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Bandyopadhyay Lab @ UCSF

Publications (listed in reverse chronological order)

    UCSF


    Preprints


  1. Kaushik S, Haderk F, Zhao X, Hu H, Shah KN, Jang GM, Olivas V, Nanjo S, Jascur J, Masto VB, Ciznadija D, Sloma I, Gross E, Weinrich SL, Johnson J, Bivona TG, Krogan NJ, Bandyopadhyay S*. A tyrosine kinase protein interaction map reveals targetable EGFR network oncogenesis in lung cancer. BioArxiv

    2. Published


  2. Kim D, Bandyopadhyay S. Aurora kinases shed light on resistance to EGFR inhibition in head and neck cancer. EBioMedicine. 2021.
  3. Maynard A, McCoach CE, Rotow JK, Harris L, Haderk F, Kerr DL, Ya EA, Schenk EL, Tan W, Zee A, Tan M, Gui P, Lea T, Wu W, Urisman A, Jones K, Sit R, Kolli PK, Seeley E, Gesthalter Y, Le DD, Yamauchi KA, Naeger DM, Bandyopadhyay S, Shah K, Cech L, Thomas NJ, Gupta A, Gonzalez M, Do H, Tan L, Bacaltos B, Gomez-Sjoberg R, Gubens M, Jahan T, Kratz JP, Jablons D, Neff N, Doebele RC, Weissman J, Blakely CM, Darmanis S, Bivona TG. Heterogeneity and targeted therapy-induced adaptations in lung cancer revealed by longitudinal single-cell RNA sequencing. [Cell] . 2020
  4. Wu C, Yang C, Wang L, Gao H, Rakhshandehroo T, Afghani S, Pincus L, Balassanian R, Rubenstein J, Gill R, Bandyopadhyay S, McCormick F, Moasser M, Ai WZ. Cutaneous T Cell Lymphoma PDX Drug Screening Platform Identifies Cooperation Between Inhibitions of PI3Kα/δ and HDAC. [J Invest Dermatol]. June 2020
  5. Ku A, Kongara S, Hu H, Zhao X, Wu D, McCormick F, Balmain A, Bandyopadhyay S*. Integration of pathway, cellular and genetic context reveals principles of synthetic lethality that affect reproducibility. [Nature Communications]. May 2020
  6. Shah KN, Bandyopadhyay S. Targeting the evolution of drug resistance in lung cancer. [Review in Molecular & Cellular Oncology]. May 2019.
  7. Shah KN, Bhatt R, Rotow J, Rohrberg J, Olivas V, Wang VE, Hemmati G, Martins MM, Maynard A, Kuhn J, Galeas J, Donnella HJ, Kaushik S, Ku, A, Dumont S, Krings G, Haringsma HH, Robillard L, Simmons AD, Harding TC, McCormick F, Goga A, Blakely CM, Bivona TG, Bandyopadhyay S*. Aurora kinase A drives the evolution of resistance to third generation EGFR inhibitors in lung cancer. [Nature Medicine]. Jan 2019.

    Nature Reviews Drug Discovery - Highlight:Combating resistance to EGFR inhibitors
    Fierce Biotech - Two pronged attack against lung cancer could overcome EGFR drug resistance
    Genetic Engineering & Biotechnology News - Two-Pronged Approach Shows Promise against Drug-Resistant Cancers
    UCSF News - Cancer Researchers ID 'Achilles Heel' of Drug-Resistant Tumors
  8. Webber JT, Kaushik S, Bandyopadhyay S*. Integration of tumor genomic data using multi-dimensional network modules improves cancer pharmacogenomics. [Cell Systems]. Nov 2018.

    GenomeWeb - Drug Response Predictions Bolstered by Combined Tumor, Cancer Cell Line Analysis
    GitHub - MAGNETIC repository
  9. 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 limits the efficacy of PI3K/mTOR-pathway inhibitors in breast cancer. [Nature Chemical Biology]. June 2018.

    Nature Chemical Biology - Uwe Rix and colleagues - Unraveling the rewired network
    American Chemical Society News - Ferreting out why some cancer drugs struggle to shrink tumors
    UCSF News - Combination Therapy May Revive Prospects for ‘Embattled’ Breast Cancer Drugs
  10. 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 factors associated with PARP inhibitor resistance. [Cell Reports]. Apr 2018.

    Cancer Today, Magazine of the AACR - Targeted Chemotherapy
    UCSF News - Gene mapping lays groundwork for precision chemotherapy
    UPI News - Gene mapping can help doctors pick most appropriate chemotherapy
    ClinicalOmics - UCSF Researchers Release Gene-Drug Interaction Map for Precision Chemotherapy
    Drug Target Review - Scientists mine gene responses to existing chemotherapies to facilitate precision cancer treatment
    Genetic Engineering & Biotechnology News - Gene–Drug Interaction Map Developed to Aid Personalized Chemotherapy
    MedicalExpress - Using big data to chart cancer's hidden genetic weaknesses
  11. Martinko AJ, Truiller C, Julien O, Diaz J, Horlbeck M, Whiteley G, Blonder J, Weissman JS, Bandyopadhyay S, Evans M, Wells JA. Targeting RAS driven human cancer cells with antibodies to upregulated and essential cell-surface proteins. [Elife]. eLife 2018;7:e31098. Jan 23 2018
  12. Brand TM, Hartmann S, Bhola N, Li H, Zang Y, O'Keefe R, Ranall M, Bandyopadhyay S, Soucheray M, Krogan N, Kemp C, Duvvuri U, LaVallee T, Johnson D, Ozbun M, Baumann J, Grandis J. Crosstalk signaling between HER3 and HPV16 E6 and E7 mediates resistance to PI3K inhibitors in head and neck cancer. [Cancer Research]. Feb 12 2018
  13. 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
  14. 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]
  15. 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]
  16. 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
  17. 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]
  18. 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.
  19. 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.
  20. 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.
  21. 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.

    Data available on NCI CTD^2 dashboard.
  22. 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)
  23. 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)
  24. 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)
  25. 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
  26. 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.
  27. 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]

    28. UCSD (2005-2010)

  28. 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]

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

  30. 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]
  31. 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

  32. 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]

  33. 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]

  34. 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

  35. 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

  36. 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]

  37. 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

  38. 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]

  39. 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]

  40. 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]

  41. 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)

  42. 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]

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