Principal Investigator

Leonid Mirny

Professor of Medical Engineering and Science, and Physics

Current Affiliations:
  • Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology
  • Associate Member of the Broad Institute
  • Associate Member of the Dana-Farber Cancer Institute



Postdoctoral Fellows

Dina Tsukrov

Albert Einstein College of Medicine, Biomedical Science, Ph.D.

Exploring the balance between passenger and driver mutations in cancer.



Johannes Nübler

Univeristy of Tübingen, Ph.D.

Johannes works on the analysis of Hi-C and Micro-C data and modeling chromosomal organization in yeast, mouse, and human cells. His particular focus is on bridging large scale polymer models of chromatin with more fine-grained models of nucleosomes. He is interested in role of active processes in chromatin organization, e.g. transcription and chromatin remodeling.


Aafke van den Berg

TU Delft, Ph.D.



Graduate Students

Anton Goloborodko

MIT Physics, Ph.D. Student

Anton's main interests are the structure of mitotic chromosomes and polymer simulations of chromosomal folding.



Nezar Abdennur

MIT Computational and Systems Biology, Ph.D. Student

My research interests lie at the intersection of nuclear organization and gene regulation.

nabdennur [at] gmail [dot] com


Martin Falk

MIT Physics, Ph.D. Student

My research interests are oriented towards a better understanding of nuclear structure and function via the construction and analysis of simple physical or mathematical models. Currently, my projects involve the use of polymer physics to study chromatin organization at the level of compartments.

mafafalk [at] gmail [dot] com


Hugo Brandão

Harvard Biophysics, Ph.D. Student

Hugo studies chromosome condensation and segregation in prokaryotes; he aims to elucidate fundamental principles of chromosome compaction by a combination of genomics, computational/theoretical modeling, and experiments.




E. M. Breville

MIT Physics (Ph.D./M.D./J.D. Harvard Biophysics/HST)

I joined MirnyLab in 2014, taking over daily caffination duties from Espresso. I continue my predecessor's research directions, including the long-term study of caffeination on H. sapiens. While I am currently the only wet-lab experimentalist in the group, I find the theorists easy to collaborate with and wonderfully open-minded.




  • Geoff Fudenberg, Ph.D. Student

    Harvard, Ph.D. in Biophysics

    3D Genome Organization: Physical models, statistical methods, and comparative genomics

  • Maxim Imakaev, Ph.D. Student

    MIT, Ph.D. in Physics

    3D genome organization: polymer models of the genomes of different organisms, and Hi-C data analysis

  • Boryana Doyle, Undergraduate Student

    MIT Physics, class of 2017

    Chromatin looping and enhancer-promoter interactions

  • Chris McFarland, Ph.D Student

    Harvard University, Ph.D. in Biophysics

    The role of deleterious passengers in cancer

  • Espresso, Staff

    MIT Physics, Ph.D., M.D., J.D.

    A longitudinal study of caffeination in H. sapiens

  • Konstantine Tchourine, Undergraduate Student

    New York University, Ph.D. Student

    Dynamics of long polymer chains supject to various restrictions

  • Jason Leith, Ph.D Student

    Harvard University, Ph.D. in Biophysics

    Theoretical and Experimental Studies of Protein-DNA Search and Recognition: p53 as a Model System

  • Michael Schnall-Levin, Ph.D Student

    MIT Mathematics, Ph.D. Student

    Transcriptional Regulation: Factors Beyond Binding Motif Matches

  • Zeba Wunderlich, Ph.D. Student

    Harvard University, Ph.D. in Biophysics

    Modeling of the transcription factor search

    Energetics of protein-protein interactions

  • Anahita Tafvizi, Ph.D. Student

    Harvard University, Ph.D. in Physics

    Transcription factor-DNA interactions

  • Victor Spirin, Postdoctoral Fellow

    Boston University, Ph.D. in Physics

    Structure and regulation of piological networks

  • Michael Slutsky, Ph.D. Student

    MIT, Ph.D. in Physics

    Biophysics of protein-DNA interactions

  • Alex Shpunt, Ph.D. Student

    MIT, Ph.D. in Physics

    Biophysics of molecular self-assemply

  • Ilya Rudkevich, Undergraduate Student

    Brandeis University, B.S.

    Prediction of natively unstructured proteins

  • Shankar Mukherji, Undergraduate Student

    MIT, B.S.

    Dynamics of signaling cascades

  • Lewyn Li, Postdoctoral Fellow

    Columpia University, Harvard University, Ph.D. in Chemistry

    Specificity determining residues in protein kinases

  • Joe Levine, Masters Student

    MIT, B.S., M.S.

    Dynamics of signaling cascades

  • Hao Yuan Kueh, Rotation Student

    Harvard Biophysics

    Princeton University, B.S.

    Information transmission in enzymatic switch

  • Grigory Kolesov, Postdoctoral Fellow

    University of Munich, Ph.D. in Biology

    Evolution and prediction of specificity-determining residues

  • Carlos Gómez-Uripe, Ph.D. Student


    Stochastic models of signaling networks

  • Juhi Chandalia, Masters Student

    MIT, B.S., M.S.

    Structure and evolution of regulatory networks

  • Vincent Berupe, Ph.D. Student>

    MIT Physics, Ph.D. Student

    Stochastic models of ion channels

  • Ivan Adzhupey

    Moscow State University, Ph.D. in Biology

    Bioinformatics infrastructure development and maintenance