Publications

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2023
Creighton CJ. Gene Expression Profiles in Cancers and Their Therapeutic Implications. Cancer J. 2023 ;29(1):9-14.
2021
Micklethwaite KP, Gowrishankar K, Gloss BS, Li Z, Street JA, Moezzi L, Mach MA, Sutrave G, Clancy LE, Bishop DC, H Y Louie R, Cai C, Foox J, MacKay M, Sedlazeck FJ, Blombery P, Mason CE, Luciani F, Gottlieb DJ, Blyth E. Investigation of product-derived lymphoma following infusion of piggyBac-modified CD19 chimeric antigen receptor T cells. Blood. 2021 ;138(16):1391-1405.
Monsivais D, Vasquez YM, Chen F, Zhang Y, Chandrashekar DS, Faver JC, Masand RP, Scheurer ME, Varambally S, Matzuk MM, Creighton CJ. Mass-spectrometry-based proteomic correlates of grade and stage reveal pathways and kinases associated with aggressive human cancers. Oncogene. 2021 ;40(11):2081-2095.
Maniakas A, Henderson YC, Hei H, Peng S, Chen Y, Jiang Y, Ji S, Cardenas M, Chiu Y, Bell D, Williams MD, Hofmann M-C, Scherer SE, Wheeler DA, Busaidy NL, Dadu R, Wang JR, Cabanillas ME, Zafereo M, Johnson FM, Lai SY. Novel Anaplastic Thyroid Cancer PDXs and Cell Lines: Expanding Preclinical Models of Genetic Diversity. J Clin Endocrinol Metab. 2021 ;106(11):e4652-e4665.
Zhang Y, Chen F, Donehower LA, Scheurer ME, Creighton CJ. A pediatric brain tumor atlas of genes deregulated by somatic genomic rearrangement. Nat Commun. 2021 ;12(1):937.
Cheng J, Zhou J, Fu S, Fu J, Zhou B, Chen H, Fu J, Wei C. Prostate adenocarcinoma and COVID-19: The possible impacts of TMPRSS2 expressions in susceptibility to SARS-CoV-2. J Cell Mol Med. 2021 ;25(8):4157-4165.
Gou X, Anurag M, Lei JT, Kim B-J, Singh P, Seker S, Fandino D, Han A, Rehman S, Hu J, Korchina V, Doddapaneni H, Dobrolecki LE, Mitsiades N, Lewis MT, Welm AL, Li S, Lee AV, Robinson DR, Foulds CE, Ellis MJ. Transcriptional Reprogramming Differentiates Active from Inactive ESR1 Fusions in Endocrine Therapy-Refractory Metastatic Breast Cancer. Cancer Res. 2021 ;81(24):6259-6272.
2020
Rheinbay E, Nielsen MMuhlig, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RIstrup, 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 CWing Yiu, 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, Van Lehmann K-, Li Y, Liu EMinwei, 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 C-Z, 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, Lopez-Bigas N, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JSkou, Getz G. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 2020 ;578(7793):102-111.
Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A, Creighton CJ. High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations. Nat Commun. 2020 ;11(1):736.
Saengboonmee C, Phoomak C, Supabphol S, Covington KR, Hampton O, Wongkham C, Gibbs RA, Umezawa K, Seubwai W, Gingras M-C, Wongkham S. NF-κB and STAT3 co-operation enhances high glucose induced aggressiveness of cholangiocarcinoma cells. Life Sci. 2020 ;262:118548.
Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JSkou, Rubin MA, Wheeler DA, Brunak S, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, S Sahinalp C, Valencia A, Reimand J, Stuart JM, Raphael BJ. Pathway and network analysis of more than 2500 whole cancer genomes. Nat Commun. 2020 ;11(1):729.
Koneru B, Lopez G, Farooqi A, Conkrite KL, Nguyen TH, Macha SJ, Modi A, Rokita JLynne, Urias E, Hindle A, Davidson H, McCoy K, Nance J, Yazdani V, Irwin MS, Yang S, Wheeler DA, Maris JM, Diskin SJ, C Reynolds P. Telomere Maintenance Mechanisms Define Clinical Outcome in High-Risk Neuroblastoma. Cancer Res. 2020 ;80(12):2663-2675.
2019
Donehower LA, Soussi T, Korkut A, Liu Y, Schultz A, Cardenas M, Li X, Babur O, Hsu T-K, Lichtarge O, Weinstein JN, Akbani R, Wheeler DA. Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas. Cell Rep. 2019 ;28(5):1370-1384.e5.
Chen F, Chandrashekar DS, Varambally S, Creighton CJ. Pan-cancer molecular subtypes revealed by mass-spectrometry-based proteomic characterization of more than 500 human cancers. Nat Commun. 2019 ;10(1):5679.
2018
Creighton CJ. The clinical applications of The Cancer Genome Atlas project for bladder cancer. Expert Rev Anticancer Ther. 2018 ;18(10):973-980.
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, A Robertson G, 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 T-W, Chiu H-S, Lefever S, Liu L, MacKenzie K, Orsulic S, Roszik J, Shelley CSimon, 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 ;33(4):690-705.e9.
Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LAverett, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, D Hayes N, Bullman S, Pedamallu CSekhar, Ojesina AI, Sadeghi S, Mungall KL, A Robertson G, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu H-S, Chen T-W, 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 ;23(1):194-212.e6.
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 ;23(11):3392-3406.
Creighton CJ. Making Use of Cancer Genomic Databases. Curr Protoc Mol Biol. 2018 ;121:19.14.1-19.14.13.
Zhang Y, Yang L, Kucherlapati M, Chen F, Hadjipanayis A, Pantazi A, Bristow CA, Lee EA, Mahadeshwar HS, Tang J, Zhang J, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Li W, Park PJ, Kucherlapati R, Creighton CJ. A Pan-Cancer Compendium of Genes Deregulated by Somatic Genomic Rearrangement across More Than 1,400 Cases. Cell Rep. 2018 ;24(2):515-527.
Chen F, Zhang Y, Gibbons DL, Deneen B, Kwiatkowski DJ, Ittmann M, Creighton CJ. Pan-Cancer Molecular Classes Transcending Tumor Lineage Across 32 Cancer Types, Multiple Data Platforms, and over 10,000 Cases. Clin Cancer Res. 2018 ;24(9):2182-2193.
2017
Sumazin P, Chen Y, Treviño LR, Sarabia SF, Hampton OA, Patel K, Mistretta T-A, Zorman B, Thompson P, Heczey A, Comerford S, Wheeler DA, Chintagumpala M, Meyers R, Rakheja D, Finegold MJ, Tomlinson G, D Parsons W, López-Terrada D. Genomic analysis of hepatoblastoma identifies distinct molecular and prognostic subgroups. Hepatology. 2017 ;65(1):104-121.
Farshidfar F, Zheng S, Gingras M-C, Newton Y, Shih J, A Robertson G, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu C-C, Shinbrot E, Stransky N, Hegde A, Yang JDong, Reznik E, Sadeghi S, Pedamallu CSekhar, Ojesina AI, Hess JM, J Auman T, Rhie SK, Bowlby R, Borad MJ, Zhu AX, Stuart JM, Sander C, Akbani R, Cherniack AD, Deshpande V, Mounajjed T, Foo WChin, Torbenson MS, Kleiner DE, Laird PW, Wheeler DA, McRee AJ, Bathe OF, Andersen JB, Bardeesy N, Roberts LR, Kwong LN. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles. Cell Rep. 2017 ;18(11):2780-2794.
Nargund AM, Pham CG, Dong Y, Wang PI, Osmangeyoglu HU, Xie Y, Aras O, Han S, Oyama T, Takeda S, Ray CE, Dong Z, Berge M, A Hakimi A, Monette S, Lekaye CL, Koutcher JA, Leslie CS, Creighton CJ, Weinhold N, Lee W, Tickoo SK, Wang Z, Cheng EH, Hsieh JJ. The SWI/SNF Protein PBRM1 Restrains VHL-Loss-Driven Clear Cell Renal Cell Carcinoma. Cell Rep. 2017 ;18(12):2893-2906.
Chandrashekar DS, Bashel B, Balasubramanya SAkshaya Ho, Creighton CJ, Ponce-Rodriguez I, Chakravarthi BVSK, Varambally S. UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and Survival Analyses. Neoplasia. 2017 ;19(8):649-658.