Gut Systems Biology, connecting microbes and host processes

Lead Research Organisation: Institute of Food Research
Department Name: Contracts

Abstract

The Korcsmaros group under this project applies network biology to analyse experimental data, develop in silico predictions and validate them with small-scale or large-scale (omics) approaches. The biological focus in this project is autophagy, gut microbes (both commensals and pathogens) that could affect the host’s autophagy process, and disease states such as IBD. The project also involves developing novel experimental protocols to measure autophagy upon infection and in organoids. The project involves a post-doc research assistant and supported by PhD students (co-)supervised by T. Korcsmaros. The project is closely connected and complement IFR projects of the Carding, Hall and Baranyi group as well as Tom Wileman’s work at the UEA. Major objectives of the project are: 1) reconstructing molecular interaction networks for gut microbes and intestinal epithelial cell specific host cells; 2) develop host-microbe interaction maps; 3) perform experiments for validation of the predictions; 4) develop new experimental approaches to measure autophagy.

Publications

10 25 50

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Csabai L (2018) SignaLink: Multilayered Regulatory Networks. in Methods in molecular biology (Clifton, N.J.)

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Csabai L (2018) SignaLink: Multilayered Regulatory Networks. in Methods in molecular biology (Clifton, N.J.)

 
Description We developed new resources to store, visualise and interpret biological data, in particular about the regulation of autophagy, an essential cellular process, critical for the intestinal well-being, and another resource, SalmoNet, which allows a comparative study of different Salmonella strains, saving tens of hours for the experts to access and use data in the public domain. We also identified connections how Salmonella can regulate autophagy to cause a more severe infection. We identified several novel autophagy regulators, and highlighted those that are relevant in specific intestinal cell types.
Exploitation Route The Autophagy Regulatory Network and the Salmonet resources can be accessed by colleagues; they can browse and download the integrated data. These users can use the databases to evaluate their experimental data or predict novel connections and functions.
Sectors Healthcare,Pharmaceuticals and Medical Biotechnology

 
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 NRP Seed fund
Amount £16,000 (GBP)
Organisation Norwich Research Park 
Sector Private
Country United Kingdom
Start 01/2018 
End 01/2019
 
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 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 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 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/
 
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 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 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 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 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 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 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 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 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 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 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 : 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 : 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: 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 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 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 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