Regulatory interactions and Complex Phenotypes

Lead Research Organisation: Earlham Institute
Department Name: UNLISTED

Abstract

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.

Publications

10 25 50
 
Description 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 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).

3) We published GeneSeqToFamily as an open-source Galaxy workflow based on the Ensembl Compara GeneTree pipeline. GeneSeqToFamily workflow is being tested internally and externally.

4) To reconstruct the circadian network we have generated a high resolution RNAseq data from the elite UK cultivar Cadenza. We are currently identifying which processes are circadian regulated, how this regulation differs across the three wheat genomes and in collaboration with IBM developing strategies to reconstruct the circadian architecture in wheat.

5) We have investigated water use efficiency and 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. The aim is to reconstruction transcription networks and understand how the networks change rather than individual genes.

6) In collaboration with the 10 plus wheat genome project we have generated transcriptomic datasets across developmental time courses for 16 international elite cultivars.

7) 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.

8) We have developed a network analysing protocol that can be used to find differences arising from different evolutionary pressures acting on closely related species, as we demonstrated in Salmonella and cichlids (https://doi.org/10.1101/496034).

9) We analysed >50 gut pathogens how they can regulate autophagy, and how autophagy is recognising these pathogen proteins. We also validated a prediction in Salmonella (Sudhakar et al, Autophagy, 2019)

10) 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 (Jones et al, Disease Models and Mechanisms, 2019; Treveil et al, https://doi.org/10.1101/575845).
Exploitation Route We continue developing further these approaches and resources. We provide if possible all the tools and databases in open access, freely accessible websites allowing other users to exploit and leverage the created resources.

In particular:
Establishing the protocols for rare cell type isolation from the gut, and analysing them by RNAseq, is generating novel datasets which will explore the cellular response to infection. These protocols can be widely adapted and by building this expertise we have established techniques that will enable internal/external researchers to analyses these cells in different models.
The development of low-input and single-cell RNAseq approaches, and their transition to our genomics pipelines group, will enable the wider research community to access these techniques as part of EI's NC1.
The list of the pathogen effectors identified to affect autophagy will serve as a short-list for experimental validation by us or external colleagues. The computational pipeline will be published allowing other researchers to identify other pathogen effectors or involved host processes.
The methodology established by analysing mice organoids will be the base for moving forward and generate similar organoids from human biopsy samples. Furthermore, our bioinformatics pipelines can be applied on data generated by external collaborators.
Sectors Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Education,Environment,Healthcare,Pharmaceuticals and Medical Biotechnology

 
Description -- The release of a high quality annotated wheat genome sequence will allow breeders to identify more rapidly genes and regulatory elements underlying complex agronomic traits, boosting wheat improvement over the next decades. Our annotation tools will support future projects that use a pan-genomic approach to explore multiple wheat genomes. -- Our novel integrative approach to gene regulatory network reconstruction can be applied to other aquaculture-relevant tilapia fish species to rapidly identify genes and their associated regulators underlying complex aquaculture traits for breeding purposes. Our transcription factor motif prediction pipeline will support future projects exploring gene regulation in animal and plant genomes. -- The data emerging from this part of the CSP is relatively new and so societal and economic impacts are difficult to predict. Again, however, through delivery of the single-cell and low-input sequencing methods to the community through EI's NC1, we anticipate that this work will support a number of researchers country-wide in delivering single-cell genomics approaches as part of their work, including clinical research and cell specific pharmacological approaches. -- Both the experimental and computational protocols/pipelines that we developed for the multi-omics analysis of organoids have already been started to be applied by clinical researchers (King's College London, 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/screen compounds with patient derived organoids (project launch soon with a London/New York based pharma company).
First Year Of Impact 2018
Sector Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Healthcare,Pharmaceuticals and Medical Biotechnology
Impact Types Societal,Economic

 
Description BBSRC ENWW panel membership
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
Impact The panel advises BBSRC exec and councillor how best to deliver BBSRC strategy. Impact is difficult to quantify
 
Description 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 advisory committee
 
Description Engagement with the Parliamentary Scientific Committee: implications of the 2018 European Court of Justice ruling on Genome Editing
Geographic Reach National 
Policy Influence Type Participation in a advisory committee
 
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 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 Gave evidence to a government review
URL https://parliamentlive.tv/Event/Index/4bdf3ff7-d1a6-4605-8b73-aca355bf9f89
 
Description Particapited in parliamentary debate on CRISPR CAS and post-BREXIT genetic engineering in crops -APPG Science & Technology in Agriculture
Geographic Reach National 
Policy Influence Type Gave evidence to a government review
 
Description 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 advisory committee
 
Description submission to UKRI infrastructure review
Geographic Reach National 
Policy Influence Type Participation in a national consultation
URL https://www.ukri.org/files/infrastructure/progress-report-summary-document-final-march-2019-pdf/
 
Description 18 BTT 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 01/2019 
End 12/2020
 
Description 18-BTT: A PATHWAY TO THE EXPLOITATION OF EPIGENETIC VARIATION IN UK, US AND INTERNATIONAL BREEDING PROGRAMMES
Amount £273,500 (GBP)
Funding ID BB/S020942/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2019 
End 03/2021
 
Description BBSRC 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 10/2018 
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 10/2018 
End 09/2022
 
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 10/2018 
End 09/2022
 
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 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 07/2018 
End 06/2019
 
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 10/2017 
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 04/2018 
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 09/2018 
End 09/2022
 
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 Charity/Non Profit
Country United Kingdom
Start 01/2018 
End 12/2018
 
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 10/2017 
End 10/2020
 
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 Academic/University
Country United Kingdom
Start 06/2017 
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 10/2018 
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 - Developing a frugal transcription factor relative affinity measurement pipeline (TRAMP)
Amount £5,000 (GBP)
Organisation University of Cambridge 
Sector Academic/University
Country United Kingdom
Start 09/2018 
End 07/2019
 
Description 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 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 09/2017 
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 10/2018 
End 10/2023
 
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 09/2018 
End 09/2021
 
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 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 Autophagy Regulatory Network 
Description A manually curated dataset of autophagy components and their interactions. Integrated resource with known protein regulators of autophagy. Contains possible transcriptional and post-transcriptional regulators (ie., transcription factors and miRNA) of autophagy and its protein regulators. Links all autophagy component and regulators to major signaling pathways. Predict novel regulators and interactions. Can be downloaded in a user-specified content and format. 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact Autophagy Regulatory Network - a systems-level bioinformatics resource for studying autophagy components and their regulation (2015). Türei D, Földvári-Nagy L, Fazekas D, Módos D, Kubisch J, Kadlecsik T, Demeter A, Lenti K, Csermely P, Vellai T, Korcsmáros T. Autophagy, 11(1):155-165. - 26 citations 
URL http://autophagyregulation.org
 
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 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 promoter exon capture data 
Description The data contain the design space for the promoter and exon used in our capture 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Whole genome shotgun re-sequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome making it difficult to unambiguously assign variation. Re-sequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. We present two gold standard capture probe sets for hexaploid bread wheat, a gene and a promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. The capture probe sets effectively enrich the high confidence genes and promoters that were identified in the genome alongside a large proportion of the low confidence genes and promoters. We use a capture design employing an 'island strategy' to enable analysis of the large gene/promoter space of wheat with only 2x160 Mb NimbelGen probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations. Here, we release the targeted sequence of the capture probe sets on the wheat RefSeqv1, the design space that was used to tile our capture probes across and finally the positions of the probes themselves across this design space for both the gene and promoter capture probe sets. 
URL https://opendata.earlham.ac.uk/wheat/under_license/toronto/Gardiner_2018-07-04_Wheat-gene-promoter-c...
 
Description Analysing Tilapia species diversity and salinity adaptation in Lake Rukwa, Tanzania. 
Organisation Bangor University
Country United Kingdom 
Sector Academic/University 
PI Contribution Full organisation and expenses for Lake Rukwa, Tanzania sampling expedition to collect Oreochromis esculentus and Oreochromis rukwaensis tissue samples. This includes sampling equipment/reagents, travel, accomodation and subsistance. This also included species handling and tissue dissection training for University of Dar Es Salaam and University of Dodoma collaborators.
Collaborator Contribution Levinus Leonard and Edward A. Moto (University of Dar Es Salaam and University of Dodoma) aided 1. Organisation and permits for sampling in Lake Rukwa upon dealing directly with the lake fisheries officers 2. Private boat hire 3. Transport hire and accomodation 4. Species identification, tissue sampling and dissection Alexandra Tyers (Bangor University) aided in tissue sampling and dissection.
Impact Tissue samples from O. rukwaensis and O. esculentus have been sequenced to include: 1. Genotyping several individuals including variant analyses for species identification, admixture and phylogenetics 2. RNA-Seq of gill, liver and kidney for genome annotation and gene expression analyses Both will be published.
Start Year 2017
 
Description Analysing Tilapia species diversity and salinity adaptation in Lake Rukwa, Tanzania. 
Organisation University of Dar es Salaam
Country Tanzania, United Republic of 
Sector Academic/University 
PI Contribution Full organisation and expenses for Lake Rukwa, Tanzania sampling expedition to collect Oreochromis esculentus and Oreochromis rukwaensis tissue samples. This includes sampling equipment/reagents, travel, accomodation and subsistance. This also included species handling and tissue dissection training for University of Dar Es Salaam and University of Dodoma collaborators.
Collaborator Contribution Levinus Leonard and Edward A. Moto (University of Dar Es Salaam and University of Dodoma) aided 1. Organisation and permits for sampling in Lake Rukwa upon dealing directly with the lake fisheries officers 2. Private boat hire 3. Transport hire and accomodation 4. Species identification, tissue sampling and dissection Alexandra Tyers (Bangor University) aided in tissue sampling and dissection.
Impact Tissue samples from O. rukwaensis and O. esculentus have been sequenced to include: 1. Genotyping several individuals including variant analyses for species identification, admixture and phylogenetics 2. RNA-Seq of gill, liver and kidney for genome annotation and gene expression analyses Both will be published.
Start Year 2017
 
Description Analysing Tilapia species diversity and salinity adaptation in Lake Rukwa, Tanzania. 
Organisation University of Dodoma
PI Contribution Full organisation and expenses for Lake Rukwa, Tanzania sampling expedition to collect Oreochromis esculentus and Oreochromis rukwaensis tissue samples. This includes sampling equipment/reagents, travel, accomodation and subsistance. This also included species handling and tissue dissection training for University of Dar Es Salaam and University of Dodoma collaborators.
Collaborator Contribution Levinus Leonard and Edward A. Moto (University of Dar Es Salaam and University of Dodoma) aided 1. Organisation and permits for sampling in Lake Rukwa upon dealing directly with the lake fisheries officers 2. Private boat hire 3. Transport hire and accomodation 4. Species identification, tissue sampling and dissection Alexandra Tyers (Bangor University) aided in tissue sampling and dissection.
Impact Tissue samples from O. rukwaensis and O. esculentus have been sequenced to include: 1. Genotyping several individuals including variant analyses for species identification, admixture and phylogenetics 2. RNA-Seq of gill, liver and kidney for genome annotation and gene expression analyses Both will be published.
Start Year 2017
 
Description 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 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 epxertise in genome engineering in plants. Contributed to two joint grant proposals.
Collaborator Contribution Contributed expertise on epigenetics and plant nitrogen reponse networks. Contributed to two joint grant proposals.
Impact Two collaborative grant proposals submitted: NSF-BIO, USDA-NIFA and BBSRC joint activity - Early Concept Grants for Exploratory Research (EAGER) - Breakthrough Technologies to Advance Crop Breeding. BBSRC-NSF Lead Agency Opportunity - Synthetic approaches to address fundamental biological questions.
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
PI Contribution Full expenses for Geraldine Kavembe (SEKU) to sample Alcolapia tissue samples from Lake Magadi, Kenya. This included sampling equipment/reagents, travel, accomodation and subsistance.
Collaborator Contribution Dr Geraldine Kavembe (SEKU) contributed in the: 1. Organisation and permits for sampling in Lake Magadi by dealing with the appropriate fisherie officers 2. Private boat hire 3. Transport hire and accomodation 4. Species identification, tissue sampling and dissection 5. Sample shipping
Impact Tissue samples from A. grahami have been sequenced to include: 1. Whole genome sequencing using short Illumina and Nanopore reads (10x Chromium pending). We currently have a whole genome assembly based on the short reads that is currently being supplemented with the long read data. 2. RNA-Seq of gill and liver for genome annotation and gene expression analyses. Both will be published. Also, Tarang Mehta hosted a year in industry student (Nicole Forrester) at the Earlham Institute where she extracted RNA, prepared cDNA libraries and sequenced the trnascriptomes of Alcolapia and other tilapia tissue samples.
Start Year 2017
 
Description Genome 10K Consortium 
Organisation University of California, Davis
Department UC Davis Genome Cente
Country United States 
Sector Academic/University 
PI Contribution The G10K consortium is an international consortium of tissue curators, biologists, conservationists, genome scientists, computer scientists, outreach educators, and more. Federica Di Palma is a council member of the Consortium and has provided advice to the current ongoing projects. Organised meetings and contributed talks to several workshops and meetings.
Collaborator Contribution The G10K leadership and community of scientists built an infrastructure from sample collection to genome sequencing, assembly, annotation, alignments, public data releases, and analyses for publications.
Impact Collaboration is multidisciplinaryand includes tissue curators, biologists, conservationists, genome scientists, computer scientists, outreach educators, and more from different countries. Outputs include press releases, workshops, meetings, publications.
Start Year 2011
 
Description 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 UK Ltd
Country United Kingdom 
Sector Private 
PI Contribution This project aims to leverage these new resources together with large gene expression data sets to reconstruct regulatory networks controlling important traits. With outputs feeding directly into UK and International wheat research and UK wheat breeding programmes. The collaboration focuses around two large data sets: the first, a high resolution time series data set for wheat and the second, a developmental time course for 16 international elite cultivars. The project aims to: 1. Develop normalisation methods for the transcriptome data sets (RNA-seq data), specific for dealing with the complexities of time course data and a complex polyploid genome. Benchmark these new approaches against existing tools. 2. Develop AI pattern matching algorithms to identify gene-expression modules and correlate these with biological processes. Use pattern matching algorithms to interrogate the high resolution data sets and to identify differences between regulatory networks in elite cultivars 3. Correlate changes in temporal or developmental expression patterns with changes in promoter architecture 4. Use network inference, co-expression and gene modules to reconstruct regulatory networks. Identify how network structure changes over time and between cultivars. This project will have impact for scientists as it will address fundamental questions about temporal regulation of processes in wheat and how a complex networks work across multiple genomes within a polyploid. By comparing networks across elite cultivars it will also have an impact for UK and international wheat breeders, identification of how breeding programmes have changed the architure of regulatory networks. This will have important impact for the selection of future networks for breeders to target or for assessing the selection of breeding material. It will allow breeders to make full use of the new resources and technologies. To ensure the impact to the UK industry is realised we aim to present this work a UK networking meeting and to visit and involve three private UK breeding companies RAGT, KWS and Elsoms seeds in early output from the project.
Collaborator Contribution IBM have are involved in applying ML and AI approaches to analyse gene expression data in wheat and reconstruct gene networks.
Impact No outputs to data
Start Year 2017
 
Description 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 Moussa Benhamed 
Organisation University of Paris-Saclay
PI Contribution WE are collaborating with Moussa Benhamed to develop Next generation sequencing technology to explore the 3D structural organisation in the wheat nucleus and epigenetic regulation in wheat.
Collaborator Contribution The have built sequencing libraries for design future wheat and are providing staff training
Impact Production of sequencing libraries analysis of histone modification, 3D genome structural organisation and Chromatin accessibility.
Start Year 2018
 
Description 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 Learned Society 
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 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 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 Charity/Non Profit 
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 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 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 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/ 
 
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 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 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 10 plus wheat genome project workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The meeting was to provide a consortium update on the 10 plus wheat genome project
Year(s) Of Engagement Activity 2018
URL http://www.10wheatgenomes.com
 
Description 17-21 July 2017_2nd Interdisciplinary Signaling Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact In this interdisciplinary workshop advanced science was combined with informal summer activities to solve multi-disciplinary scientific questions, by bringing early career scientists together with more established researchers in a relaxing and beautiful location.

Invited speakers presented talks on the topics of cell regulation, network modelling, genomics, systems biology, bioinformatics, structural biology, biochemistry, and cheminformatics. Then, selected talks from other participants will be followed by multi-disciplinary teamwork sessions in the afternoon, followed by cultural and social activities, such as medieval team building and handicraft activities in the Visegrad Castle. Poster sessions and plenty of informal opportunities allowed the participants to discuss complex and exciting questions as well as develop new collaborations. The renaissance surroundings of the venue nicely matched with the interdisciplinary nature of the workshop.
Year(s) Of Engagement Activity 2017
URL http://signalingworkshop.org/
 
Description 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 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 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 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 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 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 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 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 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 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
Year(s) Of Engagement Activity 2018
URL http://intobiology.org.uk/dr-nicola-patron-engineering-plants-for-farming-and-pharming/
 
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 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 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 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 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 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 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 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 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 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 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 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 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 - 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 - 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 - 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 : 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 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: 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 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 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 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 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
 
Description The role of structural variants n the adaptive radiation of African Cichlids, Genome Informatics 2018, Hinxton, Cambridge 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact The role of structural variants n the adaptive radiation of African Cichlids, Genome Informatics 2018, Hinxton, Cambridge
Year(s) Of Engagement Activity 2018
 
Description Tim Robinson - TechEast - 19/10/2018 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Meeting to discuss potential funding opportunities
Year(s) Of Engagement Activity 2018
 
Description Web Article - Day in the life of... a wheat bioinformatician on her own research path - 18.07.2018 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge.
This is part of our women in computing to promote this as a career addressing the skill shortage and lack of gender balance in the UK
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/day-life-%E2%80%A6-wheat-bioinformatician-her-own-research-path
 
Description Web Article - Spotlight on Synthetic Biology. Yaomin Cao 
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 Interview with Yaomin Cai of Nicola Patron's DNA Foundry at Earlham Institute, on how he got into synthetic biology, how it can help us to tackle biological questions, and what the future has in store. -SOCIAL MEDIA- Engagement x92, Impressions x70456
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/articles/spotlight-on-synthetic-biology
 
Description Web Article - Spotlight on biohacking 
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 Interview with Elliot Roth, founder of Spira and Indie-lab on biohacking and algae research. -SOCIAL MEDIA- ENgagement x88, Impressions x176657
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/articles/spotlight-biohacking-elliot-roth-%E2%80%9Cit%E2%80%99s-algae-time%...
 
Description Web Article - What is bioinformatics? - 16.10.2018 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge.

Bioinformatics is a growing field of research, existing at the cutting-edge of the biological sciences. But what is it?
Biology is going large. With the advent of next generation (and third generation) genome sequencing and along with it an explosion in the amount of biological data being produced daily, scientists are now playing with terabytes or even petabytes (lots and lots of zeros) of data at a time. It would take infinite infinities for a single person to analyse this digital abundance.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/what-is-bioinformatics
 
Description Web Article - Women in computing: a journey into bioinformatics with Erin Baggs - 08.05.2018 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. This is part of our women in computing to promote this as a career addressing the skill shortage and lack of gender balance in the UK
For many in the bioinformatics world, coding is a leap into the unknown. This was the case for Erin Baggs, who has learned from scratch how to apply computational science to biology while doing her PhD with Ksenia Krasileva. She gives us an insight into what life is like for a PhD student, and how to negotiate the intrepid plunge into the choppy sea of coding.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/women-computing-journey-bioinformatics-erin-baggs
 
Description Web article - A celebration of science in Norwich - 27.08.2018 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge.

Promoting our engagement in the Noriwch Science festival beyond our region.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/celebration-science-norwich
 
Description Web article - Decoding Living Systems: from cell to ecosystem - 28.03.2018 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/decoding-living-systems-cell-ecosystem
 
Description Web article - Fostering symbiosis in the biosciences through multiscale modelling 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact News article to highlight the "Multiscale analysis of host-microbe interactions in plants, animals & humans" workshop and it's outcomes. -SOCIAL MEDIA- Engagement x102, Impressions x113433
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/articles/fostering-symbiosis-biosciences-through-multiscale-modelling
 
Description Web article - Spotlight on Synthetic Biology 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Article with a focus on Synthetic Biology. An interview with John Cumbers, founder of SynBioBeta. -SOCIAL MEDIA- Engagement x160, Impressions x159540
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/spotlight-synthetic-biology-john-cumbers
 
Description Web article - We need to talk about food -18.04.2018 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Article about attending a BBSRC funded Early Career Researcher Policy Lab organized by the Global Food Security programme - a UK cross-government programme on food security research, with a multidisciplinary group looking to tackle the most important issue of all: how to feed 10 billion healthily and sustainably by 2050.
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/we-need-talk-about-food
 
Description Web article - Women in Computing: Alexandra Veress - 12.01.2019 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge.
This is part of our women in computing to promote this as a career addressing the skill shortage and lack of gender balance in the UK.
Alexandra Veress came to study at Earlham Institute for three months as part of the Korcsmáros Group, where she learned how to apply computational approaches to biology. Working with Tamás and his group, as many can attest, is a great experience - and Alexandra left for Hungary with the desire to learn even more about the world of bioinformatics.
Year(s) Of Engagement Activity 2019
URL http://www.earlham.ac.uk/articles/women-computing-learning-ropes-bioinformatics
 
Description Women of the Future 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact Women of the Future encourages and engages young school age women to be successful in business and careers. The event held at the Norwich Research Park showcases the science across the park to encourage participation in STEM. I presented a poster of my research to the girls and their teachers.
Year(s) Of Engagement Activity 2016
URL https://womenofthefuture.co.uk/
 
Description web article - One day in New York: bioinformatics and family life - 13.08.2018 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Articles such as this pertain to our publically funded research such that the information gleaned can be disseminated to the general public. As of March 2019, our articles have reached people in all but 6 countries worldwide, with over 50000 pageviews on our website in the year 2018. On social media, this reach has exceeded a million people, monthly. As part of an expanding portfolio covering the range of science that we do, each article forms a vital component of how we engage the wider international community with important scientific breakthroughs and knowledge. This is part of our working in computing to promote this as a flexible career addressing the skill shortage and lack of gender balance in the UK
Year(s) Of Engagement Activity 2018
URL http://www.earlham.ac.uk/articles/one-day-new-york-bioinformatics-and-family-life