Dr Padhmanand Sudhakar

Researcher

Contact via email

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

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

Big data in IBD: big progress for clinical practice.

Gut


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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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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


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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

Autophagy


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Treveil A., Sudhakar P., Matthews Z., Wrzesinski T., Jones E., Brooks J., Olbei M., Hautefort I., Hall L., Carding S., Mayer U., Powell P., Wileman T., Di Palma F., Haerty W., Korcsmaros T.. (2019)

Regulatory network analysis of Paneth cell and goblet cell enriched gut organoids using transcriptomics approaches.

Molecular omics


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Chalmers N., Stetkiewicz S., Sudhakar P., Osei-Kwasi H., Reynolds C.. (2019)

Impacts of Reducing UK Beef Consumption Using a Revised Sustainable Diets Framework

Sustainability


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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


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Metris A., Sudhakar P., Fazekas D., Demeter A., Eszter A., Olbei M., Branchu P., Kingsley R., Baranyi J., Korcsmaros T.. (2017)

SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation

Nature Partner Journals Systems Biology and Applications, 3, Article number: 31 (2017)


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