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    Sourav Bandyopadhyay, PhD

    TitleAssistant Professor
    SchoolUCSF School of Pharmacy
    DepartmentBioengineering
    Address1450 Third St
    San Francisco CA 94158
    Phone415-476-3425
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      Collapse Overview 
      Collapse Overview
      Our lab focuses on methods to map pathway rewiring in cancer. Our major goal is to understand at the systems level how the biological networks within cancer cells are fundamentally different from that in normal cells. Using our technologies, we intend to develop platforms for the rational application of personalized medicine and design of combination cancer therapies.

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      systems biology, networks, bioinformatics, precision medicine, pharmacogenomics, cancer biology, pathways

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      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
      List All   |   Timeline
      1. Kohnz RA, Roberts LS, DeTomaso D, Bideyan L, Yan P, Bandyopadhyay S, Goga A, Yosef N, Nomura DK. Protein Sialylation Regulates a Gene Expression Signature that Promotes Breast Cancer Cell Pathogenicity. ACS Chem Biol. 2016 Aug 19; 11(8):2131-9. PMID: 27380425.
        View in: PubMed
      2. Hofree M, Carter H, Kreisberg JF, Bandyopadhyay S, Mischel PS, Friend S, Ideker T. Challenges in identifying cancer genes by analysis of exome sequencing data. Nat Commun. 2016; 7:12096. PMID: 27417679.
        View in: PubMed
      3. Miller RE, Brough R, Bajrami I, Williamson CT, McDade S, Campbell J, Kigozi A, Rafiq R, Pemberton H, Natrajan R, Joel J, Astley H, Mahoney C, Moore JD, Torrance C, Gordan JD, Webber JT, Levin RS, Shokat KM, Bandyopadhyay S, Lord CJ, Ashworth A. Synthetic Lethal Targeting of ARID1A-Mutant Ovarian Clear Cell Tumors with Dasatinib. Mol Cancer Ther. 2016 Jul; 15(7):1472-84. PMID: 27364904.
        View in: PubMed
      4. Kohnz RA, Mulvihill MM, Chang JW, Hsu KL, Sorrentino A, Cravatt BF, Bandyopadhyay S, Goga A, Nomura DK. Activity-Based Protein Profiling of Oncogene-Driven Changes in Metabolism Reveals Broad Dysregulation of PAFAH1B2 and 1B3 in Cancer. ACS Chem Biol. 2015 Jul 17; 10(7):1624-30. PMID: 25945974.
        View in: PubMed
      5. Blakely CM, Pazarentzos E, Olivas V, Asthana S, Yan JJ, Tan I, Hrustanovic G, Chan E, Lin L, Neel DS, Newton W, Bobb KL, Fouts TR, Meshulam J, Gubens MA, Jablons DM, Johnson JR, Bandyopadhyay S, Krogan NJ, Bivona TG. NF-?B-activating complex engaged in response to EGFR oncogene inhibition drives tumor cell survival and residual disease in lung cancer. Cell Rep. 2015 Apr 7; 11(1):98-110. PMID: 25843712; PMCID: PMC4394036 [Available on 04/07/16].
      6. Martins MM, Zhou AY, Corella A, Horiuchi D, Yau C, Rakshandehroo T, Gordan JD, Levin RS, Johnson J, Jascur J, Shales M, Sorrentino A, Cheah J, Clemons PA, Shamji AF, Schreiber SL, Krogan NJ, Shokat KM, McCormick F, Goga A, Bandyopadhyay S. Linking tumor mutations to drug responses via a quantitative chemical-genetic interaction map. Cancer Discov. 2015 Feb; 5(2):154-67. PMID: 25501949; PMCID: PMC4407699.
      7. 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. PMID: 25127139; PMCID: PMC4294625.
      8. 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. PMID: 24738946; PMCID: PMC4076040.
      9. 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. PMID: 24550319; PMCID: PMC3932924.
      10. 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. PMID: 24302555.
        View in: PubMed
      11. 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. PMID: 23719353; PMCID: PMC3671485.
      12. 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. PMID: 23407553; PMCID: PMC3641890.
      13. 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. PMID: 21127252; PMCID: PMC3006187.
      14. 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. PMID: 20978140; PMCID: PMC2989993.
      15. 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. PMID: 20936779; PMCID: PMC2967489.
      16. 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. PMID: 20027183; PMCID: PMC2862546.
      17. 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. PMID: 19730696; PMCID: PMC2731838.
      18. 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. PMID: 19478882; PMCID: PMC2682202.
      19. 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. PMID: 19061648; PMCID: PMC2644724.
      20. 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. PMID: 18854154; PMCID: PMC2628946.
      21. 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. PMID: 18818364; PMCID: PMC2753251.
      22. 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. PMID: 18421374; PMCID: PMC2289880.
      23. 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. PMID: 17703239; PMCID: PMC2811081.
      24. Bandyopadhyay S, Sharan R, Ideker T. Systematic identification of functional orthologs based on protein network comparison. Genome Res. 2006 Mar; 16(3):428-35. PMID: 16510899; PMCID: PMC1415213.
      25. Bandyopadhyay S, Kelley R, Ideker T. Discovering regulated networks during HIV-1 latency and reactivation. Pac Symp Biocomput. 2006; 354-66. PMID: 17094252.
        View in: PubMed
      26. 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. PMID: 15181200; PMCID: PMC428480.
      27. Bandyopadhyay S, Cookson MR. Evolutionary and functional relationships within the DJ1 superfamily. BMC Evol Biol. 2004 Feb 19; 4:6. PMID: 15070401; PMCID: PMC385224.
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