Home Research People Publications Courses & Seminars

Principal Investigator:

Leonid Mirny
Junior Fellow, Harvard Society of Fellows
Ph.D., Harvard Biophysics
M.Sc. Chemistry, Weizmann Institute of Science
Biosketch @ MIT Computational and Systems Biology
Biosketch @ MIT Physics

leonid[at]mit[dot]edu
617.452.4862

Graduate Students:

Geoff Fudenberg
Harvard Biophysics, Ph.D. Student

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

geoff.fudenberg[at]gmail[dot]com
617.452.4075

Maxim Imakaev
MIT Physics, Ph.D. Student

My main research centers around 3D genome organization: polymer models of the genomes of different organisms, and Hi-C data analysis. I am also studing the effects of topological constraints on polymer melts, a follow-up to my previous work on the fractal globule model of interphase chromatin.

mimakaev[at]gmail[dot]com
617.452.4075

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
617.452.4075


Chris McFarland
Harvard Biophysics, Ph.D. Student

Precancerous cells acquire thousands of genetic alterations as they evolve into a malignant population, yet only a handful of these occur in genes believed to be directly related to the neoplastic phenotype. We have found that many of these previously overlooked mutations, called passenger alterations, have subtle effects on the cancer population that in many cases harm cancerous cells. I am interested in understanding these mutations further. Using theory from evolutionary genetics, we are trying to explain how passenger mutations arise and alter growth in the population, despite their deleterious phenotypes. In addition, these passenger mutations have genetic and biophysical features that allow us to phenotype, and potentially exacerbate, their effects on cancerous cells. We are collaborating with the Sunyaev Lab to apply their understanding of how deleterious germ-line mutations affect phenotype to our understanding of cancer. We are then testing our models of passenger mutations in two ways: against recent whole-genome DNA sequence of cancers with Dr. Gaddy Getz at The Broad Institute and by studying the effects of these mutations in cell culture in conjunction with the Sherman Lab. Lastly, we have obtained ''In silico'' results that suggest metastatic cancer cells are particularly susceptible to the effects of passenger mutations and we are testing this hypothesis in a mouse model with researchers at The Moffitt Institute.

mcfarlan[at]fas[dot]harvard[dot]edu
617.452.4075

Nezar Abdennur
MIT Computational Biology, Ph.D. Student

Structural and Functional analysis of Chromatin Conformation Capture.

nabdennur [at] gmail [dot] com



Undergraduate students:

Boryana Doyle
MIT Physics, class of 2017

boryana4 [at] mit [dot] edu


Rotation Students:

Charles Baker
Harvard Biophysics, Ph.D. Student


Staff:

Espresso Machine
MIT Physics (Ph.D./M.D./J.D. Harvard Biophysics/HST)
I joined MirnyLab in 2011 and haven't looked back! My research has primarily been a longitudinal study of over (and, yes, under) caffeination on h. sapiens. I also love studying the epigenetic nano-scale topological motifs of vitreous bacterial networks. 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
617.452.4075



Alumni:

       
Ivan Adzhubey
Moscow State University, Ph.D. in Biology
Bioinformatics infrastructure development and maintenance
 
Vincent B\E9rub\E9, Ph.D. Student
MIT Physics, Ph.D. Student
Stochastic models of ion channels
 
Juhi Chandalia, Masters Student
MIT, B.S., M.S.
Structure and evolution of regulatory networks
 
Carlos G\F3mez-Uribe, Ph.D. Student
HST MEMP/BIG, Ph.D.
Stochastic models of signaling networks
 
Grigory Kolesov, Postdoctoral Fellow
University of Munich, Ph.D. in Biology
Evolution and prediction of specificity-determining residues
 
Hao Yuan Kueh, Rotation Student
Harvard Biophysics
Princeton University, B.S.
Information transmission in enzymatic switch
 
Joe Levine, Masters Student
MIT, B.S., M.S.
Dynamics of signaling cascades
 
Lewyn Li, Postdoctoral Fellow
Columbia University
Harvard University, Ph.D. in Chemistry
Specificity determining residues in protein kinases
 
Shankar Mukherji, Undergraduate Student
MIT, B.S.
Dynamics of signaling cascades
 
Ilya Rudkevich, Undergraduate Student
Brandeis University, B.S.
Prediction of natively unstructured proteins
 
Alex Shpunt, Ph.D. Student
MIT, Ph.D. in Physics
Biophysics of molecular self-assembly
 
Michael Slutsky, Ph.D. Student
MIT, Ph.D. in Physics
Biophysics of protein-DNA interactions
 
Victor Spirin, Postdoctoral Fellow
Boston University, Ph.D. in Physics
Structure and regulation of biological networks
 
Anahita Tafvizi, Ph.D. Student
Harvard University, Ph.D. in Physics
Transcription factor-DNA interactions
 
Zeba Wunderlich, Ph.D. Student
Harvard University, Ph.D. in Biophysics
Modeling of the transcription factor search process
Energetics of protein-protein interactions

Michael Schnall-Levin, Ph.D Student
MIT Mathematics, Ph.D. Student
Transcriptional Regulation: Factors Beyond Binding Motif Matches

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

Konstantine Tchourine, Undergraduate Student
New York University, Ph.D. Student
Dynamics of long polymer chains subject to various restrictions

What have we been up to lately?

Recently discussed Journal Club articles