Principal Investigator

Leonid Mirny

Institute for Medical Engineering and Science, and
Department of Physics, MIT

leonid [at] mit [dot] edu

617.452.4862

Research Scientists

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

Postdoctoral Fellows

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 did graduate studies at the Skolkovo Institute of Science and Technology, where she studied the chromatin organization principles of the fruitfly. Her major pursuit is the dynamics of chromatin during organism development.

galitsyn [at] mit [dot] edu

Graduate Students

Emily Navarrete

MIT Biology, Ph.D. Student

Emily is studying active chromatin organization at length-scales ranging from enhancers and promoters to compartments. She is co-mentored by Job Dekker at the University of Massachusetts Medical School.

emilynav [at] mit [dot] edu

Henrik Dahl Pinholt

MIT Physics, Ph.D. Student

Henrik is interested in the emergence of biological function from the dynamics of single molecules. His main tools have been single particle tracking and statistical inference.

pinholt [at] mit [dot] edu

Staff

Katrina Norman

Katrina joined us as an administrative assistant in 2022 and quickly became an integrated part of the lab. She keeps the wheels turning on the machine that is the Mirny Lab.

pkatrina [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

Alumni

  • Sofya Gaydukova
    MSU FBB, BU
    Nucleosome and transcription factor binding, DNase-seq

  • Joseph Finkelberg
    MSU FBB, YSDA, BU
    Nucleosome and transcription factor binding, DNase-seq

  • Simon Grosse-Holz
    MIT Physics, Ph.D. Student
    Polymer physics, stochastic processes, and inference methods, with occasional forays into machine learning.

  • Neil Chowdhury
    MIT Undergraduate ‘26, MIT PRIMES (2019-2022)
    polymer simulations of chromosomal organization, understanding the interplay between loop extrusion and compartmentalization during mitosis, and Hi-C data analysis.

  • Sameer Abraham
    MIT Physics, Ph.D. Student
    SMC Proteins, physical state of mitotic chromosomes, chromosome conformation capture techniques.

  • Jeremy Owen
    MIT Physics, Ph.D. Student
    Nonequilibrium physics and mathematical biology, systems of chemical reactions coupled to polymer dynamics.

  • Hugo Brandão
    Harvard Biophysics, Ph.D. Student
    Mechanisms for how SMC proteins (cohesin and condensin) shape the 3D genome. Work combines genomics, image analysis and computational/theoretical modeling to uncover the fundamental principles of genome folding.

  • George Spracklin
    University of Wisconsin-Madison, Ph.D.
    Interested in epigenetics, chromosome conformation, and NGS technology development.

  • Kirill Polovnikov
    Moscow State University, Physics, Ph.D.
    Topological constraints and loop extrusion on chromatin folding and dynamics throughout the cell cycle, manifold learning of chromatin structure, Hi-C data analyses.

  • Nezar Abdennur
    MIT Computational and Systems Biology, Ph.D.
    Interdisciplinary computational work solving challenges of multiomic data science in biology and medicine.

  • 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