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Bell EH, Zhang P, Shaw EG, Buckner JC, Barger GR, Bullard DE, Mehta MP, Gilbert MR, Brown PD, Stelzer KJ, McElroy JP, Fleming JL, Timmers CD, Becker AP, Salavaggione AL, Liu Z, Aldape K, Brachman DG, Gertler SZ, Murtha AD, Schultz CJ, Johnson D, Laack NN, Hunter GK, Crocker IR, Won M, Chakravarti A. Comprehensive Genomic Analysis in NRG Oncology/RTOG 9802: A Phase III Trial of Radiation Versus Radiation Plus Procarbazine, Lomustine (CCNU), and Vincristine in High-Risk Low-Grade Glioma. J Clin Oncol. 2020 Oct 10;38(29):3407-3417. doi: 10.1200/JCO.19.02983. Epub 2020 Jul 24. PubMed PMID: 32706640; PubMed Central PMCID: PMC7527157.
Enache OM, Rendo V, Abdusamad M, Lam D, Davison D, Pal S, Currimjee N, Hess J, Pantel S, Nag A, Thorner AR, Doench JG, Vazquez F, Beroukhim R, Golub TR, Ben-David U. Cas9 activates the p53 pathway and selects for p53-inactivating mutations. Nat Genet. 2020 Jul;52(7):662-668. doi: 10.1038/s41588-020-0623-4. Epub 2020 May 18. PubMed PMID: 32424350; PubMed Central PMCID: PMC7343612.
Oak N, Cherniack AD, Mashl RJ, Hirsch FR, Ding L, Beroukhim R, Gümüş ZH, Plon SE, Huang KL. Ancestry-specific predisposing germline variants in cancer. Genome Med. 2020 May 29;12(1):51. doi: 10.1186/s13073-020-00744-3. PubMed PMID: 32471518; PubMed Central PMCID: PMC7260738.
Carrot-Zhang J, Chambwe N, Damrauer JS, Knijnenburg TA, Robertson AG, Yau C, Zhou W, Berger AC, Huang KL, Newberg JY, Mashl RJ, Romanel A, Sayaman RW, Demichelis F, Felau I, Frampton GM, Han S, Hoadley KA, Kemal A, Laird PW, Lazar AJ, Le X, Oak N, Shen H, Wong CK, Zenklusen JC, Ziv E, Cherniack AD, Beroukhim R. Comprehensive Analysis of Genetic Ancestry and Its Molecular Correlates in Cancer. Cancer Cell. 2020 May 11;37(5):639-654.e6. doi: 10.1016/j.ccell.2020.04.012. PubMed PMID: 32396860; PubMed Central PMCID: PMC7328015.
Touat M, Li YY, Boynton AN, Spurr LF, Iorgulescu JB, Bohrson CL, Cortes-Ciriano I, Birzu C, Geduldig JE, Pelton K, Lim-Fat MJ, Pal S, Ferrer-Luna R, Ramkissoon SH, Dubois F, Bellamy C, Currimjee N, Bonardi J, Qian K, Ho P, Malinowski S, Taquet L, Jones RE, Shetty A, Chow KH, Sharaf R, Pavlick D, Albacker LA, Younan N, Baldini C, Verreault M, Giry M, Guillerm E, Ammari S, Beuvon F, Mokhtari K, Alentorn A, Dehais C, Houillier C, Laigle-Donadey F, Psimaras D, Lee EQ, Nayak L, McFaline-Figueroa JR, Carpentier A, Cornu P, Capelle L, Mathon B, Barnholtz-Sloan JS, Chakravarti A, Bi WL, Chiocca EA, Fehnel KP, Alexandrescu S, Chi SN, Haas-Kogan D, Batchelor TT, Frampton GM, Alexander BM, Huang RY, Ligon AH, Coulet F, Delattre JY, Hoang-Xuan K, Meredith DM, Santagata S, Duval A, Sanson M, Cherniack AD, Wen PY, Reardon DA, Marabelle A, Park PJ, Idbaih A, Beroukhim R, Bandopadhayay P, Bielle F, Ligon KL. Mechanisms and therapeutic implications of hypermutation in gliomas. Nature. 2020 Apr;580(7804):517-523. doi: 10.1038/s41586-020-2209-9. Epub 2020 Apr 15. PubMed PMID: 32322066; NIHMSID:NIHMS1572083.
Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 2020 Feb;578(7793):102-111. doi: 10.1038/s41586-020-1965-x. Epub 2020 Feb 5. PubMed PMID: 32025015; PubMed Central PMCID: PMC7054214.
Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE, Imielinski M, Weischenfeldt J, Beroukhim R, Campbell PJ. Patterns of somatic structural variation in human cancer genomes. Nature. 2020 Feb;578(7793):112-121. doi: 10.1038/s41586-019-1913-9. Epub 2020 Feb 5. PubMed PMID: 32025012; PubMed Central PMCID: PMC7025897.
Clairmont CS, Sarangi P, Ponnienselvan K, Galli LD, Csete I, Moreau L, Adelmant G, Chowdhury D, Marto JA, D'Andrea AD. TRIP13 regulates DNA repair pathway choice through REV7 conformational change. Nat Cell Biol. 2020 Jan;22(1):87-96. doi: 10.1038/s41556-019-0442-y. Epub 2020 Jan 8. PubMed PMID: 31915374; PubMed Central PMCID: PMC7336368.
Horbinski C, Ligon KL, Brastianos P, Huse JT, Venere M, Chang S, Buckner J, Cloughesy T, Jenkins RB, Giannini C, Stupp R, Nabors LB, Wen PY, Aldape KJ, Lukas RV, Galanis E, Eberhart CG, Brat DJ, Sarkaria JN. The medical necessity of advanced molecular testing in the diagnosis and treatment of brain tumor patients. Neuro Oncol. 2019 Dec 17;21(12):1498-1508. doi: 10.1093/neuonc/noz119. Review. PubMed PMID: 31276167; PubMed Central PMCID: PMC6917404.
Barthel FP, Johnson KC, Varn FS, Moskalik AD, Tanner G, Kocakavuk E, Anderson KJ, Abiola O, Aldape K, Alfaro KD, Alpar D, Amin SB, Ashley DM, Bandopadhayay P, Barnholtz-Sloan JS, Beroukhim R, Bock C, Brastianos PK, Brat DJ, Brodbelt AR, Bruns AF, Bulsara KR, Chakrabarty A, Chakravarti A, Chuang JH, Claus EB, Cochran EJ, Connelly J, Costello JF, Finocchiaro G, Fletcher MN, French PJ, Gan HK, Gilbert MR, Gould PV, Grimmer MR, Iavarone A, Ismail A, Jenkinson MD, Khasraw M, Kim H, Kouwenhoven MCM, LaViolette PS, Li M, Lichter P, Ligon KL, Lowman AK, Malta TM, Mazor T, McDonald KL, Molinaro AM, Nam DH, Nayyar N, Ng HK, Ngan CY, Niclou SP, Niers JM, Noushmehr H, Noorbakhsh J, Ormond DR, Park CK, Poisson LM, Rabadan R, Radlwimmer B, Rao G, Reifenberger G, Sa JK, Schuster M, Shaw BL, Short SC, Smitt PAS, Sloan AE, Smits M, Suzuki H, Tabatabai G, Van Meir EG, Watts C, Weller M, Wesseling P, Westerman BA, Widhalm G, Woehrer A, Yung WKA, Zadeh G, Huse JT, De Groot JF, Stead LF, Verhaak RGW. Longitudinal molecular trajectories of diffuse glioma in adults. Nature. 2019 Dec;576(7785):112-120. doi: 10.1038/s41586-019-1775-1. Epub 2019 Nov 20. PubMed PMID: 31748746; PubMed Central PMCID: PMC6897368.
Gittleman H, Ostrom QT, Stetson LC, Waite K, Hodges TR, Wright CH, Wright J, Rubin JB, Berens ME, Lathia J, Connor JR, Kruchko C, Sloan AE, Barnholtz-Sloan JS. Sex is an important prognostic factor for glioblastoma but not for nonglioblastoma. Neurooncol Pract. 2019 Dec;6(6):451-462. doi: 10.1093/nop/npz019. Epub 2019 May 18. PubMed PMID: 31832215; PubMed Central PMCID: PMC6899055.
Reitman ZJ, Paolella BR, Bergthold G, Pelton K, Becker S, Jones R, Sinai CE, Malkin H, Huang Y, Grimmet L, Herbert ZT, Sun Y, Weatherbee JL, Alberta JA, Daley JF, Rozenblatt-Rosen O, Condurat AL, Qian K, Khadka P, Segal RA, Haas-Kogan D, Filbin MG, Suva ML, Regev A, Stiles CD, Kieran MW, Goumnerova L, Ligon KL, Shalek AK, Bandopadhayay P, Beroukhim R. Mitogenic and progenitor gene programmes in single pilocytic astrocytoma cells. Nat Commun. 2019 Aug 19;10(1):3731. doi: 10.1038/s41467-019-11493-2. PubMed PMID: 31427603; PubMed Central PMCID: PMC6700116.
Gao GF, Parker JS, Reynolds SM, Silva TC, Wang LB, Zhou W, Akbani R, Bailey M, Balu S, Berman BP, Brooks D, Chen H, Cherniack AD, Demchok JA, Ding L, Felau I, Gaheen S, Gerhard DS, Heiman DI, Hernandez KM, Hoadley KA, Jayasinghe R, Kemal A, Knijnenburg TA, Laird PW, Mensah MKA, Mungall AJ, Robertson AG, Shen H, Tarnuzzer R, Wang Z, Wyczalkowski M, Yang L, Zenklusen JC, Zhang Z, Liang H, Noble MS. Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data. Cell Syst. 2019 Jul 24;9(1):24-34.e10. doi: 10.1016/j.cels.2019.06.006. PubMed PMID: 31344359; PubMed Central PMCID: PMC6707074.
Bandopadhayay P, Piccioni F, O'Rourke R, Ho P, Gonzalez EM, Buchan G, Qian K, Gionet G, Girard E, Coxon M, Rees MG, Brenan L, Dubois F, Shapira O, Greenwald NF, Pages M, Balboni Iniguez A, Paolella BR, Meng A, Sinai C, Roti G, Dharia NV, Creech A, Tanenbaum B, Khadka P, Tracy A, Tiv HL, Hong AL, Coy S, Rashid R, Lin JR, Cowley GS, Lam FC, Goodale A, Lee Y, Schoolcraft K, Vazquez F, Hahn WC, Tsherniak A, Bradner JE, Yaffe MB, Milde T, Pfister SM, Qi J, Schenone M, Carr SA, Ligon KL, Kieran MW, Santagata S, Olson JM, Gokhale PC, Jaffe JD, Root DE, Stegmaier K, Johannessen CM, Beroukhim R. Neuronal differentiation and cell-cycle programs mediate response to BET-bromodomain inhibition in MYC-driven medulloblastoma. Nat Commun. 2019 Jun 3;10(1):2400. doi: 10.1038/s41467-019-10307-9. PubMed PMID: 31160565; PubMed Central PMCID: PMC6546744.
Adelmant G, Garg BK, Tavares M, Card JD, Marto JA. Tandem Affinity Purification and Mass Spectrometry (TAP-MS) for the Analysis of Protein Complexes. Curr Protoc Protein Sci. 2019 Jun;96(1):e84. doi: 10.1002/cpps.84. Epub 2019 Feb 1. PubMed PMID: 30706993; PubMed Central PMCID: PMC6579647.
Gittleman H, Cioffi G, Chunduru P, Molinaro AM, Berger MS, Sloan AE, Barnholtz-Sloan JS. An independently validated nomogram for isocitrate dehydrogenase-wild-type glioblastoma patient survival. Neurooncol Adv. 2019 May-Dec;1(1):vdz007. doi: 10.1093/noajnl/vdz007. Epub 2019 May 30. PubMed PMID: 31608326; PubMed Central PMCID: PMC6777501.
Cui T, Bell EH, McElroy J, Becker AP, Gulati PM, Geurts M, Mladkova N, Gray A, Liu K, Yang L, Liu Z, Fleming JL, Haque SJ, Barnholtz-Sloan JS, Ligon KL, Beroukhim R, Robe P, Chakravarti A. miR-4516 predicts poor prognosis and functions as a novel oncogene via targeting PTPN14 in human glioblastoma. Oncogene. 2019 Apr;38(16):2923-2936. doi: 10.1038/s41388-018-0601-9. Epub 2018 Dec 17. PubMed PMID: 30559405; PubMed Central PMCID: PMC6497411.
Wen PY, Touat M, Alexander BM, Mellinghoff IK, Ramkissoon S, McCluskey CS, Pelton K, Haidar S, Basu SS, Gaffey SC, Brown LE, Martinez-Ledesma JE, Wu S, Kim J, Wei W, Park MA, Huse JT, Kuhn JG, Rinne ML, Colman H, Agar NYR, Omuro AM, DeAngelis LM, Gilbert MR, de Groot JF, Cloughesy TF, Chi AS, Roberts TM, Zhao JJ, Lee EQ, Nayak L, Heath JR, Horky LL, Batchelor TT, Beroukhim R, Chang SM, Ligon AH, Dunn IF, Koul D, Young GS, Prados MD, Reardon DA, Yung WKA, Ligon KL. Buparlisib in Patients With Recurrent Glioblastoma Harboring Phosphatidylinositol 3-Kinase Pathway Activation: An Open-Label, Multicenter, Multi-Arm, Phase II Trial. J Clin Oncol. 2019 Mar 20;37(9):741-750. doi: 10.1200/JCO.18.01207. Epub 2019 Feb 4. PubMed PMID: 30715997; PubMed Central PMCID: PMC6553812.
Miklja Z, Pasternak A, Stallard S, Nicolaides T, Kline-Nunnally C, Cole B, Beroukhim R, Bandopadhayay P, Chi S, Ramkissoon SH, Mullan B, Bruzek AK, Gauthier A, Garcia T, Atchison C, Marini B, Fouladi M, Parsons DW, Leary S, Mueller S, Ligon KL, Koschmann C. Molecular profiling and targeted therapy in pediatric gliomas: review and consensus recommendations. Neuro Oncol. 2019 Feb 26;. doi: 10.1093/neuonc/noz022. [Epub ahead of print] PubMed PMID: 30805642; PubMed Central PMCID: PMC6682212.
Ben-David U, Beroukhim R, Golub TR. Genomic evolution of cancer models: perils and opportunities. Nat Rev Cancer. 2019 Feb;19(2):97-109. doi: 10.1038/s41568-018-0095-3. Review. PubMed PMID: 30578414; PubMed Central PMCID: PMC6493335.
Holst F, Werner HMJ, Mjøs S, Hoivik EA, Kusonmano K, Wik E, Berg A, Birkeland E, Gibson WJ, Halle MK, Trovik J, Cherniack AD, Kalland KH, Mills GB, Singer CF, Krakstad C, Beroukhim R, Salvesen HB. PIK3CA Amplification Associates with Aggressive Phenotype but Not Markers of AKT-MTOR Signaling in Endometrial Carcinoma. Clin Cancer Res. 2019 Jan 1;25(1):334-345. doi: 10.1158/1078-0432.CCR-18-0452. Epub 2018 Nov 15. PubMed PMID: 30442683; PubMed Central PMCID: PMC6384094.
Iniguez AB, Alexe G, Wang EJ, Roti G, Patel S, Chen L, Kitara S, Conway A, Robichaud AL, Stolte B, Bandopadhayay P, Goodale A, Pantel S, Lee Y, Cheff DM, Hall MD, Guha R, Davis MI, Menard M, Nasholm N, Weiss WA, Qi J, Beroukhim R, Piccioni F, Johannessen C, Stegmaier K. Resistance to Epigenetic-Targeted Therapy Engenders Tumor Cell Vulnerabilities Associated with Enhancer Remodeling. Cancer Cell. 2018 Dec 10;34(6):922-938.e7. doi: 10.1016/j.ccell.2018.11.005. PubMed PMID: 30537514; PubMed Central PMCID: PMC6352909.
Corces MR, Granja JM, Shams S, Louie BH, Seoane JA, Zhou W, Silva TC, Groeneveld C, Wong CK, Cho SW, Satpathy AT, Mumbach MR, Hoadley KA, Robertson AG, Sheffield NC, Felau I, Castro MAA, Berman BP, Staudt LM, Zenklusen JC, Laird PW, Curtis C, Greenleaf WJ, Chang HY. The chromatin accessibility landscape of primary human cancers. Science. 2018 Oct 26;362(6413). doi: 10.1126/science.aav1898. PubMed PMID: 30361341; PubMed Central PMCID: PMC6408149.
Forget MA, Haymaker C, Hess KR, Meng YJ, Creasy C, Karpinets T, Fulbright OJ, Roszik J, Woodman SE, Kim YU, Sakellariou-Thompson D, Bhatta A, Wahl A, Flores E, Thorsen ST, Tavera RJ, Ramachandran R, Gonzalez AM, Toth CL, Wardell S, Mansaray R, Patel V, Carpio DJ, Vaughn C, Farinas CM, Velasquez PG, Hwu WJ, Patel SP, Davies MA, Diab A, Glitza IC, Tawbi H, Wong MK, Cain S, Ross MI, Lee JE, Gershenwald JE, Lucci A, Royal R, Cormier JN, Wargo JA, Radvanyi LG, Torres-Cabala CA, Beroukhim R, Hwu P, Amaria RN, Bernatchez C. Prospective Analysis of Adoptive TIL Therapy in Patients with Metastatic Melanoma: Response, Impact of Anti-CTLA4, and Biomarkers to Predict Clinical Outcome. Clin Cancer Res. 2018 Sep 15;24(18):4416-4428. doi: 10.1158/1078-0432.CCR-17-3649. Epub 2018 May 30. PubMed PMID: 29848573; PubMed Central PMCID: PMC6139043.
Touat M, Gratieux J, Condette Auliac S, Sejean K, Aldea S, Savatovsky J, Perkins G, Blons H, Ligon KL, Idbaih A, Hollebecque A, Gimenez-Roqueplo AP, Laurent-Puig P, Sanson M, Villa C, Di Stefano AL. Vemurafenib and cobimetinib overcome resistance to vemurafenib in BRAF-mutant ganglioglioma. Neurology. 2018 Sep 11;91(11):523-525. doi: 10.1212/WNL.0000000000006171. Epub 2018 Aug 17. PubMed PMID: 30120137.
Ben-David U, Siranosian B, Ha G, Tang H, Oren Y, Hinohara K, Strathdee CA, Dempster J, Lyons NJ, Burns R, Nag A, Kugener G, Cimini B, Tsvetkov P, Maruvka YE, O'Rourke R, Garrity A, Tubelli AA, Bandopadhayay P, Tsherniak A, Vazquez F, Wong B, Birger C, Ghandi M, Thorner AR, Bittker JA, Meyerson M, Getz G, Beroukhim R, Golub TR. Genetic and transcriptional evolution alters cancer cell line drug response. Nature. 2018 Aug;560(7718):325-330. doi: 10.1038/s41586-018-0409-3. Epub 2018 Aug 8. PubMed PMID: 30089904; PubMed Central PMCID: PMC6522222.
Viswanathan SR, Ha G, Hoff AM, Wala JA, Carrot-Zhang J, Whelan CW, Haradhvala NJ, Freeman SS, Reed SC, Rhoades J, Polak P, Cipicchio M, Wankowicz SA, Wong A, Kamath T, Zhang Z, Gydush GJ, Rotem D, Love JC, Getz G, Gabriel S, Zhang CZ, Dehm SM, Nelson PS, Van Allen EM, Choudhury AD, Adalsteinsson VA, Beroukhim R, Taplin ME, Meyerson M. Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing. Cell. 2018 Jul 12;174(2):433-447.e19. doi: 10.1016/j.cell.2018.05.036. Epub 2018 Jun 18. PubMed PMID: 29909985; PubMed Central PMCID: PMC6046279.
Wong GS, Zhou J, Liu JB, Wu Z, Xu X, Li T, Xu D, Schumacher SE, Puschhof J, McFarland J, Zou C, Dulak A, Henderson L, Xu P, O'Day E, Rendak R, Liao WL, Cecchi F, Hembrough T, Schwartz S, Szeto C, Rustgi AK, Wong KK, Diehl JA, Jensen K, Graziano F, Ruzzo A, Fereshetian S, Mertins P, Carr SA, Beroukhim R, Nakamura K, Oki E, Watanabe M, Baba H, Imamura Y, Catenacci D, Bass AJ. Targeting wild-type KRAS-amplified gastroesophageal cancer through combined MEK and SHP2 inhibition. Nat Med. 2018 Jul;24(7):968-977. doi: 10.1038/s41591-018-0022-x. Epub 2018 May 28. PubMed PMID: 29808010; PubMed Central PMCID: PMC6039276.
Ricketts CJ, De Cubas AA, Fan H, Smith CC, Lang M, Reznik E, Bowlby R, Gibb EA, Akbani R, Beroukhim R, Bottaro DP, Choueiri TK, Gibbs RA, Godwin AK, Haake S, Hakimi AA, Henske EP, Hsieh JJ, Ho TH, Kanchi RS, Krishnan B, Kwiatkowski DJ, Lui W, Merino MJ, Mills GB, Myers J, Nickerson ML, Reuter VE, Schmidt LS, Shelley CS, Shen H, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Vincent BG, Vocke CD, Wheeler DA, Yang L, Kim WY, Robertson AG, Spellman PT, Rathmell WK, Linehan WM. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Rep. 2018 Jun 19;23(12):3698. doi: 10.1016/j.celrep.2018.06.032. PubMed PMID: 29925010; NIHMSID:NIHMS1602561.
Glioma through the looking GLASS: molecular evolution of diffuse gliomas and the Glioma Longitudinal Analysis Consortium. Neuro Oncol. 2018 Jun 18;20(7):873-884. doi: 10.1093/neuonc/noy020. Review. PubMed PMID: 29432615; PubMed Central PMCID: PMC6280138.
Shen H, Shih J, Hollern DP, Wang L, Bowlby R, Tickoo SK, Thorsson V, Mungall AJ, Newton Y, Hegde AM, Armenia J, Sánchez-Vega F, Pluta J, Pyle LC, Mehra R, Reuter VE, Godoy G, Jones J, Shelley CS, Feldman DR, Vidal DO, Lessel D, Kulis T, Cárcano FM, Leraas KM, Lichtenberg TM, Brooks D, Cherniack AD, Cho J, Heiman DI, Kasaian K, Liu M, Noble MS, Xi L, Zhang H, Zhou W, ZenKlusen JC, Hutter CM, Felau I, Zhang J, Schultz N, Getz G, Meyerson M, Stuart JM, Akbani R, Wheeler DA, Laird PW, Nathanson KL, Cortessis VK, Hoadley KA. Integrated Molecular Characterization of Testicular Germ Cell Tumors. Cell Rep. 2018 Jun 12;23(11):3392-3406. doi: 10.1016/j.celrep.2018.05.039. PubMed PMID: 29898407; PubMed Central PMCID: PMC6075738.
Konieczkowski DJ, Johannessen CM, Garraway LA. A Convergence-Based Framework for Cancer Drug Resistance. Cancer Cell. 2018 May 14;33(5):801-815. doi: 10.1016/j.ccell.2018.03.025. Review. PubMed PMID: 29763622; PubMed Central PMCID: PMC5957297.
Chapuy B, Stewart C, Dunford AJ, Kim J, Kamburov A, Redd RA, Lawrence MS, Roemer MGM, Li AJ, Ziepert M, Staiger AM, Wala JA, Ducar MD, Leshchiner I, Rheinbay E, Taylor-Weiner A, Coughlin CA, Hess JM, Pedamallu CS, Livitz D, Rosebrock D, Rosenberg M, Tracy AA, Horn H, van Hummelen P, Feldman AL, Link BK, Novak AJ, Cerhan JR, Habermann TM, Siebert R, Rosenwald A, Thorner AR, Meyerson ML, Golub TR, Beroukhim R, Wulf GG, Ott G, Rodig SJ, Monti S, Neuberg DS, Loeffler M, Pfreundschuh M, Trümper L, Getz G, Shipp MA. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018 May;24(5):679-690. doi: 10.1038/s41591-018-0016-8. Epub 2018 Apr 30. PubMed PMID: 29713087; PubMed Central PMCID: PMC6613387.
Filbin MG, Tirosh I, Hovestadt V, Shaw ML, Escalante LE, Mathewson ND, Neftel C, Frank N, Pelton K, Hebert CM, Haberler C, Yizhak K, Gojo J, Egervari K, Mount C, van Galen P, Bonal DM, Nguyen QD, Beck A, Sinai C, Czech T, Dorfer C, Goumnerova L, Lavarino C, Carcaboso AM, Mora J, Mylvaganam R, Luo CC, Peyrl A, Popović M, Azizi A, Batchelor TT, Frosch MP, Martinez-Lage M, Kieran MW, Bandopadhayay P, Beroukhim R, Fritsch G, Getz G, Rozenblatt-Rosen O, Wucherpfennig KW, Louis DN, Monje M, Slavc I, Ligon KL, Golub TR, Regev A, Bernstein BE, Suvà ML. Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq. Science. 2018 Apr 20;360(6386):331-335. doi: 10.1126/science.aao4750. PubMed PMID: 29674595; PubMed Central PMCID: PMC5949869.
Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Mokrab Y, Newman AM, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CS, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich I. The Immune Landscape of Cancer. Immunity. 2018 Apr 17;48(4):812-830.e14. doi: 10.1016/j.immuni.2018.03.023. Epub 2018 Apr 5. PubMed PMID: 29628290; PubMed Central PMCID: PMC5982584.
Liu Y, Sethi NS, Hinoue T, Schneider BG, Cherniack AD, Sanchez-Vega F, Seoane JA, Farshidfar F, Bowlby R, Islam M, Kim J, Chatila W, Akbani R, Kanchi RS, Rabkin CS, Willis JE, Wang KK, McCall SJ, Mishra L, Ojesina AI, Bullman S, Pedamallu CS, Lazar AJ, Sakai R, Thorsson V, Bass AJ, Laird PW. Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas. Cancer Cell. 2018 Apr 9;33(4):721-735.e8. doi: 10.1016/j.ccell.2018.03.010. Epub 2018 Apr 2. PubMed PMID: 29622466; PubMed Central PMCID: PMC5966039.
Taylor AM, Shih J, Ha G, Gao GF, Zhang X, Berger AC, Schumacher SE, Wang C, Hu H, Liu J, Lazar AJ, Cherniack AD, Beroukhim R, Meyerson M. Genomic and Functional Approaches to Understanding Cancer Aneuploidy. Cancer Cell. 2018 Apr 9;33(4):676-689.e3. doi: 10.1016/j.ccell.2018.03.007. Epub 2018 Apr 2. PubMed PMID: 29622463; PubMed Central PMCID: PMC6028190.
Berger AC, Korkut A, Kanchi RS, Hegde AM, Lenoir W, Liu W, Liu Y, Fan H, Shen H, Ravikumar V, Rao A, Schultz A, Li X, Sumazin P, Williams C, Mestdagh P, Gunaratne PH, Yau C, Bowlby R, Robertson AG, Tiezzi DG, Wang C, Cherniack AD, Godwin AK, Kuderer NM, Rader JS, Zuna RE, Sood AK, Lazar AJ, Ojesina AI, Adebamowo C, Adebamowo SN, Baggerly KA, Chen TW, Chiu HS, Lefever S, Liu L, MacKenzie K, Orsulic S, Roszik J, Shelley CS, Song Q, Vellano CP, Wentzensen N, Weinstein JN, Mills GB, Levine DA, Akbani R. A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. Cancer Cell. 2018 Apr 9;33(4):690-705.e9. doi: 10.1016/j.ccell.2018.03.014. Epub 2018 Apr 2. PubMed PMID: 29622464; PubMed Central PMCID: PMC5959730.
Wang Z, Yang B, Zhang M, Guo W, Wu Z, Wang Y, Jia L, Li S, Xie W, Yang D. lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer. Cancer Cell. 2018 Apr 9;33(4):706-720.e9. doi: 10.1016/j.ccell.2018.03.006. Epub 2018 Apr 2. PubMed PMID: 29622465; PubMed Central PMCID: PMC6143179.
Hoadley KA, Yau C, Hinoue T, Wolf DM, Lazar AJ, Drill E, Shen R, Taylor AM, Cherniack AD, Thorsson V, Akbani R, Bowlby R, Wong CK, Wiznerowicz M, Sanchez-Vega F, Robertson AG, Schneider BG, Lawrence MS, Noushmehr H, Malta TM, Stuart JM, Benz CC, Laird PW. Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell. 2018 Apr 5;173(2):291-304.e6. doi: 10.1016/j.cell.2018.03.022. PubMed PMID: 29625048; PubMed Central PMCID: PMC5957518.
Chen H, Li C, Peng X, Zhou Z, Weinstein JN, Liang H. A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples. Cell. 2018 Apr 5;173(2):386-399.e12. doi: 10.1016/j.cell.2018.03.027. PubMed PMID: 29625054; PubMed Central PMCID: PMC5890960.
Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim TB, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ, Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F, Ding L. Pathogenic Germline Variants in 10,389 Adult Cancers. Cell. 2018 Apr 5;173(2):355-370.e14. doi: 10.1016/j.cell.2018.03.039. PubMed PMID: 29625052; PubMed Central PMCID: PMC5949147.
Malta TM, Sokolov A, Gentles AJ, Burzykowski T, Poisson L, Weinstein JN, Kamińska B, Huelsken J, Omberg L, Gevaert O, Colaprico A, Czerwińska P, Mazurek S, Mishra L, Heyn H, Krasnitz A, Godwin AK, Lazar AJ, Stuart JM, Hoadley KA, Laird PW, Noushmehr H, Wiznerowicz M. Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation. Cell. 2018 Apr 5;173(2):338-354.e15. doi: 10.1016/j.cell.2018.03.034. PubMed PMID: 29625051; PubMed Central PMCID: PMC5902191.
Ding L, Bailey MH, Porta-Pardo E, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, Huang KL, Tokheim C, Cortés-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, Olsen C, Kim J, Taylor AM, Cherniack AD, Akbani R, Suphavilai C, Nagarajan N, Stuart JM, Mills GB, Wyczalkowski MA, Vincent BG, Hutter CM, Zenklusen JC, Hoadley KA, Wendl MC, Shmulevich L, Lazar AJ, Wheeler DA, Getz G. Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. Cell. 2018 Apr 5;173(2):305-320.e10. doi: 10.1016/j.cell.2018.03.033. PubMed PMID: 29625049; PubMed Central PMCID: PMC5916814.
Liu J, Lichtenberg T, Hoadley KA, Poisson LM, Lazar AJ, Cherniack AD, Kovatich AJ, Benz CC, Levine DA, Lee AV, Omberg L, Wolf DM, Shriver CD, Thorsson V, Hu H. An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics. Cell. 2018 Apr 5;173(2):400-416.e11. doi: 10.1016/j.cell.2018.02.052. PubMed PMID: 29625055; PubMed Central PMCID: PMC6066282.
Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S, Chakravarty D, Daian F, Gao Q, Bailey MH, Liang WW, Foltz SM, Shmulevich I, Ding L, Heins Z, Ochoa A, Gross B, Gao J, Zhang H, Kundra R, Kandoth C, Bahceci I, Dervishi L, Dogrusoz U, Zhou W, Shen H, Laird PW, Way GP, Greene CS, Liang H, Xiao Y, Wang C, Iavarone A, Berger AH, Bivona TG, Lazar AJ, Hammer GD, Giordano T, Kwong LN, McArthur G, Huang C, Tward AD, Frederick MJ, McCormick F, Meyerson M, Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell. 2018 Apr 5;173(2):321-337.e10. doi: 10.1016/j.cell.2018.03.035. PubMed PMID: 29625050; PubMed Central PMCID: PMC6070353.
Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng PK, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H, Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 2018 Apr 5;173(2):371-385.e18. doi: 10.1016/j.cell.2018.02.060. PubMed PMID: 29625053; PubMed Central PMCID: PMC6029450.
Way GP, Sanchez-Vega F, La K, Armenia J, Chatila WK, Luna A, Sander C, Cherniack AD, Mina M, Ciriello G, Schultz N, Sanchez Y, Greene CS. Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. Cell Rep. 2018 Apr 3;23(1):172-180.e3. doi: 10.1016/j.celrep.2018.03.046. PubMed PMID: 29617658; PubMed Central PMCID: PMC5918694.
Peng X, Chen Z, Farshidfar F, Xu X, Lorenzi PL, Wang Y, Cheng F, Tan L, Mojumdar K, Du D, Ge Z, Li J, Thomas GV, Birsoy K, Liu L, Zhang H, Zhao Z, Marchand C, Weinstein JN, Bathe OF, Liang H. Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers. Cell Rep. 2018 Apr 3;23(1):255-269.e4. doi: 10.1016/j.celrep.2018.03.077. PubMed PMID: 29617665; PubMed Central PMCID: PMC5916795.
Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S, Pedamallu CS, Ojesina AI, Sadeghi S, Mungall KL, Robertson AG, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW, Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER, Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK, Stuart JM, Laird PW, Hoadley KA, Weinstein JN, Peto M, Pickering CR, Chen Z, Van Waes C. Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell Rep. 2018 Apr 3;23(1):194-212.e6. doi: 10.1016/j.celrep.2018.03.063. PubMed PMID: 29617660; PubMed Central PMCID: PMC6002769.
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