UCSF


    Preprints/Submitted


  1. Webber JT, Ranall MV, Kaushik S, Bandyopadhyay S*. Connecting tumor genomics with therapeutics through multi-dimensional network modules. Submitted. Preprint on BioRxiv.
  2. Donnella HJ, Webber JT, Levin RS, Camarda R, Momcilovic O, Bayani N, Shah KN, Korkola J, Shokat KM, Goga A, Gordan J, Bandyopadhyay S*. Kinome rewiring reveals AURKA is a molecular barrier to the efficacy of PI3K/mTOR-pathway inhibitors in breast cancer. Submitted. Preprint on BioRxiv
  3. Hu H, Zhao X, Kaushik S, Robillard L, Barthelet A, Lin KK, Simmons A, Raponi M, Harding TC, Bandyopadhyay S*. A quantitative chemotherapy genetic interaction map reveals new factors associated with PARP inhibitor resistance. Submitted. Preprint on BioRxiv

  4. Published


  5. Brand TM, Stefan H, Bhola NE, Peyser ND, Li H, Zeng Y, Eschsler EI, Ranall MV, Bandyopadhyay S, Duvvuri U, LaVallee TM, Jordan RCK, Johnson DE, Grandis JR. Human Papillomavirus regulates HER3 expression in head and neck cancer: implications for targeted HER3 therapy in HPV(+) patients. Clinical Cancer Research. 2016 Dec 16
  6. Gerhard DS, Clemons PA, Shamji AF, Hon C, Wagner BK, Schreiber SL, Krasnitz A, Sordella R, Sander C, Lowe SW, Powers S, Smith K, Aburi M, Iavarone A, Lasorella A, Silva J, Stockwell BR, Califano A, Boehm JS, Vazquez F, Weir BA, Hahn WC, Khuri FR, Moreno CS, Johns M, Fu H, Nikolova O, Mendez E, Gadi VK, Margolin AA, Grandori C, Kemp CJ, Warren EH, Riddell SR, McIntosh MW, Gevaert O, Kuo CJ, Ji HP, Dhruv H, Finlay D, Kiefer J, Kim S, Vuori K, Berens ME, Hangauer M, Boettcher M, Weissman JS, Bivona TG, Bandyopadhyay S, McManus MT, McCormick F, Aksoy O, Simonds EF, Zheng T, Chen J, An Z, Balmain A, Weiss WA, Chen K, Liang H, Scott KL, Mills GB, Posner BA, MacMillan J, Minna J, White M, Roth MG, Jagu S, Mazerik J. Transforming Big Data into cancer-relevant insight: An initial, multi-tier approach to assess reproducibility and relevance. [Molecular Cancer Therapeutics]. 2016 pii: molcanres.0090.2016. [Epub ahead of print]
  7. 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 Chemical Biology].2016 Jul 22 [Epub]
  8. 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. [Nature Communications]. 2016 Jul 15;7:12096
  9. Miller RE, Brough R, Gajrami I, Williamson C, McDade S, Campbell J, Kigozi A, Rafiq R, Pemberton H, Natrajan R, Joel J, Astley H, Mahoney C, Moore J, 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. [Molecular Cancer Therapeutics]. 2016 June 30 [Epub]

  10. Fujita-Sato S, Galeas J, Truitt M, Pitt C, Urisman A, Bandyopadhyay S, Ruggero D, McCormick F. Enhanced MET translation and signaling sustains K-Ras driven proliferation under anchorage-independent growth conditions. [Cancer Research] May 2015.
  11. 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 Chemical Biology] May 2015.
  12. 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-κB-Activating Complex Engaged in Response to EGFR Oncogene Inhibition Drives Tumor Cell Survival and Residual Disease in Lung Cancer. [Cell Reports] April 2015.
  13. Martins M, Zhou A, Corella A, Horiuchi D, Yau C, Rakshandehroo T, Gordan J, Levin R, Johnson J, Jascur J, Shales M, Sorrentino A, Cheah J, Clemons P, 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 Discovery] Feb 2015.

  14. Sos ML, Levin SL, 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 Reports]. (2014)
  15. Benjamin D, Louie S, Mulvihill M, Kohnz R, Li D, Chan L, Sorrentino A, Bandyopadhyay S, Cozzo A, Ohiri A, Goga A, Ng S, Nomura DK. Inositol phosphate recycling regulates glycolytic and lipid metabolism that drives cancer aggressiveness. [ACS Chem Biol]. (2014)
  16. 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. [PNAS]. (2014) 111(7)
  17. Salt M, Bandyopadhyay S, McCormick F. Epithelial to mesenchymal transition rewires the molecular path to PI3-Kinase-dependent proliferation [Cancer Discovery]. (2014) 4(2):186-99

  18. 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]. 27(5):835-8 2013.
  19. Roguev A, Tablot D, Negri GL, Shales M, Cagney G, Bandyopadhyay S*, Panning B*, Krogan NJ*. Quantitative Genetic Interaction Mapping in Mammalian Cells. [Nature Methods]. 10(432-37) 2013. *co-corresponding

    Accompanying News and Views: Hart and Moffatt [Nature Methods]
  20. UCSD (2005-2010)

  21. 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. [Science]*Faculty of 1000 reccomended

    Accompanying News and Views: Friedman and Schuldiner [Science]; Zahn [Science Signaling]; Califano [Molecular Systems Biology]

  22. Ideker T, Bandyopadhyay S. Integrative Systems Biology. Nature Genetics. 42(12). 2010. [Nature Genetics]

  23. 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. [Pubmed]*Faculty of 1000 reccomended

    Accompanying News and Views: Baker [Nature]; Bonetta [Nature]
  24. 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. [Pubmed] *Faculty of 1000 reccomended

  25. 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. [Nature]

  26. 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. [Plos Pathogens]

  27. 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. [Plos Pathogens] *Faculty of 1000 reccomended

  28. 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. Molecular Cell. 2008 Dec 5;32(5):735-46. Featured Article, [Cell] *Equal Contribution

  29. 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. [Science]

  30. 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.[Cell] *Faculty of 1000 reccomended

  31. Bandyopadhyay S, Kelley RM, Krogan NJ, Ideker T. Functional maps of protein complexes from quantitative genetic interaction data. PLoS Computational Biology 2008 Apr 18;4(4):e1000065.[Plos] [supplement]

  32. Beyer A, Bandyopadhyay S, Ideker T. Integrating physical and genetic maps: from genomes to interaction networks. Featured Review. Nature Reviews Genetics. 2007 Sep;8(9):699-710. [Nature]

  33. Bandyopadhyay S, Sharan R, Ideker T. Cover Article: Systematic identification of functional orthologs by protein network comparison. Genome Research. 2006 Mar;16(3):428-35. [Genome Res] [supplement]

  34. Bandyopadhyay S, Kelley RM, Ideker T. Discovering regulated networks during HIV-1 latency and reactivation. Pac Symp Biocomput. 2006:354-66.[PSB]

    NIH (2002-2004)

  35. 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. [Pubmed]

  36. Bandyopadhyay S, Cookson MR. Evolutionary and functional relationships within the DJ1 superfamily. BMC Evol Biol. 2004 Feb 19;4(1):6. [Pubmed]