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About Our Alumni

Thomas Gurry

Thomas Gurry, 2015

MIT Advisor: Prof. Colin M.Stultz
Thesis Title: Order, disorder, and protein aggregation 

Current Position: Postdoctoral Associate in the Alm lab

I study the relationship between the human microbiome and disease at the new MIT Center for Microbiome Informatics and Therapeutics, with a specific emphasis on Inflammatory Bowel Disease. The main project I am working on is a clinical trial that tracks stool and blood biomarkers longitudinally, with the hope of developing a model for predicting disease relapse. In addition, I am leading the developments of an analytics platform for the Center.

Publications

Gurry T, Stultz CM. The Mechanism of Amyloid Fibril Elongation. Biochemistry 53 (44): 6981-6991; doi:10.1021/bi5000695g (2014).

Burger V, Gurry T, Stultz CM. Intrinsically Disordered Proteins: Where Computation meets Experiment. Polymers 6 (10): 2684-2719; doi:10.3390/polym6102684 (2014)

Zhong C, Gurry T, Cheng A, Down J, Deng Z, Stultz CM, Lu TK. Strong Underwater Adhesives made by self-assembling multi-protein nanobres. Nature Nanotechnology 9:858-866 (2014)

DaSilva LC, Gurry T, Stultz CM. Toward a consensus in protein structure nomenclature. Intrinsically Disordered Proteins 2:e29700 (2014)

Gurry T, Ullman O, Fisher CK, Perovic I, Pochapsky T, Stultz CM. The Dynamic Structure of Synuclein Multimers. Journal of the American Chemical Society 135(10): 3865-3872 doi:10.1021/ja310518p (2013)

Gurry T, Nerenberg PS, Stultz CM. The Contribution of Inter-chain Salt Bridges to Triple Helical Stability in Collagen. Biophysical Journal 98(11): 2634-2643 (2010) 4 of 5

Gurry T, Kahramanogullari O, Endres R. Biophysical Mechanism for Ras-Nanocluster Formation and Signaling in Plasma Membrane. PLoS ONE 4(7): e6148. doi:10.1371/ journal.pone.0006148 (2009)

Book chapter

Gurry T, Fisher CK, SchmidtM, Stultz CM.Modeling Amyloid Proteins with Bayesian Statistics. Methods in Molecular Biology 1345: 55-66. doi:10.1007/978-1-4939-2978-8 17 (2015).

   
Leyla Isik

Leyla Isik, 2015

MIT Thesis Advisor: Dr. Tomaso Poggio
Thesis Title: The dynamics of invariant object and action recognition in the human visual system

Position: Postdoc with Nancy Kanwisher and Gabriel Kreiman studying the neural basis of human visual and social perception

Publications

Invariant visual representations for human action. Isik L*, Tadchetti A, and Poggio T. (in preparation)

The dynamics of invariant object recognition in the human visual system. Isik L, Meyers EM, Leibo JZ, and Poggio T. (2014) The Journal of Neurophysiology vol. 111 no. 1 91-102.

Learning and disrupting invariance in visual recognition with a temporal association rule. Isik L, Leibo JZ, and Poggio T. (2012) Frontiers in Computational Neuroscience vol. 6 p.39. (Commentary by Bart and Hedgé)

Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. Carter H, Chen S, Isik L, Tyekucheva S, Velculescu VE, Kinzler KW, Vogelstein B, and Karchin R. (2009) Cancer research vol. 69 (16) p. 6660-7.

   
Jonathan Rameseder

Jonathan Rameseder, 2014

MIT Thesis Advisor: Prof. Michael Yaffe
Thesis Title: Multivariate methods for the statistical analysis of hyperdimensional high-content screening data

Current Position: Patent Examiner (in data mining and information retrieval) at the European Patent Office

Publications

Rameseder J, Krismer K, Dayma Y, Ehrenberger T, Hwang MK, Airoldi EM, Floyd SR, Yaffe MB.J Biomol Screen. 2015 Sep;20(8):985-97. doi: 10.1177/1087057115583037. Epub 2015 Apr 27

Cron KR, Zhu K, Kushwaha DS, Hsieh G, Merzon D, Rameseder J, Chen CC, D'Andrea AD, Kozono D. Proteasome inhibitors block DNA repair and radiosensitize non-small cell lung cancer. PLoS One. 2013 Sep 5;8(9):e73710. doi: 10.1371/journal.pone.0073710. eCollection 2013.

Floyd SR, Pacold ME, Huang Q, Clarke SM, Lam FC, Cannell IG, Bryson BD, Rameseder J, Lee MJ, Blake EJ, Fydrych A, Ho R, Greenberger BA, Chen GC, Maffa A, Del Rosario AM, Root DE, Carpenter AE, Hahn WC, Sabatini DM, Chen CC, White FM, Bradner JE, Yaffe MB. The bromodomain protein Brd4 insulates chromatin from DNA damage signalling. Nature. 2013 Jun 13;498(7453):246-50. doi: 10.1038/nature12147. Epub 2013 Jun 2.

Hegemann B, Hutchins JR, Hudecz O, Novatchkova M, Rameseder J, Sykora MM, Liu S, Mazanek M, Lénárt P, Hériché JK, Poser I, Kraut N, Hyman AA, Yaffe MB, Mechtler K, Peters JM. Systematic phosphorylation analysis of human mitotic protein complexes. Science Signaling. 2011 Nov 8;4(198):rs12. doi: 10.1126/scisignal.2001993.

Grosstessner-Hain K, Hegemann B, Novatchkova M, Rameseder J, Joughin BA, Hudecz O, Roitinger E, Pichler P, Kraut N, Yaffe MB, Peters JM, Mechtler K. Quantitative phospho-proteomics to investigate the polo-like kinase 1-dependent phospho-proteome. Molecular & Cellular Proteomics. 2011 Nov;10(11):M111.008540. doi: 10.1074/mcp.M111.008540. Epub 2011 Aug 21.

Hsu PP, Kang SA, Rameseder J, Zhang Y, Ottina KA, Lim D, Peterson TR, Choi Y, Gray NS, Yaffe MB, Marto JA, Sabatini DM. The mTOR-regulated phosphoproteome reveals a mechanism of mTORC1-mediated inhibition of growth factor signaling. Science. 2011 Jun 10;332(6035):1317-22. doi: 10.1126/science.1199498.

   
Anna Podgornaia

Anna Podgornaia, 2014

MIT Thesis Advisor: Prof. Michael Laub
Thesis Title: Pervasive degeneracy and epistasis in a protein-protein interface

Current Position: Senior Scientist at Merck

Publications

Podgornaia AI, Laub MT. Pervasive degeneracy and epistasis in a protein-protein interface. Science 347(6222): 673-677, 2015.

Podgornaia AI*, Casino P*, Marina A, Laub MT. Structural basis of a rationally rewired protein-protein interface critical to bacterial signaling. Structure 21(9):1636-47, 2013.

Podgornaia AI, Laub MT. Determinants of specificity in two-component signal transduction systems. Current Opinion in Microbiology 16(2):156-162, 2013.

Brooks AN, Aspden JL, Podgornaia AI, Rio DC, Brenner SE. Identification and experimental validation of splicing regulatory elements in Drosophila melanogaster reveals functionally conserved splicing enhancers in metazoans. RNA 17(10):1884-94, 2011.

   
Xuebing Wu

Xuebing Wu, 2014

MIT Thesis Advisors: Prof. Phillip A. Sharp and Prof. Christopher B. Burge
Thesis Title: The mechanism and function of pervasive noncoding transcription in the mammalian genome

Current Position: Postdoc, Bartel lab at Whitehead Institute

Publications

Xuebing Wu, Andrea J. Kriz, Phillip A. Sharp, Target specificity of the CRISPR-Cas9 system, Quantitative Biology, 2014, doi:10.1007/s40484-014-0030-x

Xuebing Wu, David A. Scott, Andrea J. Kriz, Anthony C. Chiu, Patrick D. Hsu, Daniel B. Dadon, Albert W. Cheng, Alexandro E. Trevino, Silvana Konermann, Sidi Chen, Rudolf Jaenisch, Feng Zhang, Phillip A. Sharp, Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells, Nature Biotechnology, 2014, 32:670-676

Sidi Chen, Yuan Xue, Xuebing Wu, Le Cong, Arjun Bhutkar, Eric Bell, Feng Zhang, Robert Langer, Phillip A. Sharp, Global microRNA depletion suppresses tumor angiogenesis, Genes & Development, 2014, 28:1054-1067,2013

Xuebing Wu, Phillip A. Sharp, Divergent transcription: a driving force for new gene origination? Cell, 2013, 155:990-996

Albert E. Almada*, Xuebing Wu*, Andrea J. Kriz, Christopher B. Burge, Phillip A. Sharp, Promoter directionality is controlled by U1 snRNP and polyadenylation signals, Nature, 2013, 499:360–363 (*equal contribution)

Le Cong, F Ann Ran, David Cox, Shuailiang Lin, Robert Barretto, Naomi Habib, Patrick D Hsu, Xuebing Wu, Wenyan Jiang, Luciano A Marraffini, Feng Zhang, Multiplex genome engineering using CRISPR/Cas systems, Science, 2013, 339 (6121):819-823.

Patrick D. Hsu, David A. Scott, Joshua A. Weinstein, F. Ann Ran, Silvana Konermann, Vineeta Agarwala, Yinqing Li, Eli J. Fine, Xuebing Wu, Ophir Shalem, Thomas J. Cradick, Luciano A. Marraffini, Gang Bao, and Feng Zhang, DNA Targeting Specificity of the RNA-guided Cas9 Nuclease, Nature Biotechnology, 2013, 31:827-832

Anna Lyubimova, Shalev Itzkovitz, Jan Philipp Junker, Zi Peng Fan, Xuebing Wu, Alexander van Oudenaarden, Single-molecule mRNA detection and counting in mammalian tissue, Nature Protocols, 2013, 8:1743–1758

Yong Chen, Xuebing Wu, Rui Jiang, Integrating human omics data to prioritize candidate genes, BMC Medical Genomics, 2013, 6:57

   
Albert We Cheng

Albert Wu Cheng, 2014

MIT Thesis Advisors: Prof. Rudolf Jaenisch and Prof. Christopher B. Burge
Thesis Title: Epigenetic and post-transcriptional regulation of gene expression in pluripotent stem cells, differentiation and metastasis

Current Position: Assistant Professor, The Jackson Laboratory for Genomic Medicine, Farmington, CT
Previous Position: JAX Scholar Postdoctoral Associate, The Jackson Laboratory, Bar Harbor, ME

Homepage | Google Scholar

Selected Publications

Cheng, A.W.*, Shi, J.*, Wong P.*, Luo, K.L., Trepman, P., Wang, E.T., Choi, H., Burge, C.B., Lodish, H.F. (2014) Muscleblind-like 1 (Mbnl1) regulates pre-mRNA alternative splicing during terminal erythropoiesis. Blood doi: 10.1182/blood-2013-12-542209 PMID: 24869935

Cheng, A.W.*, Wang, H.*, Yang, H, Shi, L., Katz, Y., Theunissen, T.W., Rangarajan, S., Shivalila, C.S., Dadon, D.B., Jaenisch, R. (2013) Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system. Cell Res. 23(10):1163-71 PMID: 23979020

Shapiro, I.M. *, Cheng, A.W. *, Flytzanis, N.C., Balsamo, M., Condeelis, J.S., Oktay, M.H., Burge, C.B., Gertler, F.B. (2011) An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype. PLoS Genet. 7(8):e1002218 PMID: 21876675

Creyghton, M.P.*, Cheng A.W.*, Welstead, G.G., Kooistra, T., Carey, B.W., Steine, E.J., Hanna, J., Lodato, M.A., Frampton, G.M., Sharp, P.A., Boyer, L.A., Young, R.A., Jaenisch, R. (2010) Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl. Acad. Sci. U.S.A. 107(50):21931-6 PMID: 21106759

Yang, H.*, Wang, H.*, Shivalila, C.S.*, Cheng, A.W., Shi, L., Jaenisch, R. (2013). One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering. Cell 154(6):1370-9 PMID: 23992847

Wang, H.*, Yang, H.*, Shivalila, C.S.*, Dawlaty, M.M., Cheng, A.W., Zhang, F., Jaenisch, R (2013). One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering. Cell 153(4):910-8 PMID: 23643243

Buganim, Y.*, Faddah D.A.*, Cheng, A.W., Itskovich, E., Markoulaki, S., Gantz, K., Klemm S.L., van Oudenaarden A., Jaenisch, R. (2012) Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase. Cell 150(6):1209-22 PMID: 22980981

*contributed equally

   
Naiyan Chen

Naiyan Chen, 2013

MIT Thesis Advisor: Prof. Mriganka Sur
Thesis Title: Cell-type specific cholinergic modulation of the cortex

Current Position: Postdoc, Agency for Science, Technology, Research, Singapore

Publications

Naiyan Chen*, Hiroki Sugihara*, Jitendra Sharma, Gertrudis Perea, Jeremy Petravicz, Chuong Le, Mriganka Sur, Nucleus basalis enabled stimulus specific plasticity in the visual cortex is mediated by astrocytes, Proc Natl Acad Sci USA, 2012 Oct 9;109(41), 16427–16428

Naiyan Chen*, Hiroki Sugihara*, Sami El Boustani, Mriganka Sur, Differential modulation of inhibitory microcircuit drives cholinergic-induced reduction in interneuronal correlations (Manuscript in preparation)

Shyh-Chyang Luo, Hong Xie, Naiyan Chen and Hsiao-Hua Yu, Trinity DNA Detection Platform by Ultrasmooth and Functionalized PEDOT Biointerfaces, ACS Applied Materials & Interfaces, 2009, 1(7), pp 1414–1419

Yu Hsiao-Hua, Ying Jackie Y, Luo Shyh-Chyang, Xie Hong, Chen Naiyan, Agency for Science Technology and Research, Polyethylenedioxythiophene Biointerfaces for DNA Detection, Patent Cooperation Treaty Application, Oct 2008

   
Jonathan Friedman

Jonathan Friedman, 2013

MIT Thesis Advisors: Prof. Eric J. Alm and Prof. Daniel H. Rothman
Thesis Title: Microbial adaptation, differentiation, and community structure

Current position: Post-doc with Jeff Gore at MIT, where I am interested in testing the principles that shape ecological communities in simple, tractable model systems.

Publications

J. Friedman, E. J. Alm, B. J. Shapiro. Sympatric speciation: when is it possible in bacteria? PLoS One.

J. Friedman, E. J. Alm. Inferring correlation networks from genomic survey data. PLoS Comp Bio, 8(9): e1002687, 2012.

A. C. Materna*, J. Friedman*, C. Bauer, C. David, S. Chen, I. B. Huang, A. Gillens, S. A. Clarke, M. F. Polz, and E. J. Alm. Shape and evolution of the fundamental niche in marine Vibrio. ISME J, 6:2168-2177, 2012.

T. Bosak, B. Liang, T.D. Wu, S. P. Templer, A. Evans, H. Vali, J. L. Guerquin-Kern, V. Klepac-Cera, J. Friedman, M. S. Sim, J. Mui. Cyanobacterial diversity and activity in modern conical microbialites. Geobiology, 10:384-401, 2012

The Human Microbiome Pro ject Consortium. Structure, function and diversity of the healthy human microbiome. Nature, 486(7402):207-214, June 2012.

The Human Microbiome Pro ject Consortium. A framework for human microbiome research. Nature, 486(7402):215-221, June 2012.

B. J. Shapiro, J. Friedman, O. X. Cordero, S. P. Preheim, S. C. Timberlake, G. Szab, M. F. Polz, and E. J. Alm. Population genomics of early events in the ecological differentiation of bacteria. Science, 336(6077):4851, 2012.

C. S. Smillie*, M. B. Smith*, J. Friedman, O. X. Cordero, L. A. David, and E. J. Alm. Ecology drives a global network of gene exchange connecting the human microbiome. Nature, 480(7376):241244, Oct. 2011

B. J. Shapiro, L. A. David, J. Friedman, and E. J. Alm. Looking for darwins footprints in the microbial world. Trends in Microbiology, 17(5):196204, May 2009

A. Madi*, Y. Friedman*, D. Roth, T. Regev, S. Bransburg-Zabary, and E. B. Jacob. Genome holography: Deciphering Function-Form motifs from gene expression data. PLoS ONE, 3(7):e2708, July 2008

   
Yuchun Guo

Yuchun Guo, 2012

MIT Thesis Advisor: Prof. David K. Gifford
Thesis Title: Simultaneous computational discovery of DNA regulatory motifs and transcription factor binding constraints at high spatial resolution 

Current Position: Postdoctoral Associate in Gifford Lab at MIT

Publications

Discovering homotypic binding events at high spatial resolution. Y Guo, G Papachristoudis, RC Altshuler, GK Gerber, TS Jaakkola, DK Gifford, Bioinformatics 26 (24), 3028 PMCID:PMC2995123

High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints. Y Guo, S Mahony, DK Gifford, PLoS computational biology 8 (8), e1002638 PMCID: PMC3415389

   
Charles Lin

Charles Lin, 2012

MIT Thesis Advisors: Prof. Christopher B. Burge and Prof. Richard A. Young
Thesis Title: c-Myc regulates transcriptional pause release and is a global amplifier of transcription

Current Position: Assistant Professor in the Molecular and Human Genetics Program at the Baylor College
of Medicine.

Publications

Revisiting global gene expression analysis. Cell. 2012 Oct 26;151(3):476-82. Lovén J, Orlando DA, Sigova AA, Lin CY, Rahl PB, Burge CB, Levens DL, Lee TI, Young RA.

Transcriptional amplification in tumor cells with elevated c-Myc. Cell. 2012 Sep 28;151(1):56-67. Lin CY, Lovén J, Rahl PB, Paranal RM, Burge CB, Bradner JE, Lee TI, Young RA.

DHODH modulates transcriptional elongation in the neural crest and melanoma. Nature. 2011 Mar 24; 471(7339):518-22. White RM, Cech J, Ratanasirintrawoot S, Lin CY, Rahl PB, Burke CJ, Langdon E, Tomlinson ML, Mosher J, Kaufman C, Chen F, Long HK, Kramer M, Datta S, Neuberg D, Granter S, Young RA, Morrison S, Wheeler GN, Zon LI.

c-Myc regulates transcriptional pause release. Cell. 2010 Apr 30;141(3):432-45. Rahl PB, Lin CY, Seila AC, Flynn RA, McCuine S, Burge CB, Sharp PA, Young RA.

   
Mei Lyn Ong

Mei Lyn Ong, 2012

MIT Thesis Advisor: Prof. Alexander van Oudenaarden
Thesis Title: Analysis of robustness and stochasticity in biochemical networks

Current position: Postdoc, Singapore Institute for Clinical Sciences, Singapore
   
Yaochung Weng

Yaochung Weng, 2012

MIT Thesis Advisor: Prof. Scott R. Manalis
Thesis Title: Measuring the effects of drugs on single cancer cell growth

Current position: Resident Physician: Radiation Oncology, UT Southwestern Medical Center, Dallas, Texas; Internal Medicine (Intern year), The Christ Hospital, Cincinnati, Ohio

Publications

Cooperative nutrient accumulation sustains growth of mammalian cells. Sci Rep. 2015 Dec 1;5:17401. doi: 10.1038/srep17401. S Son, M Stevens, HX Chao, C Thoreen, AM Hosios, Y Weng, K Wood, D Sabatini, MG Vander Heiden, SR Manalis.

Direct observation of mammalian cell growth and size regulation. Nat Methods. 2012 Sep;9(9):910-2. Epub 2012 Aug 5. Son S, Tzur A, Weng Y, Jorgensen P, Kim J, Kirschner MW, Manalis SR.

Mass sensors with mechanical traps for weighing single cells in different fluids. Lab Chip. 2011 Dec 21;11(24):4174-80. Epub 2011 Oct 28. Weng Y, Delgado FF, Son S, Burg TP, Wasserman SC, Manalis SR.

   
Surasak Chunsrivirot

Surasak Chunsrivirot, 2011

MIT Thesis Advisor: Prof. Bernhardt Trout
Thesis Title: Binding affinity of a small molecule to an amorphous polymer in a solvent

Current position: Faculty member of Biochemistry Department at Chulalongkorn University in Bangkok, Thailand

Publications

Binding affinity of a small molecule to an amorphous polymer in a solvent. Part 2: preferential binding to local sites on a surface. Langmuir. 2011 Oct 18;27(20):12396-404. Epub 2011 Sep 21. Chunsrivirot S, Santiso E, Trout BL.

Binding affinity of a small molecule to an amorphous polymer in a solvent. Part 1: free energy of binding to a binding site. Langmuir. 2011 Oct 18;27(20):12381-95. Epub 2011 Sep 21. Chunsrivirot S, Diao Y, Trout BL.

Free energy of binding of a small molecule to an amorphous polymer in a solvent. Langmuir. 2011 Jun 7;27(11):6910-9. Epub 2011 May 11. Chunsrivirot S, Trout BL.

Lee SE, Chunsrivirot S, Kamm RD, Mofrad MR. Molecular dynamics study of talin-vinculin binding. Biophys J. 2008 Aug;95(4):2027-36. Epub 2008 Apr 11. Chunsrivirot S, Trout BL.

   
Saho-shan Carol Huang

Shao-shan Carol Huang, 2011

MIT Thesis Advisor: Prof. Ernest Fraenkel
Thesis Title: A constraint optimization framework for discovery of cellular signaling and regulatory networks

Current Position: Post-doc, Salk Institute in San Diego

I joined Joe Ecker's lab as a postdoc at the Salk Institute in San Diego. I am broadly interested in using computational approaches for integrated analysis of diverse proteomics and genomics datasets, and specifically I am applying these methods to study hormone signaling in the model plant Arabidopsis.

Publications

Integrating proteomic, transcriptional, and interactome data reveals hidden components of signaling and regulatory networks. Sci Signal. 2009 Jul 28;2(81):ra40. Huang SS, Fraenkel E.

Swimming upstream: identifying proteomic signals that drive transcriptional changes using the interactome and multiple "–omics" datasets. In: Asthagiri AR and Arkin A editors. Computational Methods in Cell Biology. Academic Press. 2012. Huang SS, Fraenkel E.

SteinerNet: A Web Server for Integrating "Omic" data to Discover Hidden Components of Response Pathways. Nucleic Acids Research. 2012. 40(Web Server issue):W505-9. Tuncbag N, McCallum S, Huang SS, Fraenkel E.

Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-collecting Steiner Forest Problem. In press at Journal of Computational Biology. Tuncbag N, Braunstein A, Pagnani A, Huang SS, Chayes J, Borgs C, Zecchina R, Fraenkel E.

Linking proteomic and transcriptional data through the interactome and epigenome reveals a map of oncogene-induced signaling. In press at PLOS Computational Biology. Huang SS, Clarke DC, Gosline SJC, Labadorf A, Chouinard CR, Gordon W, Lauffenburger DA, Fraenkel E.

   
Leah Mae Octavio

Leah Mae Octavio, 2011

MIT Thesis Advisors: Prof. Gerald R. Fink and Prof. Narendra Maheshri
Thesis Title: Molecular systems analysis of a cis-encoded epigenetic switch

Current position: Associate in the Intellectual Property/Patents group at Ballard Spahr LLP in Philadelphia, PA

Publications

Epigenetic and conventional regulation is distributed among activators of FLO11 allowing tuning of population-level heterogeneity in its expression. PLoS Genet. 2009 Oct;5(10):e1000673. Epub 2009 Oct 2. Octavio LM, Gedeon K, Maheshri N.

 

 

Chadni Valiathan

Chadni Valiathan, 2011

MIT Thesis Advisor: Prof. Leona Samson
Thesis Title: Identifying a transcriptional signature for cell sensitivity to the cancer chemotherapy agent, BCNU

Current position: Modeling Research Associate at Merck

Publications

A rapid survival assay to measure drug-induced cytotoxicity and cell cycle effects. DNA Repair (Amst). 2012 Jan 2;11(1):92-8. Epub 2011 Nov 30. Valiathan C, McFaline JL, Samson LD.

Genomic predictors of interindividual differences in response to DNA damaging agents. Genes Dev. 2008 Oct 1;22(19):2621-6. Epub 2008 Sep 19. Fry RC, Svensson JP, Valiathan C, Wang E, Hogan BJ, Bhattacharya S, Bugni JM, Whittaker CA, Samson LD.

Activation of inflammation/NF-kappaB signaling in infants born to arsenic-exposed mothers. PLoS Genet. 2007 Nov;3(11):e207. Fry RC, Navasumrit P, Valiathan C, Svensson JP, Hogan BJ, Luo M, Bhattacharya S, Kandjanapa K, Soontararuks S, Nookabkaew S, Mahidol C, Ruchirawat M, Samson LD.

   
Lawrence David

Lawrence David, 2010

MIT Thesis Advisor: Prof. Eric J. Alm
Thesis Title: Novel phylogenetic approaches to problems in microbial genomics

Current Position: Assistant Professor, Duke University, Department of Molecular Genetics & Microbiology and the Institute for Genomes Sciences & Policy.

Publications

Metapopulation structure of Vibrionaceae among coastal marine invertebrates. Environ Microbiol. 2010 Sep 1. Preheim SP, Boucher Y, Wildschutte H, David LA, Veneziano D, Alm EJ, Polz MF.

Looking for Darwin's footprints in the microbial world. Trends Microbiol. 2009 May;17(5):196-204. Epub 2009 Apr 15. Shapiro BJ, David LA, Friedman J, Alm EJ.

Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science. 2008 May 23;320(5879):1081-5. Hunt DE, David LA, Gevers D, Preheim SP, Alm EJ, Polz MF.

Rapid evolutionary innovation during an Archean Genetic Expansion. Nature. 2011 Jan 469(7328):93-96. LA David, EJ Alm.

Ecology drives a global network of gene exchange connecting the human microbiome. Nature. 2011 Dec 480(7376):241-244. CS Smillie, MB Smith, J Friedman, OX Cordero, LA David & EJ Alm.

   
Ramon Salsas Escat

Ramon Salsas Escat, 2010

MIT Thesis Advisor: Prof. Collin M. Stultz
Thesis Title: The role of unfolded states in collagen degradation

Current Position: Director of Business Development, Gene Therapy Program & Orphan Disease Center at the University of Pennsylvania
Previous Position: R&D Business Strategy Manager, Esteve, Barcelona Area, Spain

Publications

Cleavage site specificity and conformational selection in type I collagen degradation. Biochemistry. 2010 May 18;49(19):4147-58. Salsas-Escat R, Nerenberg PS, Stultz CM.

Conformational selection and collagenolysis in type III collagen. Proteins. 2010 Feb 1;78(2):325-35. Salsas-Escat R, Stultz CM

Collagen--a necessary accomplice in the metastatic process. Cancer Genomics Proteomics. 2007 Sep-Oct;4(5):319-28. Nerenberg PS, Salsas-Escat R, Stultz CM.

Do collagenases unwind triple-helical collagen before peptide bond hydrolysis? Reinterpreting experimental observations with mathematical models. Proteins. 2008 Mar;70(4):1154-61. Nerenberg PS, Salsas-Escat R, Stultz CM.

   

Robin Friedman

Robin Friedman, 2010

MIT Thesis Advisors: Prof. Christopher B. Burge and Prof. David P. Bartel
Thesis Title: The specificity and evolution of gene regulatory elements

Current Position: Senior Scientist  VL34 Cambridge, MA 
Previous Position: Postdoc at Institut Pasteur in Paris

Publications

Hepatitis C Virus Infection and Hepatic Stellate Cell Activation Downregulate miR-29: miR-29 Overexpression Reduces Hepatitis C Viral Abundance in Culture. Bandyopadhyay S, Friedman RC, Marquez RT, Keck K, Kong B, Icardi MS, Brown KE, Burge CB, Schmidt WN, Wang Y, McCaffrey AP. J Infect Dis. 2011 Jun;203(12):1753-62.

Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument. Nutiu R*, Friedman RC*, Luo S, Khrebtukova I, Silva D, Li R, Zhang L, Schroth GP, Burge CB. Nature Biotechnology 2011 Jun 26. doi: 10.1038/nbt.1882.

Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 2009 Jan;19(1):92-105. Epub 2008 Oct 27. Friedman RC, Farh KK, Burge CB, Bartel DP.

Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs. Nature. 2010 Nov 17. [Epub ahead of print] Jan CH, Friedman RC, Ruby JG, Bartel DP.

   
Laura Kleiman

Laura Kleiman, 2010

MIT Thesis Advisors: Prof. Peter K. Sorger and Prof. Douglas A. Lauffenburger
Thesis Title: Experimental and computational analysis of epidermal growth factor receptor pathway phosphorylation dynamics

Current Position: Project Manager at GlobalCures
Previous Position: Postdoctoral Fellow, Kevin Haigi's lab, Massachusetts General Hospital and
Harvard Medical School

Publication

Kleiman LB*, Krebs AM*, Kim SY, Hong TS, Haigis KM. Comparative analysis of radiosensitizers for K-RAS mutant rectal cancers. PLoS ONE (2013) 8:e82982.

Huang FW, Kleiman LB, Hong TS. The clinical significance of mutations in colorectal cancer. In: Haigis KM (ed) Molecular pathogenesis of colorectal cancer. Springer, New York (2013) pp. 231-245.

Kleiman LB, Haigis KM. Future prospects for leveraging molecular information in the fight against colorectal cancer. In: Haigis KM (ed) Molecular pathogenesis of colorectal cancer. Springer, New York (2013) pp. 303-308.

Kleiman LB, Maiwald T, Conzelmann H, Lauffenburger DA, Sorger PK. Rapid phospho-turnover by receptor tyrosine kinases impacts downstream signaling and drug binding. Mol Cell (2011) 43:723-737.

Sontag LB, Lorincz MC, Luebeck EG. Dynamics, stability and inheritance of somatic DNA methylation imprints. J Theor Biol (2006) 242:890-899.

Sontag L, Axelrod DE. Evaluation of pathways for progression of heterogeneous breast tumors. J Theor Biol (2005) 232:179-189.

   
Jesse Shapiro

Jesse Shapiro, 2010

MIT Thesis Advisor: Prof. Eric J. Alm
Thesis Title: Genomic signatures of sex, selection and speciation in the microbial world

Current Position
Canada Research Chair in Microbial Evolutionary Genomics
Assistant Professor
Department of Biological Sciences
Université de Montréal
Montreal, Quebec, Canada
www.shapirolab.ca

Publications

The slow:fast substitution ratio reveals changing patterns of natural selection in gamma-proteobacterial genomes. ISME J. 2009 Oct;3(10):1180-92. Epub 2009 May 21. Shapiro BJ, Alm E.

Looking for Darwin's footprints in the microbial world. Trends Microbiol. 2009 May;17(5):196-204. Epub 2009 Apr 15. Shapiro BJ, David LA, Friedman J, Alm EJ.

Comparing patterns of natural selection across species using selective signatures. PLoS Genet. 2008 Feb;4(2):e23. Shapiro BJ, Alm EJ.

   
Grace Zheng

Grace Zheng, 2010

MIT Thesis Advisors: Prof. Phillip A. Sharp and Prof. Christopher B. Burge
Thesis Title: Exploring the regulatory roles of microRNAs in mammalian development

Current Position: Application Scientist, 10X Technologies, Pleasanton, California

Publications

Noncoding RNA landmarks of pluripotency and reprogramming. Cell Stem Cell. 2010 Dec 3;7(6):649-50. Ouyang Z, Zheng GX, Chang HY.

Dynamic regulation of miRNA expression in ordered stages of cellular development. PMID: Genes Dev. 2007 Mar 1;21(5):578-89. Neilson JR, Zheng GX, Burge CB, Sharp PA.

Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs. Nature Structural and Molecular Biology. In press. Leung AKL, Young AG, Brutkakar A, Zheng GXY, Bosson AD, Neilsen CB, Sharp PA.

Genome-wide impact of a novel rapidly expanded microRNA cluster in mouse. PNAS, 2011. Sep 20; 108(38):15804-9. Grace XY Zheng*, Avind Ravi*, Genevieve M. Gould, Christopher B. Burge, Phillip A. Sharp.

MicroRNAs can generate thresholds in target gene expression. Nature Genetics, 2011. Aug 21;43(9):854-9. Shankar Mukherji*, Margaret Ebert*, Grace XY Zheng, John S. Tsang, Phillip A. Sharp, Alex van Oudernaarden.

A latent pro-survival function for the mir-290-295 cluster in mouse embryonic stem cells. Plos Genetics, 2011. May 7(5):e1002054. Grace XY Zheng*, Avind Ravi*, Mauro J. Calabrese, Leah A. Medeiros, Oktay Kirak, Lucas M. Dennis, Rudolf Jaenisch, Christopher B. Burge, Phillip A. Sharp.

Pegasys: software for executing and integrating analyses of biological sequences. BMC Bioinformatics 2004, 5:40. Sohrab P Shah, David YM He, Jessica N Sawkins, Jeffrey C Druce, Gerald Quon, Drew Lett, Grace XY Zheng, Tao Xu, BF Francis Ouellette.

   
Sabrina Spencer

Sabrina Spencer, 2009

MIT Thesis Advisor: Prof. Peter K. Sorger
Thesis Title: Origins of cell-to-cell variability in apoptosis

Current Position: Assistant Professor, University of Colorado-Boulder, Department of Chemistry and Biochemistry, since August 2014

Lab website

Previous positions: Postdoctoral fellow, Meyer lab, Stanford University 2010-2014

First author publications

Spencer SL, Cappell, SD, Tsai FC, Overton KW, Wang CL, Meyer T (2013). The proliferation-quiescence decision is controlled by a bifurcation in CDK2 activity at mitotic exit. Cell 155:369-83.

Gaudet S*, Spencer SL*, Chen W, Sorger PK (2012). Exploring the contextual sensitivity of factors that determine cell-to-cell variability in receptor-mediated apoptosis. PLoS Computational Biology 8:e1002482.

Spencer, SL and Sorger, PK (2011). Measuring and modeling apoptosis in single cells. Cell 144:926-39.

Niepel M*, Spencer SL*, Sorger PK (2009). Non-genetic cell-to-cell variability and the consequences for pharmacology. Current Opinion in Chemical Biology 13:556-61.

Spencer SL*, Gaudet S*, Albeck JG, Burke JM, Sorger PK (2009). Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis. Nature 459:428-32.

Spencer SL*, Gerety RA*, Pienta KJ, Forrest S (2006). Modeling somatic evolution in tumorigenesis. PLoS Computational Biology 2:e108.