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

leonid[at]mit[dot]edu

617.452.4862

Postdoctoral Fellows

Nezar Abdennur

MIT Computational and Systems Biology, Ph.D.

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

nabdennur [at] gmail [dot] com

Ed Banigan

University of Pennsylvania, Ph.D.

Ed is broadly interested in cell nuclear organization and mechanics, particularly the polymer physics of chromatin structure and dynamics. He is currently using a combination of theory, simulation, and analysis of Hi-C data to understand several different aspects of genome organization.

ebanigan [at] mit [dot] edu

Maxim Imakaev

MIT Physics, Ph.D.

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

mimakaev [at] gmail [dot] com

Kirill Polovnikov

Moscow State University, Physics, Ph.D.

Kirill is interested in the role of topological constraints and loop extrusion on chromatin folding and dynamics throughout the cell cycle, manifold learning of chromatin structure, Hi-C data analyses. Kirill is a senior research scientist at Skolkovo Institute of Science and Technology.

kipolovnikov [at] gmail [dot] com

George Spracklin

University of Wisconsin-Madison, Ph.D.

George is interested in epigenetics, chromosome conformation, and NGS technology development. George is co-mentored by Job Dekker at the University of Massachusetts Medical School.

gsprack [at] mit [dot] edu

Graduate Students

Sameer Abraham

MIT Physics, Ph.D. Student

Sameer’s interests in chromosome organization are three-fold: 1) SMC Proteins and how interactions between different SMCs could allow us to explain various features observed on Hi-C maps. 2) The physical state of chromosomes when the cell is undergoing mitosis. Specifically he wants to understand how certain properties of mitotic chromosomes such as shape as reconcilable with the laws of statistical physics. 3) Modeling the biochemical process of chromosome conformation capture techniques. He seeks to understand how the varying the conformation capture protocol affects the properties of the resulting heatmaps.

sameerab [at] mit [dot] edu

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. Hugo is also a member of the Hansen lab.

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

Simon Grosse-Holz

MIT Physics, Ph.D. Student

Simon is interested in the dynamics of chromatin organization in living cells. To that end, he is developing models and analysis methods to understand tracking experiments performed by collaborators in Paris and at MIT. His work is a melange of polymer physics, stochastic processes, and inference methods, with occasional forays into machine learning.

sgh256 [at] mit [dot] edu

Jeremy Owen

MIT Physics, Ph.D. Student

Jeremy is interested in nonequilibrium physics and mathematical biology. He is studying the behavior of systems of chemical reactions coupled to polymer dynamics—such as those thought responsible for maintaining certain "epigenetic" histone modifications. He is also interested in gene regulation.

jaowen [at] mit [dot] edu

Visitors

Aleksandra (Sasha) Galitsyna

Skolkovo Institute of Science and Technology, Ph.D. Student

Aleksandra visited Mirny Lab in 2019 and learned Hi-C data analysis and polymer simulation basics. Aleksandra is a graduate student at the Skolkovo Institute of Science and Technology, where she studies the chromatin organization principles of the fruitfly. Her major pursuit is the dynamics of chromatin during organism development.

Staff

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

Alumni

  • Aafke van den Berg, Postdoctoral Fellow
    TU Delft, Ph.D.
    The interplay between transcription activity and the spatial and temporal organization of the genome.

  • Martin Falk
    MIT Physics, Ph.D. Student
    Understanding of nuclear structure and function via the construction and analysis of simple physical or mathematical models.

  • Johannes Nübler, Postdoctoral Fellow
    Univeristy of Tübingen, Ph.D.
    Analysis of Hi-C and Micro-C data, bridging large scale polymer models of chromatin with more fine-grained models, active processes in chromatin organization

  • Dina Tsukrov, Postdoctoral Fellow
    Albert Einstein College of Medicine, Biomedical Science, Ph.D.
    The balance between passenger and driver mutations in cancer.

  • Anton Goloborodko
    MIT Physics, Ph.D. Student
    The structure of mitotic chromosomes and polymer simulations of chromosomal folding.

  • Carino 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

  • 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
    HST MEMP/BIG, Ph.D.
    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