Sander Lab

Understanding and Reversing Pancreatic Beta Cell Dysfunction in Diabetes

Medhavi Mallick, Ph.D.

Postdoctoral fellow

I received my Ph.D. degree from the Institute of Molecular Biology, Johannes Gutenberg University in Germany. During my Ph.D., I worked in Prof. Christof Niehrs’ lab, where I conducted bioinformatic studies to understand the role of genomic cytosine modifications in mouse aging and Xenopus early development. My expertise in epigenetics, multi-omics datasets, and interest towards disease-oriented computational biology led me to join Sander lab in 2019. Here my research goal is to understand the mechanisms underlying genetic defects associated with human β-cell dysfunction. My main focus is to identify gene regulatory programs causing diabetes, using integration of WGBS, ox-WGBS, DIP-Seq, RNA-seq, ChIP-seq, along with scATAC-seq and scRNA-Seq data.

 

Publications:

Nutrient regulation of the islet epigenome controls adaptive insulin secretion. Journal of Clinical Investigation, 2023 Apr;133(8): e165208. Wortham M, Liu F, Harrington AR, Fleischman JY, Wallace M, Mulas F, Mallick M, Vinckier NK, Cross BR, Chiou J, Patel NA, Sui Y, McGrail C, Jun Y, Wang G, Jhala US, Schüle R, Shirihai OS, Huising MO, Gaulton KJ, Metallo CM, Sander M.

Integrating genetics with single-cell multiomic measurements across disease states identifies mechanisms of beta cell dysfunction in type 2 diabetes. Nature Genetics, 2023 Jun;55(6): 984-994. Wang G, Chiou J, Zeng C, Miller M, Matta I, Han JY, Kadakia N, Okino ML, Beebe E, Mallick M, Camunas-Soler J, Dos Santos T, Dai XQ, Ellis C, Hang Y, Kim SK, MacDonald PE, Kandeel FR, Preissl S, Gaulton KJ, Sander M.

Impaired DNA demethylation of C/EBP sites causes premature aging. Genes & Development, 2018, 32(11-12): 742-762. Andrea Schäfer*, Bernadette Mekker*, Medhavi Mallick*, Viviana Vastolo, Emil Karaulanov, Dominik Sebastian, Carina von der Lippen, Bernd Epe, Damien J. Downes, Carola Scholz, Christof Niehrs. *These authors contributed equally.

5-formylcytosine is an activating epigenetic mark for Pol III during zygotic reprogramming. Medhavi Mallick, Parasyraki, Eleftheria, Victoria Hatch, Viviana Vastolo, Emil Karaulanov, Michael U. Musheev, Simon Moxon, Christof Niehrs. (Target to submit in Cell).

NEIL1 and NEIL2 DNA glycosylases protect neural crest development against mitochondrial oxidative stress. Elife. 2019 Sep 30;8: e49044. Han D, Schomacher L, Schüle KM, Mallick M, Musheev MU, Karaulanov E, Krebs L, von Seggern A, Niehrs C.

GADD45 promotes locus-specific DNA demethylation and 2C cycling in embryonic stem cells. Genes & Development. 2019 Jul 1;33(13-14):782-798. Schüle KM, Leichsenring M, Andreani T, Vastolo V, Mallick M, Musheev MU, Karaulanov E, Niehrs C.

Meropenem: A potent drug against superbug as unveiled through bioinformatics approaches. International Journal of Bioinformatics Research and Applications, 2013, 9(2): 109-20. Medhavi Mallick, Devang Odedra, Ambarish Sharan Vidyarthi, Shankaracharya.

Tools for predicting metal binding Sites in Protein: A Review”, Current Bioinformatics, 2011, 6(4): 444-449. Medhavi Mallick, Devang Odedra, Ambarish Sharan Vidyarthi, Shankaracharya.

Homology modelling of polyphenol oxidase from Solanum melongena: sequence analysis and structural validation studies – In Silico. International Journal of Pharma and Bio Sciences, 2011, 2(3): 319-328. Medhavi Mallick, Neetha A. Udayakumar, Koel Mukherjee.

Comparative Evolutionary Analysis of Metallo-β-Lactamases with reference to NDM1. Online Journal of Bioinformatics, 2011, 12(1): 18-33. Devang Odedra*, Medhavi Mallick*, Ambarish Sharan Vidyarthi, Shankaracharya. *These authors contributed equally.

Java based diabetes type-2 prediction software to assist physicians in making better decisions. Diabetes Technology & Therapeutics, 2012, 14(3): 251–256. Shankaracharya, Devang Odedra, Medhavi Mallick, Prateek shukla, S. Samanta, Amabarish Vidyarthi.

Predict @proteommetal: A web-based tool for the prediction of metal binding domains in proteins. Software published on 2011. Software available at: www.bitmesra.ac.in/proteommetal/home.php. Medhavi Mallick, Ambarish S. Vidyarthi, Shankaracharya.

NCBI-GEO and Website Management:

The Sander laboratory website (http://msanderlab.org), project storage on Triton Shared Computing Cluster (TSCC) server and NCBI-GEO database are expertly managed by Medhavi Mallick. For any website-related queries please do not hesitate to contact us at mmallick@health.ucsd.edu.