Leonid Mirny

Core Faculty
Phone: (617) 452-4862
Website: Mirny Lab
Lab Phone: (617) 452-4862
Lab Fax: (617) 253-7498
room: E25-526C
MIT address: 77 Massachusetts Ave., Cambridge, MA 02139
Administrative Assistant: Caitlin Vinci
assistant phone: (617) 253-0009
assistant email: cburke@mit.edu

Leonid Mirny

Core Faculty


  • Professor of Medical Engineering and Science, Massachusetts Institute of Technology
  • Associate Member, Dana-Farber/Harvard Cancer Center
  • Associate Member, Broad Institute at Harvard and MIT


Leonid Mirny received his PhD in Biophysics from Harvard University. After a few years as a Junior Fellow at Harvard Society of Fellows, he was appointed to the MIT Faculty in 2001, joining the MIT Health Sciences and Technology Division and the Department of Physics. Prof. Mirny teaches classes in Statistical Physics in Biology, Quantitative Genomics, and a freshman seminar in Quantitative Biology. He is working to understand the human genome in 3D with his team at MIT in collaboration with the Dekker Lab at UMass Medical School. Using new data uncovered via Chromosome Conformation Capture (Hi-C) technology and computer simulations, the collaborators explore how the genome is organized inside a cell.

In 2015, Mirny became a co-director of the new Center for 3D Structure and Physics of the Genome at UMass Medical School and MIT, funded by the National Institutes of Health’s 4D Nucleome Program. The program, initiated by Director of the NIH, Francis Collins, is a focused, interdisciplinary directive, funding more than 25 labs to map not only the 3D architecture of the human genome, but also how this organization changes over time—the fourth dimension.

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.

Prof. Mirny is a Fellow of the American Physical Society, an Associate Faculty of the Broad Institute, and an Associate Member of the Dana-Farber Cancer Institute.


  • PhD in Biophysics, Harvard University, 1998
  • MSc in Chemistry, The Weizmann Institute of Science, 1994
  • Diploma with Honors in Physics, The Moscow Engineering Physics Institute, 1992

selected awards/societies

  • Fellow of the American Physical Society
  • NEC Fund Award
  • Samuel A. Goldblith Career Development Award
  • Alfred Sloan Research Fellow
  • John F. & Virginia B. Taplin Award
  • William F. Milton Award


The Mirny lab combines quantitative, typically physics-rooted, approaches with analysis of genomics data to address fundamental problems in biology, most recently they focused on two problems: (i) higher-order chromatin structure; (2) evolution of cancer during neoplastic progression. Studies of the Mirny lab on chromosomes aim to characterize 3D architecture of the genome and processes that lead to its organization and reorganization in the cell cycle and development. Works of the Mirny lab on cancer aim at understanding the role of multiple “passenger” genetic events, such as individual mutations and chromosomal alterations, in cancer progression.

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. The Mirny lab 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.

selected publications

  • M. V. Imakaev, G. Fudenberg, and L. A. Mirny. “Modeling chromosomes: Beyond pretty pictures.” FEBS Lett. (2015): 5893031-6.
  • B. Doyle, G. Fudenberg, M. V. Imakaev, and L. A. Mirny. “Chromatin loops as allosteric modulators of enhancer-promoter interactions.” PLoS Comput. Biol 10.10 (2014): e1003867.
  • T. Le, M. V. Imakaev, L. A. Mirny, and M. T. Laub. “High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome.” Science 342.6159 (2013): 731-4.
  • N. Naumova, M. Imakaev, G. Fudenberg, Y. Zhan, B. R. Lajoie, L. A. Mirny, and J. Dekker. “Organization of the Mitotic Chromosome.” Science 242.6161 (2013): 948-53.

A full list of Professor Mirny’s publications can be found on his website.

courses taught

  • HST 452 – SP 2013 – Statistical Physics in Biology Statistical Physics in Biology
  • HST 508 – FA 2013 – Quantitative Genomics Quantitative Genomics