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 Tskurov

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.

jnuebler [at] mit [dot] edu


Aafke van den Berg

TU Delft, Ph.D.

Aafke is interested in the interplay between transcription activity and the spatial and temporal organization of the genome. For her research, she uses a combination of computational and mathematical modeling and analysis of experimentally obtained Hi-C data.

aafkevandenberg [at] gmail [dot] com


Ed Banigan

University of Pennsylvania, Ph.D.

Ed is interested in cell nuclear organization, particularly the polymer physics of chromatin structure and dynamics. He is currently analyzing Hi-C data and developing a simulation model to probe how disruptions to chromatin's underlying polymeric structure perturb genome organization.

ebanigan [at] mit [dot] edu


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.

goloborodko [dot] anton [at] gmail [dot] com


Nezar Abdennur

MIT Computational and Systems Biology, Ph.D. Student

Nezar's research interests lie at the intersection of nuclear organization and gene regulation.

nabdennur [at] gmail [dot] com


Martin Falk

MIT Physics, Ph.D. Student

Martin's 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 aims to elucidate the mechanisms by which SMC proteins (cohesin and condensin) shape the 3D genome. He studies chromosome organization in organisms ranging from bacteria to humans, combining genomics, image analysis and computational/theoretical modeling to uncover the fundamental principles of genome folding.

hbrandao [at] g [dot] harvard [dot] edu


Sameer Abraham

MIT Physics, Ph.D. Student


sameerab [at] mit [dot] edu


Simon Grosse-Holz

MIT Physics, Ph.D. Student


sgh256 [at] mit [dot] edu



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.

espresso [at] mit [dot] edu



  • Carino Dias Gurjao
    INSA Lyon, MSEng Bioinformatics and Modeling
    Mutational burden as a predictor of response to cancer immunotherapy

  • Geoffrey 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 subject 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 process, 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 biological 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-assembly

  • 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
    Columbia 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-Uribe, Ph.D. Student
    Stochastic models of signaling networks

  • Juhi Chandalia, Masters Student
    MIT, B.S., M.S.
    Structure and evolution of regulatory networks

  • Vincent Berube, Ph.D. Student
    MIT Physics, Ph.D. Student
    Stochastic models of ion channels

  • Ivan Adzhubey
    Moscow State University, Ph.D. in Biology
    Bioinformatics infrastructure development and maintenance