Decoding Biodiversity (DECODE): Genome Enabled Analysis Of Diversity To Identify Gene Function Biosynthetic Pathways And Variation In Agri/Aquacultural Traits
Lead Research Organisation:
EARLHAM INSTITUTE
Abstract
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Technical Summary
A work package of the grant Decoding Biodiversity (DECODE) this project will use the tools we have developed to investigate biodiversity in publicly available genomes. We will use multiple analytical approaches to: assign function to genomic dark matter-genes of currently unknown function; investigate mechanisms underpinning chemical diversity in plants; and identify mechanisms driving genetic diversity in key agricultural crops and aquaculture species.
Planned Impact
unavailable
Organisations
- EARLHAM INSTITUTE (Lead Research Organisation)
- IPK Gatersleben (Collaboration)
- U.S. Department of Energy Joint Genome Institute (Collaboration)
- University of California, Berkeley (Collaboration)
- John Innes Centre (Collaboration)
- National Wildflower Centre (Collaboration)
- Elsoms Seeds (Collaboration)
- UNIVERSITY OF EAST ANGLIA (Collaboration)
- National Taiwan University (Collaboration)
- Radboud University Nijmegen (Collaboration)
- RAGT Seeds (Collaboration)
- University of Illinois at Urbana-Champaign (Collaboration)
- UNIVERSITY OF LEICESTER (Collaboration)
- Earlham Institute (Collaboration)
- Germinal (Collaboration)
- EMORSGATE SEEDS (Collaboration)
- Tropic Biosciences Ltd (Collaboration)
- Tozer Seeds (Collaboration)
- Brazilian Agricultural Research Corporation (Collaboration)
- Teagasc (Collaboration)
- HudsonAlpha Institute for Biotechnology (Collaboration)
- Royal Botanic Gardens, Kew (Collaboration)
- Syngenta International AG (Collaboration)
- IBM (Collaboration)
- Wellcome Sanger Institute (Collaboration)
- CGIAR (Collaboration)
- Centre for Environment, Fisheries and Aquaculture Science (Collaboration)
Publications
Ciezarek A
(2023)
Ancient and ongoing hybridization in the Oreochromis cichlid fishes
Coombes B
(2024)
Introgressions lead to reference bias in wheat RNA-seq analysis.
in BMC biology
Coombes B
(2023)
Whole-genome sequencing uncovers the structural and transcriptomic landscape of hexaploid wheat/Ambylopyrum muticum introgression lines.
in Plant biotechnology journal
Coombes B
(2023)
Introgressions lead to reference bias in wheat RNA-Seq analysis
Cuthbert D
(2026)
Virus Induced Gene Silencing in Calendula officinalis (pot marigold)
Denning-James KE
(2025)
Genome-wide association mapping dissects the selective breeding of determinacy and photoperiod sensitivity in common bean (Phaseolus vulgaris L.).
in G3 (Bethesda, Md.)
| Description | DECODE's WP 2 explores the link between genotype and biological function. It leverages EI's unique capabilities, large-scale genomics, and toolkit improvements from WP 1 to address questions about gene function conservation across taxonomic levels (Obj1), the genetic basis of plant bioactives (Obj2), and how complex genome-wide variation affects traits in agriculture and aquaculture production systems (Obj3). Obj 1: The growing number and diversity of complete genomes offer an opportunity to improve gene function annotation by transferring knowledge across taxa, but inconsistent annotations can mislead comparative and functional analyses. We used an annotation workflow (from WP1) to minimize artefacts in evolutionary inference and compare Fusarium genomes, reducing variation to find lifestyle differences and showed how annotation biases can mislead biological conclusions (10.1101/2025.03.12.642647). Obj 2: Although the bioactivities of plant extracts are frequently reported, the specific molecular basis is often unknown. To provide insights into the origins of novel chemodiversity in plants, we integrated bioactivity-led chemistry with functional genomics to reconstruct biosynthetic pathways and identify genetic determinants of bioactive terpenoids in UK Asteraceae. In Calendula officinalis (pot marigold), we investigated the biosynthetic origins of anti-inflammatory activity and identified C16-hydroxylated triterpenoids as key compounds. We demonstrated how integrated studies of bioactivity and biosynthesis can unlock the therapeutic potential of medicinal plants (10.1038/s41467-025-62269-w). To streamline functional validation in specialised metabolism, we also developed a virus-induced gene silencing (VIGS) approach to suppress endogenous gene expression (10.64898/2026.02.16.706131), providing methodological advances to accelerate pathway discovery and testing for a green bioeconomy (10.1016/j.pbi.2023.102346). Obj 3: Complex genetic variation, such as chromosomal rearrangements, structural variants (SVs), and introgressions, is a major source of adaptive and resistance traits, but it remains difficult to detect and interpret at scale. Across the award, we advanced this objective by combining haplotype-resolved genome assembly, population-scale analysis, and trait discovery. We generated new telomere-to-telomere and haplotype-resolved genome assemblies using PacBio HiFi and Omni-C Illumina sequencing. In male Abbassa Nile tilapia, we reconstructed X and Y haplotypes and clarified sex-determination genes for the first time (10.1038/s41598-025-01300-y). We also generated complete assemblies for two agriculturally significant species: a commercial coriander cultivar (in partnership with Elsoms) and an admixed rice accession (in partnership with RBG Kew). We demonstrated the scalability of this approach across challenging genomes, including an allo-octoploid grass with three lineages (10.1093/g3journal/jkag033), an apomictic allotetraploid in the same family (10.1093/g3journal/jkaf005), the highly heterochromatic Carpenter bee (10.1038/s41437-024-00720-2), as well as unrepresented taxa such as the weed foxtail (10.1038/s41597-024-04222-y), arctic char (10.1111/mec.70085), and wood-degrading fungus (10.1093/gbe/evaf003), showing that high-quality assembly can now be accurately achieved with appropriate long-read and scaffolding strategies. These new assemblies enabled detailed interrogation of SVs and related regulatory features. We published three studies that illustrated the phenotypic consequences of introgression and chromosomal rearrangements in farmed species and their potential role in resilience. In tilapia, we explored the role of introgression in the evolutionary history of the species complex (10.1093/molbev/msae116) and associated more than 1,000 genes associated with environmental tolerance (10.1016/j.ygeno.2023.110633). In wheat, introgression from wild species was associated with an imbalance in homoeologous expression (10.1111/pbi.13859) and spurious candidate gene signals (10.1186/s12915-024-01853-w). In bananas (10.1093/aob/mcad192), chromosomal imbalances were mapped and proposed as a source of CNV/dosage variation relevant to clonal crop traits. We also used population-level genomic resources to explore epigenetic and regulatory variation in tilapia, including chromatin accessibility and variation in transcription factor binding sites (10.1101/2025.10.09.681187). Together, these outputs establish evidence for moving from complex variation to interpretable functional hypotheses. To translate genomic diversity into trait discovery, we built on WP1 advances in automated, high-throughput, and cost-effective DNA extraction (robotics) and library preparation (LITE2). Using these capabilities, we established diversity panels for coriander and white clover with industry partners (Elsoms and Germinal) for association mapping. In common bean, we studied the relationship between domestication and early selection for photoperiod insensitivity and compact growth habits (10.1093/g3journal/jkaf141). Finally, we extended these approaches beyond agriculture into conservation genomics, including analyses of the extent of decline in British polecat populations (10.1111/mec.70091) and global cheetah populations (10.1093/evolut/qpaf005), demonstrating the broader applicability of our technological advances (10.1038/s44185-024-00054-6; 10.12688/wellcomeopenres.18499.3) to biodiversity and conservation priorities. |
| Exploitation Route | Obj 1: The multi-sample annotation workflow, together with best practices to minimise annotation artefacts, can be advanced by fungal genomics researchers, genome consortia, and data infrastructure providers seeking more consistent cross-genome comparisons. It offers a practical pathway for collaborative efforts to standardise the transfer and projection of annotations at scale. Meanwhile, single-cell sequencing research uncovering new genomic diversity in uncultured endosymbiotic bacteria lays a foundation for microbial ecologists and symbiosis scientists exploring the evolutionary shift from free-living to parasitic lifestyles. These resources can improve gene function inference and help identify genomic features linked to specific lifestyles, with implications for host-microbe interactions and disease. Obj 2: Reconstructing triterpenoid biosynthesis pathways provides a clear route for future research by plant biochemists, natural product scientists, and plant biotech groups focused on discovering and confirming new bioactive pathways in medicinal plants. Virus-induced gene silencing (VIGS) is a practical tool for academic researchers and applied R&D teams working with non-model species, where stable transformation is challenging. This technique accelerates functional validation in specialised metabolism. Obj 3: The telomere-to-telomere and haplotype-resolved assemblies provide valuable reference resources for agro- and aquaculture genetics and for academic studies of complex traits and genome variation. Population-scale analyses of structural variants (SVs) and regulatory elements can help breeders and genomics researchers identify candidate regions associated with resilience traits and adaptive alleles. The diversity panels for coriander and white clover, developed with Elsoms and Germinal and supported by high-throughput genotyping, are ready for industry use in marker-assisted selection and parental quality tests, and to build upon predictive breeding pipelines in the future. Further genomics extends beyond agriculture, offering new tools for conservation geneticists, biodiversity monitoring, and policy research on species such as polecats and cheetahs that are declining. |
| Sectors | Agriculture Food and Drink Environment |
| Description | Our WP2 translates method and tools development (WP1) into scientific discovery, enabling us to deliver impacts directly and through ISP patterns and other stakeholders. What started as foundational work linking genetic variation to biological function has evolved into (obj1) more reliable comparative genomics analyses by reducing annotation artefacts, (obj2) tractable discovery and validation of biosynthetic pathways for medicinal plant bioactives, and (obj3) breeding-ready assemblies and methods that support marker-trait discovery in agriculture and aquaculture to enhance resilience, as well as evidence that informs biodiversity conservation decisions. Among academic stakeholders, WP2 helps consolidate research that considers annotation quality and structural and regulatory variation as key aspects of genotype-phenotype inference. However, importantly, this capability also creates clearer pathways for the non-academic stakeholders to reuse outputs, lowering barriers to adopting genomic approaches. Obj1: Our multi-sample annotation workflow enhances confidence in biological conclusions derived from comparative genomics by systematically addressing annotation inconsistencies as a source of error. This reduces wasted effort caused by misleading comparisons and improves reproducibility, facilitating more reliable knowledge transfer across taxa. The approach can be directly adopted by genomics laboratories and genome consortia, and is relevant to data infrastructure providers seeking consistent, scalable standards for annotation transfer and projection to maximise the downstream value of public genome resources. Obj2: Impacts are delivered through method development, such as the VIGS method, which allows linking bioactivity to genetic mechanisms, and by their use on specific cases, enabling the identification of anti-inflammatory molecular targets. The VIGS approach reduces a key barrier in non-model plants, accelerating the functional validation of candidate genes and pathways and thereby lowering the cost and risk of pathway discovery. Applied to Calendula officinalis, the integrated bioactivity-biosynthesis work identified anti-inflammatory activity associated with specific triterpenoid chemistry, providing a clear example of how pathway elucidation can de-risk downstream translation into future products, services, and screening platforms. These outcomes are therefore relevant beyond academia to biotechnology and natural products R&D, supporting faster iteration and more evidence-led decisions on which pathways and compounds to progress. Obj3: In aquaculture and crops, our resources enable more precise identification of candidate regions that underpin resilience and adaptation, thereby strengthening the evidence base for breeding decisions and the design of follow-up studies. Translation progresses through active partnerships with industry (e.g., coriander and white clover diversity panels with Elsoms and Germinal), which offer an immediate pathway to discovering trait-associated markers and, eventually, establishing predictive breeding pipelines. Because complex genetic variation is challenging to resolve using standard references and short-read workflows, we addressed key barriers by combining robust assembly strategies (including haplotype resolution and telomere-to-telomere assembly where possible), scalable population analyses, and practical laboratory automation to generate data cost-effectively. This approach allows these methods to be applied routinely rather than on an exceptional basis. Beyond food systems, applying these same principles to endangered species, exemplified by the polecat and cheetah population projects, extends benefits into the third/public sector by supporting biodiversity monitoring and policy-relevant conservation genetics. |
| First Year Of Impact | 2025 |
| Sector | Agriculture, Food and Drink,Environment |
| Impact Types | Societal Economic |
| Description | Advocacy to the House of Lords Science and Technology Select Committee |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| Impact | As a result of EI's evidence, the Committee's report included policy recommendations aligned to the Earlham Institute's advocacy especially on investment and skills. Since the enquiry, the Government has endorsed the role of the UK's life science sector as one of the most strategically important areas for development in the Modern Industrial Strategy. This policy will generate subsequent regulatory and investment decisions that will impact our work significantly. |
| URL | https://publications.parliament.uk/pa/ld5901/ldselect/ldsctech/55/5502.htm |
| Description | Advocating for secondary legislation to implement Precision Breeding Act |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| Impact | Both the letter and the meeting between the MP and the Secretary of State were successful and the secondary legislation was introduced and passed shortly afterwards. |
| Description | Alice Macdonald MP and Jess Asato MP visit to Earlham Institute and Norwich Research Park |
| Geographic Reach | National |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | In December 2024 the newly elected MPs Alice Macdonald and Jess Asato visited the Earlham Institute and Norwich Research Park for an introduction to our research and advocacy. They met staff, saw inside our laboratories and heard about the wide range of research we do and our priority advocacy objectives for science policy. |
| Description | Ben Goldsborough MP visit to Earlham Institute and Norwich Research Park |
| Geographic Reach | National |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | In August 2024 the newly elected MP for South Norfolk, Ben Goldsborough, visited the Earlham Institute as part of his introduction to his new constituency and the Norwich Research Park. He met senior staff, heard about our policy advocacy priorities, listened to some case studies and saw colleagues working in our laboratories. Afterwards he posted on social media, praising the Norwich Research Park and saying his visit had been "life affirming" and "encouraging". Since his visit he has spoken about Norwich Research Park and the Earlham Institute in numerous parliamentary debates and policy conversations with ministers. |
| Description | DEFRA's Expert Panel on Digital sequence information on genetic resources |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | Recommendation submitted to COP15 |
| Description | EI response to Government consultation on engineering biology |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| Impact | Government invited evidence from research community to inform future policy - including regulation and funding decisions - on engineering biology |
| Description | Letter to Chancellor to protect science budget and maintain core research funding |
| Geographic Reach | National |
| Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
| Impact | The letter helped to persuade HM Treasury of the link between economic growth and a strong science research sector to drive innovation and investment. The DSIT budget and core research budgets were maintained. |
| Description | Letter to DEFRA Minister advocating against delay to implementation of legislation |
| Geographic Reach | National |
| Policy Influence Type | Implementation circular/rapid advice/letter to e.g. Ministry of Health |
| Impact | As a result from the advocacy pressure that this letter contributed to, the Government restated their intention to bring forward the secondary legislation in March 2025. |
| Description | Ministerial advocacy on science impact of immigration restrictions |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| Description | Peter Prinsley MP visit to Earlham Institute and Norwich Research Park |
| Geographic Reach | National |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | In September 2024 the newly elected MP Peter Prinsley, visited the Norwich Research Park. He met senior staff, heard about the Earlham Institute's policy advocacy priorities and listened to some case studies. He was particularly interested in the Norwich Research Park's advocacy on strategic investment in infrastructure and the strength of clusters in R&D place strategy. |
| Description | Steff Aquarone MP visit and introduction to Earlham Institute and Norwich Research Park |
| Geographic Reach | National |
| Policy Influence Type | Influenced training of practitioners or researchers |
| Impact | In September 2024 the newly elected Lib Dem MP for North Norfolk, Steff Aquarone, visited the Earlham Institute as part of an introductory visit to Norwich Research Park. He met senior staff and gave a speech about wanting to work closely with EI on science policy development and relevant legislation and regulation. |
| Description | Supporting the passage of precision breeding secondary legislation |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| Impact | Parliament passed the secondary legislation to implement the Genetic Technologies (Precision Breeding) Act 2023 which paves the way for implementation and new market authorisation in England for gene edited plant products. |
| Description | Biodiversity, wellbeing and colour: wildflower genomics to inform the creation of new habitat |
| Amount | £20,000 (GBP) |
| Funding ID | DEVEGA_E22DTP1A |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2022 |
| End | 09/2026 |
| Description | Boosting innovation in breeding for the next generation of legume crops for Europe |
| Amount | £368,936 (GBP) |
| Funding ID | 10077978 |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2023 |
| End | 02/2028 |
| Description | Characterising Rice Genetic Diversity of the Past to Safeguard the Future |
| Amount | £100,000 (GBP) |
| Funding ID | 2869278 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2023 |
| End | 09/2027 |
| Description | Connecting Research Culture Conference |
| Amount | £59,558 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2024 |
| End | 05/2025 |
| Description | Data science to feed a changing world: superior drought tolerance in nutritious traditional beans |
| Amount | £100,000 (GBP) |
| Funding ID | 2578607 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2021 |
| End | 09/2025 |
| Description | EBioAct: Environmentally sustainable production of bioactive triterpenes |
| Amount | £1,680,889 (GBP) |
| Funding ID | BB/Y007751/1 |
| Organisation | United Kingdom Research and Innovation |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2024 |
| End | 02/2026 |
| Description | Earlham Institute and Tozer Seeds Limited KTP 23_24 R5 |
| Amount | £176,013 (GBP) |
| Funding ID | 10102570 |
| Organisation | Innovate UK |
| Sector | Public |
| Country | United Kingdom |
| Start | 07/2024 |
| End | 02/2027 |
| Description | Engineering Ecosystem Resilience through the lens of genomic technologies |
| Amount | £16,632 (GBP) |
| Organisation | Advanced Research and Innovation Agency (ARIA) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2025 |
| End | 01/2026 |
| Description | Engineering Ecosystem Resilience through the lens of genomic technologies |
| Amount | £16,632 (GBP) |
| Organisation | Advanced Research and Innovation Agency (ARIA) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2025 |
| End | 01/2026 |
| Description | Engineering gene regulation in plants to yield predictable expression |
| Amount | £772,877 (GBP) |
| Funding ID | APP36048 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2025 |
| End | 04/2028 |
| Description | Germplasm relevant to DAC-listed countries |
| Amount | £495,000 (GBP) |
| Funding ID | BBS/OS/GC/000011A |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 09/2016 |
| End | 07/2017 |
| Description | Global Center: International Research Center for Enhancing Plant Resilience |
| Amount | £2,124,544 (GBP) |
| Funding ID | APP41752 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2025 |
| End | 04/2030 |
| Description | John Innes Foundation internship in data-driven plant bioinformatics |
| Amount | £38,000 (GBP) |
| Organisation | John Innes Foundation |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 04/2021 |
| End | 08/2023 |
| Description | Leverage Yellow Common Bean Native Variety Liborino as a bioproduct for the sustainable and peaceful socioeconomic development of the rural communities in Colombia |
| Amount | £49,852 (GBP) |
| Funding ID | 527023146 |
| Organisation | British Council |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2020 |
| End | 10/2021 |
| Description | Lucky and resilient: Genomic improvement of cold tolerance in red and white clover |
| Amount | £125,000 (GBP) |
| Funding ID | 2929096 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2024 |
| End | 09/2028 |
| Description | Safeguarding UK's best-loved fruit: immunity diversity in banana cultivars |
| Amount | £100,000 (GBP) |
| Funding ID | 2586708 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2021 |
| End | 09/2025 |
| Description | Summer studentship |
| Amount | £4,208 (GBP) |
| Organisation | University of East Anglia |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 05/2024 |
| End | 08/2024 |
| Description | The John Innes Foundation (JIF) International PhD Fellowships in Data-Driven Plant Science 2 |
| Amount | £138,963 (GBP) |
| Funding ID | GUIZIOU_E25JIF |
| Organisation | John Innes Foundation |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2025 |
| End | 09/2029 |
| Description | The John Innes Foundation (JIF) International PhD Fellowships in Data-Driven Plant Science Internships |
| Amount | £106,935 (GBP) |
| Organisation | John Innes Foundation |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2025 |
| End | 09/2029 |
| Description | Undergraduate (sandwich) Internship (12 months) |
| Amount | £22,924 (GBP) |
| Organisation | Royal Botanic Gardens, Kew |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 08/2023 |
| End | 09/2024 |
| Title | COPO software development policy written |
| Description | rules governing the use of jira, testing regimes, and github pull requests established |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2025 |
| Provided To Others? | No |
| Impact | Fewer bugs finding their way into production |
| Title | Method for Virus-Induced Gene Silencing of Asteraceae |
| Description | Method for Virus-Induced Gene Silencing of Asteraceae |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2026 |
| Provided To Others? | Yes |
| Impact | Characterise the function of enzymes involved in sterol and terpene biosynthesis. |
| URL | https://doi.org/10.64898/2026.02.16.706131 |
| Title | single cell metadata scraper |
| Description | Developed AI powered tool for extracting metadata from literature to manifest. 78% convergence with human. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2025 |
| Provided To Others? | Yes |
| Impact | Massive reduction in time filling out manifests if there is an accompanying manuscript |
| URL | https://github.com/EarlhamInst/Scraper_sc |
| Title | AI models for seed species classification |
| Description | we have developed two segmentation pipelines: one AI-based (Cellpose v4) and another using classic image analysis techniques (ImageJ), to generate single-seed masks for each seed starting from scanned images of seeds scattered across a domestic flatbed scanner. Then, we used an ImageJ (Schneider et al., 2012) plugin (Loddo et al. 2023) to extract numerical values for 64 features regarding the colour, texture and shape features of each seed. In parallel, we developed a Python script using OpenCV v2 to generate individual seed squared images from the masks to use with image-based classification models. We compared over 20 ML and DL classification models for tabulated phenotype scores, as well as image-based CNNs. |
| Type Of Material | Data analysis technique |
| Year Produced | 2026 |
| Provided To Others? | Yes |
| Impact | This study presented methods for classifying wildflower seeds using image analysis and AI. The optimal method depends on the balance between accuracy and computational time, the use of AutoML tools, and whether the classification involves a closed set of species. If the focus is on absolute metrics without regard for computational cost, neural networks for segmentation (CellPose) and classification (ResNet50) proved to be the best options. However, generating tabulated features was an order of magnitude faster than deep learning segmentation. In closed-set classification, the complex models from AutoGluon were the most accurate, but four models from vanilla scikit-learn performed similarly. In open-set classification, Random Forests clearly excelled because of their transparent use of calibration and thresholds to assign unseen species to the unclassified class. Our findings indicate that traditional machine learning models, such as random forests and gradient boosting, achieve high classification accuracy with lower computational demands than deep learning methods. Nonetheless, our extended analyses also demonstrated that deep learning (ResNet50) can achieve almost perfect accuracy when supplied with high-quality segmentation (e.g., Cellpose), offering a pathway towards fully automated image-to-classification pipelines at a higher computational cost. |
| URL | https://github.com/DeVegaGroup/SeedClassifier |
| Title | Adaptation of pruning pipeline |
| Description | We adapted the pruning algorithm designed by Zhang et al., 2018 in their software AllHiC to be used with OmniC data |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2023 |
| Provided To Others? | No |
| Impact | Enabled us to create our genome assembly and the method will be published |
| Title | Annotated Genome assembly |
| Description | The first haplotype aware assembly of the teatraploid Urochloa decumbens |
| Type Of Material | Data analysis technique |
| Year Produced | 2023 |
| Provided To Others? | No |
| Impact | Collaborations with Embrapa and CIAT. Increase skills in institute. Knowledge about species. Development of pipelines. |
| Title | Biosynthesis and Bioactivity of Anti-Inflammatory Triterpenoids in Calendula officinalis (pot marigold) - Supplementary Data |
| Description | Data files associated with the manuscript submission for Golubova et al. (2025) Biosynthesis and Bioactivity of Anti-Inflammatory Triterpenoids in Calendula officinalis (pot marigold). Files include Calendula officinalis functional annotation.zip All functional annotation files Filtered de-novo transcriptome assemblies of 6 Asteraceae species used to derive gene models Asteraceae transcriptome assemblies.zip De-novo transcriptome assemblies (flower and leaf) of 6 Asteraceae species for gene discovery Calendula arvensis, Eupatorium cannabinum, Inula ensifolia, Inula Britannica, Achillea millefolium and Matricaria chamomilla Calendula officinalis differential gene expression.zip Raw data files for leaf, disc and ray tissues Calendula officinalis transcriptome assembly.zip Reference-guided transcriptome assembly of Calendula officinalis GC-MS, LC-MS, NMR data files.zip Figure 2 + Supp Fig 1 - Metabolic Profile and anti-inflammatory data Figure 4 - MAS to TXSS Figure 5 + Supp Fig 25 - TXSS product ratios Figure 6 + Supp Fig 29,31 - Production of faradiol Figure 7 - Production of TFAEs Supp Fig 2 - LC-MS Supp Fig 3-5 - Standards Supp Fig 6-8 - Fractionation and purification Supp Fig 10-14 - NMR of faradiol palmitate Supp Fig 20 - Asteraceae TXSSs Supp Fig 23 - Co tissues Supp Fig 24 - Tk tissues Supp Fig 30 - Asteraceae floral extracts Supp Fig 34 - CoTXSS + ACTs Supp Fig 35 - CoTXSS + CYP + ACTs Supp Fig 37 - Flower development |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/doi/10.5281/zenodo.13869958 |
| Title | Biosynthesis and Bioactivity of Anti-Inflammatory Triterpenoids in Calendula officinalis (pot marigold) - Supplementary Data |
| Description | Data files associated with the manuscript submission for Golubova et al. (2025) Biosynthesis and Bioactivity of Anti-Inflammatory Triterpenoids in Calendula officinalis (pot marigold). Files include Calendula officinalis functional annotation.zip All functional annotation files Filtered de-novo transcriptome assemblies of 6 Asteraceae species used to derive gene models Asteraceae transcriptome assemblies.zip De-novo transcriptome assemblies (flower and leaf) of 6 Asteraceae species for gene discovery Calendula arvensis, Eupatorium cannabinum, Inula ensifolia, Inula Britannica, Achillea millefolium and Matricaria chamomilla Calendula officinalis differential gene expression.zip Raw data files for leaf, disc and ray tissues Calendula officinalis transcriptome assembly.zip Reference-guided transcriptome assembly of Calendula officinalis GC-MS, LC-MS, NMR data files.zip Figure 2 + Supp Fig 1 - Metabolic Profile and anti-inflammatory data Figure 4 - MAS to TXSS Figure 5 + Supp Fig 25 - TXSS product ratios Figure 6 + Supp Fig 29,31 - Production of faradiol Figure 7 - Production of TFAEs Supp Fig 2 - LC-MS Supp Fig 3-5 - Standards Supp Fig 6-8 - Fractionation and purification Supp Fig 10-14 - NMR of faradiol palmitate Supp Fig 20 - Asteraceae TXSSs Supp Fig 23 - Co tissues Supp Fig 24 - Tk tissues Supp Fig 30 - Asteraceae floral extracts Supp Fig 34 - CoTXSS + ACTs Supp Fig 35 - CoTXSS + CYP + ACTs Supp Fig 37 - Flower development |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/doi/10.5281/zenodo.13869957 |
| Title | Functional annotation for the Abbassa genome assembly |
| Description | Functional annotation for the Abbassa genome assembly |
| Type Of Material | Database/Collection of data |
| Year Produced | 2025 |
| Provided To Others? | Yes |
| Impact | na |
| Title | Fusarium Pan-Annotations: improved individual and collective genome annotations |
| Description | A 'pan-annotation' of genomes from 77 taxa (83 accessions) across the genus Fusarium, delivered as part of the Earlham Institute Strategic Programme Grant 'Decoding Biodiversity' (BBSRC). Manuscript and annotation workflow tutorial in prep. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | -Establishment of effective 'pan-annotation' reannotation workflow -Improved annotation quality both individually and collectively for Fusarium genomes -Detection of different rates of alternative splicing across Fusarium species complexes |
| URL | https://zenodo.org/doi/10.5281/zenodo.13829922 |
| Title | Fusarium Pan-Annotations: improved individual and collective genome annotations |
| Description | A 'pan-annotation' of genomes from 77 taxa (83 accessions) across the genus Fusarium, delivered as part of the Earlham Institute Strategic Programme Grant 'Decoding Biodiversity' (BBSRC). Manuscript and annotation workflow tutorial in prep. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| URL | https://zenodo.org/doi/10.5281/zenodo.13829921 |
| Title | MxG transcriptomic response to drought and flooding PRJEB86745 |
| Description | 105 RNAseq libraries exploring the transcriptomic response of Miscanthus x giganteus to early or late drought and flooding stresses on controlled conditions. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2025 |
| Provided To Others? | Yes |
| Impact | Collaboration between IBERS and EI demonstrates the complementary skills of both institutes. This project fits into the interest on expression dynamics on hybrid allopolyploids. The results will help design biomarkers, better understand the biology of the commercial Mxg cultivar, and feed into future research on stress priming and epigenetics. |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB86745 |
| Title | Pipeline to phasing and scaffolding heterozygous outcrossed polyploid and diploid genomes based on pruning Hi-C data |
| Description | The major problem of scaffolding polyploid genome is that Hi-C signals are frequently detected between allelic haplotypes and any existing stat of art Hi-C scaffolding program links the allelic haplotypes together. To solve the problem, we developed a new Hi-C scaffolding pipeline tailored to the polyploid genomes and tested it to anchor the tetraploid genome of Brachiaria decumbens cv. Basilisks that we previously sequenced with HiFI. We also generated Hi-C reads for the red clover cultivar cv. Milvus that we sequenced using HiFi reads in a previous funding scheme. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | No |
| Impact | The major problem of scaffolding polyploid genome is that Hi-C signals are frequently detected between allelic haplotypes and any existing stat of art Hi-C scaffolding program links the allelic haplotypes together. To solve the problem, we developed a new Hi-C scaffolding pipeline tailored to the polyploid genomes and tested it to anchor the tetraploid genome of Brachiaria decumbens cv. Basilisks that we previously sequenced with HiFI. We also generated Hi-C reads for the red clover cultivar cv. Milvus that we sequenced using HiFi reads in a previous funding scheme. |
| Title | Scraped Papers |
| Description | 183 papers on single cell were scraped and their metadata compiled into manifests |
| Type Of Material | Computer model/algorithm |
| Year Produced | 2026 |
| Provided To Others? | Yes |
| Impact | A resource for further refinement of automated metadata annotation. |
| Title | Sequencing data for the genome assembly and annotation of the Nile tilapia Abbassa elite strain |
| Description | Sequencing data for the genome assembly and annotation of the Nile tilapia Abbassa elite strain |
| Type Of Material | Database/Collection of data |
| Year Produced | 2025 |
| Provided To Others? | Yes |
| Impact | na |
| URL | https://www.ebi.ac.uk/ena/browser/view/PRJEB57170 |
| Title | Tilapia genetic diversity across the Lake Victoria Basin |
| Description | Genotypes for Oreochromis niloticus, O. leucosticus, O. variabilis, O. esculentus, Coptodon rendalli, C. zillii collected in water bodies in Kenya, Tanzania, and Uganda within the Lake Victoria Basin. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2024 |
| Provided To Others? | Yes |
| Impact | na |
| URL | https://zenodo.org/doi/10.5281/zenodo.11193181 |
| Description | Anti-inflammatory properties of plant natural products |
| Organisation | University of East Anglia |
| Department | Schools of Pharmacy and Medicine UEA |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Identification and production of plant extracts and natural products with proposed anti-inflammatory activity. |
| Collaborator Contribution | Testing the anti-inflammatory activities of plant natural products in human cell lines |
| Impact | Data on the anti-inflammatory activities of plant natural products. |
| Start Year | 2021 |
| Description | CIAT and EMBRAPA: Understanding genomics of Urochloa |
| Organisation | Brazilian Agricultural Research Corporation |
| Department | Embrapa Cerrados |
| Country | Brazil |
| Sector | Public |
| PI Contribution | We assembled and annotated a high quality genome of the polyploid Urochloa decumbens which can be used to by our collaborators to identify genes and markers relevant for breeding. |
| Collaborator Contribution | Provided us with data from another Urochloa species so we could explore and understand the ancestry of Urochloa decumbens |
| Impact | Outcome is we have added to the knowledge of the community by understanding the ancestry of Urochloa decumbens and identifying structural rearrangements that will contribute to our understanding of this forage species and its traits. |
| Start Year | 2023 |
| Description | CIAT and EMBRAPA: Understanding genomics of Urochloa |
| Organisation | Brazilian Agricultural Research Corporation |
| Department | Embrapa Genetic Resources and Biotechnology |
| Country | Brazil |
| Sector | Private |
| PI Contribution | We assembled and annotated a high quality genome of the polyploid Urochloa decumbens which can be used to by our collaborators to identify genes and markers relevant for breeding. |
| Collaborator Contribution | Provided us with data from another Urochloa species so we could explore and understand the ancestry of Urochloa decumbens |
| Impact | Outcome is we have added to the knowledge of the community by understanding the ancestry of Urochloa decumbens and identifying structural rearrangements that will contribute to our understanding of this forage species and its traits. |
| Start Year | 2023 |
| Description | CIAT and EMBRAPA: Understanding genomics of Urochloa |
| Organisation | CGIAR |
| Department | International Center for Tropical Agriculture |
| Country | Colombia |
| Sector | Charity/Non Profit |
| PI Contribution | We assembled and annotated a high quality genome of the polyploid Urochloa decumbens which can be used to by our collaborators to identify genes and markers relevant for breeding. |
| Collaborator Contribution | Provided us with data from another Urochloa species so we could explore and understand the ancestry of Urochloa decumbens |
| Impact | Outcome is we have added to the knowledge of the community by understanding the ancestry of Urochloa decumbens and identifying structural rearrangements that will contribute to our understanding of this forage species and its traits. |
| Start Year | 2023 |
| Description | Collaboration -CEFAS |
| Organisation | Centre For Environment, Fisheries And Aquaculture Science |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | Data analysis including genome assembly and annotation, pangenome reconstruction, population structure analysis |
| Collaborator Contribution | Data, samples, supervision |
| Impact | Genome assemblies for key UK fishery species |
| Start Year | 2025 |
| Description | Collaboration on white clover molecular breeding with Germinal GB Ltd |
| Organisation | Germinal |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Improving the persistency of white clover through three objectives: (1) Exploring diversity panel using landscape genomics, population analysis (2) GWAS with persistency traits from GWAS trial (3) Unlocking persistency-related traits from Caucasian clover |
| Collaborator Contribution | Germinal is providing cash contribution and supervision of PhD student, supporting summer placements |
| Impact | I have done one summer visit (investigating Caucasian hybrids and trial design). |
| Start Year | 2024 |
| Description | Collaboration with Elsoms Group (CASE - CD) - Understanding variation in flowering-related traits among commercially important Apiaceae herb species. |
| Organisation | Elsoms Seeds |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Expertise and Know-How in marker discovery for plant breeding. Expertise and Know-How in identification of genetic diversity across large biological collections. Expertise and Know-How in sequencing and bioinformatics analysis of plant genomes. Knowledge and expertise in genebanks and genotyping orphan crops. Computational and bioinformatics expertise and best practice. |
| Collaborator Contribution | Plant material and breeding knowhow for Apiaceae herb species |
| Impact | CASE Studentship agreement. |
| Start Year | 2022 |
| Description | Collaboration with IBM Research, STFC, and RAGT - HNCDI Excelerate |
| Organisation | IBM |
| Department | IBM Research in the UK |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Earlham is contributing by genomic data for 27 UK wheat varieties and wheat pan-transcriptome data. |
| Collaborator Contribution | IBM will design, develop, and test the bioinformatic workflow to enable processing of genomic and developing statistical and ML predictions of potential useful genetic variation and markers for valuable agricultural traits. RAGT brings expertise in plan breeding. STFC Hartree Centre brings expertise in supercomputing, data science and artificial intelligence (AI) technologies for enhanced productivity, smarter innovation and economic growth. |
| Impact | No outputs or outcomes yet. |
| Start Year | 2023 |
| Description | Collaboration with IBM Research, STFC, and RAGT - HNCDI Excelerate |
| Organisation | RAGT Seeds |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Earlham is contributing by genomic data for 27 UK wheat varieties and wheat pan-transcriptome data. |
| Collaborator Contribution | IBM will design, develop, and test the bioinformatic workflow to enable processing of genomic and developing statistical and ML predictions of potential useful genetic variation and markers for valuable agricultural traits. RAGT brings expertise in plan breeding. STFC Hartree Centre brings expertise in supercomputing, data science and artificial intelligence (AI) technologies for enhanced productivity, smarter innovation and economic growth. |
| Impact | No outputs or outcomes yet. |
| Start Year | 2023 |
| Description | Collaboration with Syngenta Crop Protection R&D |
| Organisation | Syngenta International AG |
| Department | Syngenta Crop Protection |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | TBA |
| Collaborator Contribution | TBA |
| Impact | TBA |
| Start Year | 2022 |
| Description | Collaboration with data management working group (Lars-Otto Gernot and Ivo Rieu) for Legume Generation |
| Organisation | IPK Gatersleben |
| Country | Germany |
| Sector | Private |
| PI Contribution | We have worked together to establish best data management practices within the legume generation project, e.g. crop and gene ontologies, and to standardise procedures across multiple partners. WE are working with BELIS to maintain these standards between projects. |
| Collaborator Contribution | They have assisted in maintaining standards at other partner institutes and providing input to us in ways to standardise procedures |
| Impact | We have worked together to establish best data management practices within the legume generation project, e.g. crop and gene ontologies, and to standardise procedures across multiple partners. WE are working with BELIS to maintain these standards between projects. |
| Start Year | 2024 |
| Description | Collaboration with data management working group (Lars-Otto Gernot and Ivo Rieu) for Legume Generation |
| Organisation | Radboud University Nijmegen |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | We have worked together to establish best data management practices within the legume generation project, e.g. crop and gene ontologies, and to standardise procedures across multiple partners. WE are working with BELIS to maintain these standards between projects. |
| Collaborator Contribution | They have assisted in maintaining standards at other partner institutes and providing input to us in ways to standardise procedures |
| Impact | We have worked together to establish best data management practices within the legume generation project, e.g. crop and gene ontologies, and to standardise procedures across multiple partners. WE are working with BELIS to maintain these standards between projects. |
| Start Year | 2024 |
| Description | Collaboration with wildflower seed companies |
| Organisation | Emorsgate Seeds |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Current work is being done under the Wildflower PhD to investigate the biological effects of the seed production process, this would potentially provide more seed samples to expand the work. |
| Collaborator Contribution | Ongoing discussions about future access to seed samples. |
| Impact | None yet |
| Start Year | 2024 |
| Description | Collaboration with wildflower seed companies |
| Organisation | National Wildflower Centre |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | Current work is being done under the Wildflower PhD to investigate the biological effects of the seed production process, this would potentially provide more seed samples to expand the work. |
| Collaborator Contribution | Ongoing discussions about future access to seed samples. |
| Impact | None yet |
| Start Year | 2024 |
| Description | Engineering triterpene production |
| Organisation | John Innes Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Expertise and methods in genome editing and pathway enginering. |
| Collaborator Contribution | Expertise in the detection of triterpenoids. |
| Impact | Collaborative grants funded: "21EBTA specialised metabolism and new cellular architectures in plants" + "EBioAct: Environmentally sustainable production of bioactive triterpenes" |
| Start Year | 2020 |
| Description | FTMA GRIT team in Sanger Insitute |
| Organisation | Wellcome Sanger Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | This was mainly a training residential stay to learn how to use their pipelines and benefit from their expertise so currently we have not made a contribution to them. |
| Collaborator Contribution | Spent a week learning how to use their pipelines and benefiting from their expertise by being taught how to perform manual curation in order to produce high quality genome assemblies. |
| Impact | High quality chromosome level haplotype aware genome assembly of Urochloa decumbens. Learning how to use GRIT curation teams pipeline and how to manually curate genomes using HiC data. |
| Start Year | 2023 |
| Description | Improving breeding of Urochloa and understanding genus |
| Organisation | University of Leicester |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Contributed expertise and will contribute data reads and assemby for Urochloa |
| Collaborator Contribution | Expertise |
| Impact | Currently exchange of expertise - collab very recent. |
| Start Year | 2024 |
| Description | Miscanthus genome, pangenome |
| Organisation | Earlham Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | Miscanthus sacchariflorus genome sequence, Miscanthus RNAseq data |
| Collaborator Contribution | Miscanthus sinensis genome sequence (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Msinensis_er), Miscanthus RNAseq data, Miscanthus molecular markers |
| Impact | Mitros et al. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nat Commun 11, 5442 (2020). https://doi.org/10.1038/s41467-020-18923-6 De Vega J, Donnison I, Dyer S, Farrar K. Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus. F1000Res. 2021 Jan 18;10:29. doi: 10.12688/f1000research.44714.1. PMID: 33732433; PMCID: PMC7921889. |
| Start Year | 2014 |
| Description | Miscanthus genome, pangenome |
| Organisation | HudsonAlpha Institute for Biotechnology |
| Country | United States |
| Sector | Charity/Non Profit |
| PI Contribution | Miscanthus sacchariflorus genome sequence, Miscanthus RNAseq data |
| Collaborator Contribution | Miscanthus sinensis genome sequence (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Msinensis_er), Miscanthus RNAseq data, Miscanthus molecular markers |
| Impact | Mitros et al. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nat Commun 11, 5442 (2020). https://doi.org/10.1038/s41467-020-18923-6 De Vega J, Donnison I, Dyer S, Farrar K. Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus. F1000Res. 2021 Jan 18;10:29. doi: 10.12688/f1000research.44714.1. PMID: 33732433; PMCID: PMC7921889. |
| Start Year | 2014 |
| Description | Miscanthus genome, pangenome |
| Organisation | Teagasc |
| Country | Ireland |
| Sector | Public |
| PI Contribution | Miscanthus sacchariflorus genome sequence, Miscanthus RNAseq data |
| Collaborator Contribution | Miscanthus sinensis genome sequence (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Msinensis_er), Miscanthus RNAseq data, Miscanthus molecular markers |
| Impact | Mitros et al. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nat Commun 11, 5442 (2020). https://doi.org/10.1038/s41467-020-18923-6 De Vega J, Donnison I, Dyer S, Farrar K. Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus. F1000Res. 2021 Jan 18;10:29. doi: 10.12688/f1000research.44714.1. PMID: 33732433; PMCID: PMC7921889. |
| Start Year | 2014 |
| Description | Miscanthus genome, pangenome |
| Organisation | U.S. Department of Energy Joint Genome Institute |
| Country | United States |
| Sector | Public |
| PI Contribution | Miscanthus sacchariflorus genome sequence, Miscanthus RNAseq data |
| Collaborator Contribution | Miscanthus sinensis genome sequence (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Msinensis_er), Miscanthus RNAseq data, Miscanthus molecular markers |
| Impact | Mitros et al. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nat Commun 11, 5442 (2020). https://doi.org/10.1038/s41467-020-18923-6 De Vega J, Donnison I, Dyer S, Farrar K. Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus. F1000Res. 2021 Jan 18;10:29. doi: 10.12688/f1000research.44714.1. PMID: 33732433; PMCID: PMC7921889. |
| Start Year | 2014 |
| Description | Miscanthus genome, pangenome |
| Organisation | University of California, Berkeley |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Miscanthus sacchariflorus genome sequence, Miscanthus RNAseq data |
| Collaborator Contribution | Miscanthus sinensis genome sequence (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Msinensis_er), Miscanthus RNAseq data, Miscanthus molecular markers |
| Impact | Mitros et al. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nat Commun 11, 5442 (2020). https://doi.org/10.1038/s41467-020-18923-6 De Vega J, Donnison I, Dyer S, Farrar K. Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus. F1000Res. 2021 Jan 18;10:29. doi: 10.12688/f1000research.44714.1. PMID: 33732433; PMCID: PMC7921889. |
| Start Year | 2014 |
| Description | Miscanthus genome, pangenome |
| Organisation | University of Illinois at Urbana-Champaign |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Miscanthus sacchariflorus genome sequence, Miscanthus RNAseq data |
| Collaborator Contribution | Miscanthus sinensis genome sequence (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Msinensis_er), Miscanthus RNAseq data, Miscanthus molecular markers |
| Impact | Mitros et al. Genome biology of the paleotetraploid perennial biomass crop Miscanthus. Nat Commun 11, 5442 (2020). https://doi.org/10.1038/s41467-020-18923-6 De Vega J, Donnison I, Dyer S, Farrar K. Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus. F1000Res. 2021 Jan 18;10:29. doi: 10.12688/f1000research.44714.1. PMID: 33732433; PMCID: PMC7921889. |
| Start Year | 2014 |
| Description | RBG Kew |
| Organisation | Royal Botanic Gardens, Kew |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | Joint PhD studentship |
| Collaborator Contribution | Joint PhD studentship |
| Impact | Joint PhD studentship |
| Start Year | 2021 |
| Description | RGBKew - EI fonio reference genome |
| Organisation | Earlham Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We characterise and provide materials for generation of genomic data (HiFi and Omni-C) for black fonio species. We provide staff time to analyse the data. |
| Collaborator Contribution | EI will optimise methodologies for black fonio and generate data for RBGKew materials. EI will advise on data processing and analyses. |
| Impact | Collaboration agreement. Short read data sequencing data for black fonio. |
| Start Year | 2023 |
| Description | Rice genomics - Taiwan |
| Organisation | National Taiwan University |
| Country | Taiwan, Province of China |
| Sector | Academic/University |
| PI Contribution | Recommendation on storage and utilising of historical rice specimens. |
| Collaborator Contribution | Provided background information for Champa rice in Taiwan. Provided test samples for genome sequencing |
| Impact | Genomic library for test samples |
| Start Year | 2026 |
| Description | Syngenta collaboration |
| Organisation | Syngenta International AG |
| Country | Switzerland |
| Sector | Private |
| PI Contribution | Facilitating regular meetings between EI and Syngenta researchers to develop 2 new collaborative projects. |
| Collaborator Contribution | Attended industry Seminar. Arranged introduction to further teams at Syngenta. |
| Impact | None yet. |
| Start Year | 2023 |
| Description | Tozer Seeds Knowledge Transfer Partnership |
| Organisation | Tozer Seeds |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Develop a project idea for a Knowledge Transfer Partnership (KTP) with Tozer Seeds, management of the application process and negotiation of IP and terms. The KTP will help Tozer to develop internal capacity to analyse genomic data for accelerated breeding. This collaboration began as a service provided by NBRI1 and JV in 2022, after which the BDI team assisted in developing it further into the KTP. |
| Collaborator Contribution | Tozer co-applied for KTP with EI and will be providing funding and in-kind support. |
| Impact | Application for a KTP submitted in November 2023. Earlham Institute gaining status as a KTN Knowledge Base. KTP was funded and started in July 2024 and will run till December 2026 (30 months) |
| Start Year | 2022 |
| Description | Tropic |
| Organisation | Tropic Biosciences Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | We continue our collaboration with the biotech company Tropic related to their interest in improving copy number variation screening in order to further improve quality control in precision breeding of clonally propagated crops, such as banana. We contributed - Oxford Nanopore genome and epigenome sequencing Protocol and the variation analysis pipeline |
| Collaborator Contribution | Expertise in banana cell biology, tissue culture, micropropagation and production, samples of proprietary elite banana embryogenic cell lines developed at Tropic, expertise in genomic/bioinformatic analysis |
| Impact | Oxford Nanopore genome and epigenome sequencing Protocols New datasets |
| Start Year | 2023 |
| Title | Data from: Ancient and recent hybridization in the Oreochromis cichlid fishes |
| Description | Cichlid fishes of the genus Oreochromis (tilapia) are among the most important fish for inland capture fisheries and global aquaculture. Deliberate introductions of non-native species for fisheries improvement and accidental escapees from farms have resulted in admixture with indigenous species. Such hybridization may be detrimental to native biodiversity, potentially leading to genomic homogenization of populations and the loss of important genetic material associated with local adaptation. By contrast, introgression may fuel diversification when combined with ecological opportunity, by supplying novel genetic combinations. To date, the role of introgression in the evolutionary history of tilapia has not been explored. Here we studied both ancient and recent hybridization in tilapia, using whole genome resequencing of 575 individuals from 23 species. We focused on Tanzania, a natural hotspot of tilapia diversity, and a country where hybridization between exotic and native species in the natural environment has been previously reported. We reconstruct the first genome-scale phylogeny of the genus and reveal prevalent ancient gene flow across the Oreochromis phylogeny. This has likely resulted in hybrid speciation of one species, O. chungruruensis. We identify multiple cases of recent hybridization between native and introduced species in the wild, linked to the use of non-native species in both capture fisheries improvement and aquaculture. This has potential implications for both conservation of wild populations and the development of the global tilapia aquaculture industry. |
| Type Of Technology | Software |
| Year Produced | 2024 |
| Impact | Enabled work with WorldFish |
| URL | https://zenodo.org/doi/10.5281/zenodo.12549228 |
| Title | Software Architectural Design of COPO |
| Description | I have been responsible for the overall design and delivery of many new features in COPO over the past 12 months. Please see recent software output entries for further details. |
| Type Of Technology | New/Improved Technique/Technology |
| Year Produced | 2023 |
| Open Source License? | Yes |
| Impact | The overall growth of COPO as a service |
| Description | A method for assembling the genome of a non-model organism |
| 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 | We supported Dr Camilla Ryan in writing a technical led blog about her methods for assembling the genome of a non-model organism, supporting the Decoding Biodiversity research programme (WP2). As part of the technical series this received good level of readership and engagement online. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/articles/method-assembling-genome-non-model-organism |
| Description | A presentation on natural product drug discovery and bioactive molecules (including DECODE Asteraceae research) was delivered to a group of students from Colby College, USA. |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Undergraduate students |
| Results and Impact | Increased interest and awareness of the role of bioactive molecules from plants and technologies to source these, which stimulated questions and discussion on the subject. |
| Year(s) Of Engagement Activity | 2025 |
| Description | A talk was given on natural product drug discovery and bioactive molecules (including DECODE Asteraceae research) to a group of Chief Medical Officers from a range of international companies |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Increased interest and awareness of the role of bioactive molecules from plants and advanced technologies to sustainably source these, which stimulated questions and discussion on the subject. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Adrian Ramsay, Green Party MP for Waveney Valley had a tour of the EI labs as part of his visit to the NRP |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | In his first visit to the research institutes at the NRP, Adrian engaged with a range of researchers. Despite his Party's long-standing opposition to gene editing, he was enthusiastic about EI's research and impact, particularly in the application of genetic research to health issues and conservation biology. Adrian met T Level students and was impressed with EI's contribution towards training and skills development. He requested a return visit to see more of our research. He posted the following on his social channels: "Thank you to @NorwichResearch Park for showing me around their impressive institutes today. Great to discuss their wide-ranging work including on microbiological research, improvements in public health & new diagnostic techniques. @EarlhamInst @TheQuadram |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://www.linkedin.com/posts/earlhaminstitute_tlevel-genomics-geneticsequencing-activity-733167721... |
| Description | Agri-Tech E REAP conference 2023 (09/11/2023) |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Attended Agri-Tech E's annual event REAP and took researchers from the DECODE and CELLGEN ISPs. Set up an EI exhibition stand, assisted JA with his talk and assisting with networking on the day. The exhibition stand was comprised of talking points to showcase the EI researchers and their work attending Agri-Tech E. This included: - a lego sequencer to demonstrate the genomics work being undertaken in clonal crops in DECODE and forage crops in CELLGEN, and how sequencing is carried out by NBRI1 - a basket of clonal crops being researched in DECODE - wheat seedlings from lines being researched in DECODE - a short presentation to compliment JA's talk, demonstrating how image analysis is used to determine diversity of seed packets |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.agri-tech-e.co.uk/microsite-page/reap-2023/ |
| Description | Article: Pangenome Annotation |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Article - showing how annotating a pangenome allows researchers to capture details of a species' genetic diversity, analyse evolution and disease resistance, and look at old data with fresh insights. |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://www.earlham.ac.uk/articles/pangenome-annotation-opens-multiverse-genes |
| Description | Article: Transforming metagenome assembly from long reads with metaMDBG |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Communicating an important new tool to share knowledge and expertise in the scientific community |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://www.earlham.ac.uk/articles/transforming-metagenome-assembly-long-reads-metamdbg |
| Description | Article: What's the power of a pangenome |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Explainer for science interested audiences on what is a pangenome |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://www.earlham.ac.uk/articles/whats-power-pangenome |
| Description | Attendance at Biocuration 2023 |
| 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 | Attended conference to network and find out latest developments. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Attended Sci-Art workshop with Edible East |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Third sector organisations |
| Results and Impact | Attended a workshop on Thursday 12th December to inform Edible East's ambitious new exhibition 'Through the Microscope - Secrets of our Changing Landscape'. Hosted by the John Innes Centre and the Centre for Microbial Interactions, and working with the Edible East team of artists and horticulturalists to share and discuss my research through the artistic formats of shadow theatre, 'Endless Landscape' tile games, and more. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Ben Goldsborough MP references Earlham Institute at Prime Minister's Question Time |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Labour's South Norfolk MP, Ben Goldsborough, mentioned the Earlham Institute in his question to Prime Minister, Sir Keir Starmer: "From heat tolerant rice trials to world leading science at the Earlham Institute and John Innes Centre on the Norwich Research Park, South Norfolk is helping feed the world. Will the Prime Minister secure a clear carve out for precision breeding in any future SPS Agreement with the EU so Britain can continue to lead tin this field?" The Prime Minister responded favourably: "Can I thank him for raising it. As negotiations are ongoing, we remain committed to, he'll be pleased to know, the Precision Breeding Act and supporting new innovative technologies. The EU accepts that there will be areas where we retain our own rules, and we will always prioritise British interests as we negotiate our SPS agreement." |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://www.linkedin.com/feed/update/urn:li:share:7424821610941140992/ |
| Description | Ben Goldsborough, Labour MP for South Norfolk visit to EI |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Local MP Ben Goldsborough returned for another visit to see EI's research in action. Given Ben's interest in health and biosecurity policy, we focused on showcasing AirSeq and its various potential routes to translation. Ben was particularly enthusiastic about this and posted on his social channels: "Another day, another mind-blowing visit to the Norwich Research Park - my fifth since being elected, and the thrill of walking onto the site never fades... a quick jog down to the Earlham Institute to catch up with Dr Richard Leggett on his latest breakthroughs in technology development for #metagenomics and rapid analysis for infection diagnostics. Brilliant, vital work... We don't just do science here. We lead it." |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://www.linkedin.com/feed/update/urn:li:ugcPost:7346852766876639232/ |
| Description | Big Data Workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Gave talk on data management to PhD students. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Biofair Roadshow EI |
| 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 | Contributed thoughts to fact finding workshop |
| Year(s) Of Engagement Activity | 2023 |
| Description | British Herbs Association Technical Meeting Talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | A BBSRC-iCASE PhD project update and plan talk to the British Herbs Association. This group consists primarily of growers and agronomists, but is also attended by breeders and other stakeholders. 15 minute presentation, follow-up questions and a networking lunch. Primary objective was to get feedback from growers on traits of interest for the project. Also to open a dialogue with British Herbs regarding closer involvement in the project. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Building capacity and resources for genomic prediction in forage grass and legume breeding |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Study participants or study members |
| Results and Impact | The workshop brought together a diverse group of researchers, practitioners, and stakeholders to exchange information and foster collaboration in the vital field of forage research. The project integrated experts from Earlham Institute in the UK and Alliance of Bioversity International and CIAT who collaborate on the application of genomic tools into the Tropical Forages breeding program. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://hdl.handle.net/10568/170303 |
| Description | COPO User feedback survey |
| 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 | User feedback survey was sent to all registered COPO users to ascertain pain points and potential new features. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Characterising gene function research project page |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Published a research project page detailing aims and activities from WP2 of Decoding Biodiversity research programme. The page is used for signposting people to more information about the work package. |
| Year(s) Of Engagement Activity | 2024,2025 |
| URL | https://www.earlham.ac.uk/research-project/characterising-gene-function-biosynthetic-pathways-and-va... |
| Description | DBT Agri-Tech Investment Specialist visit to Norwich Research Park (06/02/2024) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Policymakers/politicians |
| Results and Impact | A member from each NBI gave an introductory talk to the specialist on agri-tech development at their institute, to give the specialist an understanding of the research ongoing on the park. |
| Year(s) Of Engagement Activity | 2024 |
| Description | DSW Annual Meeting |
| 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 | Coordinated a science showcase entitled 'Cutting-edge wheat and pathogen (pan) genomics' at the annual DSW all-hands meeting. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Daniel Zeichner MP visit to Earlham Institute |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Labour's MP for Cambridge, Daniel Zeichner, visited EI as part of a wider visit to the NRP. He is a member of the House of Commons Science, Innovation and Technology Select Committee. Daniel was very keen to hear about the breadth of EI's research including precision breeding and crop science, health research, BioFAIR and the SCAnDi project using single cell analysis for forensic science research. After visiting EI he went on to meet representatives from UEA, the Hospital and the Quadram Institute and was particularly enthusiastic about the NRP's collaborative research and expertise on nutrition and childhood obesity and how that can impact patient outcomes as well as the Government's Food Strategy policy development. Until recently, Daniel was the Government's Food and Farming Minister so he was able to advise how our research fits with the DEFRA Food Strategy work. |
| Year(s) Of Engagement Activity | 2026 |
| URL | https://www.linkedin.com/posts/earlhaminstitute_biodiversity-foodsecurity-singlecell-activity-741909... |
| Description | Digital Twins in bioscience, environmental and medical science |
| 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 | Digital twins (DT) and their application are an area of growing interest within the bioscience, environmental and medical science research and innovation community. BBSRC, NERC, MRC and DTNet+ jointly ran a hybrid community workshop focussed on digital twins in bioscience, environmental and medical science on Wednesday 18 September 2024 at Rothamsted Conference Centre. The event aimed to create a better shared understanding of the DT landscape as it relates to the bioscience, environmental and medical science research and innovation communities, including better insights into the discipline-specific opportunities and challenges together with opportunities to network as a community. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://engagementhub.ukri.org/bbsrc-research-strategy-and-programmes/digital-twins-workshop/ |
| Description | EI Innovate 2023 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | A presentation by Dr Melissa Salmon at EI Innovate, an event for knowledge exchange between academics and industry, about the discovery of bioactive metabolites from UK flora and methods for their bioproduction. This was followed by a number of questions and discussion with Dr. Salmon. |
| Year(s) Of Engagement Activity | 2023 |
| Description | EI Innovate annual stakeholder engagement event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | EI Innovate is an annual engagement event that provides insight into the Earlham Institute's research, exploring opportunities for innovation and collaboration. Specialising in agri-food, biotech, med-tech and public health, we have a wealth of experience collaborating with others to develop potential solutions to urgent industrial and societal challenges. EI Innovate events foster exciting and valuable conversations between academia and industry. An example of an exciting collaboration that resulted from a previous EI Innovate is the Hybrid Wheat Initiative, which connects 25 breeding companies and research institutes worldwide, to resolve the critical challenge of hybrid wheat. In 2023, we showcased our two new strategic programmes of research - Cellular Genomics and Decoding Biodiversity - and two National Bioscience Research Infrastructures (NBRIs) - Transformative Genomics and the Earlham Biofoundry. The programme included talks about Earlham expertise and capabilities, examples of collaborations, panel discussions, Innovation Showcase, exhibition, tours of the two National Bioscience Research Infrastructures (NBRIs) - Transformative Genomics and the Earlham Biofoundry, and networking. |
| Year(s) Of Engagement Activity | 2019,2020,2021,2022,2023 |
| URL | https://www.earlham.ac.uk/events/ei-innovate-2023 |
| Description | EI Seminar |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Gave EI seminar |
| Year(s) Of Engagement Activity | 2024 |
| Description | EI Strategic Retreat |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Discussed potential avenues of research for future ISP |
| Year(s) Of Engagement Activity | 2025 |
| Description | ERGA data management training (Poland) |
| 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 | Gave talk about data management and COPO along with reps from ENA at a workshop in Poland |
| Year(s) Of Engagement Activity | 2025 |
| Description | Elected to Royal Norfolk Agricultural Agricultural Association Council |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | The RNAA Council is a volunteer body and has supervisory control over both the property and the general policy of the Association. It provides a useful check and balance to the strategic direction of the Association. Council comprises up to 48 elected members and meets twice a year, usually in the Spring and Autumn. Council members are expected to take an active interest in the development of the Association. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Elixir UK all hands - Norwich |
| 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 | Engaged in networking group discussions |
| Year(s) Of Engagement Activity | 2023 |
| Description | Elixir UK all-hands |
| 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 | Took part in various sessions and a poster session at this UK based meeting. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Elixir all-hands Dublin 2023 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented a poster, and had discussion regarding development of ROCrate which led to several hackathons. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Elixir all-hands Uppsalla |
| 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 | Presented 2 posters at all-hands meeting |
| Year(s) Of Engagement Activity | 2023 |
| Description | Engaged the DEFRA Lead on Strategy and Implementation for Digital Sequence Information and Access and Benefit Sharing in advance of COP 16 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Earlham Institute researchers met the DEFRA team working on Digital Sequence Information and Access and Benefit Sharing policy in advance of COP16 in Colombia. We discussed synergies between EI's advocacy and the UK policy position and how our advocacy could help to influence the international discussion on this subject at COP16. We published an article on this on our website: https://www.earlham.ac.uk/news/value-dsi-global-genomics-research-must-be-heard-cop16. The UK's support for DSI helped COP16 reach a ground breaking decision on operationalising a multilateral mechanism for the use of digital sequencing information from genetic resources. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/news/value-dsi-global-genomics-research-must-be-heard-cop16 |
| Description | Engaging with DEFRA and the Food Standards Agency on implementing the Genetic Technology (Precision Breeding) Act 2023 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Series of meetings with officials working on the implementation of the Genetic Technology (Precision Breeding) Act 2023 to determine key aspects of policy related to the resulting regulation. We took part in policy workshops and online briefing events organised across the Norwich Research Park. Some of these workshops involved representatives from the commercial sector involved in plant science and R&D. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Equitable Practise in Evolution Training - Applying the Equity Compass |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | This course helped me to reflect on and develop equitable and inclusive practice. It involved two in-person sessions (13 February 2024 & 13 March 2024) at the Earlham Institute to introduce The Equity Compass, a tool to address ongoing inequalities in STEM communication. These sessions were supported by a three-week online/self-motivated course via FutureLearn. |
| Year(s) Of Engagement Activity | 2024 |
| Description | FLF Development Network - Crucible |
| 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 | An interdisciplinary, cross-sector event that fosters collaborations between researchers and innovators on the Pathways FLF Development Network program. |
| Year(s) Of Engagement Activity | 2024 |
| Description | FLF Development Network - Crucible in Cardiff 21-22 March 2024 |
| 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 | An interdisciplinary, cross-sector event that fosters collaborations between researchers and innovators on the Pathways FLF Development Network program. |
| Year(s) Of Engagement Activity | 2024 |
| Description | FLF Development Network - Leadership Retreat |
| 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 | A Pathways FLF Development event to give insights into navigating the process of leading research and innovation programmes, and managing teams. |
| Year(s) Of Engagement Activity | 2024 |
| Description | FTMA visit of WorldFish at EI and training of partners from the Lake Victoria Fisheries Organisation |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Meeting at the Earlham Institute with WorldFish researchers to develop the report for the Lake Victoria Fisheries Organization to inform policy development for the sustainable exploitation of tilapia. Training of representatives from Uganda, Kenya, and Tanzania on the bioinformatics for population genetics |
| Year(s) Of Engagement Activity | 2023 |
| Description | Formal planning meetings for Earlham Data Portal |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Monthly planning meetings undertaken to develop software solution for Technical Genomics to FAIRify outputs |
| Year(s) Of Engagement Activity | 2025 |
| Description | Genetic integrity needed for Biodiversity Net Gain to flower |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | An article with PhD researcher Jonathan Ashworth, discussing his work in biodiversity genomics of wildflower seeds, and the link to Biodiversity Net Gain. This gained a huge amount of engagement online, and led to interested collaborators reaching out to Jose and Jonathan, and further work with the Business Development and Impact team signing agreements to work together. The Eden project (collaborators on the research) also reached out to ask to include it in their membership magazine. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/articles/genetic-integrity-needed-biodiversity-net-gain-flower |
| Description | Genomic resources to help boost climate resilience of fisheries |
| 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 | We issued a press release on new research around genomic resources for aquaculture breeders, which could support the development of greater resilience. The story had almost 5,000 impressions and around 75 engagements on social media, including from accounts for people and partners based outside the UK. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/news/genomic-resources-help-boost-climate-resilience-fisheries |
| Description | Hosted Nuffield Placement Student for 2 week project |
| 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 | Schools |
| Results and Impact | Hosting of two Nuffield Placement students for 2 weeks. This involved carrying out a research project in the lab. The placement also involved the student interacting with other areas at EI with other experiences such as journal clubs, lab meetings and delivering research presentations. |
| Year(s) Of Engagement Activity | 2024 |
| Description | IBERS visit |
| 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 | A group of EI staff visited IBERS in Aberystwyth from 19-21 July 2023 (Jose De Vega, Anthony Hall, Seanna McTaggart, Camilla Ryan, Christine Fosker) to discuss the DECODE ISP, find opportunties for collaboration and tour IBERS and the biorefinery. |
| Year(s) Of Engagement Activity | 2023 |
| Description | ISP all hands meetings FTMA4 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | ISP all hands meeting allow the interaction amongst all the work package members. In addition to project and impact progress updates, workshops are held to drive discussion in areas such as IDEA, policy impact, futher funding opportunities and more. |
| Year(s) Of Engagement Activity | 2023,2024 |
| Description | Image Processing Carpentries |
| 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 | Devlivered Training |
| Year(s) Of Engagement Activity | 2023 |
| Description | International Plant Pangenome Working Group |
| 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 | I coordinate this virtual international working group. The aim of these meetings is to bring together researchers and industry collaborators working in the plant pangenome space to encourage open discussions within an informal, virtual working group. We meet monthly and by sharing our knowledge, experience and challenges encountered when implementing pangenomic tools and approaches we can explore how best to apply these to achieve our different objectives. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Invited talk Syngenta |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Presentation of work on Pangenomes and work within DECODE Title:Why one genome just isn't enough: How multiple wheat genomes are changing our understanding of plant evolution. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Invited to participate in Royal Society 'Transforming Our Future' workshop, 'Innovating Agriculture' |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | This meeting explored the agricultural science and innovation that is transforming the future of food and farming to meet rising production and environmental demands. The agricultural sector needs to meet the challenge of producing more food to meet rising demand whilst also achieving environmental targets. This two-day conference examined the science and innovation aiming to transform the future of food and farming. The event brought together stakeholders from across industry, academia, government and the wider agricultural community to address three key areas: increasing sustainable yields, improving input efficiency and developing novel food production systems. Panel discussions considered how best to support and fund innovation in food and agriculture, and how to accelerate translation and take-up of new ideas. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://royalsociety.org/science-events-and-lectures/2024/06/agriculture-tof/?gad_source=1&gclid=Cjw... |
| Description | Key tilapia genome offers boost to global food security - Tarang Mehta, Graham Etherington, Will Nash, Adam Ciezarek |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | News story to highlight a new publication from EI researchers on reference genome for a key aquaculture species, designed to reach breeders, industry, and academics working in this space. Positive trade media coverage, as well as promotion from project collaborators, helped this news to reach a wide audience and enhance EI's reputation. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/news/key-tilapia-genome-offers-boost-global-food-security |
| Description | Keynote, UK Legume Conference 2024; "Adaptations and admixture in common bean and genomics for breeding" |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Keynote speaker in the Genomics and Genetics session of the UK Legume Conference in Reading, 14-15 Feb 2024 |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://uklrc.org/uklrc2024/ |
| Description | Lecture delivered on natural product drug discovery and bioactive molecules (including DECODE Asteraceae research) for the RBG Kew / Royal Holloway University of London MSc titled 'Global Health: Food security, Sustainability and Biodiversity' |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | Increased interest and awareness of the role of bioactive molecules from plants and advanced technologies to source these, which stimulated questions and discussion on the subject. Students expressed interest in applying for MSc projects on this topic. |
| Year(s) Of Engagement Activity | 2024 |
| Description | MEeting with US Joint Genome Institute |
| 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 | Talked with peers about aligning metadata standards across institutes. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Meeting with BioStudies |
| 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 | Dialog with with Biostudies to establish deposition and metadata interchange. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Meeting with MPs in Parliament to discuss precision breeding legislation implementation |
| 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 | EI staff attended an Agri-Science Summit in Parliament, hosted by the All Party Parliamentary Group or Science and Technology in Agriculture. Chair of the Group, George Freeman MP, spoke to one of our PhD students about their commercial partnership with Elsom's seeds and their precision breeding research. It was a useful opportunity to bring EI's research to the attention of parliamentarians of all parties and DEFRA civil servants in attendance, and to encourage other early career researchers to advocate to policy makers on the issues affecting their work. Discussions with MPs and Peers in the Agri-Science Summit included the Government's evolving position on the Sanitary and Phyto Sanitary Agreement with the EU about alignment on new breeding techniques. |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://www.linkedin.com/feed/update/urn:li:ugcPost:7394673937298849792/ |
| Description | Meeting with Prof Gideon Henderson, DEFRA Chief Scientific Adviser |
| 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 | Prof Gideon Henderson visited the Earlham Institute and discussed a range of DEFRA related research activity and innovation. He invited EI to have follow up engagement with DEFRA officials leading relevant policy and regulatory work. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Meeting with the UK Science & Innovation team from the UK Embassy in Mexico |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | The Science & Innovation Network (SIN) in Mexico works to encourage strategic relationships with local and national government and academic institutions between the UK and Mexico. |
| Year(s) Of Engagement Activity | 2014 |
| Description | Molecular acceleration for coriander |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Advocating the importance of molecular breeding in under resourced crops - using coriander as the example |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://www.earlham.ac.uk/articles/molecular-acceleration-coriander-breeding |
| Description | Monogram |
| 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 Monogram Network consists of UK based researchers with an active interest in small grain cereal and grass (including the C4 energy grasses) research. I attended the annual conference at the University of Reading with Jon Wright, Anthony Hall, Lucy Mahony. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Multigenome Brassica Project (MGBP) Steering Committee Meeting |
| 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 | Attended Annual MGBP Steering Committee meeting at PAG30 to discuss future opportunities to work together. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Oral Presentation - Regulatory networks evolution underlying the rapid diversification of cichlids fishes in the Great African Lakes - Tarang Mehta |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited presentation at the Society for Molecular Biology and Evolution Annual Meeting (Ferrara Italy) |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.smbe2023.org/ |
| Description | Organising committee for Elixir UK all-hands |
| 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 | Was part of the organising committee for Elixir UK all-hands in Exeter. |
| Year(s) Of Engagement Activity | 2025 |
| Description | PAG Talk 2024- Wheat Genomics to Breeding session |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Sequencing, assembling and annotating key cultivars and representatives of 7 wheat sub-populations Wheat diversity can be split into 7 subpopulations. Here I will give an update on work as part of the Design Sustainable Wheat programme to sequencing, assembly and annotating these. How these and other data sets can be added to improve the utility of existing data. |
| Year(s) Of Engagement Activity | 2024 |
| Description | PAG2024 Trticeae Genetics and Genomics |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Title: Using pangenomes in Anger to Reduce reference bias in transcriptomic experiments |
| Year(s) Of Engagement Activity | 2024 |
| Description | PCA Core Network Participant Meeting (CPN) |
| 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 | Made connections and panned for future grant submission. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Pan-European project generates genomes showcasing continent's rich biodiversity |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A news story supporting the European Reference Genome Atlas Pilot Project. The story showcases the success of the pilot project and highlights the wide-ranging involvement from the Earlham Institute including the Technical Genomics, Haerty, Anthony Hall, and Neil Hall Groups, as well as the role of the National Bioscience Research Infrastructure in Transformative Genomics. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/news/pan-european-project-generates-genomes-showcasing-continents-rich-bio... |
| Description | Pan-Pooideae Meeting at PAG32 |
| 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 | Workshop at PAG32 to discuss the international Pan-Pooideae network. Overview of current research proposals and plans for next meeting. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Pan-Pooideae Meeting, Technical University Munich 27-28 May 2025 |
| 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 | A meeting to bring together members of the Pan-pooideae consortium to discuss research plans and next steps. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Parliamentary briefings on Genetic Technology (Precision Breeding Bill) for members of the House of Commons |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Parliamentary briefings at each stage of the passage of the Bill through the House of Commons. The briefings explained the provisions in the legislation and why Earlham Institute and the Norwich Research Park supported them. We gave case studies about relevant crop research that would benefit if the legislation was passed. The purpose of the briefings were to inform the parliamentary debate, persuade the Opposition not to oppose the Bill and help legislators to understand the need for public policy based on scientific evidence. |
| Year(s) Of Engagement Activity | 2022 |
| Description | Parliamentary briefings on Genetic Technology (Precision Breeding) Bill for members of the House of Lords |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | In person and written briefings for peers interested in the Genetic Technology (Precision Breeding) Bill. Our briefings explained key provisions in the Bill, made the case for why the Bill is needed and how the legislation would work in practice. We included case studies to show current research projects that would benefit from implementation of this new legislation. We worked with the DEFRA Bill Team to target parliamentarians that needed this information to support or at least not block the Bill through the House of Lords. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Parliamentary exhibition on precision breeding |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | The Earlham Institute exhibited alongside partners from the Norwich Research Park in Parliament to draw parliamentarians' attention to secondary legislation on precision breeding. The event was designed to give parliamentarians an opportunity to discuss the legislation with researchers to prepare for the debate on the legislation. More than 20 parliamentarians attended the exhibition including the DEFRA Minister. Following their interest we have engaged these MPs and peers further with parliamentary briefings and case studies of how the new legislation will help the research sector. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Pint of Science 2023 |
| 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 by PhD student in Norwich as part of the National Pint of Science Festival 2023 followed by questions and discussion. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Plant Animal Genome Conference, San Diego |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented a poster on 'Identifying Consensus and Cultivar-Specific Gene Networks within the Wheat Pan-Transcriptome'. Attended with Anthony Hall, Jon Wright (poster on A High-Quality Genome of Paragon: A Keystone for UK Wheat Breeding), Lucy Mahony (poster on Decoding the Regulatory Regions of Wheat). |
| Year(s) Of Engagement Activity | 2023 |
| Description | Plant Pangenome Working Group |
| 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 | The aim of this group is to bring together a small group of researchers with overlapping expertise in wheat genomics and pangenome architecture to identify possible strategies and approaches that will enable a high resolution pangenome reference for the wheat community. We held an initial meeting at PAG32 in SanDiego, Jan 2025 to gauge interest, exchange experiences and plan further virtual meetings. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Poster at the EI Scientific Advisory Board meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented a poster titled "Engineering synthetic plant artificial chromosomes (synPACs) - tools for regulatory element screening at the EI Scientific Advisory Board meeting |
| Year(s) Of Engagement Activity | 2025 |
| Description | Poster presentation at the Faculty of Science, University of Bath for Chemistry undergraduates and academic staff |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Undergraduate students |
| Results and Impact | Students were required to prepare a poster about their one internship and explain the research to other undergraduates and academic staff. This raised interest in the role of plants as providers of bioactive molecules. The poster was entitled 'In search of bioactive molecules - impact of ploidy level on sesquiterpene lactones in Achillea millifolium' and it was selected as one of the top five posters out of the full undergraduate cohort, raising people's awareness of the research undertaken still further. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Posters: Research groups posters |
| Form Of Engagement Activity | A magazine, newsletter or online publication |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | We designed A0 posters for our research groups to replace existing artwork in the Earlham Institute building. Showcasing our research will help communicate our research to visitors and policy makers. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Presentation at 2025 Legume Research Conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | I delivered a 10 minute presentation with 5 minutes for questions, which allowed for futher discussion. This then resulted in discussions of future work. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Presentation at Eucarpia Fodder Crops and Amenity Grasses Conference (2025 September) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | This is an biannual conference which bring together more than 100 forage breeders and researchers from across the Europe to share the cutting-edge breeding technologies, recent breakthrough in forage breeding and blueprint future vision in the field. We had presentation sessions for most important temperate forages (clovers, alfalfa, ryegrass etc). I had a 20-minute presentation about what has been done for white clover genomic breeding between Earlham Institute and Germinal. There were plenty of networking events with breeders from different countries, providing opportunities for potential collaboration and resource-sharing for developing more sustainable and climate-resilient forages. There was also on-site visit to IBERS (Institute of Biological, Environmental and Rural Sciences at Aberystwyth University) and Germinal, which was perfect to knowledge sharing in forage breeding field. |
| Year(s) Of Engagement Activity | Pre-2006 |
| URL | https://www.forages-eucarpia.org/fcag-section-meeting-2025/ |
| Description | Presentation at the Innovation Showcase during EI Innovate 2023 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | As part of the EI Innovate event in 2023, BDI team featured winners of the internal KEC Awards as part of the Innovation Showcase. JC, TB, JdV, WH, AH, JL presented their projects showcasing their KEC work - developing a spinout, a substantial collaboration, or a knowledge exchange activity with industry. EI Innovate is an annual engagement event that provides insight into the Earlham Institute's research, exploring opportunities for innovation and collaboration. Specialising in agri-food, biotech, med-tech and public health, we have a wealth of experience collaborating with others to develop potential solutions to urgent industrial and societal challenges. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/events/ei-innovate-2023 |
| Description | Presentation given to the 'University of Bath placement conference' for students and staff of the Chemistry Department |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Undergraduate students |
| Results and Impact | The aim of the presentation was to outline the research being undertaken by Rachel Wong (MChem undergraduate intern) who is working on the DECODE project at The Royal Botanic Gardens Kew (lead supervisor Dr Melanie Howes). During the presentation she outlined the project, highlighting the importance of natural product chemistry and plant bioactives relating to the DECODE project. The presentation generated a lot of interest and questions leading to an increased interest in this research topic. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Presented EI Seminar |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Updated colleages on latest developments |
| Year(s) Of Engagement Activity | 2025 |
| Description | Presented at Monogram conference 2023 |
| 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 a talk about using HiFi and OmniC reads to create a high quality haplotype aware assembly of Urochloa decumbens. The talk title was 'Double trouble - assembling the complex allelic diversity in outcrossed tetraploid Urochloa decumbens.'. It reached the conference attendees however I am not sure exaclty how many people that was - a lecture theatre full. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://research.reading.ac.uk/monogram-2023/ |
| Description | Presented data management talk on single cell RNA course |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | half hour section as part of the course to train early career researchers about best practice in research data management |
| Year(s) Of Engagement Activity | 2024 |
| Description | Project Meeting at Syngenta Site |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Members of the Anthony Hall Group (AH, RLRP) and TraitSeq (JC, VD) met with collaborators Melissa Brazier-Hicks, Irene Gonzalez-Thuillier and Victor Labonia from Syngenta to discuss current collaboration, tour facilities and meet staff for discussions. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Quarterly Institution Strategic Programme Work package meetings |
| 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 | ISP work package meetings are hybrid and open to and involve all participants in the ISPs, including partners. The meetings include 1-3 oral presentations showcasing ongoing work and roundtable discussions on successes, barriers, and opportunities. |
| Year(s) Of Engagement Activity | 2023,2024,2025 |
| Description | Revealing the genes that build plant bioactives |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Supporting the Decoding Biodiversity research programme, we wrote an article with Mel Salmon of the Patron Group about their work revealing the genes that build plant bioactives. This includes reference to our partnership with RBG Kew. This was also used later to promote activities at the 2025 Norwich Science Festival. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/articles/revealing-genes-build-plant-bioactives |
| Description | Roundtable with Pankaj Garg Consultant |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Discussed metadata and image formats around medical imaging of liver |
| Year(s) Of Engagement Activity | 2025 |
| Description | Royal Norfolk Agricultural Show - Stewarding |
| 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 | Assistant Head Steward helping RNAA coordinate STEMM village, AgriTechE and new machinery/innovations area at the Royal Norfolk Show, over 2days. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.royalnorfolkshow.co.uk/ |
| Description | SAB Networking Dinners (x2) |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | 2 dinners during which I networked with senior advisory board of EI, to elucidate them on COPO |
| Year(s) Of Engagement Activity | 2023 |
| Description | SAB Poster Session |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented COPO at a poster session for the 2023 SAB |
| Year(s) Of Engagement Activity | 2023 |
| Description | Save the Banana! 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 | We took an activity aimed at 4-10 year old children to Norwich Science Festival 2024. This activity was based around the De Vega group's work on banana genomics. Over the three days we attended the festival we engaged with more than 1000 children and feedback (measured via feedback forms) was very positive. Many participants did not know the Cavendish banana was under threat. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Science Day at Notre Dame Prep School |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Delivered science activities as part of Sustainable Science Day at Notre Dame Prep School, Norwich. 120 pupils from Year 1 to Year 6 participated in science activities related to the DECODE ISP on the topics of "Save the Banana" (an activity previously run at the Norwich Science Festival) and "Making Medicines in Plants". Pupils listened to a presentation introducing the science, and then worked their way around the activities, filling in their results in a "Lab Notebook". The school reported that the children and teaching staff found the activities engaging and inspiring and are keen to hold another science day in the next academic year. Melissa Salmon organised and coordinated the Science Day and produced the lab notebooks and activity sheets for "Making Medicines in Plants" Sarah Guiziou, Daria Golubova and Carolina Olave-Achury volunteered to help with delivering the activities. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Science Day at Notre Dame Prep School |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Delivered science activities as part of Science Day at Notre Dame Prep School, Norwich. 105 pupils from Pre-prep to Year 6 participated in science activities related to the Biofoundry on the topics of Decoding DNA, DNA assembly and Pipetting skills. Pupils listened to a presentation introducing the science, and then worked their way around the activities. The school reported that the children and teaching staff found the activities engaging and inspiring and are keen to hold another science day in the next academic year. Melissa Salmon organised and coordinated the Science Day and produced the activity sheets. Carolina Grandellis, Erica Hawkins, Davide Annese and 2 T-Level students volunteered to help with delivering the activities. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Scilifelab presentation meeting |
| 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 | Demonstration of the efficacy of COPO as a brokering solution for Scilifelab. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Software Carpentries |
| 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 | Delivered training |
| Year(s) Of Engagement Activity | 2023 |
| Description | Syngenta Product Safety and Biological Sciences External Collaboration Event |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | This event is a forum to present academic research to peers and a wide cross-section of Syngenta colleagues. Josh Colmer and I presented an interactive poster and JC gave a flash talk. We were awarded best poster. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Talk - Postgrad Data Literacy |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Postgraduate students |
| Results and Impact | Part of an annual PGR education programme |
| Year(s) Of Engagement Activity | 2023 |
| Description | Talk at the Scientific Advisory Board Meeting 2024 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presented a talk to members of the EI Scientific Advisory Board and EI colleagues on my work on "Mining medicines from plants" |
| Year(s) Of Engagement Activity | 2024 |
| Description | Talk for UEA Pharmacology student visit |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Undergraduate students |
| Results and Impact | 15 masters students from UEA pharmacology department visited the institute for a tour and talks about the benefits of doing a PhD and a selection of talks by PIs and a post-doc to highlight the research being conducted at EI. Many of the students asked questions and provided positive feedback. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Talk in Big Data training session |
| 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 | Presented best practice in current research data management technology to UEA/NRP PhD students. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Talk on natural product drug discovery and bioactive molecules (including DECODE Asteraceae research) delivered to a group from the u3a (a UK-wide collection of charities that provide learning opportunities for those no longer in work) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Increased interest and awareness of the role of bioactive molecules from plants and technologies to source these, which stimulated questions and discussion on the subject. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Talk to PHD DTP cohort on data management and COPO |
| 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 | As part of a day of training, I talked for an hour about research data management, FAIR and the importance of these |
| Year(s) Of Engagement Activity | 2025 |
| Description | Technical blog posts |
| 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 | Three technical blog post tutorials designed to educate other researchers on how to produce various data visualisations in R. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/articles/plotting-proportional-data-nested-circles-r |
| Description | The fish, the fungus, the grass, the bee - and the brassica |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Article on Earlham Institute's membership of ERGA, gaining positive feedback and shares from external organisations. As we live through the planet's sixth mass extinction event, the Earlham Institute has joined the European Reference Genome Atlas (ERGA), a ground-breaking network of researchers across Europe documenting our vanishing lifeforms. ERGA is a continent-wide response to the threat to diversity, collecting and sequencing the genomes of all European eukaryotes to better understand them for the future. It is part of the wider Earth Biogenome Project. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.earlham.ac.uk/articles/fish-fungus-grass-bee-and-brassica |
| Description | Trip to Brussels for PROGRACE/EMPHASIS/forEVA as invited speaker |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The joint PRO-GRACE/EMPHASIS Policy Symposium and Workshop on Plant Genetic Resources and Phenotyping was held in Brussels on 27-28 June 2024. around 30-50 people attended. This sparked discussions in how to properly store data and other plant genetic -related discussions |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://grace-ri.eu/pro-grace/news-events |
| Description | Understanding Life: Using Largescale Biodiversity Reference Genomes - Short Talk - Identifying genes under positive selection in saline tolerant tilapia species |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I gave a short talk (10 mins) on "Identifying genes under positive selection in saline tolerant tilapia species" in the session on Ecological Genomics at the "Understanding Life: Using Largescale Biodiversity Reference Genomes" conference held by Welcome Connecting Science. The conference was held in a hybrid capacity over three days with short talks, posters and workshops. With over 150 attendees in person and more online. This talk was focused on the positive selection analyses, performed on 7 tilapia genomes with a range of salinity tolerances, to identify genes under positive selection in saline tolerant species that could be beneficial to the sustainable aquaculture of tilapia. I presented the annotation of 4 new tilapia genomes (O.rukwaensis, O.shiranu, O.urolepis & A.grahami) which were created using the EI REAT-Minos pipelines. This talk generated a good discussion around positive selection, tilapia aquaculture and salinity tolerance in cichlid species. |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://coursesandconferences.wellcomeconnectingscience.org/event/understanding-life-using-largescal... |
| Description | User Testing of COPO |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Unsupervised user testing of COPO to ascertain usability. So far 4 tests conducted. |
| Year(s) Of Engagement Activity | 2025 |
| Description | Video explainer to promote our Decoding Biodiversity work packages |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | A short video explainer was created to help promote our Decoding Biodiversity programme, focusing on the three areas of research. |
| Year(s) Of Engagement Activity | 2025 |
| URL | https://youtube.com/shorts/LU_ZBWdfeDE?si=UFeUGbhzlTzzF7sb |
| Description | Virtual presentation at BBSRC funded UK-Argentina wheat workshop in Buenos Aires |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited talk on wheat genomics. The goal of the workshop was to facilitate future UK-Argentina cooperation around wheat. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Visit and workshop of EI researchers to IBERS. |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Other audiences |
| Results and Impact | Crop Genomics - Earlham Institute visit to IBERS 20th July 2023 |
| Year(s) Of Engagement Activity | 2024 |
| Description | Visit from Chief Scientific Adviser |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | In February 2023, Professor Sir Patrick Vallance visited the Norwich Research Park alongside officials from the Government Office for Science and the Chief Scientific Adviser to the Food Standards Agency, Professor Robin May. Earlham Institute engaged Sir Patrick on two specific issues; reforming VAT rules applied to research, and incentivising FAIR data management. Sir Patrick gave assurances that he would raise both issues in policy discussions in Whitehall. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Visit to Kew Gardens |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Third sector organisations |
| Results and Impact | Visited collaborators at Kew Gardens to see their facilities, have a project meeting regarding our collaboration for DECODE and discuss future projects |
| Year(s) Of Engagement Activity | 2024 |
| Description | Wendling Beck DEFRA Test & Trial workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | A series of three workshops lead by the Wendling Beck Environment Project discussing biodiversity monitoring with ecologists, naturalist groups, farmers and landowners. I had a range of discussions with practitioners engaged in developing and testing technologies for monitoring and recording biodiversity trends. |
| Year(s) Of Engagement Activity | 2024,2025 |
| URL | https://www.wendlingbeck.org/ |
| Description | Workshop UK:BalticWheat workshop |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Gave a talk at the workshop "Why multiple wheat genomes are important" |
| Year(s) Of Engagement Activity | 2023 |
| Description | Workshop between Earlham and Eagle Genomics |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | A visit 7 Earlham colleagues to Eagle Genomics in London to build a collaborative framework between Eagle and Earlham, as part of collaborations with DECODE and CELLGEN ISPs. Key areas of the framework include IP management, software licensing; terms of access to EI tools and data; standardisation of tools and data to enable commercialisation; and areas of joint research interests resulting in publications (animal health and probiotics, soil health). This visit was funded through the BBSRC FTMA4. |
| Year(s) Of Engagement Activity | 2023 |
| Description | https://www.earlham.ac.uk/news/earlham-institute-BBSRC-funding-award-2023 |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | We issued a press release to mark the 5-year funding award from BBSRC, which supports the Earlham Institute, ISPs, and NBRIs. We secured widespread regional media coverage, including BBC Look East and online, ITV Anglia, and the EDP. The feedback from BBSRC on this coverage was very positive, particularly due to competing stories on life science funding. The launch campaign received around 28.5k impressions and 1,000 engagements across social media platforms, with the launch tweet achieving 330 engagements on its own. The majority of ISP partners engaged either by sharing ours posts or publishing their own messages, which included Kew Science, UK CEH, Eagle Genomics, and PacBio. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.earlham.ac.uk/news/earlham-institute-BBSRC-funding-award-2023 |