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:
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*. Nutrient regulation of the islet epigenome controls adaptive insulin secretion. J Clin Invest. 2023 Apr;133(8):e165208.
Schäfer A*, Mekker B*, Mallick M*, Vastolo V, Karaulanov E, Sebastian D, von der Lippen C, Epe B, Downes DJ, Scholz C, Niehrs C. (2018) Impaired DNA demethylation of C/EBP sites causes premature aging. Genes & Development 32(11-12): 742-762. *equal contributors
Schüle KM, Leichsenring M, Andreani T, Vastolo V, Mallick M, Musheev MU, Karaulanov E, Niehrs C. (2019) GADD45 promotes locus-specific DNA demethylation and 2C cycling in embryonic stem cells. Genes & Development 33: 782-798.
Han D, Schomacher L, Schüle KM, Mallick M, Musheev MU, Karaulanov E, Krebs L, von Seggern A, Niehrs C. (2019) NEIL1 and NEIL2 DNA glycosylases protect neural crest development against mitochondrial oxidative stress. (In revision)
Mallick M, Odedra D, Vidyarthi AS, Shankaracharya. (2013) Meropenem: A potent drug against superbug as unveiled through bioinformatics approaches. International Journal of Bioinformatics Research and Applications 9(2): 109-20.
Mallick M, Odedra D, Vidyarthi AS, Shankaracharya. (2011) Tools for predicting metal binding Sites in Protein: A Review. Current Bioinformatics 6(4): 444-449.
Mallick M, Udayakumar NA, Mukherjee K. (2011) Homology modelling of polyphenol oxidase from Solanum melongena: sequence analysis and structural validation studies – In Silico. International Journal of Pharma and Bio Sciences 2(3): 319-328.
Odedra D*, Mallick M*, Vidyarthi AS, Shankaracharya. (2011) Comparative Evolutionary Analysis of Metallo-β-Lactamases with reference to NDM1. Online Journal of Bioinformatics 12(1): 18-33. *equal contributors
Shankaracharya, Odedra D, Mallick M, Shukla P, Samanta S, Vidyarthi AS. (2012) Java based diabetes type-2 prediction software to assist physicians in making better decisions. Diabetes Technology & Therapeutics 14(3): 251–256.
Mallick M, Vidyarthi AS, Shankaracharya. (2011) Predict @proteommetal: A web-based tool for the prediction of metal binding domains in proteins. Software available at: www.bitmesra.ac.in/proteommetal/home.php
NCBI-GEO and Website Management:
The Sander laboratory website (http://msanderlab.org), project storage on Triton Shared Computing Cluster (TSCC) server and associated 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.