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Leonid Mirny, Ph.D.

Department of Health Sciences & Technology
Assistant Professor of Health Sciences & Technology and Physics

Room E25-526C
617-452-4862 (phone)

Current Projects

  • Physics of protein-DNA search and recognition
  • Modeling of chromatin organization and folding
  • Evolutionary models of cancer progression

Research Summary

Professor Mirny's research focuses on computational structural and system biology. His multidisciplinary approach combines first-principle physics with the analysis of biological systems such as genes, proteins, and metabolic pathways. His efforts in computational structural biology involve the development of novel computational tools to analyze and predict structures of proteins, their complexes, and protein-DNA interactions. In these studies, Prof. Mirny seeks to identify amino acids that determine specific DNA recognition, to test these predictions in future experiments, and to find methods to engineer proteins with novel biological functions.

Professor Mirny's system biology projects, which involve the design and simulation of genetic and biochemical networks, integrate large-scale analysis of proteomic and genomic data with molecular simulations of proteins. He is interested in developing stochastic computational models of genetic and biochemical networks, cellular regulation, and signal transduction. Professor Mirny's research seeks to extract efficiently biological knowledge from experimental genomic and proteomic data and to develop a fundamental understanding of the molecular mechanisms involved in cellular regulation. This work aims to reconstruct the cell's entire regulatory network-a goal of both genomics and bioinformatics research.

Recent Publications

  • Mirny LA. Nucleosome-mediated cooperativity between transcription factors. PNAS 2010 Dec 28;107(52):22534-9.
  • Tafvizi A, Huang F, Fersht AR, Mirny LA, van Oijen AM. A single-molecule characterization of p53 search on DNA. PNAS 2010 Dec 22. PMID: 21178072
  • Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009 Oct 9;326(5950):289-93.
  • Wunderlich Z., Mirny LA Different strategies for transcriptional regulation are revealed by information-theoretical analysis of binding motifs.
    Trends Genet. 2009 Oct;25(10):434-40.
  • Leonid Mirny, Michael Slutsky, Zeba Wunderlich, Anahita Tafvizi, Jason Leith and Andrej Kosmrlj How a protein searches for its site on DNA: the mechanism of facilitated diffusion J. Phys. A: Math. Theor. 42 No 43 (30 October 2009) 434013.

Last Updated: January 19, 2011