Publications

Selected Publications supported by the Biostatistics and Informatics Shared Resource.

Gunasekara CJ, Scott CA, Laritsky E, Baker MS, MacKay H, Duryea JD, Kessler NJ, Hellenthal G, Wood AC, Hodges KR, Gandhi M, Hair AB, Silver MJ, Moore SE, Prentice AM, Li Y, Chen R, Coarfa C, Waterland RA. A genomic atlas of systemic interindividual epigenetic variation in humans. Genome Biol. 2019 Jun 3;20(1):105.

Chen F, Zhang Y, Varambally S, Creighton CJ. Molecular Correlates of Metastasis by Systematic Pan-Cancer Analysis Across The Cancer Genome Atlas. Mol Cancer Res. 2019 Feb;17(2):476-487.

Vantaku V, Dong J, Ambati CR, Perera D, Donepudi SR, Amara CS, Putluri V, Ravi SS, Robertson MJ, Piyarathna DWB, Villanueva M, von Rundstedt FC, Karanam B, Ballester LY, Terris MK, Bollag RJ, Lerner SP, Apolo AB, Villanueva H, Lee M, Sikora AG, Lotan Y, Sreekumar A, Coarfa C, Putluri N. Multi-omics Integration Analysis Robustly Predicts High-Grade Patient Survival and Identifies CPT1B Effect on Fatty Acid Metabolism in Bladder Cancer. Clin Cancer Res. 2019 Mar 7

Yuan Y, Lee JJ, Hilsenbeck SG. Model-Assisted Designs for Early Phase Clinical Trials: Simplicity Meets Superiority. JCO Precis Oncol 2019;In Press

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 Jul 10;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 May 1;24(9):2182-2193.

Dasgupta S, Rajapakshe K, Zhu B, Nikolai BC, Yi P, Putluri N, Choi JM, Jung SY, Coarfa C, Westbrook TF, Zhang XH, Foulds CE, Tsai SY, Tsai MJ, O'Malley BW. Metabolic enzyme PFKFB4 activates transcriptional coactivator SRC-3 to drive breast cancer. Nature. 2018 Apr;556(7700):249-254.

Abbas HA, Bui NHB, Rajapakshe K, Wong J, Gunaratne P, Tsai KY, Coarfa C, Flores ER. Distinct TP63 Isoform-Driven Transcriptional Signatures Predict Tumor Progression and Clinical Outcomes. Cancer Res. 2018 Jan 15;78(2):451-462.

Riley AA, Watson M, Smith C, Guffey D, Minard CG, Currier H, Akcan Arikan A. Pediatric continuous renal replacement therapy: have practice changes changed outcomes? A large single-center ten-year retrospective evaluation. BMC Nephrol 2018;19(1):268 doi 10.1186/s12882-018-1068-1, PMID 30340544, PMC6194595.

Rimawi MF, De Angelis C, Contreras A, Pareja F, Geyer FC, Burke KA, Herrera S, Wang T, Mayer IA, Forero A, Nanda R, Goetz MP, Chang JC, Krop IE, Wolff AC, Pavlick AC, Fuqua SAW, Gutierrez C, Hilsenbeck SG, Li MM, Weigelt B, Reis-Filho JS, Kent Osborne C, Schiff R. Low PTEN levels and PIK3CA mutations predict resistance to neoadjuvant lapatinib and trastuzumab without chemotherapy in patients with HER2 over-expressing breast cancer. Breast Cancer Res Treat 2018;167(3):731-40 doi 10.1007/s10549-017-4533-9, PMID 29110152, PMC5821069.

Satterfield L, Shuck R, Kurenbekova L, Allen-Rhoades W, Edwards D, Huang S, Rajapakshe K, Coarfa C, Donehower LA, Yustein JT. miR-130b directly targets ARHGAP1 to drive activation of a metastatic CDC42-PAK1-AP1 positive feedback loop in Ewing sarcoma. Int J Cancer. 2017 Nov 15;141(10):2062-2075

Geng C, Kaochar S, Li M, Rajapakshe K, Fiskus W, Dong J, Foley C, Dong B, Zhang L, Kwon OJ, Shah SS, Bolaki M, Xin L, Ittmann M, O'Malley BW, Coarfa C, Mitsiades N. SPOP regulates prostate epithelial cell proliferation and promotes ubiquitination and turnover of c-MYC oncoprotein. Oncogene. 2017 Aug 17;36(33):4767-4777

Chen F, Zhang Y, Bossé D, Lalani AA, Hakimi AA, Hsieh JJ, Choueiri TK, Gibbons DL, Ittmann M, Creighton CJ. Pan-urologic cancer genomic subtypes that transcend tissue of origin. Nat Commun. 2017 Aug 4;8(1):199.

Zhang Y, Kwok-Shing Ng P, Kucherlapati M, Chen F, Liu Y, Tsang YH, de Velasco G, Jeong KJ, Akbani R, Hadjipanayis A, Pantazi A, Bristow CA, Lee E, Mahadeshwar HS, Tang J, Zhang J, Yang L, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Westbrook TF, Shelley CS, Choueiri TK, Ittmann M, Van Waes C, Weinstein JN, Liang H, Henske EP, Godwin AK, Park PJ, Kucherlapati R, Scott KL, Mills GB, Kwiatkowski DJ, Creighton CJ. A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations. Cancer Cell. 2017 Jun 12;31(6):820-832.e3.

Mosse YP, Voss SD, Lim MS, Rolland D, Minard CG, Fox E, Adamson P, Wilner K, Blaney SM, Weigel BJ. Targeting ALK With Crizotinib in Pediatric Anaplastic Large Cell Lymphoma and Inflammatory Myofibroblastic Tumor: A Children's Oncology Group Study. J Clin Oncol 2017;35(28):3215-21 doi 10.1200/JCO.2017.73.4830, PMID 28787259, PMC5617123.

Xu X, De Angelis C, Burke KA, Nardone A, Hu H, Qin L, Veeraraghavan J, Sethunath V, Heiser LM, Wang N, Ng CKY, Chen ES, Renwick A, Wang T, Nanda S, Shea M, Mitchell T, Rajendran M, Waters I, Zabransky DJ, Scott KL, Gutierrez C, Nagi C, Geyer FC, Chamness GC, Park BH, Shaw CA, Hilsenbeck SG, Rimawi MF, Gray JW, Weigelt B, Reis-Filho JS, Osborne CK, Schiff R. HER2 Reactivation through Acquisition of the HER2 L755S Mutation as a Mechanism of Acquired Resistance to HER2-targeted Therapy in HER2(+) Breast Cancer. Clin Cancer Res 2017;23(17):5123-34 doi 10.1158/1078-0432.CCR-16-2191, PMID 28487443