Summary
I am a systems biologist working with both computational and experimental approaches to study signalling networks in the gut. For 15 years, I have been been working in the field of intra- and inter-cellular signalling networks and the regulation of autophagy, a key cellular process for maintaining health and fight diseases. I am particularly interested in how cell-cell and cell-microbe interactions affect intestinal homeostasis, and how we could use precision medicine to tackle current challenges to treat patients with inflammatory bowel disease. In my group we have developed gap-filling computational resources and applied experimental novel systems, such as organoids, to achieve these goals. Besides leading our research group that focuses on improving our understanding on the pathomechanisms of IBD, I am also co-leading the NIHR Imperial BRC Organoid Facility to establish patient-specific multi-omics studies for various complex diseases.
A recent interview with me can be accessed HERE.
Details of our group is shown on the group website.
Short biography
I started my research as a high school student in a biochemistry lab. After four years of experimental research work on redox biology in the liver, I gained my MSc degree at Eötvös Loránd University in Budapest, Hungary. Then, as a PhD student, I developed a signalling network database, SignaLink, which filled a vital niche in the landscape of bioinformatics tools, and by now it has become one of the most used signalling network resources for human and model organism studies. In Budapest, I established and led the “NetBiol” Network Biology group, which has developed additional novel databases and web-services to meet key scientific community needs. In March 2014, I moved to the UK, to the Norwich Research Park, where I received a special 5-year BBSRC fellowship to work in the computational biology and sequencing focused Earlham Institute and in the gut microbiome centred Quadram Institute. This fellowship allowed me to establish a multi-disciplinary group that combines computational and experimental approaches, including gut organoids. Between 2017 and 2021 I was leading the systems genomics workpackage of the UKRI-BBSRC funded institute strategic programme of the Earlham Institute. In 2019, I was appointed as a Tenure-track group leader at the Earlham and the Quadram Institutes. My group has carried out multiple projects to predict, analyse and validate host-microbe interactions in the gut, especially in relation to the regulation of autophagy by microbes and upon disease conditions such as inflammatory bowel disease (IBD) and cancer. I moved to Imperial College in 2021 as a Senior Lecturer, and remained an affiliated group leader in Norwich. Thanks to the multi-disciplinary background and interest of my group as well as to the great collaborators we are lucky to work with, our group can investigate challenging and complex questions as described in the 'Research' tab.
Innovation and technology transfer: I am a strong believer that technology transfer is crucial in modern life science research. In the last 10 years, I coordinated three innovation grant programs, including one enabling the development of a biomedical software framework, NavigOmiX to facilitate multi-scale omic data analysis and precision medicine. In the last 5 years, I raised or received £1,3M worth of funding to develop a market ready product for this software. In 2013, I co-founded a US based network pharmacology company together with Laszlo Albert Barabasi (University of Notre Dame and Harvard University) and Joseph Loscalzo (Harvard Medical School), where I was an external senior scientist till 2015.
Teaching: I established a combined bioinformatics lecture and practical course for Master students (in 2010) and an introductory practical course for BSc students in Budapest (in 2011). Both courses are still going with a similar but updated curriculum. For four years, I have taught systems biology for 450 university students per year in Budapest. I was a trainer on numerous courses, including a FEBS Practical Course, sixteen EMBL-EBI courses and three other institutional courses in Norwich. In 2016, I co-organised two EMBO Practical Courses. Between 2016 and 2020, I co-ordinated the Norwich Research Park DTP course on Computational and Systems Biology for all first year PhD students.
Talent support: Since 2001, I have been participating as a volunteer in Hungarian and international talent support organisations. I organised more than 10 high-school student research conferences. Between 2004 and 2007, I established a university student leadership program for biology students to organise and manage scientific research-related programs and conferences (this program is still in action, currently with double number of students compared to 2007).
Currently, I am the Chairman of the Board of the Research Student Foundation supporting 5000 high-school research students in Eastern Europe. I took this role after the financial crisis, when most of the funding sources and donations disappeared, and the research student movement was in danger of dissolving. In two years, I was able to secure the future for this special initiative by restructuring the organisation and its programs, attracting more students, involving new sponsors (such as Microsoft) and establishing an office with three full-time staff working on operational tasks.
Organisational works: I played a major role in the organisation of eight international conferences (each with more than 1000 participants), including one FEBS Congress. As a main organiser I established the Interdisciplinary Signaling Workshop, which was organised twice already in 2014 and 2017, and the next one is scheduled for 2023.
Selected Publications
Journal Articles
Pavlidis P, Tsakmaki A, Li K, et al., 2022, Interleukin-22 regulates neutrophil recruitment in ulcerative colitis and is associated with resistance to ustekinumab therapy, Nature Communications, Vol:13, ISSN:2041-1723, Pages:1-17
Pavlidis P, Tsakmaki A, Treveil A, et al., 2022, Cytokine responsive networks in human colonic epithelial organoids unveil a molecular classification of inflammatory bowel disease, Cell Reports, Vol:40, ISSN:2211-1247, Pages:111439-111439
Demeter A, Jacomin A-C, Gul L, et al., 2022, Computational prediction and experimental validation of Salmonella Typhimurium SopE-mediated fine-tuning of autophagy in intestinal epithelial cells, Frontiers in Cellular and Infection Microbiology, Vol:12, ISSN:2235-2988
Gul L, Korcsmaros T, Hall N, 2022, Flaviviruses hijack the host microbiota to facilitate their transmission, Cell, Vol:185, ISSN:0092-8674, Pages:2395-2397
Poletti M, Treveil A, Csabai L, et al., 2022, Mapping the epithelial-immune cell interactome upon infection in the gut and the upper airways, Npj Systems Biology and Applications, Vol:8
Brooks-Warburton J, Modos D, Sudhakar P, et al., 2022, A systems genomics approach to uncover patient-specific pathogenic pathways and proteins in ulcerative colitis, Nature Communications, Vol:13
Thomas JP, Modos D, Rushbrook SM, et al., 2022, The emerging role of bile acids in the pathogenesis of inflammatory bowel disease, Frontiers in Immunology, Vol:13, ISSN:1664-3224
Csabai L, Fazekas D, Kadlecsik T, et al., 2022, SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks., Nucleic Acids Research, Vol:50, ISSN:0305-1048, Pages:D701-D709
Gul L, Modos D, Fonseca S, et al., 2022, Extracellular vesicles produced by the human commensal gut bacterium Bacteroides thetaiotaomicron affect host immune pathways in a cell-type specific manner that are altered in inflammatory bowel disease, Journal of Extracellular Vesicles, Vol:11, ISSN:2001-3078
Thomas JP, Modos D, Korcsmaros T, et al., 2021, Network Biology Approaches to Achieve Precision Medicine in Inflammatory Bowel Disease, Frontiers in Genetics, Vol:12
Ostaszewski M, Niarakis A, Mazein A, et al., 2021, COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms., Mol Syst Biol, Vol:17
Modos D, Thomas JP, Korcsmaros T, 2021, A handy meta-analysis tool for IBD research, Nature Computational Science, Vol:1, Pages:571-572
Poletti M, Arnauts K, Ferrante M, et al., 2021, Organoid-based Models to Study the Role of Host-microbiota Interactions in IBD, Journal of Crohns & Colitis, Vol:15, ISSN:1873-9946, Pages:1222-1235
Sudhakar P, Machiels K, Verstockt B, et al., 2021, Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions, Frontiers in Microbiology, Vol:12
Tuerei D, Valdeolivas A, Gul L, et al., 2021, Integrated intra- and intercellular signaling knowledge for multicellular omics analysis, Molecular Systems Biology, Vol:17, ISSN:1744-4292
Tabib NSS, Madgwick M, Sudhakar P, et al., 2020, Big data in IBD: big progress for clinical practice, Gut, Vol:69, ISSN:0017-5749, Pages:1520-1532
Andrighetti T, Bohar B, Lemke N, et al., 2020, MicrobioLink: An Integrated Computational Pipeline to Infer Functional Effects of Microbiome-Host Interactions, Cells, Vol:9
Treveil A, Sudhakar P, Matthews ZJ, et al., 2020, Regulatory network analysis of Paneth cell and goblet cell enriched gut organoids using transcriptomics approaches, Molecular Omics, Vol:16, Pages:39-58
Sudhakar P, Jacomin A-C, Hautefort I, et al., 2019, Targeted interplay between bacterial pathogens and host autophagy, Autophagy, Vol:15, ISSN:1554-8627, Pages:1620-1633
Jones EJ, Matthews ZJ, Gul L, et al., 2019, Integrative analysis of Paneth cell proteomic and transcriptomic data from intestinal organoids reveals functional processes dependent on autophagy, Disease Models & Mechanisms, Vol:12, ISSN:1754-8403
Korcsmaros T, Schneider MV, Superti-Furga G, 2017, Next generation of network medicine: interdisciplinary signaling approaches, Integrative Biology, Vol:9, ISSN:1757-9694, Pages:97-108
Modos D, Bulusu KC, Fazekas D, et al., 2017, Neighbours of cancer-related proteins have key influence on pathogenesis and could increase the drug target space for anticancer therapies, Npj Systems Biology and Applications, Vol:3