Lab Members
Ed Banigan
Research Scientist
University of Pennsylvania, Ph.D.
Ed is interested in the physical mechanisms of nuclear organization, shape, and mechanics, and how chromatin polymer physics underlies these critical cellular properties. He integrates theory, simulation, and bioinformatic analysis to develop biophysical models to understand cell and molecular biological observations.
ebanigan [at] mit [dot] edu
Aleksandra (Sasha) Galitsyna
Postdoctoral Researcher
Skolkovo Institute of Science and Technology, Ph.D. in Life Sciences
Aleksandra is a computational biologist focused on the intersection of polymer biophysics and chromatin biology, with a strong genomics perspective. A strong advocate for the power of the scientific community, Aleksandra believes teaching and sharing knowledge are absolutely vital. Inspired by regulation of cell commitment and decision-making.
galitsyn [at] mit [dot] edu
Timothy Földes
Postdoctoral Researcher
Sorbonne Université, Ph.D. Physics
Tim approaches the mysteries of chromatin architecture with the eye of a polymer physicist. Currently, he applies analytical approaches and simulations to study the kinetics of cohesin-mediated chromatin contacts and their implication for enhancer-promoter communication. When he’s not solving equations at his desk, you’ll find him brainstorming at the whiteboard with his colleagues.
foldes [at] mit [dot] edu
Irina Zhegalova
Postdoctoral Researcher
Kharkevich Institute, Ph.D.
Irina is studying the role of non-coding RNAs in shaping chromatin organization. She utilizes bioinformatics analysis of Hi-C data to investigate these phenomena and is eager to expand her expertise by learning polymer simulations.
irzhe [at] mit [dot] edu
Emily Navarrete
Graduate Student
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
Graduate Student
MIT Physics, Ph.D. Student
Henrik is interested in how cells make decisions with special emphasis on enhancer-mediated gene activation and DNA repair. His main tools have been inference on single-particle tracking, analytical methods in non-equilibrium statistical mechanics, and large-scale polymer simulations.
pinholt [at] mit [dot] edu
Maxim Imakaev
Infrastructure Administrator
MIT, Ph.D
Max is the Mirny Castle’s Calcifer, ensuring our research hearth never falters. He’s responsible for the design, construction, and maintenance of our computational infrastructure – he keeps the servers running and the data flowing. But Max’s contributions go far beyond that; his experience and vision have been instrumental in shaping the lab’s path and achievements. Lately, he’s been building Manta, a machine-learning tool to further our research. And unlike Calcifer, Max is not bound to any location and is often in touch from his global adventures.
[at] mit [dot] edu
Flavia Corsi
Postdoctoral Fellow
Flavia aims to understand the mechanisms that govern the three-dimensional organization of sister chromatids using biophysical models.
Katrina Norman
Laboratory Operations Coordinator
New School University/ Parsons School of Design
Katrina joined us in 2022 and quickly became an integrated part of the lab. She keeps the wheels turning on the machine that is the Mirny Lab. Katrina believes in a positive and productive environment where lab members can focus on their research. She also enjoys welcoming new lab members and visitors to Boston.
pkatrina [at] mit [dot] edu
E. M. Breville
Wet-Lab Experimentalist
MIT Physics (Ph.D./M.D./J.D. Harvard Biophysics/HST)
I joined MirnyLab in 2014, taking over daily caffeination 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
Andy
Visiting Canine
Emily’s Home for Adorable Doggos
Andy’s research passion lies at the intersection of gustatory sensation and reward processing. He’s eager to understand how the epigenetic modifications of taste receptor cells in the tongue, particularly those expressing umami receptors, are involved in the signaling cascades that ultimately activate the brain’s reward circuitry,
Ferris
Visiting Canine
MSPCA Angell Memorial
Ferris is focused on independent research into the release properties of collars and the un-looping of leashes. When not entangled in his own experiments, he can be found testing the structural integrity and attachment qualities of various chew toys. Ferris has yet to publish any findings.
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
