Jonathan Friedman, 2013

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

Charles Lin, 2012

Current position: Post-doc, Dana Farber Cancer Institute

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, 2012

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

Yaochung Weng, 2012

Current position: Medical Student, UT Southwestern Medical School in Dallas, Texas

Publications

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, 2011

Current position: researcher, National Center for Genetic Engineering and Biotechnology (BIOTEC), 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.

Shao-shan Carol Huang, 2011

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.

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

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, 2011

Current position: Law Student, Villanova University

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, 2011

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, 2010

I joined Harvard's Society of Fellows as a Junior Fellow. I will be conducting research on the human microbiome, studying in particular its temporal dynamics and influence on the pathology of infectious diseases.

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, 2010

I have moved to Spain and joined a cosmetics/pharma company Lipotec. I am in charge of New Business Development. My task is to be able to talk to the scientists of our client companies (L’Oreal, Dior, Channel, Estee Lauder...) and to explain to them the science of what we are researching and spark their interest in our products.

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, 2010

I accepted a three-year fellowship from the Pasteur Foundation and started postdoctoral research at the Institut Pasteur in Paris this September. I am jointly supervised by Philippe Sansonetti and Benno Schwikowski, applying tools of systems biology to better understand interactions between the human intestinal epithelium and bacteria, both commensal and pathogenic.

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, 2010

I am a postdoctoral fellow in Kevin Haigis's lab at the Massachusetts General Hospital and Harvard Medical School. I am studying how signaling pathways are altered in vivo during disease progression and drug treatment using a novel translational systems pharmacology approach, in order to identify more effective therapeutics. I am supported by a fellowship from the American Cancer Society.

Publication
Rapid Phospho-Turnover by Receptor Tyrosine Kinases Impacts Downstream Signaling and Drug Binding Molecular Cell, Volume 43, Issue 5, 723-737, 2 September 2011

Kleiman, L.B., Maiwald, T., Conzelmann H., Lauffenburger, D.A. and Sorger, P.K.

Jesse Shapiro, 2010

I have a postdoctoral fellowship through the Center for Communicable Disease Dynamics at the Harvard School of Public Health. I joined Pardis Sabeti's group in September 2011, where I will be working on intra-host evolution of Lassa virus and host-pathogen coevolution. I am also collaborating with Megan Murray's group to identify mutations associated with antibiotic resistance in M. tuberculosis. Broadly, I am interested in the ecologically and clinically important signatures of positive natural selection in populations of microbial genomes.

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, 2010

I have started my postdoc in Howard Chang's lab at Stanford. I work on long noncoding RNAs (lncRNAs) in embryonic stem cells, taking an interdisciplinary approach to look at dynamic regulation of lncRNAs in ES cell development.

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, 2009

I started in March 2010 as a Damon Runyon postdoctoral fellow in Tobias Meyer's lab in the Department of Chemical and Systems Biology at Stanford. I am collaborating with Marius Wernig's group at Stanford's new Institute for Stem Cell Biology to study the cell cycle properties of embryonic stem cells during differentiation.

Publications
Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis. Nature. 2009 May 21;459(7245):428-32. Epub 2009 Apr 12. Spencer SL, Gaudet S, Albeck JG, Burke JM, Sorger PK.

Systematic calibration of a cell signaling network model. BMC Bioinformatics. 2010 Apr 23;11:202. Kim KA, Spencer SL, Albeck JG, Burke JM, Sorger PK, Gaudet S, Kim do H.

Non-genetic cell-to-cell variability and the consequences for pharmacology. Curr Opin Chem Biol. 2009 Dec;13(5-6):556-61. Epub 2009 Oct 14. Niepel M, Spencer SL, Sorger PK.

Modeling a snap-action, variable-delay switch controlling extrinsic cell death. PLoS Biol. 2008 Dec 2;6(12):2831-52. Albeck JG, Burke JM, Spencer SL, Lauffenburger DA, Sorger PK.