Barry S. Taylor: Publications


Cancer Genome Atlas Research Network. Comprehensive molecular characterization of gastric adenocarcinoma. Nature 2014; 513(7517); 202-209

Cancer Genome Atlas Research Network. Integrated genomic characterization of papillary thyroid carcinoma. Cell 2014; 159; 676-690

Carver BS, Taylor BS, Wanjala J, Chapinski C, Hieronymus H, Wongvipat J, Chen Y, Schultz N, Xie Y, Liu S, Lu W, Yang Q, Sander C, Chen Z, Sawyers CL. MET amplification in advance stage murine and human prostate cancer. Mol Cancer Ther 2015; 14(1); 278-288

Cancer Genome Atlas Research Network. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature 2015; 517(7536); 576-582

Van Thuijl HF, Mazor T, Johnson BE, Fouse SD, Aihara K, Hong C, Malmstrom A, Hallbeck M, Heimans JJ, Kloezeman JJ, Stenmark-Askmalm M, Lamfers MLM, Saito N, Aburatan H; Berger MS, Söderkvist P, Taylor BS, Molinaro AM, Wesseling P, Reijneveld JC, Chang SM, Ylstra B, Costello JF. Evolution of DNA repair defects during malignant progression of low-grade gliomas after temozolomide treatment. Acta Neuropathol 2015; 129(4): 597-607

Cancer Genome Atlas Research Network. Genomic classification of cutaneous melanoma. Cell 2015; 161, 1681-1696

Cancer Genome Atlas Research Network. Comprehensive, integrative genomic analysis of diffuse lower grade gliomas. N. Eng. J. Med. 2015; 372(26): 2481-98

Chapman JS, Asthana S, Cade L, Chang MT, Wang Z, Zaloudek C, Ueda S, Collisson EA, Taylor BS. Clinical sequencing contributes to a BRCA-associated cancer re-diagnosis that guides an effective therapeutic course. J Natl Compr Canc Netw. 2015; 13(7): 835-845

Taylor BS, Varambally S. Chinnaiyan AM. A systems approach to model metastatic progression. Cancer Res. 2006; 66(11): 5537-9

Taylor BS, Varambally S, Chinnaiyan AM. Differential proteomic alterations between localized and metastatic prostate cancer. Br J Cancer. 2006; 95(4): 425-430

Mathew JP, Taylor BS, Bader GD, Pyarajan S, Antoniotti M, Chinnaiyan AM, Sander C, Burakoff SJ, Mishra B. From bytes to bedside: data integration and computational biology for translational cancer research. PLoS Comput Biol. 2007; 3(2): e12

Taylor BS, Pal M, Yu J, Laxman B, Kalyana-Sundaram S, Zhao R, Menon A, Wei JT, Nesvizhskii AI, Ghosh D, Omenn GM, Lubman DM, Chinnaiyan AM, Sreekumar A. Humoral response profiling reveals pathways to prostate cancer progression. Mol Cell Proteomics, 2008; 7(3): 600-11

Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008; 455(7216): 1061-8

Taylor BS, Barretina J, Socci ND, DeCarolis P, Ladanyi M, Meyerson M, Singer S, Sander C. Functional copy-number alterations in cancer. PLoS ONE. 2008; 3(9): e3179

Pratilas CA, Hanrahan AJ, Halilovic E, Persaud Y, Soh J, Chitale D, Shigematsu H, Yamamoto H, Sawai A, Janakiraman M, Taylor BS, Pao W, Toyooka S, Ladanyi M, Gazdar A, Rosen N, Solit B. Genetic predictors of MEK-dependence in non-small cell lung cancer. Cancer Res. 2008; 68(22): 9375-83

Pratilas CA, Taylor BS, Ye Q, Viale A, Sander C, Solit DB, Rosen N. (V600E)BRAF is associated with disabled feedback inhibition of RAF-MEK signaling and elevated transcriptional output of the pathway. Proc Natl Acad Sci. 2009; 106(11): 4519-24

King JC, Xu J, Wongvipat J, Hieronymus H, Carver BS, Leung DH, Taylor BS, Sander C, Couto SS, Gerald WL, Sawyers CL. Cooperativity of TMPRSS2-ERG with PI3-kinase pathway activation in prostate oncogenesis. Nature Genetics. 2009; 41(5): 524-526

Veeriah S, Brennan C, Meng S, Singh B, Fagin JA, Solit DB, Paty PB, Rohle D, Vivanco I, Chlmielecki J, Pao W, Ladanyi M, Gerald WL, Liau L, Cloughesy TC, Mischel PS, Sander C, Taylor B, Schultz N, Major J, Heguy A, Fang F, Mellinghoff IK, Chan TA. The tyrosine phosphatase PTPRD is a tumor suppressor that is frequently inactivated and mutated in glioblastoma and other human cancers. Proc Natl Acad Sci. 2009; 106(23): 9435-40

Chitale D*, Gong Y*, Taylor BS*, Broderick S*, Brennan C, Somwar R, Golas B, Wang L, Motoi N, Szoke J, Reinersman M, Major J, Sander C, Seshan VE, Zakowski MF, Rusch V, Pao W, Gerald W, Ladanyi M. An integrated genomic analysis of lung cancer reveals loss of DUSP4 in EGFR-mutant tumors. Oncogene. 2009; 28(31): 2773-2783

Veeriah S*, Taylor BS*, Meng S*, Fang F, Yilmaz E, Vivanco I, Janakiraman M, Schultz N, Hanrahan AJ, Pao W, Ladanyi M, Sander C, Heguy A, Holland EC, Paty PB, Mischel PS, Liau L, Cloughesy TF, Mellinghoff IK, Solit DB, Chan TA. Somatic mutations of the Parkinson’s disease-associated gene PARK2 in glioblastoma and other human malignancies. Nature Genetics. 2010; 42(1): 77-82

Berger AH, Niki M, Morotti A, Taylor BS, Socci ND, Viale A, Brennan C, Szoke J, Motoi N, Rothman PB, Feldstein-Teruya J, Gerald WL, Ladanyi M, Pandolfi PP. Identification of DOK genes as lung tumor suppressors. Nature Genetics. 2010; 42(3): 216-223

Cerami E, Demir E, Schultz N, Taylor BS, Sander C. Automated network analysis identifies core pathways in glioblastoma. PLoS ONE. 2010; 5(2): e8918

Dry JR, Pavey S, Pratilas CA, Harbron C, Runswick S, Hodgson D, Chresta C, McCormack R, Byrne N, Cockerill M, Graham A, Beran G, Cassidy A, Haggerty C, Brown H, Ellison G, Dering J, Taylor BS, Stark M, Bonazzi V, Ravishankar S, Packer L, Xing F, Solit DB, Finn RS, Rosen N, Hayward NK, French T, Smith PD. Transcriptional pathway signatures predict MEK addition and response to selumetinib AZD6244. Cancer Res. 2010; 70(6): 2264-73

Janakiraman M, Vakiani E, Zeng Z, Pratilas CA, Taylor BS, Chitale D, Halilovic E, Wilson M, Huberman K, Ricarte-Filho JC, Persaud Y, Levine DA, Fagin JA, Jhanwar SC, Mariadason JM, Lash A, Ladanyi M, Saltz LB, Heguy A, Paty PB, Solit DB. Genomic and biological characterization of exon 4 KRAS mutations in human cancer. Cancer Res. 2010; 70(14):5901-11

Taylor BS*, Schultz N*, Hieronymus H*, Gopalan A, Xiao Y, Carver BS, Arora VK, Kaushik P, Cerami E, Reva B, Antipin Y, Mitsiades N, Landers T, Dolgalev I, Major JE, Wilson M, Socci ND, Lash AE, Heguy A, Eastham JA, Scher HI, Reuter VE, Scardino PT, Sander C, Sawyers CL, Gerald WL. Integrative genomic profiling of human prostate cancer. Cancer Cell. 2010;   18(1): 11-22.

Barretina J*, Taylor BS*, Ramos AH, Lagos-Quintana M, Banerji S, DeCarolis PL, Shah K, Socci ND, Weir BA, Ho A, Chiang DY, Reva B, Mermel C, Getz G, Antipin Y, Beroukhim R, Major JE, Hatton C, Nicoletti R, Hanna M, Sharpe T, Fennell T, Cibulskis K, Onofrio RC, Saito T, Shukla NN, Lau C, Nelander S, Silver S, Sougnez C, Viale A, Winckler W, Maki RG, Garraway LA, Lash A, Greulich H, Root D, Sellers WR, Schwartz GK, Antonescu CR, Lander ES, Varmus HE, Ladanyi M, Sander C, Meyerson M, and Singer S. Subtype-specific genomic alterations define new targets for soft tissue sarcoma therapy. Nature Genetics. 2010; 42(8): 715-21

Joseph EW, Pratilas CA, Poulikakos PI, Tadi M, Wang W, Taylor BS, Halilovic E, Persaud Y, Xing F, Viale A, Tsai J, Chapman PB, Bollag G, Solit DB, Rosen N. The RAF inhibitor PLX4032 inhibits ERK signaling and tumor cell proliferation in a V600E BRAF-selective manner. Proc Natl Acad Sci. 2010; 107(33): 14903-14908

Brill E, Goggle R, Angeles C, Lagos-Quintana M, Crago A, Laxa B, DeCarolis P, Zhang L, Antonescu A, Socci ND, Taylor BS, Sander C, Koff A, Singer S. Zic1 over-expression is oncogenic in liposarcoma. Cancer Res. 2010; 70(17): 6891-6901

Taylor BS, Ladanyi M. Clinical cancer genomics: how soon is now. J. Pathol. 2011; 223(2): 319-27

Clegg NJ, Couto SS, Wongvipat J, Hieronymus H, Carver BS, Taylor BS, Ellwood-Yen K, Gerald WL, Sander C, Sawyers CL. MYC cooperates with AKT in prostate tumorigenesis and alters the sensitivity to mTOR inhibitors. PLoS ONE. 2011; 6(3): e17449

Bott M, Brevet M, Taylor BS, Shimizu S, Ito T, Wang L, Creaney J, Lake RA, Zakowski MF, Reva B, Sander C, Delsite R, Powell S, Zhou Q, Shen R, Olshen AB, Rusch V, Ladanyi M. The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma. Nature Genetics, 2011; 43(7): 668-72

Ugras S, Brill E, Jacobsen A, Hafner M, Socci ND, DeCarolis PL, Khanin R, O’Conner R, Mihailovic A, Taylor BS, Sheridan R, Viale A, Crago A, Antonescu CR, Sander C, Tuschl T, Singer S. Small RNA sequencing and functional characterization reveals microRNA-143 tumor suppressor activity in liposarcoma. Cancer Res, 2011; 71: 5659-69

Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature, 2011; 474(7535): 609-15

Taylor BS, Barretina J, Maki RG, Antonescu CR, Singer S, Ladanyi M. Advances in sarcoma genomics and new therapeutic targets. Nat Rev Cancer, 2011; 11: 541-557

Chen M, Pratt CP, Zeeman ME, Schultz N, Taylor BS, O’Neill A, Castillo-Martin M, Nowak DG, Naguib A, Grace DM, Murn J, Navin N, Atwal GS, Sander C, Gerald WL, Cordon-Cardo C, Newton AC, Carver BS, Trotman LC. Identification of PHLPP as a tumor suppressor reveals the role of feedback activation in PTEN-mutant prostate cancer progression. Cancer Cell, 2011; 20(2): 173-186

Morris LGT, Taylor BS, Bivona TG, Gong Y, Eng S, Banuchi VE, Brennan C, Kaufman A, Kastenhuber ER, Singh B, Heguy A, Viale A, Mellinghoff I, Huse J, Ganly I, Chan TA. Genomic dissection of the EGFR/PI3K pathway reveals frequent deletion of the EGFR phosphatase PTPRS in head and neck cancers. Proc Natl Acad Sci., 2011; 108(47): 19024-19029

Taylor BS, DeCarolis PL, Angeles CV, Brenet F, Schultz N, Antonescu CR, Scandura JM, Sander C, Viale A, Socci ND, Singer S. Frequent alterations and epigenetic silencing of differentiation pathway genes in structurally rearranged liposarcomas. Cancer Discov, 2011; 1(7): 587-597

Hanrahan AJ, Schultz N, Westfal ML, Sakr R, Giri D, Scaperi S, Janikariman M, Olvera N, She QB, Aghajanian C, King T, de Stanchina E, Spriggs D, Heguy A, Taylor BS, Sander C, Rosen N, Levine DA, Solit DB. Genetic determinants of AKT-dependence in serous ovarian cancer. Cancer Discov, 2012; 2(1): 56-67

Xing F, Persaud Y, Pratilas CA, Taylor BS, Janakiraman M, She Q-B, Gallardo H, Liu C, Merghoub T, Hefter B, Dolgalev I, Viale A, Heguy A, De Stanchina E, Cobrinik D, Bollag G, Wolchok J, Houghton A, Solit DB. Concurrent loss of the PTEN and RB1 tumor suppressors attenuates RAF dependence in melanomas harboring V600E BRAF. Oncogene, 2012; 31(4): 446-457

Crago A, Socci ND, Decarolis PL, O’Connor R, Taylor BS, Qin LX, Antonescu CR, Singer S. Copy number losses define subgroups of dedifferentiated liposarcoma with poor prognosis and genomic instability. Clin Cancer Res, 2012; 18(5): 1334-40

Cancer Genome Atlas Research Network. Comprehensive molecular characterization of human colon and rectal tumors. Nature. 2012; 487(7407): 330-337

Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012; 489(7417): 519-525

Cancer Genome Atlas Research Network. Comprehensive molecular portraits of human breast tumors. Nature. 2012; 49(7418): 61-70

Tewari AK, Yardimci GG, Shibata Y, Sheffield NC, Song L, Taylor BS, Georgiev SG, Coetzee GA, Ohler U, Furey TS, Crawford GE, Febbo PG. Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity. Genome Biol. 2012; 13:R88

Iyer G, Hanrahan AJ, Milowsky MI, Al-Ahmadie H, Scott SN, Janakiraman M, Pirun M. Sander C, Socci ND, Ostrovnaya I, Viale A, Heguy A, Peng L, Chan TA, Bochner B, Bajorin DF, Berger MF, Taylor BS**, Solit DB**. Genome sequencing identifies a basis for everolimus sensitivity. Science. 2012; 338(6104): 221

Cancer Genome Atlas Research Network. Integrated genomic characterization of endometrial carcinoma. Nature. 2013; 497(7447): 67-73

Cancer Genome Atlas Research Network. Integrative analysis of genomic and molecular alterations in clear cell renal cell carcinoma. Nature; 2013; 499(7456): 43-9

Iyer G, Al-Ahmadie H, Schultz N, Hanrahan AJ, Ostrovnaha I, Bala A, Kim P, Lin O, Weinhold N, Sander C, Zabor EC, Janakiraman M, Garcia-Grossman I, Heguy A, Viale A, Bochner B, Reuter VE, Bajorin DF, Milowsky MI, Taylor BS, Solit DB. Prevalence and co- occurrence of actionable genomic alterations in high-grade bladder cancer. J. Clin. Oncol. 2013; 31(25): 3133-3140

Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA, Mills GB, Mills Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. The cancer genome atlas pan-cancer analysis project. Nature Genetics, 2013; 45(10): 1113-20

Olshen AB, Hsieh AC, Stumpf CR, Olshen RA, Ruggero D, Taylor BS. Assessing gene-level translational control from ribosome profiling. Bioinformatics, 2013; 29(23): 2995-3002

Stumpf CR, Olshen AB, Moreno MV, Taylor BS**, Ruggero D**. The translational program of the mammalian cell cycle. Mol. Cell, 2013; 52(4): 574-582

Berger AH, Chen M, Morotti A, Jana JA, Niki M, Bronson RT, Taylor BS, Ladanyi M, Van Aelst L, Politi K, Varmus HE, Pandolfi PP. DOK2 inhibits EGFR-mutant lung adenocarcinoma. PLoS ONE, 2013; 8(11): e79526

Johnson BE, Mazor T, Hong C, Barnes M, McLean CY, Fouse SD, Yamamoto S, Ueda H, Tatsuno K, Aihara K, Asthana S, Jalbert LE, Nelson SJ, Bollen AW, Gustafson WC, Charron E, Weiss WA, Smirnov IV, Song JS, Olshen AB, Cha S, Zhao Y, Moore RA, Mungal AJ, Jones SJM, Hirst M, Marra MA, Mukasa A, Saito N, Aburatani H, Berger MS, Chang SM, Taylor BS**, Costello JF**. Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma. Science, 2014; 343(6167): 189-93

Gajan J, Tajon C, Oses-Prieto J, Lasater EA, Taylor BS, Burlingame A, Craik C, Shah NP. MEK-dependent negative feedback underlies BCR-ABL-mediated oncogene addition. Cancer Discov. 2014; 4(2): 200-15

Lin L, Asthana S, Chan E, Bandyopadhay S, Martins M, Olivas V, Yan J, Pham L, Wang M, 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. 2014; 111(7): E748-57

Nissan MH, Pratilas CA, Jones AM, Ramirez R, Won H, Liu C, Tiwari S, Kong L, Hanrahan AJ, Yao Z, Merghoub T, Ribas A, Chapman PB, Yaeger R, Taylor BS, Schultz N, Berger MF, Rosen N, Solit DB. Loss of NF1 in cutaneous melanoma is associated with RAS activation and MEK dependence. Cancer Res. 2014; 74(8): 2340-50

Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial carcinoma of the bladder. Nature, 2014; 507(7492): 315-22

Cancer Genome Atlas Research Network. Comprehensive molecular profiling of lung adenocarcinoma. Nature, In press (doi:10.1038/nature13385)

Al-Ahmadie H, Iyer G, Hohl M, Asthana S, Schultz N, Hanrahan AJ, Scott SN, Brannon AR, McDermott GC, Pirun M, Ostrovnaya I, Kim P, Socci ND, Viale A, Schwartz GK, Reuter V, Bochner B, Rosenberg JE, Bajorin DF, Berger MF, Petrini JH**, Solit DB**, Taylor BS**. Synthetic lethality in ATM-deficient RAD50-mutant tumors underlies outlier response to cancer therapy. Cancer Discov. In press (doi:10.1158/2159-8290.CD-14-0380)

Hieronymus H, Schultz N, Gopalan A, Carver BS, Chang, MT, Xiao Y, Heguy A, Huberman K, Bernstein M, Assel N, Murali R, Vickers A, Scardino PT, Sander C, Reuter VE, Taylor BS*, Sawyers CL*. Copy number alteration burden predicts prostate cancer relapse. Proc Natl Acad Sci. Proc Natl Acad Sci. 2014; 111(30): 11139-44