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Leonid Mirny leonid[at]mit[dot]edu |
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Geoff Fudenberg Harvard Biophysics, Ph.D. Student 3D Genome Organization: Physical models, statistical methods, and comparative genomics geoff.fudenberg[at]gmail[dot]com |
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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 |
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Anton Goloborodko MIT Physics, Ph.D. Student Anton: Add a description of your research project here, if you want. goloborodko[dot]anton[at]gmail[dot]com |
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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 |
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Charles Baker Harvard Biophysics, Ph.D. Student
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Espresso Machine MIT Physics (Ph.D. Harvard Biophysics/HST) 
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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 have found the theorists easy to collaborate with and wonderfully open-minded.
espresso[at]mit[dot]edu
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Ivan Adzhubey Moscow State University, Ph.D. in Biology Bioinformatics infrastructure development and maintenance |
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Vincent B\E9rub\E9, Ph.D. Student MIT Physics, Ph.D. Student Stochastic models of ion channels |
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Juhi Chandalia, Masters Student MIT, B.S., M.S. Structure and evolution of regulatory networks |
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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 |
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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 |