Regulatory interactions and Complex Phenotypes

Lead Research Organisation: Earlham Institute
Department Name: UNLISTED

Abstract

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Technical Summary

Deciphering the sources and mechanisms of variation in regulation of genes and genomes is pivotal for understanding the genotype-to-phenotype relationship underlying adaptation, evolution and health. We will integrate genetic studies with transcriptomics, epigenomics and proteomics to generate regulatory and protein-protein interaction networks, to perform systems-level analyses, and to identify and validate molecular drivers of cellular, tissue- and organism-level functions. To better understand the architecture of regulatory circuits in key relevant genomes, we will profile cis-regulatory elements and assess transcriptional regulation to deliver a systems-level view of entirely inferred networks initially in microbial species, followed by vertebrate organisms and then in more complex plants.

To better understand the interplay between genetic divergence and gene network evolution, we will compare (species-specific and tissue-specific) reconstructed regulatory networks of aquatic species (Tilapia) and crop species (starting with Arabidopsis thaliana as a model) to predict novel functions, interactions, and further candidate genes that can be collaboratively validated through genome manipulation techniques. For this, we will select species and lines that best represent the existing diversity and physiology for interrogating the fundamental molecular processes of trait and phenotype evolution. We will integrate a variety of data including genomic data, transcriptomics, interactome data, and chromatin data (ATAC-Seq), to investigate the evolution of regulatory networks and regulatory genes, and the role of regulatory networks and pathways in adaptation in the context of domestication.

Leveraging on our multi-disciplinary expertise, including our network reconstruction algorithms, and our DNA synthesis capability, we will apply a multi-scale approach to investigate the complexity of host-microbe interactions for both pathogenic and beneficial microbes. Our approach will include the following: 1) state-of-the-art and novel computational biology omics data analysis and network reconstruction methods, 2) in silico modelling of the host-microbe connections for multiple species/strains and conditions, and 3) validation of predictive systems models with synthetic biology approaches. The resulting host-microbe interactions will be used to provide an improved understanding of the mechanisms and systems-level functions of these cross-kingdom connections that are essential for host health and antimicrobial defence mechanisms.

As a complementary EI-QI joint effort, we will work with Simon Carding and other QI Research Leaders in the Gut Microbes and Health ISP to produce new fundamental insights into how the gut functions as an integrated organ system and how commensal microbes influence host homeostasis and metabolic health. In particular, we will investigate putative molecular mediators of signalling in enteric neuronal and endocrine cells, which could affect brain function (e.g. appetite control and food preferences). To uncover the mechanisms of these microbial influences on the host, we will predict and map the direct molecular interactions between gut microbes and intestinal epithelial cells as well as the subsequent inter-cellular signalling pathways between epithelial cells (primary site) and cells of the enteric nervous system (secondary sites) affected indirectly by the microbes. Bacterial influence will be modelled and key connections tested using a synthetic biology approach to obtain insights into how certain microbes affect systemic health through cross-kingdom communications in the intestinal tract.

Planned Impact

unavailable

Publications

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Abdul-Aziz A (2019) Acute myeloid leukemia induces protumoral p16INK4a-driven senescence in the bone marrow microenvironment in Blood

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Abdul-Aziz AM (2017) MIF-Induced Stromal PKCß/IL8 Is Essential in Human Acute Myeloid Leukemia. in Cancer research

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Akay A (2019) Identification of functional long non-coding RNAs in C. elegans in BMC Biology

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Al Kadhi O (2017) Increased transcriptional and metabolic capacity for lipid metabolism in the peripheral zone of the prostate may underpin its increased susceptibility to cancer. in Oncotarget

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Alexander JL (2023) The gut microbiota and metabolome are associated with diminished COVID-19 vaccine-induced antibody responses in immunosuppressed inflammatory bowel disease patients. in EBioMedicine

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Aleya F (2021) Relative expression of putative genes involved in galanthamine and other Amaryllidaceae alkaloids biosynthesis in Narcissus field and in vitro tissues in Gene

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Allahgholi M (2020) ADDI: Recommending alternatives for drug-drug interactions with negative health effects. in Computers in biology and medicine

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Andrighetti T (2019) MicrobioLink: An integrated computational pipeline to infer functional effects of microbiome-host interactions

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Andrighetti T (2020) MicrobioLink: An Integrated Computational Pipeline to Infer Functional Effects of Microbiome-Host Interactions. in Cells

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Backhaus A (2021) High expression of VRT2 increases the number of rudimentary basal spikelets in wheat

 
Description As part of the work package 2 of the Earlham Institute Genomics for Food Security Strategic Programme (CSP2), our objectives set in 2017 were to deliver: 1) orthology and annotation of complex genomes; 2) methods for reconstruction and analysis of multi-scale networks; 3) strain-specific regulatory networks to study host adaptation in food-borne bacteria; 4) species- and tissue-specific regulatory networks for aquatic species improvement; 5) network approaches for crop improvement; 6) impact of food-borne pathogens on host regulation; 7) impact of gut microbiota on systemic health. We have now completely delivered objectives 1-5. The grant was awarded a 6th year as rollover funding. As part of the rollover funding, we completed objectives 6 and 7, which were delayed due to COVID. We are also on track to deliver the rollover objectives: objective Ext 2.1 "Advanced genome and network reconstruction methods for functional annotation"; objective Ext.2.2 "Network biology of regulatory processes driving traits and adaptation". Taken together, CSP2 work led to 243 publications, 33 collaborations and 224 engagement activities and a spin-out company.

Key findings for CSP2:

Objective 1: Orthology and annotation of complex genomes and Ext2.1 "Advanced genome and network reconstruction methods for functional annotation".
1. We developed tools to support more accurate genome annotation in eukaryotic species. Improving splice junction detection from RNAseq data (Portcullis, 10.1093/gigascience/giy131) and developing an approach to integrate transcript assemblies from multiple methods, samples or sequencing technologies (Mikado, 10.1093/gigascience/giy093). We applied these developments to projects to annotate mammalian, insect and plant genomes, this includes our role in the International Wheat Genome Sequencing Consortium (IWGSC) that has delivered the most comprehensive annotation of the 21 wheat chromosomes to date (10.1126/science.aar7191).

2. We have completed genome annotations for nine wheat accessions, combining iso-seq and RNA seq from a developmental time course; publicly available from Ensembl Plants https://plants.ensembl.org/Triticum_aestivum/Info/Strains?db=core
. This was done in collaboration with Dr Spannagl and Prof. Meyer at Helmholtz-Muenchen Germany. Gene models were generated via an annotation workflow that utilised tools that we continue to develop as part of the award and a new pipeline (Minos, https://github.com/EI-CoreBioinformatics/minos) built around these tools.

3. We have brought our tools together within the framework of EIs genome annotation toolkit REAT (Robust Eukaryotic Annotation Toolkit, https://github.com/EI-CoreBioinformatics/reat) we have developed three annotation workflows. They support genome annotation from transcriptome data including utilising long noisy nanopore reads, homology data and a gene prediction workflow to facilitate ab initio and evidence-guided gene prediction via alternative methods and parameter configurations. The toolkit is also being used to support EI's Darwin Tree of Life protist project with improvements to aid the annotation of species with compact genomes and non-standard genetic codes. During the rollover period, we continued REAT development, adding support for transcript reconstruction from long noisy RNA-seq reads typical of Nanopore sequencing of RNA. Further additions to REAT included improvements to the REAT homology workflow to remove spurious protein alignments and REAT prediction to improve the confidence classification of predicted genes. The toolkit has been used to deliver Oreochromis niloticus (Abbassa), Oreochromis niloticus (GIFT; https://doi.org/10.1186/s12864-022-09065-8) and Calendula officinalis genome annotation and is currently being employed to annotate a number of wheat species and wild relatives.

4. One of the significant challenges with short-read sequencing is to accurately reconstruct alternatively spliced transcripts and quantify their expression. To assess the power of long-read RNA-Seq, we compared the power and sensitivity of short and long reads technologies in quantifying transcript expression and calling differentially expressed transcripts from undifferentiated and neuron-differentiated cells. We show that the application of long-read sequencing enables transcripts annotation, quantification and most importantly identification of differential transcript expression. Our results demonstrate the importance of investigating expression at the transcript level instead of gene level as we identified thousands of transcripts differentially expressed for genes without changes in overall gene expression (doi: 10.1093/nar/gkab1129). We contributed to the development of an algorithm enabling expression quantification from long-read data (doi: 10.1101/2021.04.27.441628). Our development enabled participation in a Marie Sklodowska-Curie Actions Doctoral Training Network (LongTrec) supported by UKRI EPSRC (EP/X035913/1).

5. We investigated the promoter sequences of genes across seven Eudicots species to identify transcription factor binding sites (TFBS) using PlantTFDB, JASPAR. We identified up to 394,786 TFBS for 153 transcription factors in the promoter regions of 21,373 genes in A. lyrata. The work also led to the implementation of an annotation pipeline for these species first developed to identify TFBS motifs in non-model organisms. This pipeline was used to identify TFBS in plant promoters in order to (i) compare the architecture of plant genes with different expression patterns in NRP DTP Studentship BB/M011216/1 Project No. 2116919 (Sam Witham; thesis submitted (ii) identify transcription factor binding sites for the development of protein-DNA binding affinity assay (doi: https://doi.org/10.1101/2023.02.13.528283); (iii) identify can compare binding sites in the promoters of nitrate-responsive genes across plant species (BB/S020853/1).


Objective 2,3.5, Ext2.2: Methods for reconstruction and analysis of multi-scale networks; species- and tissue-specific regulatory networks for aquatic species improvement; network approaches for crop improvement.

6. We developed a framework to identify which genes are co-expressed across tissues and integrated their regulators to investigate gene regulatory network evolution driving adaptations in multiple cichlid fish species, including Nile Tilapia. We report striking cases of network rewiring for genes involved with adaptation, including the visual system (https://doi.org/10.1101/496034). This network analysing protocol can be used to find differences arising from different evolutionary pressures acting on closely related species, as we have demonstrated in Salmonella and cichlids.
As part of the rollover funding, we aimed to reconstruct tissue-specific regulatory networks in sensitive and tolerant farmed species to identify network rewiring associated with acclimation (salinity, temperature) including candidate genes for future breeding programmes with WorldFish. Through collaboration with Prof Avner Cnaani (ARO, Israel), we have gained access to transcriptomic data collected during acclimation experiments in tilapia (Oreochromis niloticus - sensitive and O. urolepis - tolerant) that will form the basis of these analyses. We will apply our recent algorithm developments to this data set to characterise network rewiring during acclimation. A preprint will be submitted in early 2023.

We further extended our previous regulatory network developments to include miRNA and miRNA binding sites, identifying cases of network rewiring associated with environmental adaptation (https://doi.org/10.1093/molbev/msac146). We also investigated the pattern of regulatory regions accessibility in tilapia gills, organs directly associated with osmoregulation, using ATAC-Seq. Applying transcription factor footprinting alongside polymorphism data across Oreochromis species, we report genetic variation within transcription factor binding sites upstream of genes associated with environmental adaptation including salinity tolerance (https://doi.org/10.1101/2023.02.17.528929).

7. We expanded our previous work reconstructing regulatory networks across tissues in cichlids species to include microRNAs and their binding sites. Thus, we are assessing the impact of miRNA turnover on regulatory network rewiring identifying variants within miRNAs and transcription factor binding sites that differentially segregate between species in various ecological niches (https://doi:10.1101/2021.12.14.472604).

8. To understand the gene expression regulation during wheat spikelet development, we adapted protocols developed in model organisms to enable transcriptome sequencing from thin sections across the spikelet axis during its development. Our approach enabled to identify of differentially expressed genes along the spikelet axis, including a MADS-box transcription factor, VRT-A2, highly expressed in the basal sections and associated with increased numbers of rudimentary basal spikelets (https:// doi:10.1101/2021.08.03.454952).

9. We have investigated water use efficiency and the effects of water stress on wheat. We have identified a landrace with high levels of water use efficiency. We have now generated time course data sets for Paragon and a high water use efficiency landrace to understand how wheat responds at the molecular level to water stress. We have reconstructed transcription networks and understand how the networks change rather than individual genes. We have submitted an abstract to Frontier in Plant Science, a special issue on abiotic stress and will be submitting the paper in April.

10. We have developed an assay allowing for the first time to apply Genome-Wide Association Studies for clock phenotypes across populations, we used an Arabidopsis diversity panel and identify undiscovered natural variation in network components of the circadian clock (https://doi.org/10.1111/pce.13941). We have developed a set of bio-marker genes whose expression at a single time point can be used to measure the phase of the endogenous circadian clock (circadian time, CT). This is allowing us to predict using pre-existing or new data whether genotype or environment or a combination of the two are altering the plant circadian network (https://doi.org/10.1101/2021.02.04.429826). Having developed this approach in Arabidopsis this is now being extended to wheat and refined in collaboration with the Alan Turing Institute.
In collaboration with IBM we have developed a machine-learning approach to predict genes that are clock regulated solely based on genomic sequence, validating this approach with Arabidopsis accessions. This is now the basis for an iCASE project with BASF (https://doi.org/10.1101/2021.02.04.429826). This has led to collaborations with Anthony Dodd (John Innes Centre) and Maria Erikson (Umea University, Sweden). The tools developed are available (https://github.com/JoshuaColmer/HallCircadian). We have also used this data to mine biomarkers for complex traits in wheat as part of collaboration with the Alan Turing Institute, which has developed into a PhD project in collaboration with Anthony Dodd (John Innes Centre) funded as part of the NRP-DTP. We have now established a £0.5M collaboration with an agri-tech company to build models for a specific trait and have launched a spin-out company Traitseq Ltd and a number of agri-tech industrial partners have also expressed interest in our work.

11. Bread wheat now makes wheat an excellent experimental model to study gene regulation in complex polyploids. Circadian regulation is known to make a substantial contribution to the growth of plants, including cereals. This motivated us to investigate how a complex network like the circadian clock works across the three wheat genomes. Using high-resolution circadian transcriptomics, we show that a large proportion of wheat triads have homologues with differential patterns of circadian expression, with no specific subgenomes favoured. We reveal conserved expression of the core clock network as well as many circadian-regulated processes between distantly-related wheat and Arabidopsis. Importantly, genes that have differential regulation include several transcripts encoding enzymes for trehalose 6-phosphate and starch metabolism. These underlie a core role for circadian regulation in plant productivity, thus identifying potentially valuable targets for future wheat breeding (https://doi.org/10.1371/journal.pbio.3001802https://doi.org/10.1101/2021.09.30.462369). Associated data sets are available here (https://opendata.earlham.ac.uk/opendata/data/wheat_circadian_Rees_2021),

12. We have established a quantitative experimental system to investigate transcriptional function of plant promoters, investigating how the identity, density and position of cis-regulatory elements contribute to regulatory function. We then identified permissive architectures for minimal synthetic plant promoters enabling the computational design of synthetic promoters for which strength could be predicted from the primary sequence (https://doi.org/10.1093/nar/gkaa682). These were successfully used to control the heterologous expression of biosynthetic pathways for high-value molecules for health (BB/O014090/1; doi: 10.1101/2022.06.15.496242) and agriculture (BB/R021554/1; 10.1101/2022.06.15.496242).

13. We are applying network approaches to crop improvement, firstly by utilising the model Arabidopsis. During the rollover period, we applied our in-house assay (from 2.2) to quantify the impact of mutations within bZIP transcription factors and more specifically within their intrinsically disordered regions on the transcription of target genes in planta using transient expression and transgenic complementation assays. We have completed experiments to show that mutations to the intrinsically disordered domain of TGA1 and TGA2 affect the affinity but not specificity of binding to target binding sites. However, this also affected important interactions with other TF proteins, so we discontinued this line of investigation. Using TGA transcription factors as an exemplar, we have demonstrated how quantitative relative binding affinity data can be used to design synthetic plant promoters of varying strengths that respond to the same cellular levels of transcription factors (https://doi.org/10.1101/2023.02.13.528283).

14. As part of rollover, we aimed to investigate and compare cell-type specific transcriptional responses to nitrate availability, and the effects of network perturbations in Arabidopsis. We implemented a protocol for nuclei extraction of Arabidopsis roots. In a preliminary experiment, we isolated and sequenced the transcriptomes of ~1000 nuclei from the roots of Arabidopsis and tomato. Although we underestimated the number of nuclei and therefore had fewer reads per cell than expected, we were able to identify all the expected cell types. However, we decided to also implement a protocol for single protoplasts, as this is known to provide a greater number of reads per cell. We have now successfully established this protocol and have prepared libraries of protoplasts from wild-type Arabidopsis thaliana and Solanum lycopersicum roots grown on two nitrate concentrations. The analysis will focus on identifying the location and changes to the expression of genes in a nitrogen-responsive sub-network that our recent work (funding by NSF-BBSRC) suggests may control root growth in response to nitrate in an auxin-dependent manner.



15. During the rollover period, we extended our Machine Learning (ML) tools for predicting internal biological time beyond the model Arabidopsis to crops. We aimed to investigate circadian clock/network changes across crop diversity panels to identify loci with evidence of natural or artificial selection. We have harvested material for a time course datasets for Brassica oleracea (CC) and Brassica rapa (AA) in collaboration with Rachel Wells at the JIC. This data set will become the training set for us to develop a new ML model for Brassica allowing us to measure clock function across Brassica species. It will also allow us to investigate differential regulation of the circadian clock between these closely related species which come together to form Brassica napus (AA CC).

Objective 3,6,7: strain-specific regulatory networks to study host adaptation in food-borne bacteria; the impact of food-borne pathogens on host regulation; the impact of gut microbiota on systemic health.

16. We analysed >50 gut pathogens to identify how they can regulate autophagy, and how during autophagy pathogen proteins are recognised, and validated a prediction in Salmonella (https://doi.org/10.1080/15548627.2019.1590519). As part of the rollover, we demonstrated how Salmonella can modulate host processes, in particular, autophagy (doi: 10.3389/fcimb.2022.834895). In this study, led by EI, we combined single-cell analysis, network modelling, experimental protein-protein interaction detection and microscopy.

17. We studied how Bacteroides thetaiotaomicron modulates host processes and affects gut homeostasis, combining single-cell data with small-scale experiments and network modelling (doi: 10.1002/jev2.12189). Following this publication, we have been invited to prepare a STAR Protocol (Cell Press) paper on the methodology which we plan to submit in April 2023. Also, we recently published a related project on the Bacteroides thetaiotaomicron proteins that interact with the host (doi: 10.1128/aem.00533-22).


18. We established experimental protocols to grow and differentiate small intestinal organoids, created proteomics and transcriptomics profiles of them from wild type and autophagy deficient mice models, and developed bioinformatics pipelines for multi-omics and regulatory network analysis of these samples (https://doi.org/10.1101/575845). While establishing these models in the lab, it became clear that such an in vitro model is not easily accessed by many scientists due to scarce detailed information about how to get access and start using organoids. We address this problem through the publication of an extensive review (doi:10.1016/j.jcmgh.2022.04.012), contributing to sharing organoid model knowledge to the non-expert scientific community, wanting to use these models.

19. In our autophagy regulation projects, we used comparative genomics, protein structure and gene regulation comparisons to demonstrate that two paralogs (ULK1/ULK2) essential for autophagy induction, and thought to be interchangeable, are very different (https://doi.org/10.1038/s41598-020-67780-2). We published a unified model on how autophagy is induced upon various stress events (https://doi.org/10.1038/s41419-021-03599-7).

20. We reutilised multiple approaches we have previously developed within this programme to address key COVID-related issues. We became part of the international COVID Disease Map Consortia, and provided gap-filling network resources to the curators of the project (https://doi.org/10.1101/2020.10.26.356014).We also developed and provided the community an open-access, ready to use workflow, ViralLink, to study the effect of SARS-CoV-2 (or other viruses) on host processes (https://doi.org/10.1371/journal.pcbi.1008685). We also published two papers on the COVID-19 related cytokine storm using regulatory and host-microbe interaction networks: one comparing the cytokine responses for SARS-CoV-2 and 4 other respiratory viruses (https://doi.org/doi.org/10.3389/fimmu.2021.629193), and one highlighting the role of bacterial metalloproteases in the cytokine response to SARS-CoV-2 (https://doi.org/doi: 10.1186/s12964-020-00699-3). We showed how SARS-CoV-2 in the gut can affect key epithelial-immune processes that may contribute to the development of a potentially fatal cytokine storm (doi: 10.1038/s41540-022-00224-x). We investigated whether the gut microbiome and metabolome could explain variation in anti-SARS-CoV-2 vaccination responses in immunosuppressed inflammatory bowel disease patients. We used our network analysis and visualisation tools to interpret the complex data (10.1016/j.ebiom.2022.104430).

21. We have set up protocols for the isolation of rare cell populations from the mouse gut, including Paneth and stem cells. We have established processes for single-cell and low-input RNA sequencing, enabling us to read out the transcriptome of between 1 and 100 cells. This led us to identify Paneth cells directly infected by Salmonella, and analyse the transcriptomics changes in these cells upon infection.

22. We have used our single-cell platforms to perform RNA-seq low input (50 cells) on murine gut stem cells, intermediate cells and Paneth cells. Based on the protocol we established in the previous year, we were able to analyse the microbial effect on these cell types using samples generated by our collaborator Dana Phillpot (University of Toronto). We compared germ-free mice intestinal cells with germ-free mice that were exposed in the short or long term to microbes. The downstream computational analysis is still ongoing.

23. We updated SalmoNet, the first multi-layered interaction network resource for the pathogen Salmonella enterica, including prominent strains of both gastrointestinal, and invasive serovars. A systems-level knowledge of these pathogens has the potential to identify the complex adaptations associated with the evolution of serovars with distinct pathogenicity, host range and risk to human health, and aims to aid the design of interventions and serve as a knowledge base in the Salmonella research community. SalmoNet2 is a major update to the network database, extending the number of included Salmonella genomes from 11 to 20, including strains such as S. Typhimurium D23580, an epidemic multidrug-resistant strain leading to invasive non-typhoidal Salmonella Disease (iNTS), and a strain from Salmonella bongori, another species in the Salmonella genus. We have increased the coverage of high-quality interactions for all strains, enhanced interoperability with other interaction resources by adopting standardised formats, and created tutorials to help researchers analyse their Salmonella data with ease. SalmoNet2 is accessible at http://salmonet.org/ (doi: 10.1128/msystems.01493-21).


24. As a major demonstration of the tools we previously developed, we published a multi-disciplinary work where we led a project to study how bacterial extracellular vesicles (BEVs), released into the gut lumen, can cross the mucus layer and access underlying immune cells. To study BEV-host interactions, we examined the influence of BEVs generated by the gut commensal bacterium, Bacteroides thetaiotaomicron, on host immune cells. Single-cell RNA sequencing data and host-microbe protein-protein interaction networks were used to predict the effect of BEVs on dendritic cells, macrophages and monocytes. We identified biological processes affected by each immune cell type and cell-type-specific processes including myeloid cell differentiation (doi.org/10.1002/jev2.12189). This study, done in collaboration with the Quadram Institute, demonstrates that both cell type and health status influence BEV-host communication. The results and the pipeline (https://github.com/korcsmarosgroup/BT_BEV_project/) could facilitate BEV-based therapies for the treatment of gut-related diseases such as inflammatory bowel disease.
Exploitation Route The outcomes of work package 2 of the Earlham Institute Genomics for Food Security strategic programme (CSP2) and the extension-funded work are taken forward through collaborations and partnerships over the six years , such as:

We have built a very productive working relationship with IBM Research, who bring expertise in machine learning and AI and Hybrid Cloud Computing, while researchers at EI bring expertise in developing genomic tools for plant breeding. One of the projects in which we are translating the outcomes of the CSP2 is on the exploitation of bioinformatics and machine learning models through Hybrid Cloud technology by the British plant breeding industry. We are working on this project with STFC, IBM Research and a plant breeding company. STFC is supporting this project as part of their programme aiming to develop applications for AI and Quantum computing for industry. In this collaboration, we are developing a machine-learning model that will provide insights into the genetic components underlying key economic and agronomic traits, such as yield and sustaining environmental stress. The aim of this collaboration is to deliver the technology via Hybrid Cloud to the end user (a breeding company) as a software-as-a-service model. As part of this collaboration, staff from the EI have been seconded to IBM as part of our Flexible Talent Mobility Account and DTP-PIPS placements.

Machine learning methods for predicting regulator elements have led to an iCASE PhD studentship with an Agri-tech company on using open data and machine learning approaches to decode the regulatory regions of wheat.

The variants and network targets identified under this programme will be of direct interest to breeders and agrochemical companies working on breeding improvement programmes and sustainable disease management. Using the outcomes from the CSP2 on developing machine learning approaches to understand what regions of the genome control what genes are expressed, we are collaborating with a number of major agrochemical companies interested in applying bioinformatics expertise to identify ways to control specific crop traits of interest, aiming to develop either new breeding strategies or ways of regulating crop performance through the application of agrochemicals. Using this know-how and experience we continued developing this platform technology which is now being commercialised. This will benefit plant breeding and biotech companies helping them with product development or breeding strategies. This has led to a £0.5M collaboration which started in January 2023 with one of the major Agri-tech companies. We also participated successfully in the BBSRC ICURE programme and registered a spin-out company Traitseq Ltd to commercialise this research.


Our scientists work as part of ambitious UK and international collaborations such as the International Wheat Genome Sequencing Consortium (IWGSC), Designing Future Wheat (DFW), 10+ Wheat Genomes. In both the UK and globally, this work is supporting ongoing annual increases in wheat productivity and reducing the impact of disease outbreaks, with an estimated impact of £7.4m to the UK economy and £240m to the rest of the world over the next 10 years. The global impact is projected to rise to an estimated £1.5bn over 25 years (Socio-economic impact of the Earlham Institute, Brookdale Consulting, report 2022).

We are actively collaborating with WorldFish to improve the functional annotation of the GIFT strain, with the aim to be able to apply our network reconstruction approaches to the high-performance strains.

We are freely disseminating our genome annotation toolkits from public repositories. The REAT toolkit and documentation are freely available from a public repository https://github.com/EI-CoreBioinformatics/reat and therefore could be used by other groups in application to their own projects. The toolkit also supports annotation work provided through EI's National Capability in Genomics and Single Cell Analysis and we are providing guidance on the use of this and previous tools through our training workshops https://www.earlham.ac.uk/genome-annotation-workshop-2022.

To enable the community to access complex datasets easier and analyse them in a similar way as we did in our own studies, we published multiple practical reviews, resources and protocol papers. These papers include doi: 10.3390/genes13020370; doi: 10.3389/fimmu.2022.829525; doi: 10.3389/fgene.2021.760501; doi: 10.1093/nar/gkab909; doi: 10.3389/fmicb.2021.618856; doi: 10.15252/msb.20209923

Our outcomes in protocols and algorithms developments directly contribute to training early career researchers in genomics and bioinformatics. Our faculty hosts undergraduate students from the University of East Anglia (3rd-year Biology) for 8-week research projects and Masters's students, training the students in bioinformatics and genomics. We also hosted students as part of Genetics Society Summer Studentships and Undergraduate Research Experience Placements. We engaged with the Nuffield Foundation to offer research placements to high school students from disadvantaged backgrounds. Our faculty contributes to training courses organised by our National Capability (Single Cell Bioinformatics, Genome Annotation).

In order to help life scientists to adopt data-intensive research, the Earlham Institute, together with Institutes on the Norwich Research Park initiated a collaboration with The Alan Turing Institute supported by a £600,000 award funding six research posts to expand the application of machine learning and artificial intelligence to several key areas, including one of the CSP2 areas, i.e. characterising the circadian rhythms of plants. Machine learning offers a promising route into not only exploring that data, but also helping us to find hidden patterns and new hypotheses that we had never previously considered.This aligns strongly with the mission of the Earlham Institute, who is contributing to solving global challenges by applying data driven methods, and hosts the UK National Capability in computational infrastructure.This has led to the submission of a £11M bid for a UKRI AI Centre for Doctoral TRaining in Agri-food INnovation (TRAIN).

We developed Metagenomic Assembled Genomes (MAGS) with a new improved binning algorithm using PacBio data on chicken microbiomes. The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. This microbial community also acts as a source of pathogens associated with disease in birds or in humans including Campylobacter, Salmonella, and Escherichia coli, as well as providing a reservoir of antimicrobial resistance genes. Our improved algorithm enables us to reveal extensive taxonomic diversity within this complex microbial community, which could facilitate translation into developing new strategies for controlling these pathogens, understanding the sources of AMR, and designing new probiotics to improve chicken gut microbiota, improve animal health and improve feed conversion. Our specialist research in this area led to an invited talk on MAG reconstruction from PacBio data at the PacBio Roadshow which will take place in May 2023 to disseminate the methodology to the wider community. We are also working to disseminate our chicken metagenomics data, published in Microbiology in 2021, with several industry partners.

EI provided training to QIB on Pacbio and metagenomic sequencing, and a collaborative effort between EI and QIB researchers is ongoing to develop a metagenomic assembler.

Tools and resources developed by the CSP2 were shared and discussed during our annual stakeholder engagement event EI innovate which has been running since November 2019. EI Innovate provides an insight into the Earlham Institute's research, exploring opportunities for innovation and collaboration. We had between 70 and 200 attendees coming to these events year on year (virtual during pandemic and face-to-face before and after the pandemic). The audience is a mixture of internal staff and other research organisations on the Norwich Research Park and external organisations. The external audience comes from a range of sectors including agri-food, biotech, med-tech sectors, clinicians, developers of instrumentation, tools, products and services for genomics and bioinformatics, funders, investors, other academic organisations, and government departments. During these events we highlight areas where CSP2 research is generating impact, sharing tools that we develop, and highlighting opportunities for knowledge transfer and collaborations. An article about the event was produced by our Comms Team which enabled us to share more widely the discussions held at the event. EI Innovate events have gone on to foster exciting and valuable conversations between academia and industry. An example of an exciting collaboration that resulted from a previous EI Innovate is the Hybrid Wheat Initiative, which connects 25 breeding companies and research institutes worldwide, to resolve the critical challenge of hybrid wheat.
Sectors Agriculture

Food and Drink

Digital/Communication/Information Technologies (including Software)

Education

Environment

Healthcare

Pharmaceuticals and Medical Biotechnology
 
Description As part of the work package 2 of the Earlham Institute Core Strategic Programme Genomics for Food Security (CSP2) and the funding extension, we set out to deliver objectives focusing on genome annotation and network analysis. We have successfully delivered all these objectives making a significant impact in the area of food security, food borne pathogens and health. Deciphering the sources and mechanisms of variation in regulation of genes and genomes is pivotal for understanding the genotype-to-phenotype relationship underlying adaptation, evolution and health. Understanding the regulation of important biological processes helps to predict novel functions, interactions, and identify further candidate genes that can be collaboratively validated through genome manipulation techniques. We were able to translate the outcomes of the CSP2 in several areas listed below thus generating emerging economic and societal impacts: Improving genetic resources for wheat breeding The Earlham Institute has made major contributions to understanding the wheat genome and is leading research efforts to improve a crop vital for global food security. Releasing high quality annotated wheat genomes allows breeders to identify more rapidly genes and regulatory elements underlying complex agronomic traits. Wheat provides more global calories than any other crop, yet has historically lagged behind in genetic resources due to its large and complex genome. Methods for functional annotation developed as part of CSP2 provide a significant improvement in annotating complex genomes like wheat. Detailed annotation of the bread wheat genome was delivered using software Portcullis (https://github.com/EI-CoreBioinformatics/portcullis 10.1093/gigascience/giy131) and Mikado (https://github.com/EI-CoreBioinformatics/mikado; 10.1093/gigascience/giy093) developed as part of CSP2. Manipulating regulatory networks for breeding improvement programmes Our machine learning based pipeline helped to identify genes involved in the regulation of the circadian clock, currently not tractable for a breeder. The circadian clock enables plants to synchronise key biological processes with daily and seasonal environmental conditions in order to allocate resources. The principle was published in collaboration with IBM Research doi10.1073/pnas.2103070118. This addresses an important question of how biological networks interact to regulate complex genomes and will also allow us to understand how robustness and flexibility is built into these networks. Time and synchronisation underpin many important agricultural traits as for example nutrient use efficiency, flowering time, yield, and biomass. Understanding the regulation will help to design rational approaches to manipulating the circadian clock in wheat to achieve specific breeding targets and provide promising avenues for further crop breeding improvement, gene editing, agrichemicals and biologicals. The spin out company Traitseq Ltd will be working closely with gene editing, plant breeding, agrichemical and live-stock companies to advance trait prediction by streamlining and accelerating product testing and development. Using functional annotation tools to identify potential new treatments for human diseases The outputs of the CSP2 of functional annotation improvements have an emerging societal impact on improving human health. The application of long read sequencing enables better transcripts annotation, quantification and identification of differential transcript expression enabling to uncover new regulatory networks that could be targeted for the development of new treatments or drugs. In collaboration with the University of Oxford as part of the Medicine Discovery Catapult funded project we work with several pharmaceutical companies and two medical charities to help identify drug targets for major candidates in neuropsychiatric disorders. The full annotation for a single gene associated with neuropsychiatric disorders has now been completed enabling the identification of isoforms specifically expressed in the brain relative to the cardiac system. We individually transformed cell lines to express the newly identified isoforms, identifying different cellular localization between isoforms. A library of small molecules has been screened for their action on the regulation of specific isoforms through specific functional assays (GTPase-Glo assays, neurites outgrowth). Genome annotation tools Genome annotation tools developed as part of the CSP2 have a wide application in academic and industry. We have a growing number of projects and collaborations that use these tools. Our tools Mikado and Portcullis were used as part of the International Wheat Genome Consortium to support the annotation of the reference genome of bread wheat. More recently, the tools have been used to support the annotation of nine wheat varieties. as part of the 10+ wheat genome project (https://10wheatgenomes.com/)), with annotation released via EnsemblPlants. The REAT toolkit is being used in collaborative projects to annotate improved assemblies of Durum wheat and the Bread wheat cultivars Paragon and Cadenza. We are also deploying the toolkit to support projects delivered via EI's National Capability in Genomics and Single-Cell including annotation of wild wheat relatives. The toolkit will aid the wheat community in exploiting the growing number of genome assemblies for wheat varieties and wild relatives, providing tools to create more accurate and consistent annotation and aiding genome-wide association studies, variant analyses, and evolutionary and comparative analysis Recently the toolkit was used in an effort to produce the best ever reference genome for the GIFT strain of tilapia (10.1186/s12864-022-09065-8) - a fish of exceptional importance in global aquaculture. Having a well-annotated genome is critical to enabling end users to identify genes of interest and other genetic elements that we can target in breeding programmes. We are also applying these annotation tools as part of the Darwin Tree of Life Project to annotate novel protists (10.1101/2022.12.16.520718). Host-microbe interactions Both the experimental and computational protocols/pipelines that we developed for the multi-omics analysis of organoids have already been applied by clinical researchers (King's College London, Imperial College, The Francis Crick Institute and KU Leuven). These techniques not only enable these researchers to understand better how human intestinal cells are changing in diseased conditions but also allow pharmacology researchers to test and screen compounds with patient-derived organoids. We are in discussion with industrial partners to further develop and disseminate the tool. Impact of SARS-CoV-2 infection on host immune regulation In 2020-21 we developed the ViralLink that has been applied by multiple research groups working on SARS-CoV-2 and host transcriptomics data, in particular the COVID Disease Map consortia, a collaboration of researchers from 120 different institutes across 30 countries that coordinate computational and systems biology efforts with the ~200 researchers involved ( 10.15252/msb.202110387). To study COVID-19, we applied our expertise in multi-omics network modelling and re-utilised our resources. In particular, we have investigated how various infected cell types, especially in the gut, react to the pathogen, and how the immune response given to SARS-CoV-2 differs from other viruses(doi.org/10.3389/fimmu.2021.629193). This paper had more than 16,000 views since it was published just a year ago, making it to the top 5% of papers published in any Frontiers journal. In 2021-22 we added a new resource, the CytokineLink, to analyse immune responses during the Inflammatory Bowel Disease and COVID-19. Intercellular communication mediated by cytokines is critical to the development of immune responses, particularly in the context of infectious and inflammatory diseases. For ulcerative colitis, with CytokineLink, we demonstrated a significant rewiring of cytokine-mediated intercellular communication between non-inflamed and inflamed colonic tissues. For COVID-19, we were able to identify cell types and cytokine interactions following SARS-CoV-2 infection, highlighting important cytokine interactions that might contribute to severe illness in a subgroup of patients. These findings have the potential to inform the development of novel, cytokine-targeted therapeutic strategies. CytokineLink is freely available for the scientific community through the NDEx platform and the project github repository. Influence on Policy and Public Affairs We have continued our previous activities to provide scientific evidence to members of the government and associated agencies on the methods of production as well as the potential impacts of genome editing in agriculture. In 2021, we submitted a response to a DEFRA consultation on the regulation of genetic technologies; we worked with NRP colleagues to advocate to BEIS officials the potential for gene editing innovation as an economic development opportunity in relation to both the R&D Place Strategy and the Life Science Vision, both of which were BEIS policy papers. We hosted George Freeman MP to present the findings from his task force for Innovation, Growth and Regulatory Reform, commissioned by the Prime Minister and discussed measures that the Government could take to accelerate the UK's ability to translate gene editing research to innovate solutions to environmental and nutritional challenges; Dr Nicola Patron and Saskia Hervey advised the Parliamentary Office of Science and Technology on the content of a new POSTnote on gene editing in agriculture. The POSTnote was published with references to EI's work and has informed Parliament's response to DEFRA legislation; we hosted a policy roundtable discussion on new regulation for genetic technologies with 15 members of the DEFRA policy team and other Norwich Research Park based stakeholders including representatives from the NBIs. There have been significant changes across Westminster and Whitehall. Earlham Institute has kept abreast of all these changes and anticipated their impact. We have maintained contact with ministerial offices and initiated policy advocacy opportunities and parliamentary engagement, both on our own and in collaboration with Norwich Research Park partners. Earlham Institute staff have played a leading role in the Norwich Research Park Public Affairs Group. We have worked successfully with the Norwich Research Park partners on a series of high level visits to the Park from senior policy makers and MPs: Cabinet Office Officials (scouting for venue for Cabinet Meeting and Govt. Tech announcement aborted due to political developments) Prof Paul Monks, BEIS Chief Scientific Adviser Prof Robin May, Food Standards Agency Chief Scientific Adviser Liz Truss's Chief of Staff Genetic Technology (Precision Breeding) Bill team and DEFRA civil servants and policy officers Food Standards Agency (FSA) personnel working on implementation strategy for Genetic Technology (Precision Breeding) Bill James Wild MP Chloe Smith MP Jerome Mayhew MP Paul Cracknell, Director of Strategy, Norfolk County Council Clive Lewis MP Professor Sir Patrick Vallance and officials from the Government Office for Science Richard Bacon MP (planned May 2023) These visits have included representatives of the commercial organisations located on the Norwich Research Park to embrace the business voice and provide our visitors with a comprehensive, public and private sector innovation perspective. Since May 2022, when DEFRA's Genetic Technology (Precision Breeding) Bill was introduced to Parliament, Earlham Institute has engaged with Parliamentarians in both Houses to support the swift passage of the Bill. Earlham Institute has worked closely with Norwich Research Park colleagues to present a united front to Parliamentarians scrutinising the Bill. We have provided written material during the Committee stages and proactively sent parliamentary briefings to MPs and Peers. Our briefings have included case studies about our collective research, as well as advocacy about the potential for gene editing to contribute to tackling challenges such as climate change, food security and biodiversity loss. During the Sense About Science annual Evidence Week, representatives from the Norwich Research Park Public Affairs Group were in Parliament and met the following parliamentarians in person to present our scientific support for the Bill: Greg Clarke MP, Chair of the Science & Technology Select Committee Deirdre Brock MP Sheryll Murray MP Hilary Benn MP (former DEFRA Secretary) Liz Twist MP Alex Sobel MP Olivia Blake MP James Parton-Hughes on behalf of Richard Bacon MP Baroness Bakewell of Hardington Mandeville Nick Ross (former broadcaster and trustee of Sense About Science) Lord Best Further online engagement took place with Lord Krebs, Chloe Smith MP, Lord Benyon, Lord Cameron. At every step of the Bill's parliamentary journey, Earlham Institute has engaged with the DEFRA and the Food Standards Agency Bill teams. As part of the Norwich Research Park Public Affairs Group, Earlham Institute has responded to various policy consultations (such as the Review of Research, Development and Innovation Landscape by Professor Sir Paul Nurse) and maintained ministerial correspondence (such as a letter to George Freeman MP, Minister for Science, Research and Technology requesting a meeting to discuss strategic science investment and Plan B (Horizon)). On March 7th 2023, Dr Falk Hildebrand contributed to parliamentary questions for the Norwich Research Park Submission to the Environment, Food and Rural Affairs (EFRA) Select Committee Soil Health Enquiry. Significant impact within academia, for example the nucleation of a new research area The work of the CSP2 supported the development of single-cell and low-input sequencing methods. We implemented these methods for a wide range of biological systems and demonstrated proof-of-principle. This work is of interest to a wide range of researchers throughout the life sciences, including evolutionary studies, systems biology, cancer biology and immunology, and more recently to plant and microbial biology. Working jointly with our National Capability on Genomics and Single Cell Analysis, we established multiple platforms for the isolation and single cell sequencing of a wide range of cells. We demonstrated the feasibility of single bacterium sequencing for evolutionary studies, for single-cell isoform expression profiling, and for cell lineage tracing. We have already been able to support researchers country-wide in delivering single-cell genomics approaches as part of their work, including clinical research and cell-specific pharmacological approaches.
First Year Of Impact 2017
Sector Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Healthcare,Pharmaceuticals and Medical Biotechnology
Impact Types Cultural

Societal

Economic

Policy & public services
 
Description BBSRC ENWW panel membership
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
Impact The panel advises BBSRC exec and councillor how best to deliver BBSRC strategy. Impact is difficult to quantify
 
Description Contribution to the National Food Strategy Public Consultation
Geographic Reach National 
Policy Influence Type Contribution to a national consultation/review
URL https://consult.defra.gov.uk/agri-food-chain-directorate/national-food-strategy-call-for-evidence/
 
Description Engagement with All-Party Parliamentary Group on Agriculture and Food for Development: Implications of the 2018 European Court of Justice ruling on genome editing
Geographic Reach National 
Policy Influence Type Participation in a guidance/advisory committee
 
Description Engagement with the All Party Parliamentary Group for Science and Technology in Agriculture. EI supported this APPG's amendment to the Agriculture Bill in Summer 2020 when the Bill was going through the House of Lords. The amendment sought to give the DEFRA Secretary of State power to introduce a new regulatory regime to allow the commercial use of gene editing for crops for agricultural purposes. EI orchestrated a cross-NRP advocacy effort to brief members of the House of Lords to support the amendment and signed the NIAB letter to DEFRA Secretary of State articulating our support for the amendment. The impact of our work helped to bring about the Government's announcement of a public consultation with a view to primary legislation to establish a new regulatory regime to enable gene editing.
Geographic Reach National 
Policy Influence Type Contribution to a national consultation/review
 
Description Expert member of the plant synthetic biology working group for the European Food Standards Agency (EFSA)
Geographic Reach Europe 
Policy Influence Type Participation in a guidance/advisory committee
 
Description FNS cloud Advisory Board
Geographic Reach Europe 
Policy Influence Type Influenced training of practitioners or researchers
URL https://www.fns-cloud.eu/overview/advisory-board/
 
Description Input into "Balance and Effectiveness of Research and Innovation Spending" inquiry by the House of Commons Science and Technology Select Committee
Geographic Reach National 
Policy Influence Type Citation in other policy documents
URL https://publications.parliament.uk/pa/cm201719/cmselect/cmsctech/1453/145303.htm#_idTextAnchor000
 
Description Letter to Rt Hin Chris Skidmore to discuss science funding and science immigration post-brexit
Geographic Reach National 
Policy Influence Type Implementation circular/rapid advice/letter to e.g. Ministry of Health
 
Description Meeting with Sir John Kingman to discuss UKRI strategy and the sustainability of Institutes
Geographic Reach National 
Policy Influence Type Implementation circular/rapid advice/letter to e.g. Ministry of Health
 
Description Membership of BBSRC Transformative technology Panel
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
Impact The transformative technology strategy advisory panel have influence BBSRC policy on data intensive bioscience and big ideas pipeline
 
Description NERC 'Omics Review. I provided advice on the Environmental omics strategy as a memeber of the NERC Environmental omics steering committee
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
Impact The report generated has led to the NERC commissioning of an environmental omics facility to improve the delivery of the NERC strategy and to train the next generation of scientists.
URL http://environmentalomics.org/steering-committee-and-editors/
 
Description Nicola Patron - Cabinet Office policy roundtable discussion on synthetic biology
Geographic Reach National 
Policy Influence Type Participation in a guidance/advisory committee
 
Description Nicola Patron -Advice to the Committee Clerks on the Terms of Reference for the planned enquiry into bioscience in agriculture
Geographic Reach National 
Policy Influence Type Participation in a guidance/advisory committee
 
Description Oral Evidence to House of Commons Science and Technology Committee enquiry on Balance and effectiveness of research and innovation spending
Geographic Reach National 
Policy Influence Type Contribution to a national consultation/review
URL https://parliamentlive.tv/Event/Index/4bdf3ff7-d1a6-4605-8b73-aca355bf9f89
 
Description Particapited in parliamentary debate on CRISPR CAS and post-BREXIT genetic engineering in crops -APPG Science & Technology in Agriculture
Geographic Reach National 
Policy Influence Type Contribution to a national consultation/review
 
Description Provided input to the KTN Microbiome Strategic Roadmap Review - Section 10 Enabling Technologies - Falk Hildebrand and Christopher Quince
Geographic Reach National 
Policy Influence Type Contribution to a national consultation/review
URL https://ktn-uk.org/wp-content/uploads/2021/02/Microbiome_Strategic_Roadmap_FINAL.pdf
 
Description Science and Technology Committee, House of Commons - implications to the UK of the 2018 Euporean Court of Justice ruling on Genome Editing
Geographic Reach National 
Policy Influence Type Participation in a guidance/advisory committee
 
Description The Earlham Institute hosted a policy roundtable discussion on new regulation for genetic technologies with 15 members of the DEFRA policy team
Geographic Reach National 
Policy Influence Type Contribution to a national consultation/review
 
Description UK PLANT SCIENCE RESEARCH STRATEGY - A green roadmap for the next ten years
Geographic Reach National 
Policy Influence Type Contribution to a national consultation/review
 
Description Wilfried Haerty - meeting with French Embassy representatives to provide evidence to French Government review, gain visibility of research park and potential source of funding between France and UK
Geographic Reach Europe 
Policy Influence Type Contribution to a national consultation/review
 
Description submission to UKRI infrastructure review
Geographic Reach National 
Policy Influence Type Contribution to a national consultation/review
URL https://www.ukri.org/files/infrastructure/progress-report-summary-document-final-march-2019-pdf/
 
Description 17-ERACoBioTech - SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture
Amount £395,316 (GBP)
Funding ID BB/R021554/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2018 
End 04/2021
 
Description 18 BTT EAGER - Engineering complex traits using targeted, multiplexed genetic and epigenetic mutagenesis
Amount £202,347 (GBP)
Funding ID BB/S020853/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2019 
End 12/2022
 
Description 18-BTT: A PATHWAY TO THE EXPLOITATION OF EPIGENETIC VARIATION IN UK, US AND INTERNATIONAL BREEDING PROGRAMMES
Amount £273,500 (GBP)
Funding ID BB/S020942/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2019 
End 03/2021
 
Description 21EBTA Engineering specialised metabolism and new cellular architectures in plants
Amount £1,517,514 (GBP)
Funding ID BB/W014173/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2022 
End 01/2024
 
Description 21ENGBIO - Engineering Nucleosome Positioning in Plants
Amount £99,849 (GBP)
Funding ID BB/W010933/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 02/2023 
End 02/2024
 
Description 21ENGBIO - Engineering Nucleosome Positioning in Plants
Amount £99,849 (GBP)
Funding ID BB/W010933/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 02/2023 
End 02/2024
 
Description A proof of concept that RECQ 7 can be used as a tool to increase recombination
Amount £137,389 (GBP)
Funding ID BB/T011963/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2020 
End 09/2021
 
Description An improved bioproduction system for proteins and small molecules
Amount £459,425 (GBP)
Funding ID BB/P010490/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2017 
End 06/2021
 
Description Association of Salmonella with protists in the aquatic environment
Amount £20,879 (GBP)
Funding ID INV-051974 
Organisation Bill and Melinda Gates Foundation 
Sector Charity/Non Profit
Country United States
Start 11/2022 
End 11/2024
 
Description BBSRC IAA
Amount £10,377 (GBP)
Funding ID BB/S506679/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2021 
End 05/2021
 
Description BBSRC NRPDTP Cutting-edge approaches to understand how gut microbes promote our health
Amount £20,000 (GBP)
Funding ID 2116512 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2018 
End 09/2022
 
Description BBSRC NRPDTP Studentship - Can there be only one? Exploring heterogeneity in RNA splicing at single-cell resolution.
Amount £20,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2018 
End 09/2022
 
Description BBSRC NRPDTP iCASE Studentship - Safeguarding UK's best-loved fruit: immunity diversity in banana cultivar
Amount £28,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2021 
End 09/2025
 
Description BBSRC NRPDTP iCASE Studentship - Using open data and machine learning approaches to decode the regulatory regions of wheat
Amount £28,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2021 
End 09/2025
 
Description BBSRC NRPDTP studentship - Bioactivity and biosynthesis of triterpenoids from Asteraceae flowers
Amount £20,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2021 
End 09/2025
 
Description BBSRC NRPDTP studentship - Design principles for synthetic gene regulation: understanding how cis-regulatory functions are encoded in plant DNA.
Amount £20,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2018 
End 09/2022
 
Description BBSRC NRPDTP studentship - For everything you have missed, you have gained something else: Functional characterization of novel splicing events in human and mouse
Amount £20,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2021 
End 09/2025
 
Description BBSRC NRPDTP studentship - Functional consequences of alternative splicing on stem cell differentiation
Amount £20,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2021 
End 09/2025
 
Description Biological production of bioactives from medicinal Asteraceae
Amount £20,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2023 
End 09/2027
 
Description Brazilian PhD Sandwich Programs Abroad - PDSE/CAPES
Amount £9,000 (GBP)
Organisation Government of Brazil 
Department Coordination of Higher Education Personnel Training (CAPES)
Sector Public
Country Brazil
Start 03/2017 
End 08/2017
 
Description Business Case for a Catalyst Partnership in Artificial Intelligence between the Alan Turing Institute and the Norwich Biosciences Institutes
Amount £600,000 (GBP)
Funding ID BB/V509267/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2020 
End 06/2022
 
Description Defining mechanisms of CD8+ T-cell mediated immunity - using an integrated longitudinal model to achieve an elusive goal
Amount £321,907 (GBP)
Funding ID BB/S017178/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2020 
End 01/2023
 
Description Defining mechanisms of CD8+ T-cell mediated immunity - using an integrated longitudinal model to achieve an elusive goal.
Amount £321,908 (GBP)
Funding ID BB/S017178/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2020 
End 01/2024
 
Description Development of single-cell sequencing technology for microbial populations
Amount £149,610 (GBP)
Funding ID BB/R022526/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2018 
End 06/2019
 
Description Engineering gene regulatory networks to design disease-resistant crops
Amount £1,409,847 (GBP)
Funding ID BB/Y007786/1 
Organisation United Kingdom Research and Innovation 
Sector Public
Country United Kingdom
Start 02/2024 
End 02/2026
 
Description FTMA4 - Earlham Institute Flexible Talent Mobility Account
Amount £107,000 (GBP)
Funding ID BB/X017761/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2023 
End 03/2023
 
Description Feasibility study investigating circulating peripheral mitochondrial DNA as a potential non-invasive biomarker for diagnosis and surveillance of high risk cutaneous melanoma
Amount £97,677 (GBP)
Funding ID EDDPMA-May21\100026 
Organisation Cancer Research UK 
Sector Charity/Non Profit
Country United Kingdom
Start 02/2022 
End 02/2024
 
Description Grand Challenges Research Fund (GCRF) Data & Resources (EI) - extension
Amount £160,963 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2017 
End 07/2018
 
Description IPA Industrial Partnering Award - An improved bioproduction system for proteins and small molecules
Amount £420,676 (GBP)
Funding ID BB/P010490/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2017 
End 09/2020
 
Description IPA Industrial Partnering Award - Resistance: DNA methylation and the evolution of pesticide-resistance genes in aphids
Amount £289,489 (GBP)
Funding ID BB/R009481/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2018 
End 03/2021
 
Description Identification of prognostic indicators of healthy ageing with a machine learning based systems biology approach using gut microbiome data
Amount £99,034 (GBP)
Funding ID BB/S50743X/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2018 
End 09/2022
 
Description Identifying unique regulatory elements related to polymorphic imprinting and gestational aging in the placenta
Amount £457,956 (GBP)
Funding ID BB/V016210/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2022 
End 07/2025
 
Description Investigation of the impact of mutations within cis regulatory regions on gene and transcript regulatory network topology using computational approaches
Amount £18,400 (GBP)
Funding ID HAERTY_E19SCB 
Organisation University of Bisha 
Sector Academic/University
Country Saudi Arabia
Start 09/2019 
End 09/2023
 
Description John Innes Centre Institute Strategy Funding - The elucidation of transcription factor networks underling internode extension in wheat
Amount £13,911 (GBP)
Organisation John Innes Centre 
Sector Academic/University
Country United Kingdom
Start 01/2018 
End 12/2018
 
Description Leverage Yellow Common Bean Native Variety Liborino as a bioproduct for the sustainable and peaceful socioeconomic development of the rural communities in Colombia
Amount £49,852 (GBP)
Funding ID 527023146 
Organisation British Council 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2020 
End 10/2021
 
Description LongTREC: The Long-Reads Transcriptomics European Consortium. The next generation transcriptome biology revealed by single molecule sequencing technologies
Amount £265,251 (GBP)
Funding ID EP/X035913/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 09/2022 
End 09/2026
 
Description MSc in Plant Genetics and Crop Improvement Student Projects
Amount £2,000 (GBP)
Organisation John Innes Centre 
Sector Academic/University
Country United Kingdom
Start 03/2022 
End 03/2023
 
Description NRP Seed fund
Amount £16,000 (GBP)
Organisation Norwich Research Park 
Sector Private
Country United Kingdom
Start 01/2018 
End 01/2019
 
Description NRP Seed fund - A collaboration between the Earlham Institute (EI) and the University of East Anglia (UEA) to understand the role of small RNAs in complex gene regulatory networks in bread wheat
Amount £15,000 (GBP)
Funding ID SLSF 68 
Organisation Norwich Research Park 
Sector Private
Country United Kingdom
Start 01/2018 
End 01/2019
 
Description NRP Seed fund - Deconstructing somites using advanced genomics approaches
Amount £7,000 (GBP)
Funding ID SLSF 66 
Organisation Norwich Research Park 
Sector Private
Country United Kingdom
Start 12/2017 
End 11/2018
 
Description New Investigator Award: Developing single-cell isoform sequencing tools to explore the diversity and regulation of alternative splicing in haematopoiesis
Amount £726,658 (GBP)
Funding ID BB/P022073/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2017 
End 10/2020
 
Description Newton Bhabha PhD Placement Grant
Amount £10,200 (GBP)
Funding ID 543448553 
Organisation British Council 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2020 
End 01/2021
 
Description Open - Brain-enriched voltage-gated calcium channel isoforms: novel, genetically informed, therapeutic targets for psychiatric disorders
Amount £167,504 (GBP)
Funding ID MR/P026028/1 
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 05/2017 
End 05/2019
 
Description Open Plant Fund: Developing a frugal transcription factor relative affinity measurement pipeline (TRAMP)
Amount £5,000 (GBP)
Organisation University of Cambridge 
Sector Academic/University
Country United Kingdom
Start 09/2018 
End 09/2019
 
Description Open plant fund - Comparative analysis of cell free and in planta protein synthesis systems
Amount £5,000 (GBP)
Organisation University of Cambridge 
Sector Academic/University
Country United Kingdom
Start 01/2018 
End 01/2019
 
Description OpenPlant
Amount £14,011,253 (GBP)
Funding ID BB/L014130/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 06/2014 
End 09/2022
 
Description OpenPlant - Developing a frugal transcription factor relative affinity measurement pipeline (TRAMP)
Amount £5,000 (GBP)
Organisation University of Cambridge 
Sector Academic/University
Country United Kingdom
Start 08/2018 
End 07/2019
 
Description OpenPlant: Comparative analysis of cell free and in planta protein synthesis systems
Amount £4,000 (GBP)
Organisation University of Cambridge 
Sector Academic/University
Country United Kingdom
Start 02/2018 
End 12/2018
 
Description PhD Studentship - Using data generated by the Darwin Tree of Life to uncover chemical diversity
Amount £126,032 (GBP)
Organisation John Innes Foundation 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2021 
End 02/2025
 
Description PhD studentship - Using open data and machine learning approaches to decode the regulatory regions of plants
Amount £126,032 (GBP)
Organisation John Innes Foundation 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2021 
End 05/2025
 
Description Role of LAP in controlling liver homeostasis
Amount £566,929 (GBP)
Funding ID BB/W002450/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2022 
End 01/2025
 
Description S.Typhi and protozoa in contaminated water in Zimbabwe
Amount $100,000 (USD)
Funding ID OPP1217121 
Organisation Bill and Melinda Gates Foundation 
Sector Charity/Non Profit
Country United States
Start 11/2019 
End 04/2021
 
Description Scientific/Clinical Research Grant - Development of a 'multi-fluor-omic platform' to functionally interrogate the calcium signalling pathway in colorectal tumours: implications for cancer prevention and chemotherapy
Amount £20,124 (GBP)
Funding ID 16-12R 
Organisation Big C Cancer Charity 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2017 
End 09/2018
 
Description Single-cell cancer evolution in the clinic - zero rating
Amount £2,024,295 (GBP)
Funding ID C309/A26815 
Organisation Cancer Research UK 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2018 
End 10/2023
 
Description Strategic Priorities Fund - AI for Science, Engineering, Health and Government
Amount £38,800,000 (GBP)
Funding ID EP/T001569/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 11/2018 
End 03/2023
 
Description Structural variation in rice across modern and historical landraces and elite varieties
Amount £20,000 (GBP)
Funding ID HALLA_E23DTP 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2023 
End 09/2027
 
Description SynBioLEAP Catalyst - Open Source Foundational Tools
Amount £6,901 (GBP)
Organisation Synthetic Biology Leadership Excellence Accelerator Program 
Sector Private
Start 06/2017 
End 12/2018
 
Description The Earlham Institute 2021 Flexible Talent Mobility Account
Amount £108,000 (GBP)
Funding ID BB/W510890/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 12/2021 
End 03/2022
 
Description The cost of longevity: transgenerational consequences of parental lifespan extension for offspring fitness
Amount £468,069 (GBP)
Funding ID BB/R017387/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2018 
End 09/2021
 
Description There is more than meet the eye: reconstruction of isoform level regulatory networks in the human brain
Amount £20,000 (GBP)
Funding ID 2748728 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2022 
End 09/2026
 
Description TraitSeq - a technology platform for accelerated trait development in agritech and biotech
Amount £23,004 (CUP)
Funding ID I-BBS-A-05 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 06/2022 
End 12/2022
 
Description Transcriptomic profiling of patient-derived colonic epithelial organoids exposed to Ulcerative Colitis-relevant cytokines - a novel approach to uncover IBD pathogenesis and inform precision medicine strategies
Amount £9,950 (GBP)
Funding ID TRA2020_08 
Organisation GUTS UK 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2021 
End 11/2021
 
Description UEA Proof of Concept
Amount £7,601 (GBP)
Funding ID 1698788PA2 
Organisation University of East Anglia 
Sector Academic/University
Country United Kingdom
Start 05/2020 
End 06/2021
 
Description UKRI - Earth Biogenome Project
Amount £600,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2019 
End 03/2022
 
Description Using REC Q7 to drive increases in recombination in crop genomes
Amount £9,677 (GBP)
Funding ID BB/T010096/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 08/2019 
End 02/2020
 
Description Using machine learning to tell the time
Amount £20,000 (GBP)
Funding ID HALLA_E22DTP 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2022 
End 09/2026
 
Description Wellcome - Sir Henry Wellcome Postdoctoral Fellowship - Unravelling key regulators of thrombopoiesis using a novel RNA based clonal and molecular approaches
Amount £300,000 (GBP)
Funding ID 213731/Z/18/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 04/2019 
End 04/2023
 
Title A simple split luciferase method to assess transcription factor-DNA Interactions 
Description A luminescence-based microplate assay for quantifying the relative affinity of transcription factors for DNA probes. This method uses short, unlabelled DNA probes, which are cheaply obtained, and minimal quantities of recombinant protein with a minimal genetically-encoded tag. We have demonstrated the use of this assay to quantify the affinity of transcription factors to target sequences. We have also applied knowledge of binding affinity to modulate the strength of minimal synthetic plant promoters. 
Type Of Material Technology assay or reagent 
Year Produced 2023 
Provided To Others? Yes  
Impact This method has been used to investigate and guide the engineering of plant responses to nutrients. This is important for the development of crops that require fewer applications of agrochemicals. 
 
Title AutoRank: A python tool for giving hub and interaction context scores 
Description A biological network analysis algorithm to provide contextual scores to hubs and long distance interactors 
Type Of Material Improvements to research infrastructure 
Year Produced 2018 
Provided To Others? No  
Impact AutoRank gives identifies highly connected nodes, known as hubs, and there long distance interactors within biological networks contextual scores. These scores are generated through statistical tests, and can be used to gain an insight into structure of the network and therefore an understanding of the mechanisms driving particular phenotypes. Private github link : https://github.com/mattmadgwick/ContextTool 
 
Title Host-Microbe interaction workflow 
Description Integrated Computational workflow to infer the effect of bacterial proteins on host processes 
Type Of Material Improvements to research infrastructure 
Year Produced 2018 
Provided To Others? No  
Impact Targeted interplay between bacterial pathogens and host autophagy. Sudhakar P, Claire-Jacomin A, Hautefort I, Samavedam S, Fatemian K, Ari E, Gul L, Demeter A, Jones E, Korcsmaros T and Nezis I. Autophagy 2019. (In Press). Host-Microbe interaction pipeline based on protein-protein interactions - applicable to single species and community wide microbial proteomic data. Sudhakar P, Andrighetti T, Gul L, Fazekas D, Korcsmaros T. (in preparation - to be submitted April 2019) 
 
Title Methyl-seq methods for wheat 
Description Background: Bread wheat has a large complex genome that makes whole genome resequencing costly. Therefore, genome complexity reduction techniques such as sequence capture make re-sequencing cost effective. With a high- quality draft wheat genome now available it is possible to design capture probe sets and to use them to accurately genotype and anchor SNPs to the genome. Furthermore, in addition to genetic variation, epigenetic variation provides a source of natural variation contributing to changes in gene expression and phenotype that can be profiled at the base pair level using sequence capture coupled with bisulphite treatment. Here, we present a new 12 Mbp wheat capture probe set, that allows both the profiling of genotype and methylation from the same DNA sample. Furthermore, we present a method, based on Agilent SureSelect Methyl-Seq, that will use a single capture assay as a starting point to allow both DNA sequencing and methyl-seq. Results: Our method uses a single capture assay that is sequentially split and used for both DNA sequencing and methyl-seq. The resultant genotype and epi-type data is highly comparable in terms of coverage and SNP/methylation site identification to that generated from separate captures for DNA sequencing and methyl-seq. Furthermore, by defining SNP frequencies in a diverse landrace from the Watkins collection we highlight the importance of having genotype data to prevent false positive methylation calls. Finally, we present the design of a new 12 Mbp wheat capture and demonstrate its successful application to re-sequence wheat. Conclusions: We present a cost-effective method for performing both DNA sequencing and methyl-seq from a single capture reaction thus reducing reagent costs, sample preparation time and DNA requirements for these complementary analyses. 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? Yes  
Impact As yet not known 
 
Title Minimal synthetic promoters for plants 
Description We have established a quantitative experimental system to investigate transcriptional function, investigating how identity, density and position contribute to regulatory function. We then identified permissive architectures for minimal synthetic plant promoters enabling the computational design of a suite of synthetic promoters of different strengths. These have been used to regulate the relative expression of output genes in simple genetic devices. 
Type Of Material Biological samples 
Year Produced 2020 
Provided To Others? Yes  
Impact Requests for materials from other research groups and organisations 
URL https://academic.oup.com/nar/article/48/21/11845/5897334
 
Title MulEA: An R package for Multi Enrichment Analysis 
Description Bioinformatics, genomics analysis tool MulEA is a comprehensive gene set overrepresentation and enrichment Bioconductor R package and Galaxy tool Github link : https://github.com/TGAC/Mulea 
Type Of Material Improvements to research infrastructure 
Year Produced 2017 
Provided To Others? No  
Impact MulEA will provide extensive analytical means using diverse databases, statistical models and p-value correction procedures that can extend our understanding of the results of various high-throughput analyses. 
 
Title Systems biology of gut organoids 
Description Since its first publication in 2009, the in vitro organoid model has been recognized as a major technological breakthrough tool in many basic biology and clinical applications. Organoids are near-physiological 3D model systems that facilitate studying a range of in vivo biological processes including cell differentiation, antimicrobial peptide production, host-microbe interactions and cell-cell communications. Organoids can also used to examine the effect of certain mutations by generating organoids from transgenic mice strains. The key aim of this joint project is to perform 'omics analyses of the generated organoids, examine the differences between cell-types and disease conditions using computational approaches, as well as generate and validate testable hypotheses regarding the affect of the identified functional differences. 
Type Of Material Model of mechanisms or symptoms - in vitro 
Year Produced 2017 
Provided To Others? No  
Impact In the last 12 months we 1) performed proteomics analysis of the organoids that allowed to identify biomedically relevant and scientifically interesting differences ; 2) tested and established a protocol/pipeline to perform RNAseq and microRNA profiling at Earlham Institute. ; 3) Our in silico analysis of the proteomic datasets also confirmed the differentiated organoids do express proteins expected for the given cell types (e.g., enzymes important in peptide synthesis in Paneth cell differentiated organoids). By analysing interaction data we interestingly pointed out that autophagy (cellular self-eating) could degrade many of the cell-specific key proteins. ATG16L1 is an autophagy protein involved in selecting proteins for autophagy-driven degradation, and it also contributes to the general autophagy process.; 4) In a second series of experiments we have generated organoids from the intestine of mice generated at UEA that lack expression of Atg16L1 specifically in intestinal epithelial cells (Atg16L1 dIEC). The proteomic profiles of these autophagy deficient Paneth cell and goblet cell organoids were also carried out at the University of Liverpool. Strikingly, when we analysed the proteins whose protein levels differed in the autophagy deficient background, we found several of them are known or predicted to be degraded through autophagy. In Paneth cell organoids, the functional analysis of those proteins whose level was significantly higher in the ATG16L1 knock-out background (potentially as they have not been degraded properly) pointed out their importance in 'acute inflammatory response', 'immune response', 'negative regulation of gene expression', and 'protein processing'. This list indicates that autophagy malfunction negatively affects protein (antimicrobial peptide) production as well as deregulates inflammatory responses. Failure of these process are well known for Paneth cells in Crohn's disease but so far they have not been connected directly with autophagy malfunction. We found similar results for the mucosa producing goblet cells. To confirm these findings, we will directly examine some affected key functions using organoids. Reference: Integrative analysis of Paneth cell proteomic and transcriptomic data from intestinal organoids reveals functional processes dependent on autophagy. Emily Jones*, Zoe Matthews*, Lejla Gul*, Padhmanand Sudhakar, Agatha Treveil, Devina Divekar, Jasmine Buck, Tomasz Wrzesinski, Matthew Jefferson, Stuart Armstrong, Lindsay Hall, Alastair Watson, Simon Carding, Wilfried Haerty, Federica Di Palma, Ulrike Mayer, Penny Powell, Isabelle Hautefort, Tom Wileman, Tamas Korcsmaros. Disease Models and Mechanisms 2019. http://dmm.biologists.org/content/early/2019/02/26/dmm.037069. (* joint first authors) 
 
Title promoter exon capture platform 
Description Whole genome shotgun re-sequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome making it difficult to unambiguously assign variation. Re-sequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. Previous studies have implemented cDNA/exon or gene-based probe sets where promoter and intron sequence is largely missing alongside newly characterized genes from the recent improved reference sequences. Results We present and validate two gold standard capture probe sets for hexaploid bread wheat, a gene and a putative promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high confidence genes and putative promoter regions that were identified in the genome alongside a large proportion of the low confidence genes and associated promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for SNP calling while significantly reducing cost per sample for gene and putative promoter capture. Conclusions We show that a capture design employing an 'island strategy' can enable analysis of the large gene/putative promoter space of wheat with only 2x160 Mb probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations. 
Type Of Material Technology assay or reagent 
Year Produced 2018 
Provided To Others? Yes  
Impact Currently being used by DFW, CIMMYT and US CAPS projects 
 
Title Additional file 1 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus 
Description Additional file 1: Supplementary Table 1. Assembly statistics. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_1_of_Chromosome-level_genome_se...
 
Title Additional file 1 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus 
Description Additional file 1: Supplementary Table 1. Assembly statistics. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_1_of_Chromosome-level_genome_se...
 
Title Additional file 3 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus 
Description Additional file 3: Supplementary Table 2. Genomics regions in GIFT with evidence of O. mossambicus introgression. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_3_of_Chromosome-level_genome_se...
 
Title Additional file 3 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus 
Description Additional file 3: Supplementary Table 2. Genomics regions in GIFT with evidence of O. mossambicus introgression. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_3_of_Chromosome-level_genome_se...
 
Title Additional file 6 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus 
Description Additional file 6: Supplementary Table 3. Genes identified within O. mossambicus introgressed regions including corresponding orthologs in medaka. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_6_of_Chromosome-level_genome_se...
 
Title Additional file 6 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus 
Description Additional file 6: Supplementary Table 3. Genes identified within O. mossambicus introgressed regions including corresponding orthologs in medaka. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_6_of_Chromosome-level_genome_se...
 
Title Additional file 8 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus 
Description Additional file 8: Supplementary Table 4. Ontology terms significantly enriched among genes identified within O. mossambicus introgressed regions. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_8_of_Chromosome-level_genome_se...
 
Title Additional file 8 of Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus 
Description Additional file 8: Supplementary Table 4. Ontology terms significantly enriched among genes identified within O. mossambicus introgressed regions. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
URL https://springernature.figshare.com/articles/dataset/Additional_file_8_of_Chromosome-level_genome_se...
 
Title CytokineLink: an interactive cytokine communication map to analyse immune responses in inflammatory and infectious diseases 
Description In this project, we built a communication map between tissues and blood cells to show how cytokine feedback loops can build (and thus, possibly break) under pathophysiological conditions. We collated the most prevalent cytokines from literature, and assigned the proteins and their receptors to source tissue and blood cell types based on consensus RNA-Seq data from the Human Protein Atlas. To assign more confidence to the interactions, we integrated cytokine-cell interaction data from two systems immunology databases, immuneXpresso and ImmunoGlobe. 
Type Of Material Computer model/algorithm 
Year Produced 2021 
Provided To Others? No  
Impact I gave a virtual poster presentation on the tool at the ISMB 2020 conference. 
 
Title Epigenomic variation across a polyploid wheat diversity collection 
Description We survey genotype and DNA methylation across the core Watkins bread wheat landrace collection. We observe high transposable element variability and expansion, most frequently in retrotransposons, alongside high epigenomic diversity; while there is an association between methylation and genotype, methylation is a standalone source of variation between closely related accessions. Both methylation and genotype are influenced by geographic origin. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Lead to an EAGER grant to translate the research 
URL https://www.ebi.ac.uk/ena/data/view/PRJEB23320
 
Title PRJEB32354 - Small RNA transcriptomics comparison of mouse small intestinal organoids grown to be normally differentiated, enriched for Paneth cells or enriched for goblet and enteroendocrine cells. 
Description Small RNA transcriptomics comparison of mouse small intestinal organoids grown to be normally differentiated, enriched for Paneth cells or enriched for goblet and enteroendocrine cells. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact This dataset has resulted in a peer reviewed publication 
URL https://www.ebi.ac.uk/ena/data/view/PRJEB32354
 
Title PRJEB32366 - RNA-seq comparison of mouse small intestinal organoids grown to be normally differentiated, enriched for Paneth cells or enriched for goblet and enteroendocrine cells. 
Description RNA-seq comparison of mouse small intestinal organoids grown to be normally differentiated, enriched for Paneth cells or enriched for goblet and enteroendocrine cells. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact This dataset has resulted in a peer-reviewed publication 
URL https://www.ebi.ac.uk/ena/data/view/PRJEB32366
 
Title PRJEB35461 - Secale cereale L. inbred line 'Lo7' genome assembly 
Description Thie database contains the Illumina RNA-Seq and the PacBio Sequel reads for the submission of the Secale cereale L. inbred line 'Lo7' genome assembly paper 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact This dataset has resulted in a bioRxiv pre-print publication. This is a key KWS rye line so will be used in their rye breeding programme. 
URL https://www.ebi.ac.uk/ena/data/view/PRJEB35461
 
Title PRJEB37024 - Nicotiana benthamiana 
Description The research dataset contains sequencing reads to build a high quality genome assembly for the model tobacco species Nicotiana benthamiana. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? No  
Impact The resulting assembly was essential for an ongoing project in the Patron lab to genetically engineer N. benthamiana as an improved bio-based production system for useful plant metabolites. 
 
Title PRJEB37025 - Nicotiana benthamiana 
Description The research dataset contains sequencing reads to build a high quality genome assembly for the model tobacco species Nicotiana benthamiana. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? No  
Impact The resulting assembly was essential for an ongoing project in the Patron lab to genetically engineer N. benthamiana as an improved bio-based production system for useful plant metabolites. 
 
Title PRJEB37026 - Nicotiana benthamiana 
Description The research dataset contains sequencing reads to build a high quality genome assembly for the model tobacco species Nicotiana benthamiana. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? No  
Impact The resulting assembly was essential for an ongoing project in the Patron lab to genetically engineer N. benthamiana as an improved bio-based production system for useful plant metabolites. 
 
Title PRJEB38337 - THE HUMAN BRAIN MICROBIOME IN HEALTH AND PARKINSONS's DISEASE MUCH ADO ABOUT NOTHING 
Description This dataset contains putative 16S amplicon sequences of brain matter in healthy and Parkinson's Disease patients. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? No  
Impact Using this dataset, we could show that there is no brain microbiome, but this seems to be a methods artifact in a few other publications. 
 
Title Paneth cell, stem cell - Salmonella infection transcriptomics data 
Description We orally infected mice with GFP-tagged Salmonella, and then isolated small intestinal crypts, containing Paneth cells and stem cells. We also did the same for uninfected (control) mice. Follwoing the cell isolation, we sorted the cells for those that were GFP positive (contained Salmonella). Then we generated a transcriptomics profile of Paneth cells directly infected with Salmonella; stem cells directly infected with Salmonella; Paneth cells not directly infected with Salmonella but cells from the infected mice; stem cells not directly infected with Salmonella but cells from the infected mice as well as Paneth cells and stem cells from the control mice. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? No  
Impact The data now enables us to identify transcriptomics changes in host cells directly or indirectly infected by Salmonella. Also, we can now test Salmonella mutants and compare those gene expression profiles with this wild-type Salmonella induced changes. 
 
Title Recombination landscape of hexaploid bread wheat 
Description Sequence exchange between homologous chromosomes through crossing over and gene conversion is highly conserved among eukaryotes, contributing to genome stability and genetic diversity. Lack of recombination limits breeding efforts in crops, therefore increasing recombination rates can reduce linkage-drag and generate new genetic combinations. We use computational analysis of open access data from 13 recombinant inbred mapping populations to assess crossover and gene conversion frequency in the hexaploid genome of wheat (Triticum aestivum). We find that high frequency crossover sites are shared between populations and that closely related parental founders lead to populations with more similar crossover patterns. We have identified QTL for altered gene conversion and crossover frequency and confirm functionality for a novel candidate RecQ helicase gene that belongs to an ancient clade that is missing in some plant lineages. Harnessing the RecQ helicase has the potential to break linkage-drag utilizing widespread gene conversions conserved across recombination sparse centromeric regions. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Demonstrates high rates of recombination in wheat previously not seen 
URL https://www.ebi.ac.uk/ena/data/view/PRJEB28231
 
Title SalmoNet2.0 
Description An integrated network resource containing regulatory, metabolic and protein-protein interactions For multiple Salmonella strains classified as gastro-intestinal or extra-intestinal pathogens An interaction resource with manually curated, high-throughput and predicted interactions Provides a strain specific and consensus networks Can be downloaded in a user-specified content and format 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation Métris A., Sudhakar P., Fazekas D., Demeter A., Ari E., Branchu P, Kingsley R.A., Baranyi J., Korcsmáros T. npj Systems Biology and Applications 3, Article number: 31 (2017) doi:10.1038/s41540-017-0034-z 
URL http://salmonet.org/
 
Title Sherlock - big data analytics platform for bioinformatics data 
Description The Sherlock tool is utilizing standard, open source big data technologies (like S3, Presto and docker) in order to execute simple analytical SQL queries on top of the integrated bioinformatics data organized into an S3-based data lake. 
Type Of Material Data analysis technique 
Year Produced 2019 
Provided To Others? No  
Impact The method will help to increase the productivity of data heavy bioinformatics projects, easing the data cleaning, filtering and integration related tasks which are usually the first steps in each complex bioinformatics pipeline. Github link : https://github.com/NetBiol/sherlock 
 
Title Supporting data for "A Galaxy-based training resource for single-cell RNA-seq quality control and analyses" 
Description It is not a trivial step to move from single-cell RNA-seq (scRNA-seq) data production to data analysis. There is a lack of intuitive training materials and easy-to-use analysis tools, and researchers can find it difficult to master the basics of scRNA-seq quality control and the later analysis.
We have developed a range of practical scripts, together with their corresponding Galaxy wrappers, that make scRNA-seq training and quality-control accessible to researchers previously daunted by the prospect of scRNA-seq analysis. We implement a 'visualise-filter-visualise' paradigm through simple command-line tools that use the Loom format to exchange data between the tools. The point-and-click nature of Galaxy makes it easy to assess, visualise, and filter scRNA-seq data from short-read sequencing data.
We have developed a suite of scRNA-seq tools that can be used for both training and more in-depth analyses. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
 
Title promoter exon capture data 
Description The data contain the design space for the promoter and exon used in our capture 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Whole genome shotgun re-sequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome making it difficult to unambiguously assign variation. Re-sequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. We present two gold standard capture probe sets for hexaploid bread wheat, a gene and a promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. The capture probe sets effectively enrich the high confidence genes and promoters that were identified in the genome alongside a large proportion of the low confidence genes and promoters. We use a capture design employing an 'island strategy' to enable analysis of the large gene/promoter space of wheat with only 2x160 Mb NimbelGen probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations. Here, we release the targeted sequence of the capture probe sets on the wheat RefSeqv1, the design space that was used to tile our capture probes across and finally the positions of the probes themselves across this design space for both the gene and promoter capture probe sets. 
URL https://opendata.earlham.ac.uk/wheat/under_license/toronto/Gardiner_2018-07-04_Wheat-gene-promoter-c...
 
Description Analysing Tilapia species diversity and salinity adaptation in Lake Rukwa, Tanzania. 
Organisation Bangor University
Country United Kingdom 
Sector Academic/University 
PI Contribution Full organisation and expenses for Lake Rukwa, Tanzania sampling expedition to collect Oreochromis esculentus and Oreochromis rukwaensis tissue samples. This includes sampling equipment/reagents, travel, accomodation and subsistance. This also included species handling and tissue dissection training for University of Dar Es Salaam and University of Dodoma collaborators.
Collaborator Contribution Levinus Leonard and Edward A. Moto (University of Dar Es Salaam and University of Dodoma) aided 1. Organisation and permits for sampling in Lake Rukwa upon dealing directly with the lake fisheries officers 2. Private boat hire 3. Transport hire and accomodation 4. Species identification, tissue sampling and dissection Alexandra Tyers (Bangor University) aided in tissue sampling and dissection.
Impact Tissue samples from O. rukwaensis and O. esculentus have been sequenced to include: 1. Genotyping several individuals including variant analyses for species identification, admixture and phylogenetics 2. RNA-Seq of gill, liver and kidney for genome annotation and gene expression analyses Both will be published.
Start Year 2017
 
Description Analysing Tilapia species diversity and salinity adaptation in Lake Rukwa, Tanzania. 
Organisation University of Dar es Salaam
Country Tanzania, United Republic of 
Sector Academic/University 
PI Contribution Full organisation and expenses for Lake Rukwa, Tanzania sampling expedition to collect Oreochromis esculentus and Oreochromis rukwaensis tissue samples. This includes sampling equipment/reagents, travel, accomodation and subsistance. This also included species handling and tissue dissection training for University of Dar Es Salaam and University of Dodoma collaborators.
Collaborator Contribution Levinus Leonard and Edward A. Moto (University of Dar Es Salaam and University of Dodoma) aided 1. Organisation and permits for sampling in Lake Rukwa upon dealing directly with the lake fisheries officers 2. Private boat hire 3. Transport hire and accomodation 4. Species identification, tissue sampling and dissection Alexandra Tyers (Bangor University) aided in tissue sampling and dissection.
Impact Tissue samples from O. rukwaensis and O. esculentus have been sequenced to include: 1. Genotyping several individuals including variant analyses for species identification, admixture and phylogenetics 2. RNA-Seq of gill, liver and kidney for genome annotation and gene expression analyses Both will be published.
Start Year 2017
 
Description Analysing Tilapia species diversity and salinity adaptation in Lake Rukwa, Tanzania. 
Organisation University of Dodoma
Country Tanzania, United Republic of 
Sector Academic/University 
PI Contribution Full organisation and expenses for Lake Rukwa, Tanzania sampling expedition to collect Oreochromis esculentus and Oreochromis rukwaensis tissue samples. This includes sampling equipment/reagents, travel, accomodation and subsistance. This also included species handling and tissue dissection training for University of Dar Es Salaam and University of Dodoma collaborators.
Collaborator Contribution Levinus Leonard and Edward A. Moto (University of Dar Es Salaam and University of Dodoma) aided 1. Organisation and permits for sampling in Lake Rukwa upon dealing directly with the lake fisheries officers 2. Private boat hire 3. Transport hire and accomodation 4. Species identification, tissue sampling and dissection Alexandra Tyers (Bangor University) aided in tissue sampling and dissection.
Impact Tissue samples from O. rukwaensis and O. esculentus have been sequenced to include: 1. Genotyping several individuals including variant analyses for species identification, admixture and phylogenetics 2. RNA-Seq of gill, liver and kidney for genome annotation and gene expression analyses Both will be published.
Start Year 2017
 
Description Analysis of IBD large scale metatranscriptomic datasets, Dr Rob Finn, Sequence Families Team Leader, European Bioinformatics Institute, Cambridge 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution Decoding the molecular functions of the microbial protein-coding elements in the IBD metatranscriptomes using the microbe-host interaction analysis approach.
Collaborator Contribution Functional annotation of the multiple IBD metatranscriptomic datasets
Impact No outputs yet
Start Year 2018
 
Description BASF 
Organisation BASF
Country Germany 
Sector Private 
PI Contribution We are using the the promoter capture platform developed in (https://doi.org/10.1093/gigascience/giz018) to sequence wheat cultivars
Collaborator Contribution Paying for sequencing and capture
Impact Funded ICASE studentship "Using open data and machine learning approaches to decode the regulatory regions of wheat"
Start Year 2020
 
Description Cibus 
Organisation Cibus
Country United States 
Sector Private 
PI Contribution Meet with them online and at their company in San Diego
Collaborator Contribution Confidential
Impact Confidential
Start Year 2022
 
Description Collaboration - WorldFish 
Organisation Worldfish
Country Malaysia 
Sector Charity/Non Profit 
PI Contribution As part of this collaboration we have been generating genomic resources and identifying the genetic bases of traits of interest
Collaborator Contribution WorldFish has been providing samples for sequencing, genetic data
Impact 10.1186/s12864-022-09065-8
Start Year 2020
 
Description Collaboration with Oxford Nanopore Technologies 
Organisation Oxford Nanopore Technologies
Country United Kingdom 
Sector Private 
PI Contribution As part of the upcoming EI strategic programme we will be producing novel protocols for single cell long read RNA and DNA sequencing as well as novel approaches to detect DNA replication through base modification
Collaborator Contribution ONT will contribute through providing expertise in machine learning models applications (base modification), technology solutions and protocols developments for single cell RNA / DNA seq
Impact Engagement with ONT on March 7th to develop the collaboration as part of the upcoming ISPs
Start Year 2022
 
Description Computational biology for Genomics 
Organisation IBM
Department IBM UK Labs Ltd
Country United Kingdom 
Sector Private 
PI Contribution We have had scoping meetings and with work with Ritesh Krishna on the project
Collaborator Contribution Initial sharing of expertise
Impact Paper https://doi.org/10.1101/2021.02.04.429826 Code https://github.com/JoshuaColmer/HallCircadian
Start Year 2017
 
Description Cytiva - Single-cell transcriptomes 
Organisation Cytiva
Country United Kingdom 
Sector Private 
PI Contribution Data comparing the new device with other methods available on the market. EI performed single-cell transcriptomic analysis using EI's 10X Genomics Chromium platform and Illumina NovaSeq 6000 system, followed by detailed bioinformatic analysis and generated data.
Collaborator Contribution Cytiva have developed a new device for the disaggregation of human and animal solid tissue and tumors into viable single cells.
Impact New product application note
Start Year 2020
 
Description Dr Spannagl and Prof. Meyer 
Organisation Helmholtz Association of German Research Centres
Department Helmholtz Zentrum Munchen
Country Germany 
Sector Academic/University 
PI Contribution We work in collaboration to analyse and annotate complex plant genomes
Collaborator Contribution The have supplied expertise and staff time to collabrative projects
Impact Rabanus-Wallace, M. T., Hackauf, B., Mascher, M., Lux, T., Wicker, T., Gundlach, H., et al. (2019). Chromosome-scale genome assembly provides insights into rye biology, evolution, and agronomic potential. bioRxiv, 5, 2019.12.11.869693. http://doi.org/10.1101/2019.12.11.869693 L.-J. Gardiner, R. Joynson, J. Omony, R. Rusholme-Pilcher, L. Olohan, D. Lang, C. Bai, M. Hawkesford, D. Salt, M. Spannagl, K. F. X. Mayer, J. Kenny, M. Bevan, N. Hall, and A. Hall, "Hidden variation in polyploid wheat drives local adaptation.," Genome Res, http://doi.org/10.1101/gr.233551.117 Walkowiak, S., Gao, L., Monat, C. et al. Multiple wheat genomes reveal global variation in modern breeding. Nature 588, 277-283 (2020). https://doi.org/10.1038/s41586-020-2961-x
Start Year 2016
 
Description EI- IBM 
Organisation IBM
Department IBM Research in the UK
Country United Kingdom 
Sector Private 
PI Contribution EPSRC CASE studentship 'Development of new machine learning methods and algorithms for the efficient integration of 'omics data to quantify the role of the host microbiome in therapeutic diets'. Develop innovative technical approaches that (a) exploit large-scale longitudinal datasets from dietary treatments of Crohn's disease (b) combine metagenomics data with metabolomics
Collaborator Contribution EPSRC CASE studentship 'Development of new machine learning methods and algorithms for the efficient integration of 'omics data to quantify the role of the host microbiome in therapeutic diets'. IBM contributes to development and application of ML approach and statistical algorithms on networks.
Impact Collaborations, Research databases & models
Start Year 2022
 
Description Engineering Regulatory Networks 
Organisation John Innes Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution Expertise in synthetic biology, engineering regulatory networks and gene editing.
Collaborator Contribution Expertise in systems biology, network reconstruction and modelling.
Impact Funded grant proposal: Engineering Gene Regulatory Networks To Design Disease Resistant Crops
Start Year 2023
 
Description Engineering Regulatory Networks 
Organisation University of York
Department Centre for Novel Agricultural Products (CNAP)
Country United Kingdom 
Sector Academic/University 
PI Contribution Expertise in synthetic biology, engineering regulatory networks and gene editing.
Collaborator Contribution Expertise in systems biology, network reconstruction and modelling.
Impact Funded grant proposal: Engineering Gene Regulatory Networks To Design Disease Resistant Crops
Start Year 2023
 
Description Engineering plant responses to environmental nitrogen 
Organisation University of California, Davis
Department UC Davis Genome Cente
Country United States 
Sector Academic/University 
PI Contribution Contributed expertise in genome engineering, synthetic biology and regulatory networks in plants. Contributed to joint grant proposals.
Collaborator Contribution Contributed expertise on systems biology, root growth and plant nitrogen responses. Contributed to joint grant proposals.
Impact Collaborative grant funded: "18 BTT EAGER - Engineering complex traits using targeted, multiplexed genetic and epigenetic mutagenesis" Collaborative manuscript submitted: Bian et al doi: 10.1101/2023.07.17.549299v2
Start Year 2018
 
Description Evolution of cis-regulatory activity associated with rapid phenotypic diversity 
Organisation University of Basel
Country Switzerland 
Sector Academic/University 
PI Contribution To further analyse gene regulatory network evolution associated with traits of cichlid phenotypic diversity, we 1. developed and optimised the assay for transposable active chromatin sequencing (ATAC-seq) protocol for cichlid fish tissues, and 2. characterised and compared the tissue-specific activity of regulatory regions in representative species of the great lake radiations. This can then be carried over
Collaborator Contribution Our collaborators include Domino Joyce (University of Hull) and Walter Salzburger (University of Basel) that provided live fish and tissues to isolate cells for ATAC-Seq.
Impact We have: 1. Developed and optimised the assay for transposable active chromatin sequencing (ATAC-seq) protocol for cichlid fish tissues, and 2. Carried out a single lane of Hi-Seq sequencing of 20 ATAC and genomic DNA control libraries to test the protocol Since the protocol has been largely optimised, we are now preparing libraries for more tissue samples and species for higher-coverage sequencing.
Start Year 2017
 
Description Evolution of cis-regulatory activity associated with rapid phenotypic diversity 
Organisation University of Hull
Country United Kingdom 
Sector Academic/University 
PI Contribution To further analyse gene regulatory network evolution associated with traits of cichlid phenotypic diversity, we 1. developed and optimised the assay for transposable active chromatin sequencing (ATAC-seq) protocol for cichlid fish tissues, and 2. characterised and compared the tissue-specific activity of regulatory regions in representative species of the great lake radiations. This can then be carried over
Collaborator Contribution Our collaborators include Domino Joyce (University of Hull) and Walter Salzburger (University of Basel) that provided live fish and tissues to isolate cells for ATAC-Seq.
Impact We have: 1. Developed and optimised the assay for transposable active chromatin sequencing (ATAC-seq) protocol for cichlid fish tissues, and 2. Carried out a single lane of Hi-Seq sequencing of 20 ATAC and genomic DNA control libraries to test the protocol Since the protocol has been largely optimised, we are now preparing libraries for more tissue samples and species for higher-coverage sequencing.
Start Year 2017
 
Description Genetic basis of adaptation to extreme environments: insights from the genome of Alcolapia grahami 
Organisation University College London
Country United Kingdom 
Sector Academic/University 
PI Contribution Sequencing of A. grahami genome with short and long read technology and transcriptome sequencing
Collaborator Contribution Our collaborators Julia Day and Kanchon Dasmahapatra are able to source live Alcolapia and preserved fish samples for sequencing. As such we have used O. amphimelas for whole genome and transcriptome sequencing.
Impact O. amphimelas DNA/RNA is currently being extracted for genome and transcriptome sequencing. For the purpose of this collaboration, we are also improving the Alcolapia genome assembly for chromosome level contiguity. Our collaborators are interested in carrying out functional testing of interesting candidate genes in Alcolapia that may be important in their adaptations. Julia Day and Lewis White recently travelled to Tanzania, bringing back live Alcolapia to the UK to set up experimental stocks for functional testing. As such, Lewis White has succcesfully carried out gene knock-outs and rescue in Alcolapia that will be useful for future functional validations.
Start Year 2017
 
Description Genetic basis of adaptation to extreme environments: insights from the genome of Alcolapia grahami 
Organisation University of York
Country United Kingdom 
Sector Academic/University 
PI Contribution Sequencing of A. grahami genome with short and long read technology and transcriptome sequencing
Collaborator Contribution Our collaborators Julia Day and Kanchon Dasmahapatra are able to source live Alcolapia and preserved fish samples for sequencing. As such we have used O. amphimelas for whole genome and transcriptome sequencing.
Impact O. amphimelas DNA/RNA is currently being extracted for genome and transcriptome sequencing. For the purpose of this collaboration, we are also improving the Alcolapia genome assembly for chromosome level contiguity. Our collaborators are interested in carrying out functional testing of interesting candidate genes in Alcolapia that may be important in their adaptations. Julia Day and Lewis White recently travelled to Tanzania, bringing back live Alcolapia to the UK to set up experimental stocks for functional testing. As such, Lewis White has succcesfully carried out gene knock-outs and rescue in Alcolapia that will be useful for future functional validations.
Start Year 2017
 
Description Genetic basis of adaptation to extreme environments: insights from the genome of the soda tilapia (Alcolapia grahami) 
Organisation South Eastern Kenya University
Country Kenya 
Sector Academic/University 
PI Contribution Full expenses for Geraldine Kavembe (SEKU) to sample Alcolapia tissue samples from Lake Magadi, Kenya. This included sampling equipment/reagents, travel, accomodation and subsistance.
Collaborator Contribution Dr Geraldine Kavembe (SEKU) contributed in the: 1. Organisation and permits for sampling in Lake Magadi by dealing with the appropriate fisherie officers 2. Private boat hire 3. Transport hire and accomodation 4. Species identification, tissue sampling and dissection 5. Sample shipping
Impact Tissue samples from A. grahami have been sequenced to include: 1. Whole genome sequencing using short Illumina and Nanopore reads (10x Chromium pending). We currently have a whole genome assembly based on the short reads that is currently being supplemented with the long read data. 2. RNA-Seq of gill and liver for genome annotation and gene expression analyses. Both will be published. Also, Tarang Mehta hosted a year in industry student (Nicole Forrester) at the Earlham Institute where she extracted RNA, prepared cDNA libraries and sequenced the trnascriptomes of Alcolapia and other tilapia tissue samples.
Start Year 2017
 
Description Genetic determinants of transcriptional stochasticity 
Organisation Biochemistry and Plant Molecular Physiology
Country France 
Sector Public 
PI Contribution Collaborative experiments to investigate the role of transcription-factor-DNA interactions in stochastic gene expression
Collaborator Contribution Collaborative experiments to investigate the role of transcription-factor-DNA interactions in stochastic gene expression
Impact Ongoing
Start Year 2021
 
Description Genome 10K Consortium 
Organisation University of California, Davis
Department UC Davis Genome Cente
Country United States 
Sector Academic/University 
PI Contribution The G10K consortium is an international consortium of tissue curators, biologists, conservationists, genome scientists, computer scientists, outreach educators, and more. Federica Di Palma is a council member of the Consortium and has provided advice to the current ongoing projects. Organised meetings and contributed talks to several workshops and meetings.
Collaborator Contribution The G10K leadership and community of scientists built an infrastructure from sample collection to genome sequencing, assembly, annotation, alignments, public data releases, and analyses for publications.
Impact Collaboration is multidisciplinaryand includes tissue curators, biologists, conservationists, genome scientists, computer scientists, outreach educators, and more from different countries. Outputs include press releases, workshops, meetings, publications.
Start Year 2011
 
Description Gut - microbiome single cell project 
Organisation University of Toronto
Country Canada 
Sector Academic/University 
PI Contribution We have sequenced and analysed samples provided by the partner.
Collaborator Contribution These samples were from an experiment the partner have previously carried out. We were not able to generate such samples, and as the cell isolation protocol was the same that we normally use, processing their samples and then compare the different conditions were straightforward for us.
Impact Single-cell sequence data generated (stem cell, Paneth cell, transit amplifying cells) from mouse (germ-free, ex-germ-free, normal). Data analysis and publication is ongoing.
Start Year 2018
 
Description IBD Multi-omics, Prof. Severine Vermeire, KU Leuven 
Organisation University of Leuven
Country Belgium 
Sector Academic/University 
PI Contribution Stemming from our strategic collaboration with the IBD unit headed by Prof. Séverine Vermeire at KU Leuven, we have access to patient -omic datasets (such as genotyping, tissue and immune cell transcriptomics, blood proteomics, gut microbiome etc). We use data integration approaches aided by systems biology and machine learning to disentangle the complexity of IBD by exploiting the benefits delivered by the cumulative insights rendered by multiple -omic layers.
Collaborator Contribution Clinical datasets including -omic and phenotypic trait data. Scientific advice on grants
Impact The project is multi-disciplinary involving concepts from systems biology, statistics, microbiology, mathematics, computational biology (software resources etc) and experimental validation where appropriate and necessary. Outcomes Machine Learning and Big Data integration in the clinical research of Inflammatory Bowel Disease. Seyed-Tabib N, Madgwick M, Sudhakar P, Verstockt B, Korcsmaros T, Vermeire S. (under review) Systems genomics of ulcerative colitis: combining GWAS and signalling networks for patient stratification and individualised drug targeting in ulcerative colitis. J. Brooks*, D. Modos*, P. Sudhakar*, D. Fazekas, A. Zoufir, A. Watson, M. Tremelling, B. Verstockt, S. Vermeire, A. Bender, S. Carding, T. Korcsmaros. (in preparation - to be submitted March 2019) (*joint first authors)
Start Year 2018
 
Description IBM 
Organisation IBM
Department IBM Research in the UK
Country United Kingdom 
Sector Private 
PI Contribution As part of this collaboration the Earlham Institute is providing data, genomic expertise to the collaborator
Collaborator Contribution IBM is providing expertise in machine learning application, and software development
Impact no output yet
Start Year 2022
 
Description IBM 
Organisation IBM
Department IBM UK Ltd
Country United Kingdom 
Sector Private 
PI Contribution This project aims to leverage these new resources together with large gene expression data sets to reconstruct regulatory networks controlling important traits. With outputs feeding directly into UK and International wheat research and UK wheat breeding programmes. The collaboration focuses around two large data sets: the first, a high resolution time series data set for wheat and the second, a developmental time course for 16 international elite cultivars. The project aims to: 1. Develop normalisation methods for the transcriptome data sets (RNA-seq data), specific for dealing with the complexities of time course data and a complex polyploid genome. Benchmark these new approaches against existing tools. 2. Develop AI pattern matching algorithms to identify gene-expression modules and correlate these with biological processes. Use pattern matching algorithms to interrogate the high resolution data sets and to identify differences between regulatory networks in elite cultivars 3. Correlate changes in temporal or developmental expression patterns with changes in promoter architecture 4. Use network inference, co-expression and gene modules to reconstruct regulatory networks. Identify how network structure changes over time and between cultivars. This project will have impact for scientists as it will address fundamental questions about temporal regulation of processes in wheat and how a complex networks work across multiple genomes within a polyploid. By comparing networks across elite cultivars it will also have an impact for UK and international wheat breeders, identification of how breeding programmes have changed the architure of regulatory networks. This will have important impact for the selection of future networks for breeders to target or for assessing the selection of breeding material. It will allow breeders to make full use of the new resources and technologies. To ensure the impact to the UK industry is realised we aim to present this work a UK networking meeting and to visit and involve three private UK breeding companies RAGT, KWS and Elsoms seeds in early output from the project.
Collaborator Contribution IBM have are involved in applying ML and AI approaches to analyse gene expression data in wheat and reconstruct gene networks.
Impact https://github.com/AHallLab/PredictingCircadianTime Joint grant with the Alan Turing Institute https://doi.org/10.1101/2021.02.04.429826
Start Year 2017
 
Description KWS 
Organisation KWS UK
Country United Kingdom 
Sector Private 
PI Contribution Generated double haploid population for the IWYP project and provide material for INTREPID and the BBSRC/EAGER work
Collaborator Contribution Know of the techniques and approaches we are using, early access to the data we generate
Impact Double haploid seed population
Start Year 2017
 
Description Molecular Medicine Catapult - Psychiatry Consortium 
Organisation Medicines Discovery Catapult
Country United Kingdom 
Sector Private 
PI Contribution As part of the Psychaitry Consortium my group will be leading on all the bioinformatic analyses for the project aiming to identfy transcripts with tissue specific expression for a primary candidate in neuropsychaitric disorder. The aim it be able to identify proteins with brain specific expressions that can be used as targets for frug development
Collaborator Contribution The University of Oxford leads on the molecular work, generating the data that are analysed by my group. As industrial partners, lead scientists at Boehringer Ingelheim and Biogen provide feedback on their needs, the selection of transcripts to pursue, further analyses.
Impact The project started n December 1st 2020, it is too early to list outputs. The major outcome is the funding to support the work as part of the project (£120,000). The collaboation is highly disciplinary inculding molecular biology, neurobiology and bioinformatics.
Start Year 2020
 
Description Moussa Benhamed 
Organisation University of Paris-Saclay
Country France 
Sector Academic/University 
PI Contribution WE are collaborating with Moussa Benhamed to develop Next generation sequencing technology to explore the 3D structural organisation in the wheat nucleus and epigenetic regulation in wheat.
Collaborator Contribution The have built sequencing libraries for design future wheat and are providing staff training
Impact Production of sequencing libraries analysis of histone modification, 3D genome structural organisation and Chromatin accessibility.
Start Year 2018
 
Description Organoid Technologies, Dr. Tom Wileman, UEA 
Organisation University of East Anglia
Country United Kingdom 
Sector Academic/University 
PI Contribution Analysis of -omic datasets; integration into networks; hypothesis generation and experimental validation
Collaborator Contribution Training in organoid culture
Impact Integrative analysis of Paneth cell proteomic and transcriptomic data from intestinal organoids reveals functional processes dependent on autophagy. Jones EJ, Matthews ZJ, Gul L, Sudhakar P, Treveil A, Divekar D, Buck J, Wrzesinski T, Jefferson M, Armstrong SD, Hall LJ, Watson AJM, Carding SR, Haerty W, Di Palma F, Mayer U, Powell PP, Hautefort I, Wileman T, Korcsmaros T. Dis Model Mech. 2019 Feb 27. pii: dmm.037069. doi: 10.1242/dmm.037069. [Epub ahead of print] PMID: 30814064
Start Year 2017
 
Description RAGT 
Organisation RAGT Seeds
Country United Kingdom 
Sector Private 
PI Contribution Identify key material for our EAGER project and Design future wheat. Support for collaboration with IBM.
Collaborator Contribution Discussion of methods and analysis of material relevant to RAGT.
Impact none yet
Start Year 2018
 
Description REC Q7 accelerator of recombination in crops and as a tool to increase recombination 
Organisation KWS UK
Country United Kingdom 
Sector Private 
PI Contribution CSP researchers contributed scientific background and expertise
Collaborator Contribution Consultancy services on commercialisation and IP from JMB consulting using Follow-on Pathfinder funding (BB/T010096/1) led to this collaboration TRDF grant application with Syngenta, KWS, RAGT (BB/T011963/1)
Impact led to a TRDF grant application with Syngenta, KWS, RAGT (BB/T011963/1)
Start Year 2019
 
Description REC Q7 accelerator of recombination in crops and as a tool to increase recombination 
Organisation RAGT Seeds
Country United Kingdom 
Sector Private 
PI Contribution CSP researchers contributed scientific background and expertise
Collaborator Contribution Consultancy services on commercialisation and IP from JMB consulting using Follow-on Pathfinder funding (BB/T010096/1) led to this collaboration TRDF grant application with Syngenta, KWS, RAGT (BB/T011963/1)
Impact led to a TRDF grant application with Syngenta, KWS, RAGT (BB/T011963/1)
Start Year 2019
 
Description REC Q7 accelerator of recombination in crops and as a tool to increase recombination 
Organisation Syngenta International AG
Department Syngenta Ltd (Bracknell)
Country United Kingdom 
Sector Private 
PI Contribution CSP researchers contributed scientific background and expertise
Collaborator Contribution Consultancy services on commercialisation and IP from JMB consulting using Follow-on Pathfinder funding (BB/T010096/1) led to this collaboration TRDF grant application with Syngenta, KWS, RAGT (BB/T011963/1)
Impact led to a TRDF grant application with Syngenta, KWS, RAGT (BB/T011963/1)
Start Year 2019
 
Description Role of selective autophagy in bacterial-host interactions, Prof. Ioannis Nezis, University of Warwick 
Organisation University of Warwick
Department School of Life Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution Selective autophagy and LC3 target predictions for pathogen-autophagy interplay with Dr. Ioannis Nezis, Department of Life Sciences, University of Warwick. We investigated using a combination of computational approaches the possible interactions between the proteins encoded by several bacterial pathogens and the core autophagy proteins of the host. We also carried out a part of the experimental validation using assays on cell lines to determine the effect of the effector protein on autophagy.
Collaborator Contribution Predictions between the autophagy adaptor LC3 and bacterial proteins using the custom made tool iLIR (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5079668/) Second part of the experimental validation assessing the binding between LC3 and selected bacterial effectors.
Impact What We Learned From Big Data for Autophagy Research. Jacomin AC, Gul L, Sudhakar P, Korcsmaros T, Nezis IP. Front Cell Dev Biol. 2018 Aug 17;6:92. doi: 10.3389/fcell.2018.00092. eCollection 2018. Review. Sudhakar P., Claire-Jacomin A., Hautefort I., Samavedam S., Fatemian K., Ari E., Gul L., Demeter A., Jones E., Korcsmaros T., Nezis I.(2019) Targeted interplay between bacterial pathogens and host autophagy In Press. Autophagy 2019.
Start Year 2017
 
Description Single cell sequencing of plant leaves 
Organisation Dolomite Microfluidics
Country United Kingdom 
Sector Private 
PI Contribution Microfluidic sorting, encapsulation and transcriptome sequencing of single cells isolated from plant leaves.
Collaborator Contribution Use of the microfluidic platform, preparation and sequencing of transcriptome libraries.
Impact No outputs yet.
Start Year 2019
 
Description The 200 mammals project: sequencing genomes by a novel cost-effective method, yielding a high resolution annotation of the human genome. 
Organisation Broad Institute
Country United States 
Sector Charity/Non Profit 
PI Contribution Part of the consortium which is analysing the data.
Collaborator Contribution Proposal submitted to NHGRI and funded
Impact In combination with the ~50 already existing high quality placental mammalian assemblies, the project produced the sequence of one placental mammal per family for a total of 150 species. The new assembly method: DISCOVAR de novo, was used to allow the production of a good quality novel genome assembly using only a single sequencing library type.
Start Year 2016
 
Description Uncovering regulators of autophagy in pancreatic cancer, Francis Crick Institute 
Organisation Francis Crick Institute
Country United Kingdom 
Sector Academic/University 
PI Contribution Target prioritization using a combination of biological interaction networks, HT screens and -omic datasets. Hypothesis generation for experimental verification
Collaborator Contribution Experimental verification of the short-listed targets and delineating their mechanisms of action
Impact MDH1 and MPP7 regulate autophagy in pancreatic ductal adenocarcinoma. Tooze SA, New M, Van Acker T, Sakamaki JI, Jiang M, Saunders RE, Long J, Wang VM, Behrens A, Sudhakar P, Korcsmaros T, Ryan KM, Howell M, Cerveira J, Jefferies HBJ. Cancer Res. 2019 Feb 14. pii: canres.2553.2018. doi: 10.1158/0008-5472.CAN-18-2553. [Epub ahead of print] PMID: 30765601
Start Year 2017
 
Title GENOMIC ANALYSIS 
Description A method of identifying contribution of a genomic variation to a phenotypic feature is disclosed. The method comprises determining a degree of a genomic variation (51; Fig. ) in each individual in a set of individuals and recording the degree of genomic variation in each individual in a database, for example, in a first table (6). The method comprises determining a location of the genomic variation to allow determination, by virtue of the location, of whether the genomic variation affects a gene product directly and/or regulates production of a gene product (53, 54; Fig. 5). The method comprises determining a first gene (51; Fig. 5) affected by the genomic variation. When the genomic variation affects a gene product directly, recording the gene, in the coding sequence of which the genomic variation is located, as the first gene, for example, in a second table (7). When the genomic variation regulates the production of a gene product, recording the gene, in the promoter region or other regulatory region of which the genomic variation is located, as the first gene. The method comprises determining an outcome of the genomic variation on the first gene and recording the outcome of the genomic variation in the database, for example, in the second table and determining the presence or absence of one or more other gene products (i) interacting with the first gene, (ii) encoded by the first gene; and/or (iii) regulating the first gene and, if present, recording the identity of the gene encoding the one or more other gene products in the database as the second gene, for example, in the second table. 
IP Reference WO2020095035 
Protection Patent application published
Year Protection Granted 2020
Licensed No
Impact This application is abandoned, there is limited potential for exploitation and impact realisation.
 
Title Genomic analysis 
Description A method of identifying contribution of a genomic variation to a phenotypic feature, comprising determining a degree of a genomic variation (51; Fig. 5) in each individual in a set of individuals and recording the degree of genomic variation in each individual in a database, in a first table (6), determining a location of the genomic variation to allow determination of whether the genomic variation affects a gene product directly and/or regulates production of a gene product (53, 54; Fig. 5), thus determining a first gene (51; Fig. 5) affected by the genomic variation. The genomic variation may affect a gene product directly or indirectly, either of which may be recorded as the first gene, for example, in a second table (7). The method may include determining the presence or absence of one or more other gene products (i) interacting with the first gene, (ii) encoded by the first gene; and/or (iii) regulating the first gene and, if present, recording the identity of the other gene products in the database as the second gene in the second table. The method may determine appropriate treatment pathways. 
IP Reference GB2578727 
Protection Patent application published
Year Protection Granted 2020
Licensed No
Impact This application is allowed to lapse, there is limited potential for exploitation and impact realisation.
 
Title Mikado - Leveraging multiple transcriptome assembly methods for improved gene structure annotation 
Description Mikado is a lightweight Python3 pipeline to identify the most useful or "best" set of transcripts from multiple transcript assemblies. Our approach leverages transcript assemblies generated by multiple methods to define expressed loci, assign a representative transcript and return a set of gene models that selects against transcripts that are chimeric, fragmented or with short or disrupted CDS. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact Mikado has been utilised to deliver improved gene annotation for Ash doi:10.1038/nature20786 and wheat doi: 10.1101/gr.217117.116 and was utilised by the international wheat genome sequencing consortium. 
 
Title Pipeline for long non coding RNA identification 
Description Pipeline enabling long non coding identification taking as input RNA-Seq data, genome sequence, and annotation. The pipeline handle the read mapping, de noo transcript assembly, comparison with existing annotations to identify novel intergenic transcript, assess the coding potential of the noevl transcripts report those identified as non coding and at least 200 nt long. 
Type Of Technology Webtool/Application 
Year Produced 2021 
Open Source License? Yes  
Impact Long non codig RNAs are generally associated with gene expression regulation and previouly identified to have major roles in both animals and plant biology. The pipeline is organism agnostic, enabling the identification of lon non coding RNAs in any eukaryotic species. The aim is to make the pipeline available on Galaxy for the community to use. 
URL https://github.com/TGAC/lncRNA-analysis
 
Title Portcullis - Efficient and accurate detection of splice junctions from RNAseq 
Description Portcullis stands for PORTable CULLing of Invalid Splice junctions from pre-aligned RNA-seq data. It is known that RNAseq mapping tools generate many invalid junction predictions, particularly in deep datasets with high coverage over splice sites. In order to address this, instead for creating a new RNAseq mapper, with a focus on SJ accuracy we created a tool that takes in a BAM file generated by an RNAseq mapper of the user's own choice (e.g. Tophat2, Gsnap, STAR2 or HISAT2) as input (i.e. it's portable). It then, analyses and quantifies all splice junctions in the file before, filtering (culling) those which are unlikely to be genuine. Portcullis output's junctions in a variety of formats making it suitable for downstream analysis (such as differential splicing analysis and gene modelling) without additional work. Portcullis can also filter the original BAM file removing alignments associated with bad junctions. Both the filtered junctions and BAM files are cleaner and more usable resources which can more effectively be used to assist in downstream analyses such as gene prediction and genome annotation. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact Porcullis has been utilised to deliver improved gene annotation for Ash doi:10.1038/nature20786 and wheat doi: 10.1101/gr.217117.116 and was utilised by the international wheat genome sequencing consortium. 
 
Title PredictingCircadianTime 
Description We developed a ML based pipeline to predict the circadian time (phase) at any single transcriptomic sampling time point using gene expression data from a set of marker genes. This code uses an artificial neural network (with Tensorflow). 
Type Of Technology Webtool/Application 
Year Produced 2020 
Open Source License? Yes  
Impact https://doi.org/10.1101/2021.02.04.429826 This work was done in collaboration with IBM and is being taken forward in a collaboration with the Alan Turing Institute 
 
Title REAT - Robust and Extendable eukaryotic Annotation Toolkit 
Description REAT is a robust easy-to-use genome annotation toolkit for turning high-quality genome assemblies into usable and informative resources. REAT makes use of state-of-the-art annotation tools and is robust to varying quality and sources of molecular evidence. REAT provides an integrated environment that comprises both a set of workflows geared towards integrating multiple sources of evidence into a genome annotation, and an execution environment (Docker, Singularity) for these workflows. 
Type Of Technology Webtool/Application 
Year Produced 2021 
Open Source License? Yes  
Impact Being used to support EI's annotation projects including the DToL Protist project Components of the toolkit were developed to support the annotation of wheat accessions as part of the 10+ Wheat Genome Project. 
URL https://plants.ensembl.org/Triticum_aestivum/Info/Strains?db=core
 
Title ei-annotation - eukaryotic annotation pipeline 
Description Eukaryotic genome annotation pipeline 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact Annotation pipeline being utilised to support http://www.10wheatgenomes.com/10-wheat-genomes-project-and-the-wheat-initiative/ 
 
Title minos - a gene model consolidation pipeline for genome annotation projects 
Description Minos is a Python3/Snakemake - based pipeline that generates and utilises metrics derived from protein, transcript and expression data sets to consolidate gene models obtained from gene annotation workflows. 
Type Of Technology Webtool/Application 
Year Produced 2020 
Open Source License? Yes  
Impact The tool has bee used to deliver annotation for 9 wheat accessions as part of the 10+ Wheat Genomes Project (http://www.10wheatgenomes.com/) and is being used to support a variety of Earlham Institute annotation projects 
URL http://www.10wheatgenomes.com/
 
Company Name TraitSeq 
Description TraitSeq develops a platform for the agricultural industry, which uses AI to identify and predict complex traits and breed optimised crops. 
Year Established 2023 
Impact We are currently in the start up stage and wait for UKRI follow on funding, the company was developed as part of the iCURE process.
Website https://traitseq.com/
 
Description 10 plus wheat genome project workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The meeting was to provide a consortium update on the 10 plus wheat genome project
Year(s) Of Engagement Activity 2018
URL http://www.10wheatgenomes.com
 
Description 10 years of impact: Keeping living things healthy - 23/05/2019 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Website article highlighting the impact of our research so far including working delivered through the CSP from a report commissioned by EI (Brookdale Consulting).
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/articles/10-years-impact-keeping-living-things-healthy
 
Description 17-21 July 2017_2nd Interdisciplinary Signaling Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact In this interdisciplinary workshop advanced science was combined with informal summer activities to solve multi-disciplinary scientific questions, by bringing early career scientists together with more established researchers in a relaxing and beautiful location.

Invited speakers presented talks on the topics of cell regulation, network modelling, genomics, systems biology, bioinformatics, structural biology, biochemistry, and cheminformatics. Then, selected talks from other participants will be followed by multi-disciplinary teamwork sessions in the afternoon, followed by cultural and social activities, such as medieval team building and handicraft activities in the Visegrad Castle. Poster sessions and plenty of informal opportunities allowed the participants to discuss complex and exciting questions as well as develop new collaborations. The renaissance surroundings of the venue nicely matched with the interdisciplinary nature of the workshop.
Year(s) Of Engagement Activity 2017
URL http://signalingworkshop.org/
 
Description 24-25 April 2017_Multiscale analysis of host-microbe interactions in plants, animals and humans 
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 The aim of this workshop was to bring together key experts and early-stage scientists working on host-microbe interactions, including pathogen infections, commensals and microbiome level studies, to share novel scientific ideas on the multiscale investigation of host-microbe interactions and to provide an exciting opportunity to establish and improve cross-disciplinary and UK-wide collaborations.

After kick off with three keynote speakers on current challenges, the program provides structured study groups to discuss 1) novel methodological approaches; 2) potential future projects requiring participants from different disciplines; 3) the best ways to get funding for such multi-disciplinary projects. We facilitated these goals with short presentations and brainstorming opportunities in coordinated team works, and with panel discussion with representatives of key relevant funding agencies and charities.
Year(s) Of Engagement Activity 2017
URL http://www.multiscalebiology.org.uk/events/event/multiscale-analysis-of-host-microbe-interactions/
 
Description 5 ways EI is improving global food security 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact 5 ways EI is improving global food security
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/articles/5-ways-earlham-institute-improving-global-food-security
 
Description 600k machine learning collaboration to supercharge data driven science 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact 600k machine learning collaboration to supercharge data driven science
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/newsroom/%C2%A3600k-machine-learning-collaboration-supercharge-data-driven...
 
Description A PhD, is it worth it? Just ask our students 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact A PhD, is it worth it? Just ask our students
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/articles/phd-it-worth-it-just-ask-our-students
 
Description A kaleidoscope of colours, shapes and sustainable plates: diving into cichlid fish diversity, Earlham Institute 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact A kaleidoscope of colours, shapes and sustainable plates: diving into cichlid fish diversity, Earlham Institute
Year(s) Of Engagement Activity 2018
 
Description A systems-level approach in studying autophagy modification by Salmonella Typhimurium. Early Career Researcher Symposium on Microbial Interactions Norwich 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact A systems-level approach in studying autophagy modification by Salmonella Typhimurium. Early Career Researcher Symposium on Microbial Interactions Norwich
Year(s) Of Engagement Activity 2019
 
Description A vedolizumab specific four-gene colonic signature accurately predicting future endoscopic remission in patients with inflammatory bowel disease, 14th congress of European Crohn's and colitis organisation Copenhagen, Denmark 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A vedolizumab specific four-gene colonic signature accurately predicting future endoscopic remission in patients with inflammatory bowel disease, 14th congress of European Crohn's and colitis organisation Copenhagen, Denmark
Year(s) Of Engagement Activity 2019
 
Description ARN2: Uncovering the multi-layered regulation of autophagy From Functional Genomics to Systems Biology 
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 ARN2: Uncovering the multi-layered regulation of autophagy From Functional Genomics to Systems Biology
Year(s) Of Engagement Activity 2019
 
Description Activity - DNA sequencer at Great Hockham Primary School 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Activity at the Great Hockham Primary School
Year(s) Of Engagement Activity 2019
 
Description Activity - Pink Pigeon Trail at the Norfolk Show 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Activity Pink Pigeon Trail at the Norfolk Show
Year(s) Of Engagement Activity 2019
 
Description Activity - Where have you BEEn? 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Activity at the Norwich Science Festival
Year(s) Of Engagement Activity 2019
 
Description Affordable genome sequencing for pathogen analysis to help tackle global epidemics 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact Blog post for the publication of the development of an affordable sequencing protocol applied to the sequencing of over 10,000 Salmonella isolates
Year(s) Of Engagement Activity 2022
URL https://www.earlham.ac.uk/newsroom/affordable-genome-sequencing-pathogen-analysis-help-tackle-global...
 
Description Agritech East Week 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact In order to stimulate a dialogue and discussion between scientists, farmers, breeders and more, we organised an interactive, show-and-tell style workshop for members of AgriTech East, who came to EI for three hours on a Tuesday evening.

The event showcased the latest advances in genome sequencing and bioinformatics, while then allowing groups to explore themes relevant to modern agriculture and research together.
Year(s) Of Engagement Activity 2018
 
Description An integrated multi-omics biomarker predicting endoscopic response in ustekinumab treated patients with Crohn's disease, 14th congress of European Crohn's and colitis organisation Copenhagen, Denmark 
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 An integrated multi-omics biomarker predicting endoscopic response in ustekinumab treated patients with Crohn's disease, 14th congress of European Crohn's and colitis organisation Copenhagen, Denmark
Year(s) Of Engagement Activity 2019
 
Description Analysing dynamic changes in the microbiome through systems biology approaches Scientific Advisory Board Meeting 
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 Analysing dynamic changes in the microbiome through systems biology approaches Scientific Advisory Board Meeting
Year(s) Of Engagement Activity 2019
 
Description Analysing intestinal organoids in a multi-omics, systems biology framework to investigate functional processes affected in Crohn's disease due to autophagy impairment, 14th congress of European Crohn's and colitis organisation Copenhagen, Denmark 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Analysing intestinal organoids in a multi-omics, systems biology framework to investigate functional processes affected in Crohn's disease due to autophagy impairment, 14th congress of European Crohn's and colitis organisation Copenhagen, Denmark
Year(s) Of Engagement Activity 2019
 
Description Analysing intestinal organoids in a multi-omics, systems biology framework to investigate gut health and host-microbe interactions Scientific Advisory Board Meeting Earlham Institute 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact Analysing intestinal organoids in a multi-omics, systems biology framework to investigate gut health and host-microbe interactions Scientific Advisory Board Meeting Earlham Institute
Year(s) Of Engagement Activity 2019
 
Description Analyzing intestinal organoids in a multi-omics, systems biology framework to investigate gut health and host-microbe interactions SYSBIO 2018 - Advanced Lecture Course on Systems Biology 
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 Analyzing intestinal organoids in a multi-omics, systems biology framework to investigate gut health and host-microbe interactions SYSBIO 2018 - Advanced Lecture Course on Systems Biology
Year(s) Of Engagement Activity 2019
 
Description Antibiotic resistance: people will die when antibiotics fail - 09/03/2010 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Audio interview to highlight work on antibiotic resistance in salmonella, combining big data and computational biology with single cell analysis to understand the rapid evolution going on at the fine scale, which draws out work carried out through the CSP.
Year(s) Of Engagement Activity 2019
URL https://www.earlham.ac.uk/articles/antibiotic-resistance-people-will-die-when-antibiotics-fail
 
Description Article: 'Should we genetically edit the food we eat?' The Conversation. 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Article co-written with an editor and social scientist and published at 'The Conversation'. This article is part of The Conversation's 'Head to Head' series, which feature academics from different disciplines chewing over current debates.
Year(s) Of Engagement Activity 2021
URL https://theconversation.com/should-we-genetically-edit-the-food-we-eat-we-asked-two-experts-162959
 
Description Bacterial regulation of host processes. A seminar in the Technical School of Agronomy and Engineering to BsC and MsC students. UPCT, Cartagena, Spain 
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 Bacterial regulation of host processes. A seminar in the Technical School of Agronomy and Engineering to BsC and MsC students. UPCT, Cartagena, Spain
Year(s) Of Engagement Activity 2019
 
Description Blog post "N is for nitrogen: how can we make our crops more sustainable?" 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Blog post "N is for nitrogen: how can we make our crops more sustainable?"
Year(s) Of Engagement Activity 2021
URL https://www.earlham.ac.uk/articles/n-nitrogen-how-can-we-make-our-crops-sustainable
 
Description Blog post - 'Unlocking power of gene editing to protect the natural environment' 
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 Blog post - 'Unlocking power of gene editing to protect the natural environment'
Year(s) Of Engagement Activity 2021
URL https://www.earlham.ac.uk/newsroom/unlocking-power-gene-editing-protect-natural-environment-earlham-...
 
Description Blog post: New legislation granted to progress plant gene editing in UK 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Blog post: New legislation granted to progress plant gene editing in UK
Year(s) Of Engagement Activity 2022
URL https://www.earlham.ac.uk/newsroom/new-legislation-granted-progress-plant-gene-editing-uk
 
Description Bob Damms - Department for International Trade - 18/12/2018 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Meeting to discuss potential funding opportunity
Year(s) Of Engagement Activity 2018
 
Description Breeding diversity into the future of aquaculture 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A feature for International Aquaculture Magazine, which has an international reach among aquaculture professionals.

The feature highlighted Earlham Institute's important work in understanding cichlid diversity in East Africa, while offering answers to how to breed tilapia in a more sustainable way.
Year(s) Of Engagement Activity 2018
 
Description British/ Colombian HE collaboration embedded within the Bio Parc Concept, Earlham Institute 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact British/ Colombian HE collaboration embedded within the Bio Parc Concept, Earlham Institute
Year(s) Of Engagement Activity 2017
 
Description Clive Lewis - Member of Parliment for Norwich South - 08/03/2019 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Policymakers/politicians
Results and Impact Visit from local MP to discuss Institute research activity and input into policy
Year(s) Of Engagement Activity 2019
URL https://twitter.com/EarlhamInst/status/1104040111401066496
 
Description Comparative analysis of Paneth cell and enteroendocrine cell transcriptomics: organoid and signalling network based approaches Research in progress talk at Quadram Institute. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Comparative analysis of Paneth cell and enteroendocrine cell transcriptomics: organoid and signalling network based approaches
Research in progress talk at Quadram Institute.
Year(s) Of Engagement Activity 2019
 
Description Computational Systems Biology 2: Analysing and visualising networks 
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 Training for local PhD students: Computational Systems Biology 2: Analysing and visualising networks
Year(s) Of Engagement Activity 2019
 
Description Conference Poster at Gordon Research Conference 
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 I presented my poster about the upcoming update to the SalmoNet database at the 2019 Gordon Research Conference on Salmonella Pathogenesis.
Year(s) Of Engagement Activity 2019
 
Description Conference Presentation - Genomics in Aquaculture - Evolutionn of chromatin accessibility in Nile tilapia 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Genomics in Aquaculture
Year(s) Of Engagement Activity 2022
 
Description Conference poster: Evolution of gene regulatory networks controlling traits under natural selection in cichlids 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Poster presentation on work on Evolution of gene regulatory networks controlling traits under natural selection in cichlids at Evolutionary Systems Biology conference, Cambridge, UK
Year(s) Of Engagement Activity 2018
 
Description Conference poster: Networks to catch the difference: Construction and analysis of Regulatory Networks applied to East African Lake Cichlids 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact poster presentation on work involving the construction and analysis of regulatory networks applied to East African Lake Cichlids
Year(s) Of Engagement Activity 2018
 
Description Cytokine responsive transcriptional networks in inflammatory bowel disease 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Oral presentation to ~50 scientists and clinicians at the 6th Young European Crohns and colitis organisation basic science program in Vienna, Austria.
Year(s) Of Engagement Activity 2020
URL https://www.ecco-ibd.eu/discover-the-programme-2020/educational-programme-2020/6th-y-ecco-basic-scie...
 
Description Dialogue: food and health, what matters to you? - 24/10/2019 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Dialogue: food and health, what matters to you? was a new event at the Norwich Science Festival supported by Professor Neil Hall and Dr Nicola Patron. The event was an invitation to the public to join Norwich Research Park scientists and work together with them to solve the problems that you see, and inspire the science of the future.
Year(s) Of Engagement Activity 2019
URL https://docs.google.com/document/d/13yGwFkzh-9YDVUYMBzkhm7i_E4NnytZt74LBFrmjhNU/edit?usp=sharing
 
Description Digital oral presentation at 14th congress of European Crohn's and colitis organisation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Conference oral presentation at the 14th congress of European Crohn's and colitis organisation. Presentation tited "the regulatory landscape of intestinal cells - investigating the transcriptional effect of autophagy impairment observed in Crohn's disease using organoid and network biology approaches". Digital oral presentation at main congress and also an oral presentation at the Y-ECCO basic science workshop.
Year(s) Of Engagement Activity 2019
URL https://www.ecco-ibd.eu/ecco19.html
 
Description Dr Paul Kersey - Royal Botanic Gardens Kew - 14/12/2018 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Meeting to discuss collaborative project
Year(s) Of Engagement Activity 2018
 
Description EI Innovate - 09/01/2019 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Website article highlighting the importance of knowledge exchange, reflecting on the success of the first EI Innovate KEC focussed event which including showcasing the CSP.
Year(s) Of Engagement Activity 2019
URL https://www.earlham.ac.uk/articles/ei-innovate-why-knowledge-exchange-important
 
Description EI Innovate 17 November 2022 (In-Person) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact In its fourth year, EI Innovate is an annual engagement event that explores opportunities for innovation and collaboration among attendees from agri-food, biotech and med-tech sectors. The theme of EI Innovate 2022 was 'tackling urgent global challenges through pioneering research' and served to highlight specific areas where EI's research is generating impact, driven by a targeted programme delivered by Group Leaders, members of faculty and departmental heads. This year was held purely in an in-person format, and on a single day to maximise accessibility for attendees. Three key themes were represented across the programme of talks: Food Security and Environment Sustainability (the impact of genomes on crop breeding, and improving aquaculture with genomic resources for tilapia breeding); Enabling others to advance research and innovate (advancing and enabling data-intensive bioscience, and sharing expertise through training); and Improving Human Health (Genomic approaches to understand the emergence of virulence and AMR in Salmonella, and preventative lifestyle modifications). A registration fee of £50 covered refreshments and lunch for delegates.
Year(s) Of Engagement Activity 2022
URL https://www.earlham.ac.uk/events/ei-innovate-2022#programme
 
Description EI Innovate 17-18 November 2021 (Virtual) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact In its third year, EI Innovate aimed to explore opportunities for collaboration and innovation with external organisations. This year the event was delivered as an online-only format, spread across two days, with each half-day session focusing on one of the three themes: 1) Natural products & biomanufacturing - exploring how synthetic biology and data-driven approaches can facilitate the discovery of new bioactive compounds and develop biomanufacturing platforms based on plants 2) AI in plant science - exploring how AI and ML tools and techniques can help with the understanding of many biological functions in plants that underline important economic traits such as resistance to pathogens, nutrient utilisation and structural development 3) Omics approaches to study the human gut microbiome - exploring how bioinformatics, systems biology and machine learning approaches can be used for advanced microbiome analysis and to facilitate personalised microbiome treatments, identification of novel biomarkers and pathogens, and antimicrobial resistant features of our microbiota. Sharing examples of existing collaborations, this event was a chance to explore new opportunities. The two sessions on day 1 were structured with three talks, one from EI faculty and two from external collaborators, a Q&A panel discussion, and group networking on Spatial. The second session on AI also included flash talks from the Alan Turing Institute Fellows. The third session on the morning of day 2 took the format of several short talks from groups leaders and PhD students, followed by a Q&A panel discussion and further networking opportunities in spatial in the afternoon.
Year(s) Of Engagement Activity 2021
URL https://www.earlham.ac.uk/ei-innovate-2021-linking-datasets-and-bioscience
 
Description EI Innovate 17-19 November 2020 (Virtual) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact In its second year, EI Innovate aimed to explore opportunities for collaboration and innovation with external organisations. This year the event was converted to an online only format, spread across three days, with each day focussing on one of the three themes:

1) Disease identification and monitoring - how genomics and bioinformatics are used for disease identification and monitoring, from COVID-19, to AMR to agricultural pathogens.
2) Finding a needle in a haystack - Identifying specific targets in health and disease with long read RNA and single cell sequencing.
3) Accelerating plant breeding with next generation genetics, genomics and epigenetics.

Sharing examples of existing collaborations, this event was a chance to explore new opportunities. Each day was structured with two talks, one from EI faculty and one from an external collaborator, a Q&A panel discussion, facilitated break out discussions and then slots to arrange one-to-one meetings with other participants in the afternoon (event times 09:30-15:30), arranged using the software Meeting Mojo.
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/ei-innovate-2020
 
Description EI Innovate event - 13/11/2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact The inaugural EI innovate event showcased EIs capabilities and expertise in genomics, bioinformatics, synthetic biology, crop phenotyping, and high-performance computing including the CSP. This event aimed to help industry, academics, charity and voluntary organisations fully understand the opportunities for collaboration with EI, and how engaging with EI science and services can be of benefit. EI Innovate: genomics data to advance bioscience, held on 13th November 2019, was a success. It was attended by 82 people, 26 EI staff who delivered talks, tours and discussion sessions, prepared posters and came to network, 31 representatives from industry (across agri-food, biotech and life sciences sectors), 2 BBSRC staff, 2 representatives from Food Standards Agency, representatives from KTN, NALEP, National Biofilms Centre and Centre for Process Innovation, and 14 representatives from (9 from UEA) academic institutions. We attracted 3 high profile external speakers from: Natural History Museum (Director of Research); Royal Botanic Gardens Kew (Director of Science); and Oxford Nanopore Technologies (Vice President for Applications). We delivered 5 talks, prepared 11 posters, led 2 tours of Genomics Pipelines and Bio-Foundry to showcase EI expertise and capabilities. The afternoon programme had 3 breakout sessions, aiming to explore opportunities for collaborative projects: 1. New Frontiers in Next-Generation Sequencing 2. Data Mining of the UK Tree of Life to Understand and Utilise Biodiversity of British Species 3. A guided discussion about the value of data for driving research, innovation and commercialisation This was EI's first externally-facing KEC event, bringing together various stakeholders to learn about EI expertise and how it can add value to their projects. We received a lot of informal positive feedback and following upon the interactions that this event enabled. A date has already been secured for November 2020.
Year(s) Of Engagement Activity 2019
URL https://www.earlham.ac.uk/innovate2019-0
 
Description EI Innovate: a platform for collaboration and new ideas 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact EI Innovate: a platform for collaboration and new ideas
Year(s) Of Engagement Activity 2020
URL https://www.earlham.ac.uk/articles/ei-innovate-platform-collaboration-and-new-ideas
 
Description Earlham Institute open day 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Discussions with variety of audiences about gut bacteria and probiotics.
Year(s) Of Engagement Activity 2019
URL https://www.earlham.ac.uk/open-day-2019
 
Description Earlham Institute open day 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Talk to ~50 members of the public sparking questions and discussion about probiotics and a healthy gut microbiome.
Year(s) Of Engagement Activity 2019
URL https://www.earlham.ac.uk/open-day-2019
 
Description Engagement with General Public: Royal Norfolk Show 2022 - Will Nash 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Engagement activities with the general public as part of the Royal Norfolk Show 2022, demonstrating our activities focusing on the application of new technologies to characterise biodiversity
Year(s) Of Engagement Activity 2022
 
Description Evolution of regulatory networks controlling adaptive traits in cichlids, Network Biology CSHL, NY, USA Mar 19-23 2019 
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 Evolution of regulatory networks controlling adaptive traits in cichlids, Network Biology CSHL, NY, USA Mar 19-23 2019
Year(s) Of Engagement Activity 2019
 
Description Evolutionary Systems Biology 2020: Conference Flash Talk and Poster on Evolution of chromatin accessibility associated with traits of cichlid phenotypic diversity 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Conference Flash Talk and Poster on Evolution of chromatin accessibility associated with traits of cichlid phenotypic diversity. Owing to the flash talk, questions and discussions were initiated on the application of our methods to other systems and future work.
Year(s) Of Engagement Activity 2020
URL https://coursesandconferences.wellcomegenomecampus.org/our-events/evolutionary-systems-biology-2020/
 
Description Evolutionary arms race pits out cellular defence mechanisms against invading bacteria - 26/03/2019 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact A website article outlining a new systemic analysis of the complex molecular interactions between bacteria and our own cells has mapped out an arms race that may provide clues to what makes bacteria successful invaders through work led by Dr Tamás Korcsmáros, a research leader at EI and Quadram Bioscience. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/newsroom/evolutionary-arms-race-pits-our-cellular-defence-mechanisms-agains...
 
Description Examining genetic diversity and traits under selection in several aquaculture-relevant tilapia species, Genome Science 
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 Examining genetic diversity and traits under selection in several aquaculture-relevant tilapia species, Genome Science
Year(s) Of Engagement Activity 2018
 
Description FTMA3 - Eagle Genomics Workshop for ECRs on engagement with industry and exploratory meetings to identify new collaborations - 23-24 March 2022 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact A 2-day workshop with Eagle Genomics' Director of Microbiome Solutions and Director of Bioinformatics. The workshop consisted of short sessions and networking lunch to facilitate ECR identification of transferrable skills for industry to improve employability within this sector, plus networking and engagement with industry skills. Further to this several 1:1 meetings and a networking dinner were facilitated with group leaders to explore potential longer-term collaborations between EI and Eagle Genomics. This includes identification of potential involvement in one of EI's future ISPs plus the opportunity to apply for joint CASE studentship funding.
Year(s) Of Engagement Activity 2022
 
Description From oral and scalp microbial communities to host responses - a network and multi-omics based approach to connect microbes and human PhD student workshop 
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 From oral and scalp microbial communities to host responses - a network and multi-omics based approach to connect microbes and human PhD student workshop
Year(s) Of Engagement Activity 2019
 
Description Gatsby plant science summer school: engineering plants for farming and pharming 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact Presented a lecture and particilaped in a discussion session with undergraduates as part of the Gatsby Plant Science Summer School. The summer school is an opportunity for first year undergraduate students in the UK to discover the challenge and opportunities of studying plant science. 76% of students rated this particular talk as good or very good with some very positive comments such as, 'I realised how much I loved to learn about Synthetic aspect of biology after the talk by Dr Nicola Patron'. 69% of students atteneding the whole summer school responded that they were more interested in plant science as a result of attending and one third of students reported in their feedback that they are now thinking of doing a PhD with some plant science, an increase in 12% from when asked before attending. 93% of students reported that they are interested in or are considering a career in or with plant science as a result of attending.
Year(s) Of Engagement Activity 2018
URL http://intobiology.org.uk/dr-nicola-patron-engineering-plants-for-farming-and-pharming/
 
Description Genome Science - Presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Invited talk on single-cell isoform sequencing at Genome Science Conference. Gave opportunity to highlight the work we are doing on the BBSRC New Investigator Grant.
Year(s) Of Engagement Activity 2019
URL http://genomescience.co.uk/programme/
 
Description George Freeman MP, Minister for Transport visit - 20/09/2019 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Policymakers/politicians
Results and Impact In September 2019, George Freeman MP, Transport Minister, visited EI and address NRP staff. EI and CSP researchers lobbied him on our priorities and policy asks and staff were able to question him on the Government's Brexit policy as well as its wider science strategy
Year(s) Of Engagement Activity 2019
URL https://www.georgefreeman.co.uk/content/earlham-institute-visit
 
Description Gugs Lushai - Life Health Sciences Ltd - 18/12/2018 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Meeting to discuss collaborative project
Year(s) Of Engagement Activity 2018
 
Description Gut feeling: a network approach to studying IBD - 10/12/2019 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Website article on the development of a novel combined experimental and computational pipeline that tells us what genes are the important 'master regulators' in the gut, and which of these genes overlap with those associated with IBD, suggesting new angles to research in the future in collaboration from Korcsmaros Group at EI and the Quadram Bioscience.
Year(s) Of Engagement Activity 2019
URL https://www.earlham.ac.uk/newsroom/gut-feeling-network-approach-towards-understanding-ibd
 
Description Host-microbe interactions in oral cavity Conference: Unilever Microbiology Symposium Location: Unilever R&D Colworth Science Park, Bedfordshire Date: 4-5 July, 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Industry/Business
Results and Impact Host-microbe interactions in oral cavity Conference: Unilever Microbiology Symposium Location: Unilever R&D Colworth Science Park, Bedfordshire Date: 4-5 July,
Year(s) Of Engagement Activity 2019
 
Description Hosting undergraduate summer student, Giorgio Koufous for work experience in lab. 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Undergraduate students
Results and Impact We hosted Giorgio Koufous, an international student for one month to gain experience in wet lab research - he thorougly enjoyed the research project on characterising polymorphisms associated with fin egg spot diversity in cichlid fish.
Year(s) Of Engagement Activity 2019
 
Description I'm a Scientist - why talk to young people? - 13/05/2019 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Showcase of PhD student in Korcsmaros group and their work in public engagement through the "I'm a scientist, get me out of here" programme which engages with schools and the general public to inform them about research and possible career pathways.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/articles/i'm-scientist-why-talk-young-people
 
Description I'm a Scientist Get me out of here" programme 2019. 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact Engaging with school students about STEM related questions and promoting discussions between scientists and students.
Year(s) Of Engagement Activity 2019
URL https://drugm19.imascientist.org.uk/
 
Description Identification of master regulators in goblet cells and Paneth cells using transcriptomics profiling of gut organoids and multi-layered networks. QIB Research in Progress 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact Identification of master regulators in goblet cells and Paneth cells using transcriptomics profiling of gut organoids and multi-layered networks. QIB Research in Progress
Year(s) Of Engagement Activity 2019
 
Description Identification of prognostic indicators of healthy ageing with a machine learning based systems biology approach using gut microbiome data Microbes in Norwich 2019 
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 Identification of prognostic indicators of healthy ageing with a machine learning based systems biology approach using gut microbiome data Microbes in Norwich 2019
Year(s) Of Engagement Activity 2019
 
Description Identification of prognostic indicators of healthy ageing with a machine learning based systems biology approach using gut microbiome data RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges 
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 Identification of prognostic indicators of healthy ageing with a machine learning based systems biology approach using gut microbiome data RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges
Year(s) Of Engagement Activity 2019
 
Description Identifying signalling pathways regulating antimicrobial peptide production in the gut using network biology and organoid transcriptomics Modularity of signaling proteins and networks 
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 Identifying signalling pathways regulating antimicrobial peptide production in the gut using network biology and organoid transcriptomics Modularity of signaling proteins and networks
Year(s) Of Engagement Activity 2018
 
Description Inside EI - 21/05/2019 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Inside EI is an open day when the public are invited to learn more about the work at the Earlham Institute, meet our team and engage with our research and understand its relevance and impact. There were talks and posters based on CSP-led research.
Year(s) Of Engagement Activity 2019
URL https://earlhaminstitute.coveragebook.com/b/0ee62ba7
 
Description Inside EI - Open Day 2019 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact One day in May 2019 EI opened its doors to the public and schools from the region. Offering an overview of the Tree of Life with the branches of our tree culminating in posters displaying colourful imagery of our research, visitors were able to talk to researchers about their projects and why the research is important. There were hands on activities providing insight into de novo genome assembly, nanopore sequencing technology, synthetic biology and high performance/cloud computing.

In addition to the activities, there were talks and tours of the laboratories, which were fully subscribed.

We were joined by schools from across the region in the morning, and opened our doors to the general public for the afternoon, with a total of over 400 visitors, media coverage (TV and radio) reaching an estimated 500+. The feedback was incredibly positive and we achieved an unbelievably successful set of outcomes. Comparison of pre- and post Open Day attitudes demonstrated that: Participants reported very high increases in understanding of a range of topics, while overwhelmingly agreed that research at EI should be funded by the government. The majority of people left with an increased appreciation of the importance of bioinformatics, genomics, etc. for their every day life, the environment, and more.
Year(s) Of Engagement Activity 2019
URL https://www.earlham.ac.uk/articles/inside-ei-public-engagement-science-impact
 
Description Inside EI 2019: Diving into cichlid diversity (Oral Presentation) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Around 100 people attended the 'Inside EI' open day; there were several talks and informal discussions based on this. As a result, there was increased interest in several of the research areas, including our work on fish.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/open-day-2019#Programme-7
 
Description Inside EI: Public engagement with impact - 06/08/2019 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Website highlighting the Inside EI event for the public to explore our fascinating and diverse range of important scientific research projects including talks and posters on our CSP work and the importance and impact of public engagement in research
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/articles/inside-ei-public-engagement-science-impact
 
Description Internal Seminar on 'Evolution of regulatory networks associated with traits of cichlid phenotypic diversity' 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Other audiences
Results and Impact Earlham Institute Internal Seminar (also open to NBI colleagues) on the 'Evolution of regulatory networks associated with traits of cichlid phenotypic diversity'. There was a round of questions and discussion afterwards.
Year(s) Of Engagement Activity 2020
 
Description Interview on institute website on our recent publication on COVID-19 
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 Following our publication on cytokine responses caused by SARS-CoV-2 and similar viruses, the institute communications team made an interview with us to describe our findings
Year(s) Of Engagement Activity 2021
URL https://www.earlham.ac.uk/newsroom/could-our-immune-system-be-why-covid-19-so-deadly
 
Description Interview with Medscape about COVID-19 publication 
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 I gave an interview following our publication on cytokine responses caused by SARS-CoV-2 and similar viruses. The interviewer asked great questions, and has asked medical professionals for comments on our publication.
Year(s) Of Engagement Activity 2021
URL https://www.medscape.com/viewarticle/946900?src=soc_tw_share
 
Description Interview with iNews 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact Interview with iNews Science and Environment correspondent. This resulted in the article: "Scientists welcome Government plans to lift ban on gene editing in agriculture" published March 16, 2021.
Year(s) Of Engagement Activity 2021
URL https://inews.co.uk/news/science/scientists-welcome-government-plans-to-lift-ban-on-gene-editing-in-...
 
Description Interview, Farming Today, BBC Radio 4 
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 Media (as a channel to the public)
Results and Impact Interview with BBC Radio 4 Farming Today "Anna Hill visits the Earlham Institute in Norwich where scientists are gene mapping wildflowers to find out which genes govern the creation of molecules with medicinal potential."
Year(s) Of Engagement Activity 2019
URL https://www.bbc.co.uk/programmes/m000c4z4
 
Description Interviewed for a BBC news feature on the Darwin Tree of LIFE project - shown worldwide on BBC world news 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact The feature covered the Darwin Tree of Life project and the involvement of EI. Particularly focussing on Protists
Year(s) Of Engagement Activity 2019
 
Description Intestinal autophagy regulation by Salmonella Typhimurium. Coffee Break Science 
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 Intestinal autophagy regulation by Salmonella Typhimurium. Coffee Break Science
Year(s) Of Engagement Activity 2019
 
Description Introduction to Multiomics Data Integration 
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 Tamas Korcsmaros delivered a talk on the nature of different data types, and provided a training on Cytoscape
Year(s) Of Engagement Activity 2009,2018
URL https://www.ebi.ac.uk/training/events/2018/introduction-multiomics-data-integration-0
 
Description Investigating regulation of intestinal function by Bifidobacteria using network biology and organoid approaches, Microbes in Norwich 
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 Investigating regulation of intestinal function by Bifidobacteria using network biology and organoid approaches, Microbes in Norwich
Year(s) Of Engagement Activity 2019
 
Description Invited seminar - Swedish University of Agricultural Sciences, Uppsala, Faculty of Veterinary Medicine and Animal Sciences - Complex evolutionary history of tilapia 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited presentation at the Swedish University of Agricultural Sciences, Uppsala, Faculty of Veterinary Medicine and Animal Sciences
Year(s) Of Engagement Activity 2023
 
Description Jolly good fellows: building a career at Earlham Institute - 20/02/2020 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Website article showcasing fellowship programmes at EI including Tamas Korcsmaros, whose five year fellowship which has led to a large and successful group investigating computational and network-based approaches to understanding complex systems such as the gut. Dr Korcsmaros is the CSP WP2 Lead.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/articles/jolly-good-fellows-building-career-earlham-institute
 
Description KTN Agri-tech mission in Colombia 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Attended and contributed to Agri-tech Catalyst Colombia organised by the agri tech KTN and innovate UK. Talked and participated in workshops across Colombia
Year(s) Of Engagement Activity 2018
 
Description Leszek Wysocki (Department for International Trade ) 10/06/2019 - visit to EI 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Policymakers/politicians
Results and Impact Leszek Wysocki (Department for International Trade) visited EI and met with CSP researchers to discuss their work in relation to International Trade
Year(s) Of Engagement Activity 2019
 
Description Machine learning approaches to identify prognosis indicators from microbiome data, 14th congress of European Crohn's and colitis organisation Copenhagen, Denmark 
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 Machine learning approaches to identify prognosis indicators from microbiome data, 14th congress of European Crohn's and colitis organisation Copenhagen, Denmark
Year(s) Of Engagement Activity 2019
 
Description Microbial Community Analysis Workshop 29 - 31 March 2022 (Virtual) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact This was a three-day course covering microbiome analysis - going from samples, to sequencing, to numerical ecology analysis. It provided an overview from raw sequencing reads to publication ready analysis and figures. Lecture materials comprised the theory of DNA extraction, sample storage and existing pipelines for amplicon sequencing. Use of the LotuS2 pipeline was applied to an example dataset via a Galaxy interface. R was also used to explore abundance data from producing diversity measures to visualisation of taxonomic differences. We had 25 participants comprising PhD students (~53%), Postdocs (~30%), Professors/PIs (12%) and other representatives from research organisations in attendance. The overall quality of the course was rated as 'Very Good' or 'Excellent' (92%) and there are plans to host this again in Q4 2023. Participants reported this allowed them unique hands-on experience with 16S/amplicon sequencing data, and that after attending the course it allowed them to present papers in the field of bioinformatics.
Year(s) Of Engagement Activity 2022
URL https://www.earlham.ac.uk/events/microbial-community-analysis-workshop-2022
 
Description Molecular Training Workshop for African Scientists, University of Cambridge 
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 Lectures deleivered as part of a two week training evint for agricultural research scientists, academics and PhD students from across Africa. This was followed by discussion and follow-up questions by email.
Year(s) Of Engagement Activity 2018
URL http://www.jrbiotekfoundation.org/cambridge-lab-training-2018/
 
Description Multi-omic data integration assisted identification of molecular features contributing to disease heterogeneity in Crohn's disease, 14th congress of European Crohn's and colitis organisation Copenhagen, Denmark 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Multi-omic data integration assisted identification of molecular features contributing to disease heterogeneity in Crohn's disease, 14th congress of European Crohn's and colitis organisation Copenhagen, Denmark
Year(s) Of Engagement Activity 2019
 
Description Nanopore Metagenomics: from sample to analysis 26-28 April 2022 (Virtual) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The first iteration of this 3-day course covered Nanopore Metagenomics and provided an overview of in-field, real-time nanopore sequencing using the Oxford Nanopore Technologies (ONT) platform. It covered experimental considerations, sample collection and preparation theory, plus data analysis and visualisation. Hands-on opportunities for data analysis of metagenomic data covered the use of EI's in-house software MARTi via virtual machines, accessed remotely by the participants. Participants also had the opportunity to discuss and apply lessons to their own projects with EI's experts and a representative from Oxford Nanopore Technologies during an optional Q&A session. Attendees were predominantly from the UK (65%) with remaining participants from Sweden, Norway, Germany and Hong Kong. The majority were Postdoctoral researchers (~33%), and PhD students (~27%), while the remainder comprised Undergraduates (~7%), Professor/PIs (~7%) and 'other' job functions. These included a research scientist, senior engineer (food technologist) and laboratory technician. Delegates rated the course overall as "Very Good" or "Excellent" (40% and 60% respectively), while 67% rated the trainers "Excellent". 100% would recommend the course.
Year(s) Of Engagement Activity 2022
URL https://www.earlham.ac.uk/events/nanopore-metagenomics-sample-analysis-2022
 
Description Neo.Life - 25 Visions for the Future of our Species (Book) 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Contributed a book section to Neo.Life - 25 Visions for the Future of our Species (Book). Editors: Jane Metcalf and Brian Bergstein
Year(s) Of Engagement Activity 2020
URL https://neo.life/visions/
 
Description Network Biology, CSHL, USA: Conference Talk on Evolution of regulatory networks controlling adaptive traits in cichlids 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Conference Talk on Evolution of regulatory networks controlling adaptive traits in cichlids. This conference talk was very well received and as a result, questions and discussions were initiated on the application of our methods to other systems and future work.
Year(s) Of Engagement Activity 2019
URL https://meetings.cshl.edu/meetings.aspx?meet=network&year=19
 
Description Network biology approaches to understanding life - 29/04/2019 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Website article highlighting the work of a PhD student in the Korcsmaros group on how systems biology approaches can help us to understand the interactions between living systems and how the information we can glean is important for improving human health and better understanding the evolution of host-specificity of bacteria, among many other things. This article also provide insight into carrying out a PhD at EI and working in the field of systems biology and Salmonella research.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/articles/network-biology-approaches-to-understanding-life
 
Description New clue to triggers of gut inflammation 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. Collectively, our international reach as of March 2019 has extended across the globe, with highlight pieces in the Guardian, the BBC World Service, the Washington Post and more, as well as local TV and radio. In 2018, the estimated readership of news stories we shared was well in excess of 1 million.
Year(s) Of Engagement Activity 2018
URL https://medicalxpress.com/news/2019-02-interdisciplinary-approach-uncovers-clues-triggers.html
 
Description Newsletter - Developing a frugal and medium throughput method for assessing protein-DNA binding affinity 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact News Letter for Open Plant
Year(s) Of Engagement Activity 2019
URL https://www.openplant.org/blog/2019/4/4/developing-a-frugal-and-medium-throughput-method-for-assessi...
 
Description Norwich 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 Earlham Institute Bee trail at the Norwich science festival
Year(s) Of Engagement Activity 2019
URL https://norwichsciencefestival.co.uk/about/norwich-science-festival-2019/
 
Description Norwich Science Festival - 22/10/2019 to 24/10/2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Norwich Science Festival is a wonderful showcase of science from Norwich and beyond for learning and excellent public engagement. This year, EI presented 11 talks and poems covering a fascinating range of science topics, from Salmonella and guts through to sequencing algae in the Antarctic, covering the whole tree of life in the process, bringing an innovative Bee Trail, LEGO sequencer, robots and more. Researchers from the CSP participated, presented their work and engaged with the public. Coverage on TV, radio and media with estimated coverage views of 698K
Year(s) Of Engagement Activity 2019
URL https://earlhaminstitute.coveragebook.com/b/02819684cc7da5de
 
Description Norwich Science Festival Ops Note 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media. Collectively, our international reach as of March 2019 has extended across the globe, with highlight pieces in the Guardian, the BBC World Service, the Washington Post and more, as well as local TV and radio. In 2018, the estimated readership of news stories we shared was well in excess of 1 million.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/newsroom/first-ei-lego-sequencer-human-dna-and-endangered-species-earlham-i...
 
Description Norwich Single-Cell Symposium - 8 May 2017 
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 With the developments in single-cell genomics technologies, particularly in the broadening of applications, we organised this symposium to bring together researchers who were curious about single-cell genomics with external speakers engaged in advanced single-cell research as well as highlighting the single-cell capabilities available at Earlham Institute. The idea was that this would provide an informal platform to catalyse future development and application of single-cell genomics across the region. The one-day symposium covered single-cell genomics topics in the following areas: technology development, developmental biology, health and disease, plant science and data analysis. The inaugural event had over 90 registrations, including a small number of industry representatives who had the option to sponsor and exhibit at the meeting. Feedback received suggested that the symposium offered a great diversity of topics in an informal and friendly setting. Many respondents providing feedback commented upon the high standard of presentations and enjoyable networking opportunities citing that they would like to see a repeat symposium the following year and that the meeting should be a little longer, with more networking.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/norwich-single-cell-symposium
 
Description Nuffield Research Experience Placements Summer 2020 (Virtual) 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact Nuffield reported a dramatic loss of placements due to the COVID-19 pandemic and the need to move these placements online. Earlham Institute were able to host 6 students, 5 to completion, through a four week research programme. Students worked in pairs, with each pair being assigned a different supervisor and organism to study, however, the cohort was combined in twice-weekly meetings to go over the tools and resources that were relevant to each project on a weekly basis so that they could see the data analysis approaches were similar across the different projects, and in a final presentation to all of the project supervisors and the training team at the end of their placement.

The presentations at completion of the placements demonstrated just how much the students had each learned and achieved in such a short time, despite the difficulties in having to host these placements entirely remotely.
Year(s) Of Engagement Activity 2020
 
Description Oceans Day at Norwich Science Festival 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Tarang Mehta gave a well-received talk on how he delves into cichlid fish diversity for the Norwich Science Festival.

He had given a similar talk the year before, and this was an update due to its roaring success the first time around.

The talk helped to promote an awareness of the importance of understanding the evolution of interesting groups of organisms such as cichlid fish, and how this can be applied to a number of interesting research projects, from better understanding human disease through to improving aquaculture practice in East Africa.
Year(s) Of Engagement Activity 2018
 
Description Open source data management: Sherlock open for all - 14/06/2019 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Website article on customisable method of data management for smaller research groups who don't have the resources to develop a modern, big data solution using software developed at EI and made open-source.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/articles/sherlock-open-source-data-management
 
Description Oral Presentation - Genomics in Aquaculture (GIA) 6th, Granada, Spain - EXAMINING GENETIC DIVERSITY AND CHROMATIN ACCESSIBILITY IN AQUACULTURE-RELEVANT TILAPIA SPECIES - Tarang Mehta 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Oral presentation as part of the Genomics in Aquaculture (GIA) 6th, Granada, Spain
Year(s) Of Engagement Activity 2022
 
Description Oral Presentation - Characterization of noncoding expression and splicing diversity in the human brain 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Seminar at the Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
Year(s) Of Engagement Activity 2019
 
Description Oral Presentation - EI Innovate - Computational prediction of novel regulatory elements as potential drug targets 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Presentation as part of EI Innovate
Year(s) Of Engagement Activity 2022
 
Description Oral Presentation - Regulatory networks evolution underlying the rapid diversification of cichlids fishes in the Great African Lakes - Tarang Mehta 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited presentation at the Society for Molecular Biology and Evolution Annual Meeting (Ferrara Italy)
Year(s) Of Engagement Activity 2023
URL https://www.smbe2023.org/
 
Description Oral presentation - Building gene Families and assessing gene structure 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Presentation at the Genome Annotation Workshop 2021
Year(s) Of Engagement Activity 2021
 
Description Oral presentation - Characterization of splicing diversity and gene fusions through Nanopore sequencing 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Oral presentation at the Long Read Sequencing Meeting, SciLifeLab Uppsala, Sweden
Year(s) Of Engagement Activity 2019
 
Description Oral presentation - Characterization of splicing diversity in bulk samples and single cells using long read technologies 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Seminar at the Maurice Wohl Clinical Neuroscience Institute King's College London
Year(s) Of Engagement Activity 2019
 
Description Oral presentation - Detection of differential isoform expression and usage during cellular differentiation using long read RNA sequencing 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation at the London Calling 2021 meeting
Year(s) Of Engagement Activity 2021
 
Description Oral presentation - Enter the Nanoporium 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Oral presentation as part of the Pint of Science
Year(s) Of Engagement Activity 2019
 
Description Oral presentation - How well do you know your family tree? 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Oral presentation at the Norwich Science Festival
Year(s) Of Engagement Activity 2019
 
Description Oral presentation - Intestinal organoids in a multi-omics, systems biology framework to investigate gut health and host-microbe interactions 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Oral presentation at the Cell Symposia: Engineering Organoids and Organs 25th-27th August 2019 Paradise Point, San Diego, California, United States
Year(s) Of Engagement Activity 2019
 
Description Oral presentation - Population level cis-regulatory variation highlights the importance of DNA shape to transcription factor binding affinity 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Oral presentation at the SMBE Annual Meeting 2019, Manchester, UK 21-25 July 2019
Year(s) Of Engagement Activity 2019
 
Description Oral presentation - Taking the long (read) view of alternative splicing during cell differentiation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Presentation at the EI Long Read Symposium, Earlham Institute (virtual) 15 - 17th June 2021
Year(s) Of Engagement Activity 2021
 
Description Organoid transcriptomics to study cell regulation Internal research presentation at the Earlham Institute 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Organoid transcriptomics to study cell regulation Internal research presentation at the Earlham Institute
Year(s) Of Engagement Activity 2019
 
Description Padhmanand Sudhakar : Selected and Participated in the "ECR Policy Lab on the determinants of food choice for healthy and sustainable diets" organized by Global Food Security (a UK cross-government programme on food security research). 
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 Selected and Participated in the "ECR Policy Lab on the determinants of food choice for healthy and sustainable diets" organized by Global Food Security (a UK cross-government programme on food security research).
Year(s) Of Engagement Activity 2018
 
Description Padhmanand Sudhakar : participated in 2018 Royal Society's pairing programme between Scientists and Parliamentarians. 
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 Padhmanand Sudhakar : participated in 2018 Royal Society's pairing programme between Scientists and Parliamentarians.
Year(s) Of Engagement Activity 2019
 
Description Paneth cells secrete lysozyme via secretory autophagy during bacterial infection of the intestine Stem Cells @ Lunch, a fortnightly lunchtime seminar series, hosted by Dr. Davide Danovi at the Centre for Stem Cells & Regenerative Medicine at Guy's Hospital, King's College London, UK. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Paneth cells secrete lysozyme via secretory autophagy during bacterial infection of the intestine Stem Cells @ Lunch, a fortnightly lunchtime seminar series, hosted by Dr. Davide Danovi at the Centre for Stem Cells & Regenerative Medicine at Guy's Hospital, King's College London, UK.
Year(s) Of Engagement Activity 2019
 
Description Participated in promotional video for research park 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact I participated in the shooting of a promotional video for the NBI.
Year(s) Of Engagement Activity 2020
URL https://www.youtube.com/watch?v=jH_fmWD692s&feature=emb_title
 
Description Pathway Analysis to Study the Effect of Bifidobacteria on Autophagy in the Intestine 2nd Interdisciplinary Signaling Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Pathway Analysis to Study the Effect of Bifidobacteria on Autophagy in the Intestine 2nd Interdisciplinary Signaling Workshop
Year(s) Of Engagement Activity 2017
 
Description Pint of Science 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Will Nash gave a well-received talk about his work understanding the koala genome, and what we can learn from understanding it - particularly how koalas can somehow withstand a toxic diet of eucalyptus.

Pint of Science is a great occasion to share information with the public in an informal setting, which stimulates and encourages debate and discussion, therefore the opportunity for a dialogue - which is a valuable outcome for any public engagement event.
Year(s) Of Engagement Activity 2018
 
Description Plants can be larks or night owls just like us 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Plants can be larks or night owls just like us
Year(s) Of Engagement Activity 2020
URL https://www.telegraph.co.uk/news/2020/12/18/plants-night-owls-early-birds-just-like-humans-scientist...
 
Description Podcast - Genetics Unzipped Podcast by the Genetics Society - S5.20 Bread and fishes: the future of food in a changing climate - Tarang Mehta 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Podcast to highlight activities focusing on building genomic resources for aquaculture
Year(s) Of Engagement Activity 2022
URL https://geneticsunzipped.com/blog/2022/10/6/bread-and-fishes
 
Description Poster Presentation - Intelligent Systems for Molecular Biology - Scaling up GeneSeqToFamily to handle pan transcriptomes and million of genes 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation as part of the Intelligent Systems for Molecular Biology 2022 conference
Year(s) Of Engagement Activity 2022
 
Description Poster Presentation - Analysing intestinal organoids in a multi-omics, systems biology framework to investigate gut health and host-microbe interactions 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Presentation in front of the Earlham Institute Scientific Advisory Board
Year(s) Of Engagement Activity 2018
 
Description Poster Presentation - Cambridge Stem Cell Symposium - Characterization of splicing in the haematopoietic landscape using combined short and long read single-cell sequencing 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Poster presentation at the Cambridge Stem Cell Symposium
Year(s) Of Engagement Activity 2018
 
Description Poster Presentation - Cichlid Science 2022, Cambridge - Evolution of regulatory networks associated with traits of cichlid phenotypic diversity - Tarang Mehta 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Poster presentation as part of the Cichlid Science 2022 conference
Year(s) Of Engagement Activity 2022
 
Description Poster Presentation - Modularity of signaling proteins and networks - Identifying signalling pathways regulating antimicrobial peptide production in the gut using network biology and organoid transcriptomics Modularity of signaling proteins and networks 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation at the Modularity of signaling proteins and networks, Seefeld, Austria
Year(s) Of Engagement Activity 2018
 
Description Poster Presentation : Decoding Plant-infecting Viruses and Bacteria to Inform the Rational Design of Synthetic Regulatory Elements for Plants. Open Plant Forum. University of Cambridge, UK. July 2017. 
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 Decoding Plant-infecting Viruses and Bacteria to Inform the Rational Design of Synthetic Regulatory Elements for Plants. Open Plant Forum. University of Cambridge, UK. July 2017.
Year(s) Of Engagement Activity 2017
 
Description Poster Presentation : Targeted interplay between bacterial pathogens and host autophagy. 2017 EMBO India Conference : Autophagy: Cellular mechanisms and significance in health and disease 
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 Targeted interplay between bacterial pathogens and host autophagy. Autophagy: Cellular mechanisms and significance in health and disease . 2017
Year(s) Of Engagement Activity 2017
URL http://meetings.embo.org/event/17-autophagy-health
 
Description Poster presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation as part of the Biodiversity Genomics Conference
Year(s) Of Engagement Activity 2020
 
Description Poster presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation at the annual PopGroup meeting
Year(s) Of Engagement Activity 2021
 
Description Poster presentation - Evolution of gene regulatory networks controlling traits under natural selection in cichlids 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation at the volutionary Systems Biology Conference, Wellcome Trust Sanger Centre. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 2018
 
Description Poster presentation - Characterising and visualising gene families with GeneSeqToFamily and Aequatus 
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 Poster presentation at the Genome Informatics 2018, Cambridge, UK . The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 2018
 
Description Poster presentation - Gene regulatory network evolution in East African lake cichlids 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation at the Evolution 2018 conference, Montpellier. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 2018
 
Description Poster presentation - Identifying signalling pathways regulating antimicrobial peptide production in the gut using network biology and organoid transcriptomics 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation at the Modularity of signaling proteins and networks conference Seefeld, Austria. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 2018
 
Description Poster presentation - Networks to catch the difference: Construction and analysis of Regulatory Networks applied to East African Lake Cichlids 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation at the Evolutionary Systems Biology conference, Wellcome Trust Sanger Centre. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 2018
 
Description Poster presentation - Aequatus.js: a plugin to visualise gene trees in Galaxy 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation at the Galaxy Community Conference (GCC2019) - Freiburg, Germany
Year(s) Of Engagement Activity 2019
 
Description Poster presentation - Annotation and characterization of splicing diversity in complex genes of relevance for psychiatric disorders 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation at the Frontiers of Science, joint meeting between the Royal Society and JSPS , Tokyo, Japan
Year(s) Of Engagement Activity 2019
 
Description Poster presentation - Characterising and visualising gene families within Galaxy using GeneSeqToFamily and Aequatus 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation at the SMBE Annual Meeting 2019, Manchester, UK 21-25 July 2019
Year(s) Of Engagement Activity 2019
 
Description Poster presentation - Evolution of chromatin accessibility associated with traits of cichlid phenotypic diversity 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation at the Evolutionary Systems Biology 2020 , Wellcome Genome Campus Conference Centre UK
Year(s) Of Engagement Activity 2020
 
Description Poster presentation - Gene regulatory network evolution in East African lake cichlids 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Poster presentation as part of the PopGroup 52, Oxford. The audience included group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 2019
 
Description Poster presentation - Investigating regulation of intestinal function by Bifidobacteria using network biology and organoid approaches 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Poster presentation at the Microbes in Norwich workshop. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students.
Year(s) Of Engagement Activity 2019
 
Description Poster presentation - Single-cell Analysis of Alternative Splicing in Hematopoietic Stem and Progenitor Cells 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster presentation at the Hematopoesis, Keystone Conference
Year(s) Of Engagement Activity 2021
 
Description Poster presentation - ULK1 and ULK2: siblings or distant cousins? A bioinformatics analysis characterising the differences between two autophagy induction complex members 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Poster presentation at the 2019 annual Autophagy UK Network meeting, Glasgow UK
Year(s) Of Engagement Activity 2019
 
Description Poster presentation : An integrated computational approach to infer the targeted interplay between bacterial pathogens and host autophagy 2nd Interdisciplinary Signalling Workshop 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Sudhakar P., Jones E., Fatemian K., Samadevam S., Gul L., Korcsmaros T., Nezis I. (2017) An integrated computational approach to infer the targeted interplay between bacterial pathogens and host autophagy 2nd Interdisciplinary Signalling Workshop 2017
Year(s) Of Engagement Activity 2017
URL http://signalingworkshop.org/
 
Description Poster presentation : Decoding Plant-infecting Viruses and Bacteria to Inform the Rational Design of Synthetic Regulatory Elements for Plants. SynBioUK, Manchester, UK. November 2017. 
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 Cai Y., Patron NJ. Decoding Plant-infecting Viruses and Bacteria to Inform the Rational Design of Synthetic Regulatory Elements for Plants. SynBioUK, Manchester, UK. November 2017.
Year(s) Of Engagement Activity 2017
 
Description Poster presentation : Evolution of tissue-specific regulatory programs in cichlids. Biology of Genomes, Cold Spring Harbor, New York, USA; 9-13 May 2017. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Mehta T. K., Sudhakar P., Dolfin L. P., Wrzesinski T., Nash W., Korcsmaros T., Haerty W., Roy S., Koch C., Di Palma F. (2017) Evolution of tissue-specific regulatory programs in cichlids. Biology of Genomes, Cold Spring Harbor, New York, USA; 9-13 May 2017.
Year(s) Of Engagement Activity 2017
URL https://meetings.cshl.edu/meetings.aspx?meet=genome&year=17
 
Description Poster presentation : Mutational analysis of cell lines to uncover undesired changes in the regulation of autophagy 2nd Interdisciplinary Signalling Workshop 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Demeter A., Sudhakar P., Hautefort I., Korcsmaros T. (2017) Mutational analysis of cell lines to uncover undesired changes in the regulation of autophagy 2nd Interdisciplinary Signalling Workshop 2017
Year(s) Of Engagement Activity 2017
URL http://signalingworkshop.org/
 
Description Poster presentation : Pathway Analysis to Study the Effect of Bifidobacteria on Autophagy in the Intestine 2nd Interdisciplinary Signaling Workshop 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact Treveil A. T., Korcsmaros T. K. (2017) Pathway Analysis to Study the Effect of Bifidobacteria on Autophagy in the Intestine 2nd Interdisciplinary Signaling Workshop
Year(s) Of Engagement Activity 2017
URL http://signalingworkshop.org/
 
Description Poster presentation : Resistant Escherichia coli Interactome identifies putative novel drug combinations to break antimicrobial resistance 2nd Interdisciplinary Signaling Workshop 2017 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Modos D., Bulusu K., Afzal A., Sudhakar P., Korcsmaros T., Cokol M., Bender A. (2017) Resistant Escherichia coli Interactome identifies putative novel drug combinations to break antimicrobial resistance 2nd Interdisciplinary Signaling Workshop 2017
Year(s) Of Engagement Activity 2017
URL http://signalingworkshop.org/
 
Description Poster presentation : SalmoNet: an integrated multi-layered network for Salmonella 2nd Interdisciplinary Signaling Workshop 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact Olbei M. L. O., Metris A. M., Sudhakar P. S., Fazekas D. F., Demeter A. D., Ari E. A., Branchu P. B., Kingsley R. K., Baranyi J. B., Korcsmaros T. K. (2017) SalmoNet: an integrated multi-layered network for Salmonella 2nd Interdisciplinary Signaling Workshop
Year(s) Of Engagement Activity 2017
URL http://signalingworkshop.org/
 
Description Poster presentation : SalmoNet: an integrated multi-layered network for Salmonella Genome 10K and Genome Science Conference. Genome 10K and Genome Science Conference 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact Olbei M. L. O., Metris A. M., Sudhakar P. S., Fazekas D. F., Demeter A. D., Ari E. A., Branchu P. B., Kingsley R. K., Baranyi J. B., Korcsmaros T. K. (2017)
SalmoNet: an integrated multi-layered network for Salmonella Genome 10K and Genome Science Conference
Year(s) Of Engagement Activity 2017
URL https://genome10k.soe.ucsc.edu/node/130
 
Description Poster presentation at 2nd Interdisciplinary Signaling Workshop: SalmoNet: an integrated multi-layered network for Salmonella 
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 I presented my poster on SalmoNet, an integrated Salmonella network resource, at the 2nd Interdisciplinary Signaling Workshop.
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/2nd-interdisciplinary-signaling-workshop-isw
 
Description Poster presentation at Exploring Human Host-Microbiome Interactions in Health and Disease conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Poster presentation titled "Investigating regulation of intestinal function by Bifidobacteria using network biology and organoid approaches" at the Exploring Human Host-Microbiome Interactions in Health and Disease conference 2017.
Year(s) Of Engagement Activity 2017
URL https://coursesandconferences.wellcomegenomecampus.org/our-events/exploring-human-host-microbiome-in...
 
Description Poster presentation at ICSB2019 
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 I presented my poster at a prestigious systems biology conference (ICSB) where I got a lot of important feedback about my work.
Year(s) Of Engagement Activity 2019
 
Description Poster presentation: SignaLink 3, a tissue specific and extended multi-layered signaling network resource 2nd Interdisciplinary Signalling Workshop 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Fazekas D., Kadlecsik T., Sudhakar P., Modos D., Turei D., Csabai L., Gul L., Korcsmaros T. (2017) SignaLink 3, a tissue specific and extended multi-layered signaling network resource 2nd Interdisciplinary Signalling Workshop 2017
Year(s) Of Engagement Activity 2017
URL http://signalingworkshop.org/
 
Description Presentation - Evolution of regulatory networks controlling adaptive traits in cichlids Network Biology CSHL, NY, USA Mar 19-23 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation at the Network Biology meeting Cold Spring Harbor Laboratory. The audience included group leaders, university lecturers, postdoctoral researchers, graduate students and industry representatives.
Year(s) Of Engagement Activity 2019
 
Description Presentation - GeneSeqToFamily: a Galaxy workflow to find gene families based on the Ensembl Compara GeneTrees pipeline 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation at the 2018 Galaxy Community Conference (GCC2018), Portland, OR, USA, 25-30/06/2018. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students and industry representatives
Year(s) Of Engagement Activity 2018
 
Description Presentation - Aequatus: An open-source homology browser 
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 13th International Conference on Genomics (ICG13) Shenzhen, China. The audience consisted group leaders, University professors, University Lecturers, postdoctoral researchers, graduates and undergraduates students and industrial representatives.
Year(s) Of Engagement Activity 2018
 
Description Presentation - Festival of Genomics 2023 - Long Read RNA Seq Applications for Targets Identification 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Presentation at the Festival of Genomics
Year(s) Of Engagement Activity 2023
URL https://www.festivalofgenomics.com/
 
Description Presentation - Invited Seminar - Roslin Institute, Edinburgh - Complex evolutionary history of tilapia and impact on elite breeds for aquaculture 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Invited Seminar at the Roslin Institute, Edinburgh
Year(s) Of Engagement Activity 2022
 
Description Presentation - Invited Seminar - University College Dublin - Characterization of novel splicing events across tissues and during cellular differentiation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited seminar at the School of Biology and Environmental Science University College Dublin
Year(s) Of Engagement Activity 2023
 
Description Presentation - Long Read Sequencing Uppsala - Comprehensive human brain transcriptome characterisation using long-read CaptureSeq 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation as part of the Annual Long Read Sequencing Uppsala meeting
Year(s) Of Engagement Activity 2022
 
Description Presentation - Winter Conference on Brain Research - Characterisation of Transcript and Protein Diversity in Major Candidates for Neuropsychiatric Disorders 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation at the Winter Conference on Brain Research
Year(s) Of Engagement Activity 2023
 
Description Presented a virtual poster at the ISMB 2020 conference 
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 virtual poster on CytokineLink, a cytokine communication interaction resource I have developed, in a special COVID-19 focused poster session.
Year(s) Of Engagement Activity 2020
 
Description Presented poster at the Network Inference in Biology and Disease workshop in Pozzuoli 
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 I presented my poster at the conference, which led to some interesting discussions regarding the project.
Year(s) Of Engagement Activity 2019
 
Description Press Release - Network science unravels the secrets of the evolution of Salmonella's disease adaptations 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Press release to introduce SalmoNet, a systems biology approach that uses network biology and bioinformatic techniques to collate molecular interactions within Salmonella, and to link information on how genes and metabolic pathways are regulated in Salmonella, and how proteins interact with each other. -SOCIAL MEDIA- Engagement x45, Impressions x54800
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/newsroom/network-science-unravels-secrets-evolution-salmonella%E2%80%99s-di...
 
Description Press article - Improved strain of tilapia genome sequencing highlighted by UKRI and BBSRC Impact Showcase of 2022 - Tarang Mehta, Will Nash, Adam Ciezarek, Graham Etherington 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Article as part of BBSRC Impact showcase 2022
Year(s) Of Engagement Activity 2022
URL https://preview.shorthand.com/uG7dbZH9ZkAyeO0M#group-section-Collaboration-Tv0V86lglL
 
Description Press article - UKRI BBSRC Strategic Delivery Plan 2022 - Cichlid GRNs work 'A role for non-coding DNA in biodiversity' - Tarang Mehta 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Article highlighting activities to characterise regulatory networks in cichlids published in UKRI BBSRC Strategic Delivery Plan 2022
Year(s) Of Engagement Activity 2022
URL https://www.ukri.org/wp-content/uploads/2022/09/BBSRC-010922-StrategicDeliveryPlan2022.pdf
 
Description Press release - The genetic machinery that drives biodiversity - Tarang Mehta 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Press release for the publication of the article describing approaches to reconstruct regulatory networks
Year(s) Of Engagement Activity 2022
URL https://www.earlham.ac.uk/articles/genetic-machinery-drives-biodiversity
 
Description Press release - regulatory networks in cichlids 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact Press release for the publication of the article describing regulatory network rewiring in cichlids
Year(s) Of Engagement Activity 2021
 
Description Professor Ian Boyd - Chief Scientific Adviser to DEFRA - 04/02/2019 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Meeting to discuss Institute influence and impact into government policy and input into Select Committees
Year(s) Of Engagement Activity 2019
URL http://data.parliament.uk/writtenevidence/committeeevidence.svc/evidencedocument/science-and-technol...
 
Description Robert Bulstrode - PwC - 18/12/2018 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Meeting to discuss commercial project
Year(s) Of Engagement Activity 2018
 
Description Royal Society Summer Science Exhibition 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact Led by Dr Lindsay Hall, myself and colleagues brought a 'walk through gut' stand to the Royal Society Summer Science Exhibition. This was an interactive exhibition where myself and colleagues talked to (and visually showed) students and the public, from 2 to 90 years old, about gut microbiomes. Many visitors, students and public alike, were very interested in the topic and expressed an interest in learning more on it in the future. We felt we contributed to increased awareness of the impact of lifestyle factors and antibiotics on gut microbiomes. Lindsay spoke on local news about the exhibition.
Year(s) Of Engagement Activity 2018
URL http://royalsociety.org/science-events-and-lectures/2019/summer-science-exhibition/
 
Description SMBE 2019: Conference Poster on Evolution of chromatin accessibility associated with traits of cichlid phenotypic diversity 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Conference Poster on Evolution of chromatin accessibility associated with traits of cichlid phenotypic diversity. At the poster session there were several questions and discussions were initiated on the application of our methods to other systems and future work.
Year(s) Of Engagement Activity 2019
URL http://smbe2019.org/
 
Description Salmonella - how the body fights back - 14/11/2019 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Website article highlighting collaborative research from the University of East Anglia, supported by Earlham Institute (EI) which shows how the human body powers its emergency response to salmonella infection. Contributions from the Macaulay and Di Palma groups. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/newsroom/salmonella-how-body-fights-back
 
Description Salmonella, who gives a faeces? - 23/04/2019 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Website article showcasing the CSPs work on a number of different aspects of Salmonella Researchers through understanding its invasiveness, pathogenicity, genetics and evolution, especially with regard to the growing threat of multidrug resistance and alarmingly devastating new strains arising in sub-Saharan Africa. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/articles/salmonella-who-gives-a-faeces
 
Description Scientific Advisory Board for Cluster of Excellence on Plant Sciences (CEPLAS), a joint initiative of Heinrich Heine University Düsseldorf (HHU), University of Cologne (UoC), Max Planck Institute for Plant Breeding Research Cologne (MPIPZ) and Forschungszentrum Jülich (FZJ). 
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 Member of the Science Advisory Board for the Cluster of Excellence on Plant Sciences (CEPLAS), a joint initiative of Heinrich Heine University Düsseldorf (HHU), University of Cologne (UoC), Max Planck Institute for Plant Breeding Research Cologne (MPIPZ) and Forschungszentrum Jülich (FZJ).
Year(s) Of Engagement Activity 2019,2020
URL https://www.ceplas.eu/en/home/
 
Description Selected Talk : Systems genomics of ulcerative colitis: combining GWAS and signalling networks identifies novel pathways in disease pathogenesis 2nd Interdisciplinary Signaling Workshop 2017, Visegrad, Hungary 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Brooks J., Modos D., Sudhakar P., Fazekas D., Zoufir A., Kapuy O., Harnisch L., Hall L., Carding S., Korcsmaros T. (2017) Systems genomics of ulcerative colitis: combining GWAS and signalling networks identifies novel pathways in disease pathogenesis 2nd Interdisciplinary Signaling Workshop 2017, Visegrad, Hungary
Year(s) Of Engagement Activity 2017
URL http://signalingworkshop.org/
 
Description Selected Talk : argeted interplay between bacterial pathogens and host autophagy UK Autophagy Meeting, London 2017 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Sudhakar P., Jones E., Samavedam S., Fatemian K., Gul L., Korcsmaros T., Nezis I. (2017) Targeted interplay between bacterial pathogens and host autophagy UK Autophagy Meeting, London
Year(s) Of Engagement Activity 2017
URL http://autophagy.uk/2017-london-meeting-2/
 
Description Sherlock: elementary genomics 18/03/2019 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Website article highlighting the Sherlock platform developed at EI to store and analyse bioinformatics data using modern big data technologies. News stories highlight important updates that also have broad relevance and interest to the national and/or specialised media.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/articles/sherlock-elementary-genomics
 
Description Signalling Networks: From Data to Modelling 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Contributed to a training course run at the Earlham institute entitled 'Signalling Networks: From Data to Modelling'.
Year(s) Of Engagement Activity 2019
URL https://www.earlham.ac.uk/signalling-networks-data-modelling
 
Description Signalling Networks: From Data to Modelling 1-5 April 2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Providing an introductory overview of tools and resources to investigate signalling pathways and networks, delegates received hands-on experience in how to reconstruct, analyse and visualise networks, plus how to develop models of signalling events. The course was well received with 100% recommendation of the course from feedback respondents and 100% rating the trainers as Very Good or Excellent.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/signalling-networks-data-modelling
 
Description Signalling and transcriptional network propagation uncovers novel ulcerative colitis pathogenetic pathways from single-nucleotide polymorphisms, 14th congress of European Crohn's and colitis organisation Copenhagen, Denmark 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Signalling and transcriptional network propagation uncovers novel ulcerative colitis pathogenetic pathways from single-nucleotide polymorphisms, 14th congress of European Crohn's and colitis organisation Copenhagen, Denmark
Year(s) Of Engagement Activity 2019
 
Description Single-cell RNAseq Training Course Delivered 3-7 Dec 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This was the first iteration of this course, demonstrating EI's both introducing Single Cell Genomics and demonstrating EI's capability. It covered several aspects such as: the experimental design, cell sorting and processing for production of quality samples for sequencing, in the three-days of laboratory hands-on sessions; generation of sequencing data, assessing the quality of sequence data, data visualisation, differential expression analyses and identifying Copy Number Variants at the single cell level in the following two-days of theory and computational hands-on sessions. A total of twelve (12) delegates attended this course, with ten (10) attending the full five days. Also included was a short half-day session with practical elements on single molecule FISH, delivered by EI faculty, and an overview of 10X Genomics' data analysis platform, presented by one of their Field Application Specialists.

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

Following the unprecedented success of delegates producing high quality data to analyse, course organisers wish to review the programme. The proposal for the second iteration is to run the course as 3 or 4 days in the laboratory, with sequencing running over a weekend, and then extending the bioinformatics from 2 days to 4 days, running this on the following week.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/single-cell-rnaseq-training-course
 
Description Susan Duncan Conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Plant Molecular Biology, Gordon Research Seminar and Conference conference: Working triple time: Elucidating the circadian gene network in hexaploid bread wheat

In Arabidopsis, circadian regulation has been found to underpin many important fitness traits including flowering time, dormancy, water use efficiency, nitrogen metabolism and vegetative yield. However, it is not clear the extent to which the underlying Arabidopsis clock gene network has been conserved in the three separate genomes, (AA, BB, DD) of allohexaploid bread wheat (Triticum aestivum). To address this we are using phylogenetic analyses to identify wheat clock gene homologues. In addition, we are carrying out an RNA-Seq time course to identify genes with oscillatory expression patterns and using network inference tools to rebuild the circadian network and identify transcriptional outputs. DNA affinity purification sequencing (DAP-Seq) assays are also being set up to identify genomic binding sites of wheat clock transcription factors and high-throughput delayed fluorescence assays are being used to reveal endogenous circadian rhythms in wheat cultivars and mutant tilling populations. The core clock transcriptional network affects many important agricultural traits and together our experiments will enable us to identify how it works in this complex polyploid crop. They will also allow us to determine whether polyploid organisms benefit from enhanced clock network robustness and flexibility or whether multiple genomes function independently.
Year(s) Of Engagement Activity 2018
URL https://www.grc.org/plant-molecular-biology-conference/2018/
 
Description Susan Duncan PAG talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact San Diego, PAG XXVII - Plant & Animal Genome Conference, January 12-16th 2019

Talk entitled: Insights into Arabidopsis Gene Regulation and Wheat Nuclear Organisation using Single Molecule RNA FISH
Year(s) Of Engagement Activity 2019
 
Description Systems genomics of ulcerative colitis: combining GWAS and signalling networks for patient stratification and individualised drug targeting in ulcerative colitis, Conference: 14th Congress of ECCO 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Systems genomics of ulcerative colitis: combining GWAS and signalling networks for patient stratification and individualised drug targeting in ulcerative colitis, Conference: 14th Congress of ECCO
Year(s) Of Engagement Activity 2019
 
Description Talk and discussion with Elsoms seeds 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact The talk was to breeders and crop scientist work at Elsoms seed, The aim was to raise awareness of the work that Design future wheat and my group were doing. This lead to a letter of support for our BBSRC grant and a line of communication with their wheat and brassica breeders.
Year(s) Of Engagement Activity 2018
 
Description Talk: A kaleidoscope of colours, shapes and sustainable plates: diving into cichlid fish diversity 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Around 30 people from age range 5-60 attended a talk on "A kaleidoscope of colours, shapes and sustainable plates: diving into cichlid fish diversity" at the Norwich Science Festival. This sparked widespread questions and discussion afterwards and reported an all-round interest in the work and research carried out at Earlham Institute.
Year(s) Of Engagement Activity 2018
URL https://norwichsciencefestival.co.uk/events/water-day-gallery-stage/
 
Description Talk: Evolution of regulatory networks controlling adaptive traits in cichlids 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact A talk on our work on "Evolution of regulatory networks controlling adaptive traits in cichlids" at the Network Biology conference in Cold Spring Harbor, USA.
Year(s) Of Engagement Activity 2019
URL https://meetings.cshl.edu/abstracts.aspx?meet=network&year=19
 
Description Techology Day at Norwich Science Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact 7500 members of the general public attended Nature Day at Norwich Science Festival. A number of activities were available to engage the general public with the work of the institute. A number of talks/presentations were scheduled also.
Year(s) Of Engagement Activity 2018
 
Description The Essex Synthetic Biology School (ESBS), University of Essex, UK : 
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 Presented lectures on "Engineering Plant Genomes for Farming and Pharming" and "Sharing Biology in the Information Age: Perceived Threats of Dematerialisation and Open Data". These were followed by discussions on the use of biotechnologies in agricultures and a debate on access and benefit sharing of genetic resources. Participants reported changes in their views on the common practices used to share information relating to genetic resources as well as physical resources.
Year(s) Of Engagement Activity 2018
URL https://esbs.essex.ac.uk
 
Description The regulatory landscape of intestinal cells - investigating the transcriptional effect of autophagy impairment observed in Crohn's disease using organoid and network biology approaches 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presentation at the 14th congress of European Crohn's and colitis organisation Copenhagen, Denmark . The audience included group leaders, university lecturers, postdoctoral researchers, graduate students, industry representatives
Year(s) Of Engagement Activity 2019
 
Description The regulatory landscape of intestinal cells - investigating the transcriptional effect of autophagy impairment observed in Crohn's disease using organoid and network biology approaches 14th congress of European Crohn's and colitis organisation Copenhagen, Denmark 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Updating the Inflammatory Bowel Disease community about the regulatory landscape and the role of autophagy in various types of intestinal cells
Year(s) Of Engagement Activity 2019
URL https://academic.oup.com/ecco-jcc/article/13/Supplement_1/S031/5300677
 
Description The regulatory landscape of intestinal cells - investigating the transcriptional effect of autophagy impairment observed in Crohn's disease using organoid and network biology approaches, 14th congress of European Crohn's and colitis organisation Copenhagen, Denmark 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The regulatory landscape of intestinal cells - investigating the transcriptional effect of autophagy impairment observed in Crohn's disease using organoid and network biology approaches
Year(s) Of Engagement Activity 2019