asked to concentrate on: -Meat from livestock is the main source of world protein and also source of GHG. What are the challenges for scientists to provide enough protein from livestock while coping with climate change?
-The latest livestock (and fisheries) research innovations that suitable to LMICs
-How LMICs can feed themselves?
-Do we have enough sources to provide protein for the world?
Year(s) Of Engagement Activity 2017