Dr Padhmanand Sudhakar


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Systems Biology of Gut-Microbe Interactions

I have an academic background in Microbial Computational Systems Biology mostly focused on the reconstruction of bacterial regulatory networks and integration of heterogeneous datasets.

My current research interests revolve around using various bioinformatics methods and approaches to study the molecular cross-talk between bacteria and humans in the gut environment particularly in the context of autophagy, immunomodulation, and homeostasis as well as in disease states such as Ulcerative Colitis and Crohn’s Disease. Towards this goal, I use a wide variety of methods and data sources to enable the integration and interpretation of different kinds of –omic datasets using biological networks derived from both predicted and experimental data.

Key Publications

Olbei M., Kingsley R. A., Korcsmaros T., Sudhakar P. (2019) Network Biology Approaches to Identify Molecular and Systems-Level Differences Between Salmonella Pathovars. Methods Mol Biol. Springer 1918 265-273 DOI: 10.1007/978-1-4939-9000-9_21

Tooze S. A., New M., Van Acker T., Sakamaki J. I., Jiang M., Saunders R. E., Long J., Wang V. M., Behrens A., Sudhakar P., Korcsmaros T., Ryan K. M., Howell M., Cerveira J., Jefferies H. B. J. (2019) MDH1 and MPP7 regulate autophagy in pancreatic ductal adenocarcinoma. Cancer Research 10.1158/0008-5472.CAN-18-2553

Jones E., Matthews Z., Gul L., Sudhakar P., Treveil A., Divekar D., Buck J., Wrzesinski T., Jefferson M., Armstrong S., Hall L., Watson A., Carding S., Haerty W., Di Palma F., Mayer U., Powell P., Hautefort I., Wileman T., Korcsmaros T. (2019) Integrative analysis of Paneth cell proteomic and transcriptomic data from intestinal organoids reveals functional processes dependent on autophagy Disease Models and Mechanisms DOI: doi: 10.1242/dmm.037069

Jacomin A. C., Gul L., Sudhakar P., Korcsmaros T., Nezis I. P. (2018) What We Learned From Big Data for Autophagy Research. Frontiers in cell and developmental biology 6 92 DOI: 10.3389/fcell.2018.00092

Métris A., Sudhakar P., Fazekas D., Demeter A., Ari E., Branchu P, Kingsley R.A., Baranyi J., Korcsmáros T.
SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation, In Press, npj Systems Biology and Applications, doi: 10.1038/s41540-017-0034-z

P. Sudhakar, M. Reck, W. Wang, F. He, IW. Dobler, AP. Zeng. Construction and verification of the transcriptional regulatory network of the human dental pathogen Streptococcus mutans upon treatment with the biofilm inhibitor Carolacton. BMC Genomics 2014, 15:362 http://www.biomedcentral.com/1471-2164/15/362

F. He, W. Wang, P. Zheng, P. Sudhakar, J. Sun and AP. Zeng. Essential O2-responsive genes of Pseudomonas aeruginosa and their network revealed by integrating dynamic data from inverted conditions. Integrative Biology 2014, 6: 215-223. http://pubs.rsc.org/en/content/articlelanding/2014/ib/c3ib40180d

L. Song, P. Sudhakar, W. Wang, G. Conrads, A. Brock, J. Sun, I. Wagner-Döbler, A.-P. Zeng (2012) A genome-wide study of two-component signal transduction systems in eight newly sequenced mutans streptococci strains. BMC Genomics 2012, 13:128 http://www.biomedcentral.com/1471-2164/13/128

Brooks-Warburton J, Modos D, Sudhakar P, Madgwick M, Thomas JP, Bohar B, Fazekas D, Zoufir A, Kapuy O, Szalay-Beko M, Verstockt B, Hall LJ, Watson A, Tremelling M, Parkes M, Vermeire S, Bender A, Carding SR, Korcsmaros . (2022)

A systems genomics approach to uncover patient-specific pathogenic pathways and proteins in ulcerative colitis.

Nature communications

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Gul LEJLA, Modos DEZSO, Fonseca SONIA, Madgwick M, Thomas J, Sudhakar P, Booth C, Stentz R, Carding S, Korcsmaros . (2022)

Extracellular vesicles produced by the human commensal gutbacteriumBacteroides thetaiotaomicronaffect host immunepathways in a cell-type specific manner that are altered ininflammatory bowel disease

Journal of Extracellular Vesicles

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Treveil A,Bohar B,Sudhakar P,Gul L,Csabai L,Olbei M,Poletti M,Madgwick M,Andrighetti T,Hautefort I,Modos D,Korcsmaros T. (2021)

ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways

PLoS Computational Biology

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Csabai L, Fazekas D, Kadlecsik T, Szalay-Beko M, Bohár B, Madgwick M, Módos D, Olbei M, Gul L, Sudhakar P, Kubisch J, Oyeyemi OJ, Liska O, Ari E, Hotzi B, Billes VA, Molnár E, Földvári-Nagy L, Csályi K, Demeter A, Pápai N, Koltai M, Varga M, Lenti K, Farkas IJ, Türei D, Csermely P, Vellai T, Korcsmáros . (2021)

SignaLink3: a multi-layered resource to uncover tissue-specific signaling networks.

Nucleic acids research

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Sudhakar P, Machiels K, Verstockt B, Korcsmaros T, Vermeire . (2021)

Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions

Frontiers in Microbiology

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Seyed Tabib N., Madgwick M., Sudhakar P., Verstockt B., Korcsmaros T., Vermeire S.. (2020)

Big data in IBD: big progress for clinical practice.


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Tooze S. A., New M., Van Acker T., Sakamaki J. I., Jiang M., Saunders R. E., Long J., Wang V. M., Behrens A., Sudhakar P., Korcsmaros T., Ryan K. M., Howell M., Cerveira J., Jefferies H. B. J.. (2019)

MDH1 and MPP7 regulate autophagy in pancreatic ductal adenocarcinoma.

Cancer research

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