CURRICULUM VITAE: SUSHMITA ROY CONTACT INFORMATION Broad institute, 7 Cambridge center, Cambridge, MA 02142 sroy@broadinstitute.org Mobile: +1 505-­‐610-­‐7712 Work: + 1 617-­‐714-­‐7861 EDUCATION •
Doctor of Philosophy, Computer Science, University of New Mexico, Albuquerque, New Mexico, USA, Sep 2009. Advisor, Dr. Terran Lane (CS), co-­‐advisor Dr. Margaret Werner-­‐Washburne (Biology). Thesis topic: Learning condition-­‐specific networks. •
Master of Science, Computer Science, University of New Mexico, Albuquerque, New Mexico, USA, May 2005. Thesis topic: A Machine Learning Approach for Biological Information Extraction. •
Bachelor of Engineering, Computer Engineering, University of Pune, India, May 2000. WORK EXPERIENCE •
Nov 2009-­‐Present: Postdoctoral Associate at the Broad institute of MIT and Harvard (Dr. Aviv Regev’s laboratory), Visiting scientist at MIT CSAIL (Dr. Manolis Kellis’ laboratory). •
Jan 2009-­‐July 2009: Research assistant for Dr. Margaret Werner-­‐Washburne, Department of Biology, Univeristy of New Mexico. •
June 2007-­‐Dec 2008: Research assistant for Dr. Terran Lane, Department of Computer Science, Univeristy of New Mexico. •
Aug 2006-­‐May 2007: Research assistant for Dr. Jim Brown, Department of Biology, University of New Mexico. •
Jan 2006-­‐May 2006: Research Assistant for Dr. Terran Lane, Department of Computer Science, University of New Mexico. •
Dec 2002-­‐Dec 2005: Research Assistant for Dr. Margaret Werner-­‐Washburne, Department of Biology, University of New Mexico. •
September 2002-­‐Nov 2002: System Administrator for computer laboratory, Department of Chemistry, University of New Mexico. •
June 2000-­‐June 2002: Software developer for Persistent Systems Pvt. Ltd., Pune, India FELLOWSHIPS & AWARDS •
Computing Innovation Fellowship from the Computing Community Consortium and Computing Research Association (2009-­‐2011). •
Student scholarship for attending the 26th International Conference on Machine Learning (2009). •
Outstanding graduate student, Department of Computer Science, University of New Mexico (2009). •
Travel award to Pacific Symposium of Biocomputing 2009, from the International Society for Computational Biology ($1000) and the National Library of Medicine/National Institutes of Health ($250). •
Best graduate student talk in the annual student conference organized by Department of Computer Science, University of New Mexico (2008). •
Best graduate student poster in the annual student conference, Department of Computer Science, University of New Mexico (2007). •
Howard Hughes Interfaces fellowship from the Program in Interdisciplinary Biological and Biomedical Science (2006). •
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University of New Mexico student award for innovation in informatics (2005). Third prize in graduate poster presentation competition for the Department of Biology, University of New Mexico (2004, 2007). PUBLICATIONS •
G. S. Davidson, R. M. Joe, S. Roy, O. Meirelles, C. P. Allen, M. R. Wilson, P. H. Tapia, E. E. Manzanilla, A. E. Dodson, S. Chakraborty, M. Carter, S. Young, B. Edwards, L. Sklar, and M. Werner-­‐
Washburne (2011). The proteomics of quiescent and non-­‐quiescent cell differentiation in yeast stationary-­‐phase cultures. Molecular Biology of the Cell. •
The modENCODE Consortium, S. Roy+, J. Ernst+, P. V. Kharchenko+, P. Kheradpour+, N. Negre+, M. L. Eaton+, J.M. Landolin+, C. A. Bristow+, L. Ma+, M. F. Lin+, S. Washietl+, B. I. Arshinoff+, F. Ay+, P. E. Meyer+, N. Robine+, N. L. Washington+, L. D. Stefano+, E. Berezikov, C. D. Brown, R. Candeias, J. W. Carlson, A. Carr, I. Jungreis, D. Marbach, R. Sealfon, M. Y. Tolstorukov, S.Will, A. Alekseyenko, C. Artieri, B.W. Booth, A. N. Brooks, Qi. Dai, C. A. Davis, M. O. Duff, X. Feng, A. Gorchakov, T. Gu, J. G. Henikoff, P. Kapranov, R. Li, H. MacAlpine, J. Malone, A. Minoda, J. Nordman, K. Okamura, M. Perry, S. Powell, N. C. Riddle, A. Sakai, A. Samsonova, J. E. Sandler, Y. Schwartz, N. Sher, R. Spokony, D. Sturgill, M. van Baren, K. H. Wan, L.Yang, C. Yu, E. Feingold, P. Good, M. Guyer, R. Lowdon, K. Ahmad, J. Andrews, B. Berger, S. E. Brenner, M. R. Brent, L. Cherbas, S. C. R. Elgin, T. R. Gingeras, R. Grossman, R. A. Hoskins, T. C. Kaufman, W. Kent, M. Kuroda, T. Orr-­‐Weaver, N. Perrimon, V. Pirrotta, J. W. Posakony, B. Ren, S. Russell, P. Cherbas, B. R. Graveley, S. Lewis, G. Micklem, B. Oliver, P. J. Park S. E. Celniker, S. Henikoff, G. H. Karpen, E. C. Lai, D. M. MacAlpine, L. D. Stein, K. P. White, and M. Kellis (2010). Identification of functional elements and regulatory circuits in Drosophila modENCODE. Science. +Co-­‐first authors. •
S. Roy, D. Martinez, H. Platero, T. Lane, M. Werner-­‐Washburne (2009). Exploiting Amino Acid Composition for Predicting Protein-­‐protein Interactions. PLoS ONE. •
S. Roy, T. Lane, M. Werner-­‐Washburne (2009). Learning structurally consistent undirected probabilistic graphical models. Proceedings of the 26th International Conference on Machine Learning. •
S. Roy, S. Plis, M. Werner-­‐Washburne, T. Lane (2009). Scalable learning of large networks. q-­‐bio 2008 Special Issue for IET Systems Biology. •
S. Roy, T. Lane, M. Werner-­‐Washburne and D. Martinez (2009). Inference of functional networks of condition-­‐specific response -­‐ A case study of quiescence in yeast. Pacific Symposium of Biocomputing. •
S. Roy, M. Werner-­‐Washburne, and T. Lane (2008). A system for generating transcription regulatory net-­‐ works with combinatorial control of transcription. Bioinformatics, 24(10). •
A.D.Aragon, A.L.Rodriguez, O.Meirelles, S.Roy, G.S.Davidson, P.H.Tapia, C.Allen, R.Joe, D.Benn, and M. Werner-­‐Washburne (2008). Characterization of differentiated quiescent and nonquiescent cells in yeast stationary-­‐phase cultures. Mol. Biol. Cell, 19(3). •
Stark, M. F. Lin, P. Kheradpour, J. S. Pedersen, L. Parts, J. W. Carlson, M. A. Crosby, M. D. Rasmussen, S. Roy, A. N. Deoras, J. G. Ruby, J. Brennecke, Harvard FlyBase curators, Berkeley Drosophila Genome Project, E. Hodges, A. S. Hinrichs, A. Caspi, B. Paten, S. Park, M. V. Han, M. L. Maeder, B. J. Polansky, B. E. Robson, S. Aerts, J. Helden, B. Hassan, D. G. Gilbert, D. A. Eastman, M. Rice, M. Weir, M. W. Hahn, Y. Park, C. N. Dewey, L. Pachter, W. J. Kent, D. Haussler, E. C. Lai, D. P. Bartel, G. J. Hannon, T. C. Kaufman, M. B. Eisen, A. G. Clark, D. Smith, S. E. Celniker, W. M. Gelbart, and M. Kellis (2007). Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature, 450. •
P. Kheradpour, A. Stark, S. Roy, M. Kellis (2007). Reliable prediction of regulator targets using 12 Drosophila genomes. Genome Research, 17. •
S. Roy, T. Lane, C. Allen, A. D. Aragon, M. Werner-­‐Washburne (2006). A Hidden-­‐state Markov Model for Cell Population Deconvolution. Journal of Computational Biology, 13(10). •
P. D. Wentzell, T. K. Karakach, S. Roy, M. J. Martinez, C. P. Allen, M. Werner-­‐Washburne (2006). Multi-­‐ variate curve resolution of time course microarray data. BMC Bioinformatics, 7(343). •
D. Aragon, G. A. Quinones, E. V. Thomas, S. Roy, G. S. Davidson, and M. Werner-­‐Washburne (2006). Release of extraction-­‐resistant mRNA in stationary phase Saccharomyces cerevisiae produces a massive increase in transcript abundance in response to stress. Genome Biology, •
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7(R9). A.D.Aragon, G.A.Quinones, C.Allen, J.Thomas, S.Roy, G.S.Davidson, P.D.Wentzell, B.Millier, J..E. Jaetao, A. L. Rodriguez, and M. Werner-­‐Washburne (2005). An Automated, Pressure-­‐Driven Sampling De-­‐ vice for Harvesting from Liquid Cultures for Genomic and Biochemical Analyses. Journal of Biochemical Analysis, 65(2). M. J. Martinez, S. Roy, A. B. Archueletta, P. D. Wentzell, S. A. Anna-­‐Arriola, A. L. Rodriguez, A. D. Aragon, G. A. Quinones, C. Allen, M. Werner-­‐Washburne (2004). Analysis of Stationary Phase and Exit in Saccharomyces cerevisiae: Gene Expression and Identification of Novel Essential Genes. Molecular Biology of the Cell, 15. TECHNICAL REPORTS •
S. Roy, T. Lane, M. Werner-­‐Washburne (2009). Learning Probabilistic Networks of Condition-­‐
Specific Response: Digging Deep in Yeast Stationary Phase. UNM Computer Science Technical Report, TR-­‐CS-­‐ 2009-­‐07. •
S. Roy, T. Lane, M. Werner-­‐Washburne (2008). Learning structurally consistent undirected probabilistic graphical models. UNM Computer Science Technical Report, TR-­‐CS-­‐2008-­‐14. •
S. Roy, T. Lane, M. Werner-­‐Washburne (2007). A Simulation Framework for Modeling Combinatorial Control in Transcription Regulatory Networks. UNM Computer Science Technical Report, TR-­‐CS-­‐2007-­‐ 06. •
S. Roy, T. Lane, C. Allen, A. D. Aragon, M. Werner-­‐Washburne (2004). A Sequential Monte Carlo Sampling Approach for Cell Population Deconvolution from Microarray Data. POSTERS & WORKSHOPS •
S. Roy, C. A. Bristow, J. Konieczka, P. Kheradpour, A. Regev, M. Kellis. A Mixture of Experts model for predicting expression from sequence (2010). Intelligent Systems in Molecular Biology. •
S. Roy, T. Lane, M. Werner-­‐Washburne (2009). Learning condition-­‐specific networks. Third Annual q-­‐bio Conference on Cellular Information Processing. Santa Fe. New Mexico, USA. •
S. Roy, S. Plis, M. Werner-­‐Washburne (2008). Scalable learning of large networks. Second Annual q-­‐bio Conference on Cellular Information Processing. Santa Fe. New Mexico, USA. •
S. Roy, A. Stark, P. Kheradpour, M. Kellis, M. Werner-­‐Washburne, T. Lane (2008). A relational framework for predicting tissues and links in the Drosophila regulatory network. Poster at RECOMB Satellite on Regulatory Genomics and Systems Biology. •
S. Roy, T. Lane, M. Werner-­‐Washburne (2008). Integrative Construction and Analysis of Condition-­‐specific Biological Network. Thirteenth AAAI Doctoral Consortium. Chicago. Illinois, USA •
S. Roy, T. Lane, M. Werner-­‐Washburne (2007). Intergative construction and analysis of condition-­‐specific biological networks. AAAI Student Abstract and Poster Program. Vancouver, Canada. •
S. Roy, T. Lane, M. Werner-­‐Washburne (2006). Predicting protein-­‐protein interactions using amino-­‐acid composition. Second Annual RECOMB Satellite Workshop on Systems Biology. •
S.Roy, T. Lane, C. Allen, A. D. Aragon, M. Werner-­‐Washburne (2006). Cell population deconvolution using particle filter. Poster presentation at the Tenth Annual International Conference on Research in Computa-­‐ tional Molecular Biology (RECOMB). •
S. Roy, T. Lane, C. Allen, A. D. Aragon, M. Werner-­‐Washburne (2005). A Datamining approach to cell population deconvolution from gene expressions using particle filters. Fifth ACM SIGKDD Workshop on Data Mining in Bioinformatics. RESEARCH INTERESTS •
Algorithms for inference and analysis of regulatory and functional networks. •
Development of integrative frameworks of high-­‐throughput genomic data such as sequence, gene expression, chromatin, ChIP-­‐chip binding. •
Comparative analysis of context-­‐specific networks. ACTIVITIES •
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Poster presentation at 2nd, 3rd and 5th Computer Science student conference, University of New Mexico, 2006, 2007, 2009. Talk at the 1st and 4th Computer Science student conference, University of New Mexico, 2005, 2008. Student volunteer for the Computational Systems Bioinformatics conference (CSB) 2004. President of the Computer Science graduate student association. Reviewer for conference (AAAI, KDD, PSB) and journal (BMC Genomics, PLoS One) articles. Mentoring a high-­‐school student on his facial recognition project for an upcoming science project competition. Mentoring a biology undergraduate student for developing computational algorithms for analyzing cross-­‐species data. Mentoring computer science and biology undergraduate students for their computational biology class projects at MIT.