Sourav Bandyopadhyay, PhD

Assistant Professional Researcher (Cancer Center Fellow), UCSF Helen Diller Family Comprehensive Cancer Center

bandyopadhyays@cc.ucsf.edu

Phone: (415) 476-3425 (voice)
Box 0128, UCSF
San Francisco, CA 94143-0128

Professional Experience

• 2011-present
  Assistant Professional Researcher (Cancer Center Fellow), Helen Diller Family Comprehensive Cancer Center, UCSF


• Research Interests
  The Bandyopadhyay Lab is focused on systems-wide functional analysis of pathways that are deregulated and mutated in different types of cancers. While a number of large-scale efforts are underway to catalog the genetic aberrations in a variety of cancers, there is a lack of systematic efforts to understand which of these aberrations mediate the transformation from a normal to malignant cancer cell. The lab focuses on adapting existing technologies into a high-throughput network-mapping framework and then developing novel computational techniques to generate biologically meaningful hypotheses that can be subsequently tested using more traditional biochemical techniques.
  
  The lab focuses on the role of RAS-activated signal transduction pathways, which are mutated in 25 percent of all human cancers with a much higher prevalence in skin, pancreatic, and lung cancer. Through a combination of RNAi screening and immuno-precipitation coupled with mass spectrometry, the lab is focused on elucidating mechanisms by which members of the RAS-RAF-MEK-ERK signaling cascade alters cell growth and survival in cancer cells.

Selected Publications

• Bandyopadhyay S, Mehta M, Kuo D, Sung M, Licon K, Chuang R, Jaehnig E, Bodenmiller B, Licon K, Copeland W, Shales M, Fiedler D, Dutkowski J, Guenole A, van Attikum H, Shokat K, Kolodner R, Huh W, Aebersold R, Keogh MC, Krogan NJ, Ideker T. Rewiring of Genetic Networks in Response to DNA Damage. Science. 330(6009):1385-89. 2010. [link]
• Ideker T, Bandyopadhyay S. Integrative Systems Biology. Nature Genetics. 42(12). 2010. [link]
• Bandyopadhyay S, Chiang C, Srivastava J, Gersten M, White S, Bell R, Kurschner C, Martin CH, Smoot M, Sahasrabudhe S, Barber DL, Chanda SK, Ideker T. A Human MAP Kinase Interactome. Nature Methods. 7(10):801-5 2010. [link]
• Kuo D, Licon K, Bandyopadhyay S, Chuang R, Luo C, Catalana J, Ravasi T, Tan K, Ideker T. Co-evolution within a transcriptional network by compensatory trans and cis mutations. Genome Research. Genome Research 20(12):1672-8. 2010. [link]
• Konig R, Stertz S, Zhou Y, Inoue A, Hoffmann HH, Bhattacharyay S, Alamares J, Tscherne DM, Ortigoza MB, Liang Y, Gao Q, Andrews SE, Bandyopadhyay S, De Jesus P, Tu B, Pache L, Shih C, Orth A, Bonamy G, Miraglia L, Ideker T, Garcia-Sastre A, Young JAT, Palese P, Shaw ML, Chanda SK. Human Host Factors Required for Influenza Virus Replication. Nature. 2010 Feb 11;463(7282):813-7. [link]
• Fossum E, Friedel CC, Rajagopala SV, Titz B, Baiker A, Schmidt T, Kraus T, Stelberger T, Rutenberg C, Suthram S, Bandyopadhyay S, Rose D, Von Brunn A, Uhlmann M, Zeretzke C, Dong Y, Boulet H, Koegl M, Bailer SM, Koszinowski U, Ideker T, Uetz P, Zimmer R, Haas J. Evolutionarily conserved herpesviral protein interaction networks. PLoS Pathog. 2009 Sep;5(9):e1000570. Epub 2009 Sep 4. [link]
• Bushman FD, Malani N, Fernandes J, D'Orso I, Cagney G, Diamond TL, Zhou H, Hazuda DJ, Espeseth AS, Konig R, Bandyopadhyay S, Ideker T, Goff S, Krogan N, Frankel A, Young JAT, Chanda SK. Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathog. 2009 May;5(5):e1000437. Epub 2009 May 29. [link]
• Wilmes G*, Bergkessel M*, Bandyopadhyay S, Chan A, Braberg H, Shales M, Collins SR, Whitworth BG, Kress TL, Weissman JS, Ideker T, Guthrie C, Krogan NJ. Cover Article: A Genetic Interaction Map of RNA Processing Factors Reveals Links Between Sem1/Dss1-Containing Complexes and mRNA Export and Splicing. Mol Cell. 2008 Dec 5;32(5):735-46. Featured Article, [link] *Equal Contribution
• Roguev A, Bandyopadhyay S, Zofall M, Zhang K, Fischer T, Collins SR, Qu H, Shales M, Park H, Hayles J, Hoe K, Kim D, Ideker T, Grewal SI, Weissman JS, Krogan NJ. Conservation and Rewiring of Functional Modules Revealed by an Epistasis Map in Fission Yeast. Science. 2008 Oct 17;322(5900):405-10. Epub 2008 Sep 25. [link]
• Konig R, Zhou Y, Elleder D, Diamond TL, Bonamy GMC, Irelan JT, Chiang C, Tu BP, De Jesus PD, Lilley CE, Seidel S, Opaluch AM, Caldwell JS, Weitzman MD, Kuhen KL, Bandyopadhyay S, Ideker T, Orth AP, Miraglia LJ, Bushman FD, Young JA, Chanda SK. Global Analysis of Host-Pathogen Interactions that Regulate Early-Stage HIV-1 Replication. Cell. 2008 Oct 3;135(1):49-60.[link]
• Bandyopadhyay S, Kelley RM, Krogan NJ, Ideker T. Functional maps of protein complexes from quantitative genetic interaction data. PLoS Comput Biol. 2008 Apr 18;4(4):e1000065.[link] [supplement]
• Beyer A, Bandyopadhyay S, Ideker T. Integrating physical and genetic maps: from genomes to interaction networks. Featured Review. Nat Rev Genet. 2007 Sep;8(9):699-710. [link]
• Bandyopadhyay S, Sharan R, Ideker T. Cover Article: Systematic identification of functional orthologs by protein network comparison. Genome Res. 2006 Mar;16(3):428-35. [link] [supplement]
• Bandyopadhyay S, Kelley RM, Ideker T. Discovering regulated networks during HIV-1 latency and reactivation. Pac Symp Biocomput. 2006:354-66.[link]
• Canet-Aviles RM, Wilson MA, Miller DW, Ahmad R, McLendon C, Bandyopadhyay S, Baptista MJ, Ringe D, Petsko GA, Cookson MR. The Parkinson's disease protein DJ-1 is neuroprotective due to cysteine-sulfinic acid-driven mitochondrial localization. Proc Natl Acad Sci U S A. 2004 Jun 15;101(24):9103-8. [link]
• Bandyopadhyay S, Cookson MR. Evolutionary and functional relationships within the DJ1 superfamily. BMC Evol Biol. 2004 Feb 19;4(1):6. [link]