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: Sean Clarke
assistant phone: (617) 253-9757
assistant email: clarke_1@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


A researcher in biophysics and computational biology, Professor Leonid Mirny has taught HST.558 (Introduction to Modeling and Simulation), and has served on HST’s PhD Admissions Committee. Following his appointment to the MIT faculty in 2001, he taught Statistical Physics in Biology (8.398). He was a Harvard University graduate with a PhD in Biophysics and later served as a Junior Fellow at the Harvard Society of Fellows. He attended the Weizmann Institute of Science (MSc ’94, Chemistry) and the Moscow Engineering Physics Institute (Dip ’92, Physics).


  • 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


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, Professor 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.

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