Sourav Bandyopadhyay, PhD

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
bandyopadhyay_sourav

Assistant Professor, Bioengineering and Therapeutic Sciences, UCSF

bandyopadhyays@cc.ucsf.edu

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

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Additional Websites


Education

University of Wisconsin - Madison, BS, 5/02, Molecular Biology
University of Wisconsin - Madison, BS, 5/02, Computer Science
University of California, San Diego, PhD, 5/10, Bioinformatics and Systems Biology

Professional Experience

  • 2002 - 2003
    Informatics Programmer, Eragen Biosciences, Madison, WI
  • 2003 - 2004
    Research Staff, National Institute on Aging / NIH
  • 2004 - 2010
    Doctoral Dissertation, Advisor Trey Ideker, UCSD
  • 2010 - 2013
    Assistant Professional Researcher/Faculty Fellow, Helen Diller Family Comprehensive Cancer Center, UCSF
  • 2013 - present
    Assistant Professor, Bioengineering and Therapeutic Sciences, 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.

Honors & Awards

  • 2009-2010
    Associate Member, Faculty of 1000
  • 2010-2012
    UCSF QB3/Cancer Center Faculty Fellow
  • 2011
    UCSF Breast SPORE Career Development Award

Selected Publications

  1. Sos ML, Levin RS, Gordan JD, Oses-Prieto JA, Webber JT, Salt M, Hann B, Burlingame AL, McCormick F, Bandyopadhyay S, Shokat KM. Oncogene Mimicry as a Mechanism of Primary Resistance to BRAF Inhibitors. Cell Rep. 2014 Aug 21; 8(4):1037-48.
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  2. Benjamin DI, Louie SM, Mulvihill MM, Kohnz RA, Li DS, Chan LG, Sorrentino A, Bandyopadhyay S, Cozzo A, Ohiri A, Goga A, Ng SW, Nomura DK. Inositol phosphate recycling regulates glycolytic and lipid metabolism that drives cancer aggressiveness. ACS Chem Biol. 2014 Jun 20; 9(6):1340-50.
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  3. Lin L, Asthana S, Chan E, Bandyopadhyay S, Martins MM, Olivas V, Yan JJ, Pham L, Wang MM, Bollag G, Solit DB, Collisson EA, Rudin CM, Taylor BS, Bivona TG. Mapping the molecular determinants of BRAF oncogene dependence in human lung cancer. Proc Natl Acad Sci U S A. 2014 Feb 18; 111(7):E748-57.
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  4. Salt MB, Bandyopadhyay S, McCormick F. Epithelial-to-Mesenchymal Transition Rewires the Molecular Path to PI3K-Dependent Proliferation. Cancer Discov. 2014 Feb; 4(2):186-99.
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  5. Bushman FD, Barton S, Bailey A, Greig C, Malani N, Bandyopadhyay S, Young J, Chanda S, Krogan N. Bringing it all together: big data and HIV research. AIDS. 2013 Mar 13; 27(5):835-8.
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  6. Roguev A, Talbot D, Negri GL, Shales M, Cagney G, Bandyopadhyay S, Panning B, Krogan NJ. Quantitative genetic-interaction mapping in mammalian cells. Nat Methods. 2013 May; 10(5):432-7.
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  7. Bandyopadhyay S, Mehta M, Kuo D, Sung MK, Chuang R, Jaehnig EJ, Bodenmiller B, Licon K, Copeland W, Shales M, Fiedler D, Dutkowski J, Guénolé A, van Attikum H, Shokat KM, Kolodner RD, Huh WK, Aebersold R, Keogh MC, Krogan NJ, Ideker T. Rewiring of genetic networks in response to DNA damage. Science. 2010 Dec 3; 330(6009):1385-9.
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  8. Kuo D, Licon K, Bandyopadhyay S, Chuang R, Luo C, Catalana J, Ravasi T, Tan K, Ideker T. Coevolution within a transcriptional network by compensatory trans and cis mutations. Genome Res. 2010 Dec; 20(12):1672-8.
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  9. Bandyopadhyay S, Chiang CY, Srivastava J, Gersten M, White S, Bell R, Kurschner C, Martin C, Smoot M, Sahasrabudhe S, Barber DL, Chanda SK, Ideker T. A human MAP kinase interactome. Nat Methods. 2010 Oct; 7(10):801-5.
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  10. König R, Stertz S, Zhou Y, Inoue A, Hoffmann HH, Bhattacharyya S, Alamares JG, Tscherne DM, Ortigoza MB, Liang Y, Gao Q, Andrews SE, Bandyopadhyay S, De Jesus P, Tu BP, Pache L, Shih C, Orth A, Bonamy G, Miraglia L, Ideker T, García-Sastre A, Young JA, Palese P, Shaw ML, Chanda SK. Human host factors required for influenza virus replication. Nature. 2010 Feb 11; 463(7282):813-7.
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  11. Fossum E, Friedel CC, Rajagopala SV, Titz B, Baiker A, Schmidt T, Kraus T, Stellberger T, Rutenberg C, Suthram S, Bandyopadhyay S, Rose D, von Brunn A, Uhlmann M, Zeretzke C, Dong YA, 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.
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  12. Bushman FD, Malani N, Fernandes J, D'Orso I, Cagney G, Diamond TL, Zhou H, Hazuda DJ, Espeseth AS, König R, Bandyopadhyay S, Ideker T, Goff SP, Krogan NJ, Frankel AD, Young JA, Chanda SK. Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathog. 2009 May; 5(5):e1000437.
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  13. Wilmes GM, Bergkessel M, Bandyopadhyay S, Shales M, Braberg H, Cagney G, Collins SR, Whitworth GB, Kress TL, Weissman JS, Ideker T, Guthrie C, Krogan NJ. 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.
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  14. König R, Zhou Y, Elleder D, Diamond TL, Bonamy GM, Irelan JT, Chiang CY, 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.
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  15. Roguev A, Bandyopadhyay S, Zofall M, Zhang K, Fischer T, Collins SR, Qu H, Shales M, Park HO, Hayles J, Hoe KL, Kim DU, 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.
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  16. Bandyopadhyay S, Kelley R, Krogan NJ, Ideker T. Functional maps of protein complexes from quantitative genetic interaction data. PLoS Comput Biol. 2008 Apr; 4(4):e1000065.
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  17. Beyer A, Bandyopadhyay S, Ideker T. Integrating physical and genetic maps: from genomes to interaction networks. Nat Rev Genet. 2007 Sep; 8(9):699-710.
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  18. Bandyopadhyay S, Sharan R, Ideker T. Systematic identification of functional orthologs based on protein network comparison. Genome Res. 2006 Mar; 16(3):428-35.
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  19. Bandyopadhyay S, Kelley R, Ideker T. Discovering regulated networks during HIV-1 latency and reactivation. Pac Symp Biocomput. 2006; 354-66.
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  20. Canet-Avilés 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.
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