Hoadley Publications - Hoadley Lab

Kothiyal P, Eley G, Ilangovan H, Hoadley KA, Elgart SR, Mao XW, Eslami P. A multi-omics longitudinal study of the murine retinal response to chronic low-dose irradiation and simulated microgravity. Sci Rep. 2022 Oct 7;12(1):1-4. 16825. doi:10-1038/s41598-022-19360-9. PMID: 36207342.

Walens A, Van Alsten SC, Olsson LT, Smith MA, Lockhart A, Gao X, Hamilton AM, Kirk EL, Love MI, Gupta GP, Perou CM, Vaziri C, Hoadley KA, Troester MA. RNA-based classification of homologous recombination deficiency in racially-diverse patients with breast cancer. Cancer Epidemiol Biomarkers Prev. 2022 Sep 21:EPI-22-0590. doi:10.1158/1055-9965.EPI-22-0590. PMID: 36129803.

Smith MA, Van Alsten SC, Walens A, Damrauer JS, Maduekwe UN, Broaddus RR, Love MI, Troester MA, and Hoadley KA. DNA damage repair classifier defines distinct groups in hepatocellular carcinoma. Cancers. 2022 Sep 1;14(17):4282. doi: 10.3390/cancers14174282. PMID: 36077818

Chambwe N, Sayaman RW, Hu D, Huntsman S; Cancer Genome Analysis Network, Kemal A, Caesar-Johnson S, Zenklusen JC, Ziv E, Beroukhim R, Cherniack AD. Analysis of germline-driven ancestry-associated gene expression in cancers. STAR Protoc. 2022 Jul 31;3(3):101586. doi: 10.1016/j.xpro.2022.101586. eCollection 2022 Sep 16. PMID: 35942349

Hamilton AM, Hurson AN, Olsson LT, Walens A, Nsonwu-Farley J, Kirk EL, Abdou Y, Downs-Canner SM, Serody JS, Perou CM, Calhoun BC, Troester MA, Hoadley KA. The landscape of immune microenvironments in racially-diverse breast cancer patients. Cancer Epidemiol Biomarkers Prev. 2022 Jul 1;31(7):1341-1350. Epub 2022 Apr 18. doi: 10.1158/1055-9965.EPI-21-1312. PMID: 35437570

Gadd S, Huff V, Skol AD, Renfro LA, Fernandez CV, Mullen EA, Jones CD, Hoadley KA, Yap KL, Ramirez NC, Aris S, Phung QH, Perlman EJ. Genetic changes associated with relapse in favorable histology Wilms tumor: A Children’s Oncology Group AREN03B2 study. Cell Rep Med. 2022 June 21;3(6):100644. doi: 10.1016/j.xcrm.2022/100644. Epub 2022 May 25. PMID: 35617957

Samorodnitsky S, Hoadley KA, Lock EF. A hierarchical spike-and-slab model for pan-cancer survival using pan-omic data. BMC Bioinformatics. 2022 June 17;23(1):235. doi: 10.1186/s12859-022-04770-3. PMID: 35710340

Hurson AN, Abubakar M, Hamilton AM, Conway K, Hoadley KA, Love MI, Olshan AF, Perou CM, Garcia-Closas M, Troester MA. Prognostic significance of RNA-based TP53 pathway function among estrogen receptor positive and negative breast cancer cases. NPJ breast cancer. 2022 Jun 14;8(1):74. doi:10.1038/s41523-022-00437-7. PMID: 35701440

Fassler DJ, Torre-Healy LA, Gupta R, Hamilton AM, Kobayashi S, Van Alsten SC, Zhang Y, Kurc T, Moffitt RA, Troester MA, Hoadley KA, Saltz J. Spatial Characterization of Tumor-Infiltrating Lymphocytes and Breast Cancer Progression. Cancers. 2022 Apr 26;14(9):2148. doi: 10.3390/cancers14092148. PMID: 35565277

Shepherd JH, Ballman K, Polley MC, Campbell JD, Fan C, Selitsky S, Fernandez-Martinez A, Parker JS, Hoadley KA, Hu Z, Li Y, Soloway MG, Spears PA, Singh B, Tolaney SM, Somlo G, Port ER, Ma C, Kuzma C, Mamounas E, Golshan M, Bellon JR, Collyar D, Hahn OM, Hudis CA, Winer EP, Partridge A, Hyslop T, Carey LA, Perou CM, Sikov WM. CALGB 40603 (Alliance): Long-Term Outcomes and Genomic Correlates of Response and Survival After Neoadjuvant Chemotherapy With or Without Carboplatin and Bevacizumab in Triple-Negative Breast Cancer. J Clin Oncol. 2022 Apr 20;40(12):1323-1334. doi: 10.1200/JCO.21.01506. Epub 2022 Jan 19. PMID: 35044810

Jones GS, Hoadley KA, Benefield H, Olsson LT, Hamilton AM, Bhattacharya A, Kirk EL, Tipaldos HJ, Fleming JM, Williams KP, Love MI, Nichols HB, Olshan AF, Troester MA. Racial differences in breast cancer outcomes by hepatocyte growth factor pathway expression. Breast Cancer Res Treat. 2022 Apr;192(2):447-455. doi: 10.1007/s10549-021-06497-w. Epub 2022 Jan 16. PMID: 35034243

Lock EF, Park JY, and Hoadley KA. BIODIMENSIONAL LINKED MATRIX FACTORIZATION FOR PAN-OMICS PAN-CANCER ANALYSIS. Ann Appl Stat. 2022 Mar;16(1):193-215. doi: 10.1214/21-AOAS1495. Epub 2022 Mar 28. PMID: 35505906

Hurson AN, Abubakar M, Hamilton AM, Conway K, Hoadley KA, Love MI, Olshan AF, Perou CM, Garcia-Closas M, Troester MA. TP53 Pathway Function, Estrogen Receptor Status, and Breast Cancer Risk Factors in the Carolina Breast Cancer Study. Cancer Epidemiol Biomarkers Prev. 2022 Jan;31(1):124-131. doi: 10.1158/1055-9965.EPI-21-0661. Epub 2021 Nov 4. PMID: 34737209

Carrot-Zhang J, Han S, Zhou W, Damrauer JS, Kemal A; Cancer Genome Atlas Analysis Network, Cherniack AD, Beroukhim R. Analytical protocol to identify local ancestry-associated molecular features in cancer. STAR Protoc. 2021 Sep 20;2(4):100766. doi: 10.1016/j.xpro.2021.100766. eCollection 2021 Dec 17. PMID: 34585150

Thennavan A, Beca F, Xia Y, Recio SG, Allison K, Collins LC, Tse GM, Chen YY, Schnitt SJ, Hoadley KA, Beck A, Perou CM. Molecular analysis of TCGA breast cancer histologic types. Cell Genom. 2021 Dec 8;1(3):100067. doi: 10.1016/j.xgen.2021.100067. PMID: 35465400

Carmichael I, Calhoun BC, Hoadley KA, Troester MA, Geradts J, Couture HD, Olsson L, Perou CM, Niethammer M, Hannig J, Marron JS. JOINT AND INDIVIDUAL ANALYSIS OF BREAST CANCER HISTOLOGIC IMAGES AND GENOMIC COVARIATES. Ann Appl Stat. 2021 Dec;15(4):1697-1722. doi: 10.1214/20-aoas1433. Epub 2021 Dec 21. PMID: 35432688

Little P, Jo H, Hoyle A, Mazul A, Zhao X, Salazar AH, Farquhar D, Sheth S, Masood M, Hayward MC, Parker JS, Hoadley KA, Zevallos J, Hayes DN. UNMASC: tumor-only variant calling with unmatched normal controls. NAR Cancer. 2021 Oct 6;3(4):zcab040. doi: 10.1093/narca/zcab. eCollection 2021 Dec. PMID: 34632388

Damrauer JS*, Smith MA*, Walter V, Thennavan A, Mose LE, Selitsky SR, Hoadley KA. Genomic characterization of rare molecular subclasses of hepatocellular carcinoma. Commun Biol. 2021 Oct 4;4(1):1150. doi: 10.1038/s42003-021-02674-1. PMID: 34608257

Cao L, Huang C, Cui Zhou D, Hu Y, Lih TM, Savage SR, Krug K, Clark DJ, Schnaubelt M, Chen L, da Veiga Leprevost F, Eguez RV, Yang W, Pan J, Wen B, Dou Y, Jiang W, Liao Y, Shi Z, Terekhanova NV, Cao S, Lu RJ, Li Y, Liu R, Zhu H, Ronning P, Wu Y, Wyczalkowski MA, Easwaran H, Danilova L, Mer AS, Yoo S, Wang JM, Liu W, Haibe-Kains B, Thiagarajan M, Jewell SD, Hostetter G, Newton CJ, Li QK, Roehrl MH, Fenyö D, Wang P, Nesvizhskii AI, Mani DR, Omenn GS, Boja ES, Mesri M, Robles AI, Rodriguez H, Bathe OF, Chan DW, Hruban RH, Ding L, Zhang B, Zhang H; Clinical Proteomic Tumor Analysis Consortium. Proteogenomic characterization of pancreatic ductal adenocarcinoma. Cell. 2021 Sep 16;184(19):5031-5052.e26. doi: 10.1016/j.cell.2021.08.023. PMID: 34534465

Damrauer JS, Roell KR, Smith MA, Sun X, Kirk EL, Hoadley KA, Benefield HC, Iyer G, Solit DB, Milowsky MI, Kim WY, Nielsen ME, Wobker SE, Dalbagni G, Al-Ahmadie HA, Olshan AF, Bochner BH, Furberg H, Troester MA, Pietzak EJ. Identification of a novel inflamed tumor microenvironment signature as a predictive biomarker of bacillus Calmette-Guerin immunotherapy in non-muscle invasive bladder cancer. Clin Cancer Res. 2021 Aug 15;27(16):4599-4609. doi: 10.1158/1078-0432.CCR-21-0205. Epub 2021 Jun 11. PMID: 34117034.

Satpathy S, Krug K, Jean Beltran PM, Savage SR, Petralia F, Kumar-Sinha C, Dou Y, Reva B, Kane MH, Avanessian SC, Vasaikar SV, Krek A, Lei JT, Jaehnig EJ, Omelchenko T, Geffen Y, Bergstrom EJ, Stathias V, Christianson KE, Heiman DI, Cieslik MP, Cao S, Song X, Ji J, Liu W, Li K, Wen B, Li Y, Gümüş ZH, Selvan ME, Soundararajan R, Visal TH, Raso MG, Parra ER, Babur Ö, Vats P, Anand S, Schraink T, Cornwell M, Rodrigues FM, Zhu H, Mo CK, Zhang Y, da Veiga Leprevost F, Huang C, Chinnaiyan AM, Wyczalkowski MA, Omenn GS, Newton CJ, Schurer S, Ruggles KV, Fenyö D, Jewell SD, Thiagarajan M, Mesri M, Rodriguez H, Mani SA, Udeshi ND, Getz G, Suh J, Li QK, Hostetter G, Paik PK, Dhanasekaran SM, Govindan R, Ding L, Robles AI, Clauser KR, Nesvizhskii AI, Wang P, Carr SA, Zhang B, Mani DR, Gillette MA; Clinical Proteomic Tumor Analysis Consortium. A proteogenomic portrait of lung squamous cell carcinoma. 2021 Aug 5;184(16):4348-4371.e40. doi: 10.1016/j.cell.2021.07.016. PMID: 34358469

Jones GS, Hoadley KA, Olsson LT, Hamilton AM, Bhattacharya A, Kirk EL, Tipaldos HJ, Fleming JM, Love MI, Nichols HB, Olshan AF, Troester MA. Hepatocyte growth factor pathway expression in breast cancer by race and subtype. Breast Cancer Res. 2021 Aug 3;23(1):80. doi: 10.1186/s13058-021-01460-5. PMID: 34344422

Robertson AG, Yau C, Carrot-Zhang J, Damrauer JS, Knijnenburg TA, Chambwe N, Hoadley KA, Kemal A, Zenklusen JC, Cherniack AD, Beroukhim R, Zhou W. Integrative modeling identifies genetic ancestry-associated molecular correlates in human cancer. STAR Protoc. 2021 Apr 19;2(2):100483. doi:10.1016/j.xpro.2021.100483. eCollection 2021 Jun 18. PMID: 33982016

Walens A, Olsson LT, Gao X, Hamilton AM, Kirk EL, Cohen SM, Midkiff BR, Xia Y, Sherman ME, Nikolaishvili-Feinberg N, Serody JS, Hoadley KA, Troester MA, Calhoun BC. Protein-based immune profiles of basal-like vs. luminal breast cancers. Lab Invest. 2021 Jun;101(6):785-793. doi: 10.1038/s41374-020-0056-0. Epub 2021 Feb 23. PMID: 33623115

Bhattacharya A, Hamilton AM, Furberg H, Pietzak E, Purdue MP, Troester MA, Hoadley KA, Love MI. An approach for normalization and quality control for NanoString RNA expression data. Brief Bioinform. 2020 Aug 13:bbaa163. doi: 10.1093/bib/bbaa163. Online ahead of print. PMID: 32789507

Gillette MA, Satpathy S, Cao S, Dhanasekaran SM, Vasaikar SV, Krug K, Petralia F, Li Y, Liang WW, Reva B, Krek A, Ji J, Song X, Liu W, Hong R, Yao L, Blumenberg L, Savage SR, Wendl MC, Wen B, Li K, Tang LC, MacMullan MA, Avanessian SC, Kane MH, Newton CJ, Cornwell M, Kothadia RB, Ma W, Yoo S, Mannan R, Vats P, Kumar-Sinha C, Kawaler EA, Omelchenko T, Colaprico A, Geffen Y, Maruvka YE, da Veiga Leprevost F, Wiznerowicz M, Gümüş ZH, Veluswamy RR, Hostetter G, Heiman DI, Wyczalkowski MA, Hiltke T, Mesri M, Kinsinger CR, Boja ES, Omenn GS, Chinnaiyan AM, Rodriguez H, Li QK, Jewell SD, Thiagarajan M, Getz G, Zhang B, Fenyö D, Ruggles KV, Cieslik MP, Robles AI, Clauser KR, Govindan R, Wang P, Nesvizhskii AI, Ding L, Mani DR, Carr SA; Clinical Proteomic Tumor Analysis Consortium. Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma. Cell. 2020 Jul 9;182(1):200-225.e35. PMID: 32649874

Oak N, Cherniack AD, Mashl RJ; TCGA Analysis Network, 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. PMID: 32471518

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; Cancer Genome Atlas Analysis Network, 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. PMID: 32396860

Samorodnitsky S, Hoadley KA, Lock EF. A Pan-Cancer and Polygenic Bayesian Hierarchical Model for the Effect of Somatic Mutations on Survival. Cancer Inform. 2020 Feb 17;19:1176935120907399. eCollection 2020. PMID: 32116467

Dou Y, Kawaler EA, Cui Zhou D, Gritsenko MA, Huang C, Blumenberg L, Karpova A, Petyuk VA, Savage SR, Satpathy S, Liu W, Wu Y, Tsai CF, Wen B, Li Z, Cao S, Moon J, Shi Z, Cornwell M, Wyczalkowski MA, Chu RK, Vasaikar S, Zhou H, Gao Q, Moore RJ, Li K, Sethuraman S, Monroe ME, Zhao R, Heiman D, Krug K, Clauser K, Kothadia R, Maruvka Y, Pico AR, Oliphant AE, Hoskins EL, Pugh SL, Beecroft SJI, Adams DW, Jarman JC, Kong A, Chang HY, Reva B, Liao Y, Rykunov D, Colaprico A, Chen XS, Czekański A, Jędryka M, Matkowski R, Wiznerowicz M, Hiltke T, Boja E, Kinsinger CR, Mesri M, Robles AI, Rodriguez H, Mutch D, Fuh K, Ellis MJ, DeLair D, Thiagarajan M, Mani DR, Getz G, Noble M, Nesvizhskii AI, Wang P, Anderson ML, Levine DA, Smith RD, Payne SH, Ruggles KV, Rodland KD, Ding L, Zhang B, Liu T, Fenyö D; Clinical Proteomic Tumor Analysis Consortium. Proteogenomic Characterization of Endometrial Carcinoma. Cell. 2020 Feb 20;180(4):729-748.e26. Epub 2020 Feb 13. PMID: 32059776

PCAWG Transcriptome Core Group, Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H; PCAWG Transcriptome Working Group, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z; PCAWG Consortium. Genomic basis for RNA alterations in cancer. Nature. 2020 Feb;578(7793):129-136. Epub 2020 Feb 5. PMID: 32025019

ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-cancer analysis of whole genomes. Nature. 2020 Feb;578(7793):82-93. Epub 2020 Feb 5. PMID: 32025007

Jiao W, Atwal G, Polak P, Karlic R, Cuppen E; PCAWG Tumor Subtypes and Clinical Translation Working Group, Danyi A, de Ridder J, van Herpen C, Lolkema MP, Steeghs N, Getz G, Morris Q, Stein LD; PCAWG Consortium. A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns. Nat Commun. 2020 Feb 5;11(1):728. PMID: 32024849

Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A; PCAWG Transcriptome Working Group; PCAWG Structural Variation Working Group, Creighton CJ; PCAWG Consortium. High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations. Nat Commun. 2020 Feb 5;11(1):736. PMID: 32024823

Selitsky SR, Marron D, Hollern D, Mose LE, Hoadley KA, Jones C, Parker JS, Dittmer DP, Perou CM. Virus expression detection reveals RNA-sequencing contamination in TCGA. BMC Genomics. 2020 Jan 28;21(1):79. PMID: 31992194

Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, da Veiga Leprevost F, Reva B, Lih TM, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L, Krek A, Li Y, Rykunov D, Li QK, Chen LS, Ozbek U, Vasaikar S, Wu Y, Yoo S, Chowdhury S, Wyczalkowski MA, Ji J, Schnaubelt M, Kong A, Sethuraman S, Avtonomov DM, Ao M, Colaprico A, Cao S, Cho KC, Kalayci S, Ma S, Liu W, Ruggles K, Calinawan A, Gümüş ZH, Geiszler D, Kawaler E, Teo GC, Wen B, Zhang Y, Keegan S, Li K, Chen F, Edwards N, Pierorazio PM, Chen XS, Pavlovich CP, Hakimi AA, Brominski G, Hsieh JJ, Antczak A, Omelchenko T, Lubinski J, Wiznerowicz M, Linehan WM, Kinsinger CR, Thiagarajan M, Boja ES, Mesri M, Hiltke T, Robles AI, Rodriguez H, Qian J, Fenyö D, Zhang B, Ding L, Schadt E, Chinnaiyan AM, Zhang Z, Omenn GS, Cieslik M, Chan DW, Nesvizhskii AI, Wang P, Zhang H; Clinical Proteomic Tumor Analysis Consortium. Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma. Cell. 2020 Jan 9;180(1):207. PMID: 31923397

Xia Y, Fan C, Hoadley KA, Parker JS, Perou CM. Genetic determinants of the molecular portraits of epithelial cancers. Nat Commun. 2019 Dec 11;10(1):5666. PMID: 31827079

Zhang H, Schaefer A, Wang Y, Hodge RG, Blake DR, Diehl JN, Papageorge AG, Stachler MD, Liao J, Zhou J, Wu Z, Akarca FG, de Klerk LK, Derks S, Pierobon M, Hoadley KA, Wang TC, Church G, Wong KK, Petricoin EF, Cox AD, Lowy DR, Der CJ, Bass AJ. Gain-of-Function RHOA Mutations Promote Focal Adhesion Kinase Activation and Dependency in Diffuse Gastric Cancer. Cancer Discov. 2019 Nov 26. pii: CD-19-0811. PMID: 31771969

Smith CC, Bixby LM, Miller KL, Selitsky SR, Bortone DS, Hoadley KA, Vincent BG, Serody JS. Using RNA Sequencing to Characterize the Tumor Microenvironment. Methods Mol Biol. 2020;2055:245-272. doi: 10.1007/978-1-4939-9773-2_12. PMID: 31502156

Kamoun A, Reyniès A, Allory Y, Sjödahl G, Robertson AG, Seiler R, Hoadley KA, Groeneveld CS, Al-Ahmadie H, Choi W, Castro MAA, Fontugne J, Eriksson P, Mo Q, Kardos J, Zlotta A, Hartmann A, Dinney CP, Bellmunt J, Powles T, Malats N, Chan KS, Kim WY, McConkey DJ, Black PC, Dyrskjøt L, Höglund M, Lerner SP, Real FX, Radvanyi F; Bladder Cancer Molecular Taxonomy Group. A Consensus Molecular Classification of Muscle-invasive Bladder Cancer. Eur Urol. 2019 Sep 26. pii: S0302-2838(19)30695-5. doi: 10.1016/j.eururo.2019.09.006. [Epub ahead of print] PMID: 31563503

Yu NY, Iftimi A, Yau C, Tobin NP, van ‘t Veer L, Hoadley KA, Benz CC, Nordenskjöld B, Fornander T, Stål O, Czene K, Esserman LJ, Lindström LS. Assessment of Long-term Distant Recurrence-Free Survival Associated With Tamoxifen Therapy in Postmenopausal Patients With Luminal A or Luminal B Breast Cancer. JAMA Oncol. 2019 Aug 8. doi: 10.1001/jamaoncol.2019.1856. [Epub ahead of print] PMID: 31393518

Waks AG, Stover DG, Guerriero JL, Dillon DA, Barry WT, Gjini E, Hartl CA, Lo WT, Savoie J, Brock J, Wesolowski R, Li Z, Damicis A, Philips AV, Wu Y, Yang F, Sullivan A, Danaher P, Brauer HA, Osmani W, Lipschitz M, Hoadley KA, Goldberg MS, Perou CM, Rodig S, Winer EP, Krop I, Mittendorf EA, Tolaney SM. The immune microenvironment in hormone receptor-positive breast cancer before and after preoperative chemotherapy. Clin Cancer Res. 2019 Aug 1;25(15):4644-4655. doi: 10.1158/1078-0432.CCR-19-0173. Epub 2019 May 6. PMID: 31061067

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; Genomic Data Analysis Network, 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: 0.1016/j.cels.2019.06.006. PMID: 31344359

Selitsky SR, Mose LE, Smith CC, Chai S, Hoadley KA, Dittmer DP, Moschos SJ, Parker JS, Vincent BG. Prognostic value of B cells in cutaneous melanoma. Genome Med. 2019 May 28;11(1):36. doi: 10.1186/s13073-019-0647-5. PMID: 31138334

Sikic D, Wirtz RM, Wach S, Dyrskjøt L, Erben P, Bolenz C, Breyer J, Otto W, Hoadley KA, Lerner SP, Eckstein M, Hartmann A, Keck B. Androgen Receptor mRNA Expression in Urothelial Carcinoma of the Bladder: A Retrospective Analysis of Two Independent Cohorts. Transl Oncol. 2019 Apr;12(4):661-668. doi: 10.1016/j.tranon.2019.01.005. Epub 2019 Mar 2. PMID: 30831560

Arceci A, Bonacci T, Wang X, Stewart K, Damrauer JS, Hoadley KA, Emanuele MJ. FOXM1 Deubiquitination by USP21 Regulates Cell Cycle Progression and Paclitaxel Sensitivity in Basal-like Breast Cancer. Cell Rep. 2019 Mar 12;26(11):3076-3086.e6. doi: 10.1016/j.celrep.2019.02.054. PMID: 30865895

Williams LA, Hoadley KA, Nichols HB, Geradts J, Perou CM, Love MI, Olshan AF, Troester MA. Differences in race, molecular and tumor characteristics among women diagnosed with invasive ductal and lobular breast carcinomas. Cancer Causes Control. 2019 Jan 8. doi: 10.1007/s10552-018-1121-1. [Epub ahead of print] PMID: 30617775

Zhao X, Little P, Hoyle AP, Pegna GJ, Hayward MC, Ivanova A, Parker JS, Marron DL, Soloway MG, Jo H, Salazar AH, Papakonstantinou MP, Bouchard DM, Jefferys SR, Hoadley KA, Ollila DW, Frank JS, Thomas NE, Googe PB, Ezzell AJ, Collichio FA, Lee CB, Earp HS, Sharpless NE, Hugo W, Wilmott JS, Quek C, Waddell N, Johansson PA, Thompson JF, Hayward NK, Mann GJ, Lo RS, Johnson DB, Scolyer RA, Hayes DN, Moschos SJ. The Prognostic Significance of Low-Frequency Somatic Mutations in Metastatic Cutaneous Melanoma. Front Oncol. 2019 Jan 4;8:584. doi: 10.3389/fonc.2018.00584. eCollection 2018. PMID: 30662871

Kensler KH, Sankar VN, Wang J, Zhang X, Rubadue CA, Baker GM, Parker JS, Hoadley KA, Stancu AL, Pyle ME, Collins LC, Hunter DJ, Elissen AH, Hankinson SE, Tamimi RM, Heng YJ. PAM50 Molecular Intrinsic Subtypes in the Nurses’ Health Study Cohorts. Cancer Epidemiol Biomarkers Prev. 2018 Dec 27. pii: cebp.0863.2018. doi: 10.1158/1055-9965.EPI-18-0863. [Epub ahead of print] PMID: 30591591

Wang Y, Xu X, Maglic D, Dill MT, Mojumdar K, Ng PK, Jeong KJ, Tsang YH, Moreno D, Bhavana VH, Peng X, Ge Z, Chen H, Li J, Chen Z, Zhang H, Han L, Du D, Creighton CJ, Mills GB; Cancer Genome Atlas Research Network, Camargo F, Liang H. Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer. Cell Rep. 2018 Oct 30;25(5):1304-1317.e5. doi: 10.1016/j.celrep.2018.10.001. PMID:30380420

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; Cancer Genome Atlas Analysis Network, Greenleaf WJ, Chang HY. The chromatin accessibility landscape of primary human cancers. Science. 2018 Oct 26;362(6413). pii: eaav1898. doi: 10.1126/science.aav1898. PMID: 30361341

Hmeljak J, Sanchez-Vega F, Hoadley KA, Shih J, Stewart C, Heiman DI, Tarpey P, Danilova L, Drill E, Gibb EA, Bowlby R, Kanchi R, Osmanbeyoglu HU, Sekido Y, Takeshita J, Newton Y, Graim K, Gupta M, Gay CM, Diao L, Gibbs DL, Thorsson V, Iype L, Kantheti HS, Severson DT, Ravegnini G, Desmeules P, Jungbluth AA, Travis WD, Dacic S, Chirieac LR, Galateau-Salle F, Fujimoto J, Husain AN, Silveira HC, Rusch VW, Rintoul RC, Pass H, Kindler H, Zauderer MG, Kwiatkowski DJ, Bueno R, Tsao AS, Creaney J, Lichtenberg T, Leraas K, Bowen J, The Cancer Genome Atlas Research Network, Felau I, Zenklusen JC, Akbani R, Cherniack AD, Byers LA, Noble MS, Fletcher JA, Robertson G, Shen R, Aburatani H, Robinson BW, Campbell P, Ladanyi M. Integrative Molecular Characterization of Malignant Pleural Mesothelioma. Cancer Discov. 2018 Oct 15. pii: CD-18-0804. doi: 10.1158/2159-8290.CD-18-0804. [Epub ahead of print] PMID: 30322867

Thomas A, Routh ED, Pullikuth A, Jin G, Su J, Chou JW, Hoadley KA, Print C, Knowlton N, Black MA, Demaria S, Wang E, Bedognetti D, Jones WD, Mehta GA, Gatza ML, Perou CM, Page DB, Triozzi P, and Miller, LD. Tumor mutational burden is a determinant of immune-mediated survival in breast cancer. Oncoimmunology. 2018 Jul 30;7(10):e1490854. doi: 10.1080/2162402X.2018.1490854. eCollection 2018. PMID:30386679

Korkut A, Zaidi S, Kanchi RS, Rao S, Gough NR, Schultz A, Li X, Lorenzi PL, Berger AC, Robertson G, Kwong LN, Datto M, Roszik J, Ling S, Ravikumar V, Manyam G, Rao A, Shelley S, Liu Y, Ju Z, Hansel D, de Velasco G, Pennathur A, Andersen JB, O’Rourke CJ, Ohshiro K, Jogunoori W, Nguyen BN, Li S, Osmanbeyoglu HU, Ajani JA, Mani SA, Houseman A, Wiznerowicz M, Chen J, Gu S, Ma W, Zhang J, Tong P, Cherniack AD, Deng C, Resar L; Cancer Genome Atlas Research Network, Weinstein JN, Mishra L, Akbani R. A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β Superfamily. Cell Syst. 2018 Sep 14. pii: S2405-4712(18)30357-0. doi: 10.1016/j.cels.2018.08.010. [Epub ahead of print] PMID: 30268436

Lei JT, Shao J, Zhang J, Iglesia M, Chan DW, Cao J, Anurag M, Singh P, He X, Kosaka Y, Matsunuma R, Crowder R, Hoog J, Phommaly C, Goncalves R, Ramalho S, Peres RMR, Punturi N, Schmidt C, Bartram A, Jou E, Devarakonda V, Holloway KR, Lai WV, Hampton O, Rogers A, Tobias E, Parikh PA, Davies SR, Li S, Ma CX, Suman VJ, Hunt KK, Watson MA, Hoadley KA, Thompson EA, Chen X, Kavuri SM, Creighton CJ, Maher CA, Perou CM, Haricharan S, Ellis MJ. Functional Annotation of ESR1 Gene Fusions in Estrogen Receptor-Positive Breast Cancer. Cell Rep. 2018 Aug 7;24(6):1434-1444.e7. PMID: 30089255

Tanioka M, Fan C, Parker JS, Hoadley KA, Hu Z, Li Y, Hyslop TM, Pitcher BN, Soloway MG, Spears PA, Henry NL, Tolaney S, Dang CT, Krop I, Harris LN, Berry DA, Mardis ER, Winer EP, Hudis CA, Carey LA, Perou CM. Integrated analysis of RNA and DNA from a phase III trial of trastuzumab-based neoadjuvant chemotherapy identifies response predictors in HER2-positive breast cancer. Clin Cancer Res. 2018 Jul 23. pii: clincanres.3431.2017. doi: 10.1158/1078-0432.CCR-17-3431. [Epub ahead of print] PMID: 30037817

Williams LA, Butler EN, Sun X, Allott EH, Cohen SM, Fuller AM, Hoadley KA, Perou CM, Geradts J, Olshan AF, Troester MA. TP53 protein levels, RNA-based pathway assessment, and race among invasive breast cancer cases. NPJ Breast Cancer. 2018 Jun 25;4:13. doi: 10.1038/s41523-018-0067-5. eCollection 2018. PMID: 29951581

Greytak SR, Engel KB, Zmuda E, Casas-Silva E, Guan P, Hoadley KA, Mungall AJ, Wheeler DA, Doddapaneni HV, Moore HM. National Cancer Institute Biospecimen Evidence-Based Practices: Harmonizing Procedures for Nucleic Acid Extraction from Formalin-Fixed, Paraffin-Embedded Tissue. Biopreserv Biobank. 2018 Jun 19. doi: 10.1089/bio.2018.0046. [Epub ahead of print] PMID: 29920119

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; Cancer Genome Atlas Research Network, 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. PMID: 29898407

Tutt A, Tovey H, Cheang MCU, Kernaghan S, Kilburn L, Gazinska P, Owen J, Abraham J, Barrett S, Barrett-Lee P, Brown R, Chan S, Dowsett M, Flanagan JM, Fox L, Grigoriadis A, Gutin A, Harper-Wynne C, Hatton MQ, Hoadley KA, Parikh J, Parker P, Perou CM, Roylance R, Shah V, Shaw A, Smith IE, Timms KM, Wardley AM, Wilson G, Gillett C, Lanchbury JS, Ashworth A, Rahman N, Harries M, Ellis P, Pinder SE, Bliss JM. Carboplatin in BRCA1/2-mutated and triple-negative breast cancer BRCAness subgroups: the TNT Trial. Nat Med. 2018 May;24(5):628-637. PMID: 29713086

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; Cancer Genome Atlas Network, 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. PMID: 29625048. Cover article.

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; Cancer Genome Atlas Research Network, Hu H. An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics. Cell. 2018 Apr ;173(2):400-416.e11. doi: 10.1016/j.cell.2018.02.052. PMID: 29625055

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; Cancer Genome Atlas Research Network, 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. PMID: 29625051

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; Cancer Genome Atlas Research Network. 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. PMID: 29625049

Chen H, Li C, Peng X, Zhou Z, Weinstein JN; Cancer Genome Atlas Research Network, 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. PMID: 29625054

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; MC3 Working Group; Cancer Genome Atlas Research Network, 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. PMID: 29625053

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; Cancer Genome Atlas Research Network, 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. PMID: 29625052

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; Cancer Genome Atlas Research Network, 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. PMID: 29625050

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; Cancer Genome Atlas Research Network, 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. PMID: 29622466

Wang Z, Yang B, Zhang M, Guo W, Wu Z, Wang Y, Jia L, Li S; Cancer Genome Atlas Research Network, 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. PMID: 29622465
*Cancer Cell’s “Best of 2018” reprint collection

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; Cancer Genome Atlas Research Network, 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. PMID: 29622464

Taylor AM, Shih J, Ha G, Gao GF, Zhang X, Berger AC, Schumacher SE, Wang C, Hu H, Liu J, Lazar AJ; Cancer Genome Atlas Research Network, 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. PMID: 29622463

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, Kwaitkowski 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 WT, Robertson AG; Cancer Genome Atlas Research Network, Spellman PT, Rathmell WK, Linehan WM. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Rep. 2018 Apr 3;23(1):313-326.e5. doi: 10.1016/j.celrep.2018.03.075. PMID: 29617669

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, 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 CE; Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich L. The Immune Landscape of Cancer. Immunity. 2018 Apr 4. pii: S1074-7613(18)30121-3. doi: 10.1016/j.immuni.2018.03.023. [Epub ahead of print] PMID: 29628290
*Immunity’s “Best of 2018” reprint collection

Chiu HS, Somvanshi S, Patel E, Chen TW, Singh VP, Zorman B, Patil SL, Pan Y, Chatterjee SS; Cancer Genome Atlas Research Network, Sood AK, Gunaratne PH, Sumazin P. Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context. Cell Rep. 2018 Apr 3;23(1):297-312.e12. doi: 10.1016/j.celrep.2018.03.064. PMID: 29617668

Seiler M, Peng S, Agrawal AA, Palacino J, Teng T, Zhu P, Smith PG; Cancer Genome Atlas Research Network, Buonamici S, Yu L. Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types. Cell Rep. 2018 Apr 3;23(1):282-296.e4. doi: 10.1016/j.celrep.2018.01.088. PMID: 29617667

Jayasinghe RG, Cao S, Gao Q, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-González H, Chai S, Wang F, Varghese R, Huang M, Liang WW, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyö D, Miner JH, Walter MJ; Cancer Genome Atlas Research Network, Vincent B, Eyras E, Chen K, Shmulevich I, Chen F, Ding L. Systematic Analysis of Splice-Site-Creating Mutations in Cancer. Cell Rep. 2018 Apr 3;23(1):270-281.e3. doi: 10.1016/j.celrep.2018.03.052. PMID: 29617666

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; Cancer Genome Atlas Research Network, 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. PMID: 29617665

Knijnenburg TA, Wang L, Zimmermann MT, Chambwe N, Gao GF, Cherniack AD, Fan H, Shen H, Way GP, Greene CS, Liu Y, Akbani R, Feng B, Donehower LA, Miller C, Shen Y, Karimi M, Chen H, Kim P, Jia P, Shinbrot E, Zhang S, Liu J, Hu H, Bailey MH, Yau C, Wolf D, Zhao Z, Weinstein JN, Li L, Ding L, Mills GB, Laird PW, Wheeler DA, Shmulevich I; Cancer Genome Atlas Research Network, Monnat RJ Jr., Xiao Y, Wang C. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Rep. 2018 Apr 3;23(1):239-254.e6. doi: 10.1016/j.celrep.2018.03.076. PMID: 29617664
*Cell Reports “Best of 2018” reprint collection

Gao Q, Liang WW, Foltz SM, Mutharasu G, Jayasinghe RG, Cao S, Liao WW, Reynolds SM, Wyczalkowski MA, Yao L, Yu L, Sun SQ; Fusion Analysis Working Group; Cancer Genome Atlas Research Network, Chen K, Lazar AJ, Fields RC, Wendl MC, Van Tine BA, Vij R, Chen F, Nykter M, Shmulevich I, Ding L. Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell Rep. 2018 Apr 3;23(1):227-238.e3. doi: 10.1016/j.celrep.2018.03.050. PMID: 29617662
*Cell Reports “Best of 2018” reprint collection

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; Cancer Genome Atlas Research Network, 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. PMID: 29617660

Ge Z, Leighton JS, Wang Y, Peng X, Chen Z, Chen H, Sun Y, Yao F, Li J, Zhang H, Liu J, Shriver CD, Hu H; Cancer Genome Atlas Research Network, Piwnica-Worms H, Ma L, Liang H. Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types. Cell Rep. 2018 Apr 3;23(1):213-226.e3. doi: 10.1016/j.celrep.2018.03.047. PMID: 29617661

Saltz J, Gupta R, Hou L, Kurc T, Singh P, Nguyen V, Samaras D, Shroyer KR, Zhao T, Batiste R, Van Arnam J; Cancer Genome Atlas Research Network, Shmulevich I, Rao AUK, Lazar AJ, Sharma A, Thorsson V. Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images. Cell Rep. 2018 Apr 3;23(1):181-193.e7. doi: 10.1016/j.celrep.2018.03.086. PMID: 29617659

Way GP, Sanchez-Vega F, La K, Armenia J, Chatila WK, Luna A, Sander C, Cherniack AD, Mina M, Ciriello G, Schultz N; Cancer Genome Atlas Research Network, 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. PMID: 29617658

Schaub FX, Dhankani V, Berger AC, Trivedi M, Richardson AB, Shaw R, Zhao W, Zhang X, Ventura A, Liu Y, Ayer DE, Hurlin PJ, Cherniack AD, Eisenman RN, Bernard B, Grandori C; Cancer Genome Atlas Network. Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas. Cell Syst. 2018 Mar 28;6(3):282-300.e2. doi: 10.1016/j.cels.2018.03.003. PMID: 29596783

Ellrott K, Bailey MH, Saksena G, Covington KR, Kandoth C, Stewart C, Hess J, Ma S, Chiotti KE, McLellan M, Sofia HJ, Hutter C, Getz G, Wheeler D, Ding L; MC3 Working Group; Cancer Genome Atlas Research Network. Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Cell Syst. 2018 Mar 28;6(3):271-281.e7. doi: 10.1016/j.cels.2018.03.002. PMID: 29596782

Siegel MB, He X, Hoadley KA, Hoyle A, Pearce JB, Garrett AL, Kumar S, Moylan VJ, Brady CM, Van Swearingen AE, Marron D, Gupta GP, Thorne LB, Kieran N, Livasy C, Mardis ER, Parker JS, Chen M, Anders CK, Carey LA, Perou CM. Integrated RNA and DNA sequencing reveals early drivers of metastatic breast cancer. J Clin Invest. 2018 Feb 26. pii: 96153. doi: 10.1172/JCI96153. [Epub ahead of print] PMID: 29480819

Radovich M, Pickering CR, Felau I, Ha G, Zhang H, Jo H, Hoadley KA, Anur P, Zhang J, McLellan M, Bowlby R, Matthew T, Danilova L, Hegde AM, Kim J, Leiserson MDM, Sethi G, Lu C, Ryan M, Su X, Cherniack AD, Robertson G, Akbani R, Spellman P, Weinstein JN, Hayes DN, Raphael B, Lichtenberg T, Leraas K, Zenklusen JC; Cancer Genome Atlas Network, Fujimoto J, Scapulatempo-Neto C, Moreira AL, Hwang D, Huang J, Marino M, Korst R, Giaccone G, Gokmen-Polar Y, Badve S, Rajan A, Ströbel P, Girard N, Tsao MS, Marx A, Tsao AS, Loehrer PJ. The Integrated Genomic Landscape of Thymic Epithelial Tumors. Cancer Cell. 2018 Feb 12;33(2):244-258.e10. doi: 10.1016/j.ccell.2018.01.003. PMID: 29438696

Echavarría I, López-Tarruella S, Picornell AC, Garcia-Saenz JA, Jerez-Gilarranz Y, Hoadley KA, Gomez H, Moreno F, Del Monte-Millán M, Marquez-Rodas I, Alvarez EL, Ramos-Medina R, Gayarre J, Massarrah T, Ocaña I, Cebollero M, Fuentes H, Barnadas A, Ballesteros AI, Bohn U, Perou CM, Martín M. Pathological response in a triple negative breast cancer cohort treated with neoadjuvant carboplatin and docetaxel according to Lehmann’s refined classification. Clin Cancer Res. 2018 Jan 29. pii: clincanres.1912.2017. doi: 10.1158/1078-0432.CCR-17-1912. [Epub ahead of print] PMID: 29378733

Lindström LS, Yau C, Czene K, Thompson CK, Hoadley KA, Van’t Veer LJ, Balassanian R, Bishop JW, Carpenter PM, Chen YY, Datnow B, Hasteh F, Krings G, Lin F, Zhang Y, Nordenskjöld B, Stål O, Benz CC, Fornander T, Borowsky AD, Esserman LJ; STO Trialists Group. Intratumor Heterogeneity of the Estrogen Receptor and the Long-term Risk of Fatal Breast Cancer. J Natl Cancer Inst. 2018 Jan 19. doi: 10.1093/jnci/djx270. [Epub ahead of print] PMID: 29361175.

Williams LA, Nichols HB, Hoadley KA, Tse CK, Geradts J, Bell ME, Perou CM, Love MI, Olshan AF, Troester MA. Reproductive risk factor associations with lobular and ductal carcinoma in the Carolina Breast Cancer Study. Cancer Causes Control. 2017 Nov 9. doi: 10.1007/s10552-017-0977-9. [Epub ahead of print]. PMID: 29124544

The Cancer Genome Atlas Research Network. Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas. Cell. 2017 Nov 2;171(4):950-965.e28. doi: 10.1016/j.cell.2017.10.014. PMID:29100075

Robertson AG, Kim J, Al-Ahmadie H, Bellmunt J, Guo G, Cherniack AD, Hinoue T, Laird PW, Hoadley KA, Akbani R, Castro MAA, Gibb EA, Kanchi RS, Gordenin DA, Shukla SA, Sanchez-Vega F, Hansel DE, Czerniak BA, Reuter VE, Su X, de Sa Carvalho B, Chagas VS, Mungall KL, Sadeghi S, Pedamallu CS, Lu Y, Klimczak LJ, Zhang J, Choo C, Ojesina AI, Bullman S, Leraas KM, Lichtenberg TM, Wu CJ, Schultz N, Getz G, Meyerson M, Mills GB, McConkey DJ; TCGA Research Network, Weinstein JN, Kwiatkowski DJ, Lerner SP. Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer. Cell. 2017 Oct 19;171(3):540-556.e25. doi: 10.1016/j.cell.2017.09.007. PMID: 28988769

Troester MA, Sun X, Allott EH, Geradts J, Cohen SM, Tse CK, Kirk EL, Thorne LB, Mathews M, Li Y, Hu Z, Robinson WR, Hoadley KA, Olopade OI, Reeder-Hayes KE, Earp HS, Olshan AF, Carey LA, Perou CM. Racial Differences in PAM50 Subtypes in the Carolina Breast Cancer Study. J Natl Cancer Inst. 2018 Feb 1;110(2). doi: 10.1093/jnci/djx135. PMID:28859290

Robertson AG, Shih J, Yau C, Gibb EA, Oba J, Mungall KL, Hess JM, Uzunangelov V, Walter V, Danilova L, Lichtenberg TM, Kucherlapati M, Kimes PK, Tang M, Penson A, Babur O, Akbani R, Bristow CA, Hoadley KA, Iype L, Chang MT; TCGA Research Network, Cherniack AD, Benz C, Mills GB, Verhaak RGW, Griewank KG, Felau I, Zenklusen JC, Gershenwald JE, Schoenfield L, Lazar AJ, Abdel-Rahman MH, Roman-Roman S, Stern MH, Cebulla CM, Williams MD, Jager MJ, Coupland SE, Esmaeli B, Kandoth C, Woodman SE. Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma.Cancer Cell. 2017 Aug 14;32(2):204-220.e15. doi: 10.1016/j.ccell.2017.07.003. PMID:28810145

The Cancer Genome Atlas Research Network. Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma. Cancer Cell. 2017 Aug 14;32(2):185-203.e13. doi: 10.1016/j.ccell.2017.07.007. PMID:28810144

Esserman LJ, Yau C, Thompson CK, van ‘t Veer LJ, Borowsky AD, Hoadley KA, Tobin NP, Nordenskjöld B, Fornander T, Stål O, Benz CC, Lindström LS. Use of Molecular Tools to Identify Patients With Indolent Breast Cancers With Ultralow Risk Over 2 Decades. JAMA Oncol. 2017 Jun 29. doi: 10.1001/jamaoncol.2017.1261. [Epub ahead of print] PMID:28662222

The Cancer Genome Atlas Research Network. Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma. Cell. 2017 Jun 15;169(7):1327-1341.e23. PMID:28622513

Huo D, Hu H, Rhie SK, Gamazon ER, Cherniack AD, Liu J, Yoshimatsu TF, Pitt JJ, Hoadley KA, Troester M, Ru Y, Lichtenberg T, Sturtz LA, Shelley CS, Benz CC, Mills GB, Laird PW, Shriver CD, Perou CM, Olopade OI. Comparison of Breast Cancer Molecular Features and Survival by African and European Ancestry in The Cancer Genome Atlas. JAMA Oncol. 2017 May 4. doi: 10.1001/jamaoncol.2017.0595. [Epub ahead of print] PMID:28472234

Bower JJ, Vance LD, Psioda M, Smith-Roe SL, Simpson DA, Ibrahim JG, Hoadley KA, Perou CM, and Kaufmann WK. Patterns of cell cycle checkpoint deregulation associated with intrinsic molecular subtypes of human breast cancer cells. npj Breast Cancer. 2017 3:9. PMID:28649649

Seiler R, Ashab HA, Erho N, van Rhijn BW, Winters B, Douglas J, Van Kessel KE, Fransen van de Putte EE, Sommerlad M, Wang NQ, Choeurng V, Gibb EA, Palmer-Aronsten B, Lam LL, Buerki C, Davicioni E, Sjödahl G, Kardos J, Hoadley KA, Lerner SP, McConkey DJ, Choi W, Kim WY, Kiss B, Thalmann GN, Todenhöfer T, Crabb SJ, North S, Zwarthoff EC, Boormans JL, Wright J, Dall’Era M, van der Heijden MS, Black PC. Impact of Molecular Subtypes in Muscle-invasive Bladder Cancer on Predicting Response and Survival after Neoadjuvant Chemotherapy. Eur Urol. 2017 Apr 5. pii: S0302-2838(17)30251-8. PMID: 28390739

Sun X, Hoadley KA, Kim WY, Furberg H, Olshan AF, Troester MA. Age at diagnosis, obesity, smoking, and molecular subtypes in muscle-invasive bladder cancer. Cancer Causes Control. 2017 Jun;28(6):539-544. PMID:28321693

Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu CC, Shinbrot E, Stransky N, Hegde A, Yang JD, Reznik E, Sadeghi S, Pedamallu CS, Ojesina AI, Hess JM, Auman JT, Rhie SK, Bowlby R, Borad MJ; Cancer Genome Atlas Network., Zhu AX, Stuart JM, Sander C, Akbani R, Cherniack AD, Deshpande V, Mounajjed T, Foo WC, 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 Mar 14;18(11):2780-2794. PMID: 28297679

Cherniack AD, Shen H, Walter V, Stewart C, Murray BA, Bowlby R, Hu X, Ling S, Soslow RA, Broaddus RR, Zuna RE, Robertson G, Laird PW, Kucherlapati R, Mills GB; Cancer Genome Atlas Research Network., Weinstein JN, Zhang J, Akbani R, Levine DA. Integrated Molecular Characterization of Uterine Carcinosarcoma. Cell Rep. 2017 Mar 14;18(11):2780-2794. PMID: 28292439

Mehta GA, Parker JS, Silva GO, Hoadley KA, Perou CM, Gatza ML. Amplification of SOX4 promotes PI3K/Akt signaling in human breast cancer. Breast Cancer Res Treat. Breast Cancer Res Treat. 2017 Apr;162(3):439-450. PMID:28176176

Fishbein L, Leshchiner I, Walter V, Danilova L, Robertson AG, Johnson AR, Lichtenberg TM, Murray BA, Ghayee HK, Else T, Ling S, Jefferys SR, de Cubas AA, Wenz B, Korpershoek E, Amelio AL, Makowski L, Rathmell WK, Gimenez-Roqueplo AP, Giordano TJ, Asa SL, Tischler AS; Cancer Genome Atlas Research Network., Pacak K, Nathanson KL, Wilkerson MD. Comprehensive Molecular Characterization of Pheochromocytoma and Paraganglioma. Cancer Cell. 2017 Feb 13;31(2):181-193. PMID:28162975

Cancer Genome Atlas Research Network. Integrated genomic and molecular characterization of cervical cancer. Nature. 2017 Mar 16;543(7645):378-384. PMID: 28112728

The Cancer Genome Atlas Research Network. Integrated genomic characterization of oesophageal carcinoma. Nature. 2017 Jan 12;541(7636):169-175. PMID: 28052061

Hoadley KA, Siegel MB, Kanchi KL, Miller CA, Ding L, Zhao W, He X, Parker JS, Wendl MC, Fulton RS, Demeter RT, Wilson RK, Carey LA, Perou CM, Mardis ER. Tumor Evolution in Two Patients with Basal-like Breast Cancer: A Retrospective Genomics Study of Multiple Metastases. PLoS Med. 2016 Dec 6;13(12):e1002174. PMID: 27923045

Heng YJ, Lester SC, Tse GM, Factor RE, Allison KH, Collins LC, Chen YY, Jensen KC, Johnson NB, Jeong JC, Punjabi R, Shin SJ, Singh K, Krings G, Eberhard DA, Tan PH, Korski K, Waldman FM, Gutman DA, Sanders M, Reis-Filho JS, Flanagan SR, Gendoo DM, Chen GM, Haibe-Kains B, Ciriello G, Hoadley KA, Perou CM, Beck AH. The molecular basis of breast cancer pathological phenotypes. J Pathol. 2017 Feb;241(3):375-391. PMID: 27861902

Reaves DK, Hoadley KA, Fagan-Solis K, Jima DD, Bereman M, Thorpe L, Hicks J, McDonald D, Troester MA, Perou CM, Fleming JM. Nuclear localized LSR, a novel regulator of breast cancer behavior and tumorigenesis. Mol Cancer Res. 2017 Feb;15(2):165-178. PMID: 27856957

Liu W, Snell JM, Jeck WR, Hoadley KA, Wilkerson MD, Parker JS, Patel N, Mlombe YB, Mulima G, Liomba NG, Wolf LL, Shores CG, Gopal S, Sharpless NE. Subtyping sub-Saharan esophageal squamous cell carcinoma by comprehensive molecular analysis. JCI Insight. 2016 Oct 6;1(16):e88755. PMID: 27734031

Iglesia MD, Parker JS, Hoadley KA, Serody JS, Perou CM, Vincent BG. Genomic Analysis of Immune Cell Infiltrates Across 11 Tumor Types. J Natl Cancer Inst. 2016 Jun 22;108(11). PMID:27335052

Li H, Zhu Y, Burnside ES, Huang E, Drukker K, Hoadley KA, Fan C, Conzen SD, Zuley M, Net JM, Sutton E, Whitman GJ, Morris E, Perou CM, Ji Y, Giger ML. Quantitative MRI radiomics in the prediction of molecular classifications of breast cancer subtypes in the TCGA/TCIA data set. npj Breast Cancer 2, Article number: 16012 (2016) doi:10.1038/npjbcancer.2016.12. PMID: 27853751

Troester MA, Hoadley KA, D’Arcy M, Cherniack AD, Stewart C, Koboldt DC, Robertson AG, Mahurkar S, Shen H, Wilkerson MD, Sandhu R, Johnson NB, Allison KH, Beck AH, Yau C, Bowen J, Sheth M, Hwang ES, Perou CM, Laird PW, Ding L, Benz CC. DNA defects, epigenetics, and gene expression in cancer-adjacent breast: a study from The Cancer Genome Atlas. NPJ Breast Cancer. 2016 2, 16007 doi:10.1038/npjbcancer.2016.7; published online 4 May 2016. PMID:28721375

Zheng S, Cherniack AD, Dewal N, Moffitt RA, Danilova L, Murray BA, Lerario AM, Else T, Knijnenburg TA, Ciriello G, Kim S, Assie G, Morozova O, Akbani R, Shih J, Hoadley KA, Choueiri TK, Waldmann J, Mete O, Robertson AG, Wu HT, Raphael BJ, Shao L, Meyerson M, Demeure MJ, Beuschlein F, Gill AJ, Sidhu SB, Almeida MQ, Fragoso MC, Cope LM, Kebebew E, Habra MA, Whitsett TG, Bussey KJ, Rainey WE, Asa SL, Bertherat J, Fassnacht M, Wheeler DA; Cancer Genome Atlas Research Network, Hammer GD, Giordano TJ, Verhaak RG. Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. Cancer Cell. 2016 May 9;29(5):723-36. doi: 10.1016/j.ccell.2016.04.002. PMID:27165744

Campbell JD, Alexandrov A, Kim J, Wala J, Berger AH, Pedamallu CS, Shukla SA, Guo G, Brooks AN, Murray BA, Imielinski M, Hu X, Ling S, Akbani R, Rosenberg M, Cibulskis C, Ramachandran A, Collisson EA, Kwiatkowski DJ, Lawrence MS, Weinstein JN, Verhaak RG, Wu CJ, Hammerman PS, Cherniack AD, Getz G; Cancer Genome Atlas Research Network, Artyomov MN, Schreiber R, Govindan R, Meyerson M. Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas. Nat Genet. 2016 May 9. doi: 10.1038/ng.3564. [Epub ahead of print] PMID:27158780

Li H, Zhu Y, Burnside ES, Drukker K, Hoadley KA, Fan C, Conzen SD, Whitman GJ, Sutton EJ, Net JM, Ganott M, Huang E, Morris EA, Perou CM, Ji Y, Giger ML. MR Imaging Radiomics Signatures for Predicting the Risk of Breast Cancer Recurrence as Given by Research Versions of MammaPrint, Oncotype DX, and PAM50 Gene Assays. Radiology. 2016 May 5:152110. [Epub ahead of print] PMID:27144536

Zhao W, Hoadley KA, Parker JS, Perou CM. Identification of mRNA isoform switching in breast cancer. BMC Genomics. 2016 Mar 3;17(1):181. doi: 10.1186/s12864-016-2521-9. PMID: 24888378

Ceccarelli M, Barthel FP, Malta TM, Sabedot TS, Salama SR, Murray BA, Morozova O, Newton Y, Radenbaugh A, Pagnotta SM, Anjum S, Wang J, Manyam G, Zoppoli P, Ling S, Rao AA, Grifford M, Cherniack AD, Zhang H, Poisson L, Carlotti CG Jr, Tirapelli DP, Rao A, Mikkelsen T, Lau CC, Yung WK, Rabadan R, Huse J, Brat DJ, Lehman NL, Barnholtz-Sloan JS, Zheng S, Hess K, Rao G, Meyerson M, Beroukhim R, Cooper L, Akbani R, Wrensch M, Haussler D, Aldape KD, Laird PW, Gutmann DH; TCGA Research Network, Noushmehr H, Iavarone A, Verhaak RG. Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma. Cell. 2016 Jan 28;164(3):550-63. PMID:26824661

Wang P, Wu J, Ma S, Zhang L, Yao J, Hoadley KA, Wilkerson MD, Perou CM, Guan KL, Ye D, Xiong Y. Oncometabolite D-2-Hydroxyglutarate Inhibits ALKBH DNA Repair Enzymes and Sensitizes IDH Mutant Cells to Alkylating Agents. Cell Rep. 2015 Dec 22;13(11):2353-61. PMID:26686626

Prat A, Fan C, Fernández A, Hoadley KA, Martinello R, Vidal M, Viladot M, Pineda E, Arance A, Muñoz M, Paré L, Cheang MC, Adamo B, Perou CM. Response and survival of breast cancer intrinsic subtypes following multi-agent neoadjuvant chemotherapy. BMC Med. 2015 Dec 18;13:303. PMID:26684470

Ruggles KV, Tang Z, Wang X, Grover H, Askenazi M, Teubl J, Cao S, McLellan MD, Clauser KR, Tabb DL, Mertins P, Slebos R, Erdmann-Gilmore P, Li S, Gunawardena HP, Xie L, Liu T, Zhou JY, Sun S, Hoadley KA, Perou CM, Chen X, Davies SR, Maher CA, Kinsinger CR, Rodland KD, Zhang H, Zhang Z, Ding L, Townsend RR, Rodriguez H, Chan D, Smith RD, Liebler DC, Carr SA, Payne S, Ellis MJ, Fenyo D. An analysis of the sensitivity of proteogenomic mapping of somatic mutations and novel splicing events in cancer. Mol Cell Proteomics. 2016 Mar;15(3):1060-71. PMID:26631509

Cancer Genome Atlas Research Network. The Molecular Taxonomy of Primary Prostate Cancer. Cell. 2015 Nov 5;163(4):1011-25. PMID:26544944

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Carey LA, Berry DA, Cirrincione CT, Barry WT, Pitcher BN, Harris LN, Ollila DW, Krop IE, Henry NL, Weckstein DJ, Anders CK, Singh B, Hoadley KA, Iglesia M, Cheang MC, Perou CM, Winer EP, Hudis CA. Molecular Heterogeneity and Response to Neoadjuvant Human Epidermal Growth Factor Receptor 2 Targeting in CALGB 40601, a Randomized Phase III Trial of Paclitaxel Plus Trastuzumab With or Without Lapatinib. J Clin Oncol. 2016 Feb 20;34(6):542-9. PMID:26527775

Ciriello G, Gatza ML, Beck AH, Wilkerson MD, Rhie SK, Pastore A, Zhang H, McLellan M, Yau C, Kandoth C, Bowlby R, Shen H, Hayat S, Fieldhouse R, Lester SC, Tse GM, Factor RE, Collins LC, Allison KH, Chen YY, Jensen K, Johnson NB, Oesterreich S, Mills GB, Cherniack AD, Robertson G, Benz C, Sander C, Laird PW, Hoadley KA, King TA; TCGA Research Network, Perou CM. Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer. Cell. 2015 Oct 8; 163(2):506-19. PMID:26451490

Moffitt RA, Marayati R, Flate EL, Volmar KE, Loeza SG, Hoadley KA, Rashid NU, Williams LA, Eaton SC, Chung AH, Smyla JK, Anderson JM, Kim HJ, Bentrem DJ, Talamonti MS, Iacobuzio-Donahue CA, Hollingsworth MA, Yeh JJ. Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma. Nature Genetics. 2015 Oct;47(10):1168-78. PMID:26343385

Cancer Genome Atlas Research Network, Brat DJ, Verhaak RG, Aldape KD, Yung WK, Salama SR, Cooper LA, Rheinbay E, Miller CR, Vitucci M, Morozova O, Robertson AG, Noushmehr H, Laird PW, Cherniack AD, Akbani R, Huse JT, Ciriello G, Poisson LM, Barnholtz-Sloan JS, Berger MS, Brennan C, Colen RR, Colman H, Flanders AE, Giannini C, Grifford M, Iavarone A, Jain R, Joseph I, Kim J, Kasaian K, Mikkelsen T, Murray BA, O’Neill BP, Pachter L, Parsons DW, Sougnez C, Sulman EP, Vandenberg SR, Van Meir EG, von Deimling A, Zhang H, Crain D, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton T, Sherman M, Yena P, Black A, Bowen J, Dicostanzo K, Gastier-Foster J, Leraas KM, Lichtenberg TM, Pierson CR, Ramirez NC, Taylor C, Weaver S, Wise L, Zmuda E, Davidsen T, Demchok JA, Eley G, Ferguson ML, Hutter CM, Mills Shaw KR, Ozenberger BA, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Ayala B, Baboud J, Chudamani S, Jensen MA, Liu J, Pihl T, Raman R, Wan Y, Wu Y, Ally A, Auman JT, Balasundaram M, Balu S, Baylin SB, Beroukhim R, Bootwalla MS, Bowlby R, Bristow CA, Brooks D, Butterfield Y, Carlsen R, Carter S, Chin L, Chu A, Chuah E, Cibulskis K, Clarke A, Coetzee SG, Dhalla N, Fennell T, Fisher S, Gabriel S, Getz G, Gibbs R, Guin R, Hadjipanayis A, Hayes DN, Hinoue T, Hoadley K, Holt RA, Hoyle AP, Jefferys SR, Jones S, Jones CD, Kucherlapati R, Lai PH, Lander E, Lee S, Lichtenstein L, Ma Y, Maglinte DT, Mahadeshwar HS, Marra MA, Mayo M, Meng S, Meyerson ML, Mieczkowski PA, Moore RA, Mose LE, Mungall AJ, Pantazi A, Parfenov M, Park PJ, Parker JS, Perou CM, Protopopov A, Ren X, Roach J, Sabedot TS, Schein J, Schumacher SE, Seidman JG, Seth S, Shen H, Simons JV, Sipahimalani P, Soloway MG, Song X, Sun H, Tabak B, Tam A, Tan D, Tang J, Thiessen N, Triche T Jr, Van Den Berg DJ, Veluvolu U, Waring S, Weisenberger DJ, Wilkerson MD, Wong T, Wu J, Xi L, Xu AW, Yang L, Zack TI, Zhang J, Aksoy BA, Arachchi H, Benz C, Bernard B, Carlin D, Cho J, DiCara D, Frazer S, Fuller GN, Gao J, Gehlenborg N, Haussler D, Heiman DI, Iype L, Jacobsen A, Ju Z, Katzman S, Kim H, Knijnenburg T, Kreisberg RB, Lawrence MS, Lee W, Leinonen K, Lin P, Ling S, Liu W, Liu Y, Liu Y, Lu Y, Mills G, Ng S, Noble MS, Paull E, Rao A, Reynolds S, Saksena G, Sanborn Z, Sander C, Schultz N, Senbabaoglu Y, Shen R, Shmulevich I, Sinha R, Stuart J, Sumer SO, Sun Y, Tasman N, Taylor BS, Voet D, Weinhold N, Weinstein JN, Yang D, Yoshihara K, Zheng S, Zhang W, Zou L, Abel T, Sadeghi S, Cohen ML, Eschbacher J, Hattab EM, Raghunathan A, Schniederjan MJ, Aziz D, Barnett G, Barrett W, Bigner DD, Boice L, Brewer C, Calatozzolo C, Campos B, Carlotti CG Jr, Chan TA, Cuppini L, Curley E, Cuzzubbo S, Devine K, DiMeco F, Duell R, Elder JB, Fehrenbach A, Finocchiaro G, Friedman W, Fulop J, Gardner J, Hermes B, Herold-Mende C, Jungk C, Kendler A, Lehman NL, Lipp E, Liu O, Mandt R, McGraw M, Mclendon R, McPherson C, Neder L, Nguyen P, Noss A, Nunziata R, Ostrom QT, Palmer C, Perin A, Pollo B, Potapov A, Potapova O, Rathmell WK, Rotin D, Scarpace L, Schilero C, Senecal K, Shimmel K, Shurkhay V, Sifri S, Singh R, Sloan AE, Smolenski K, Staugaitis SM, Steele R, Thorne L, Tirapelli DP, Unterberg A, Vallurupalli M, Wang Y, Warnick R, Williams F, Wolinsky Y, Bell S, Rosenberg M, Stewart C, Huang F, Grimsby JL, Radenbaugh AJ, Zhang J. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med. 2015 Jun 25; 372(26):2481-98. PMID:26061751

The Cancer Genome Atlas Network. Genomic Classification of Cutaneous Melanoma. Cell. 2015 Jun 18; 161(7):1681-96. PMID:26091043

The Cancer Genome Atlas Network. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature. 2015 Jan 29; 517(7536):576-82. PMID:25631445 cover article

Brown KE, Chagoya G, Kwatra SG, Yen T, Keir ST, Cooter M, Hoadley KA, Rasheed A, Lipp ES, Mclendon R, Ali-Osman F, Bigner DD, Sampson JH, Kwatra MM. Proteomic profiling of patient-derived glioblastoma xenografts identifies a subset with activated EGFR: Implications for drug development. J Neurochem. 2015 June; 133(5):730-8. PMID:25598002

The Cancer Genome Atlas Research Network. Integrated genomic characterization of papillary thyroid carcinoma. Cell. 2014 Oct 23; 159(3):676-90. PMID:25417114

Parfenov M, Pedamallu CS, Gehlenborg N, Freeman SS, Danilova L, Bristow CA, Lee S, Hadjipanayis AG, Ivanova EV, Wilkerson MD, Protopopov A, Yang L, Seth S, Song X, Tang J, Ren X, Zhang J, Pantazi A, Santoso N, Xu AW, Mahadeshwar H, Wheeler DA, Haddad RI, Jung J, Ojesina AI, Issaeva N, Yarbrough WG, Hayes DN, Grandis JR, El-Naggar AK, Meyerson M, Park PJ, Chin L, Seidman JG, Hammerman PS, Kucherlapati R; Cancer Genome Atlas Network. Characterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci U S A. 2014 Oct 28; 111(43):15544-9. PMID:25313082

Davis CF, Ricketts CJ, Wang M, Yang L, Cherniack AD, Shen H, Buhay C, Kang H, Kim SC, Fahey CC, Hacker KE, Bhanot G, Gordenin DA, Chu A, Gunaratne PH, Biehl M, Seth S, Kaipparettu BA, Bristow CA, Donehower LA, Wallen EM, Smith AB, Tickoo SK, Tamboli P, Reuter V, Schmidt LS, Hsieh JJ, Choueiri TK, Hakimi AA; The Cancer Genome Atlas Research Network, Chin L, Meyerson M, Kucherlapati R, Park WY, Robertson AG, Laird PW, Henske EP, Kwiatkowski DJ, Park PJ, Morgan M, Shuch B, Muzny D, Wheeler DA, Linehan WM, Gibbs RA, Rathmell WK, Creighton CJ; The Cancer Genome Atlas Research Network. The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma. Cancer Cell. 2014 Sep 8; 26(3):319-30. PMID:25155756

Sandhu R, Rein J, D’Arcy M, Herschkowitz JI, Hoadley KA, Troester MA. Over-expression of miR-146a in basal-like breast cancer cells confers enhanced tumorigenic potential in association with altered p53 status. Carcinogenesis. 2014 Nov; 35(11):2567-75. PMID:25123132

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The Cancer Genome Atlas Research Network. Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014 Jul 31; 511(7511):543-50. PMID:25079552

Prat A, Cruz C, Hoadley KA, Díez O, Perou CM, Balmaña J. Molecular features of the basal-like breast cancer subtype based on BRCA1 mutation status. Breast Cancer Res Treat. 2014 Aug; 147(1):185-91. PMID:25048467

Wilkerson MD, Cabanski CR, Sun W, Hoadley KA, Walter V, Mose LE, Troester MA, Hammerman PS, Parker JS, Perou CM, Hayes DN. Integrated RNA and DNA sequencing improves mutation detection in low purity tumors. Nucleic Acids Res. 2014 Sep 1; 42(13):e107. PMID:24970867

Iglesia MD, Vincent BG, Parker JS, Hoadley KA, Carey LA, Perou CM, Serody JS. Prognostic B-cell signatures using mRNA-seq in patients with subtype-specific breast and ovarian cancer. Clin Cancer Res. 2014 Jul 15; 20(14):3818-29. PMID:24916698

Zhao W, He X, Hoadley KA, Parker JS, Hayes DN, Perou CM. Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling. BMC Genomics. 2014 Jun 2; 15:419. PMID:24888378

Damrauer JS, Hoadley KA, Chism DD, Fan C, Tiganelli CJ, Wobker SE, Yeh JJ, Milowsky MI, Iyer G, Parker JS, Kim WY. Intrinsic subtypes of high-grade bladder cancer reflect the hallmarks of breast cancer biology. Proc Natl Acad Sci U S A. 2014 Feb 25; 111(8):3110-5. PMID:24520177

The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature. 2014 Mar 20; 507(7492):315-22. PMID:24476821

Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, Barnholtz-Sloan J, Zou L, Vegesna R, Shukla SA, Ciriello G, Yung WK, Zhang W, Sougnez C, Mikkelsen T, Aldape K, Bigner DD, Van Meir EG, Prados M, Sloan A, Black KL, Eschbacher J, Finocchiaro G, Friedman W, Andrews DW, Guha A, Iacocca M, O’Neill BP, Foltz G, Myers J, Weisenberger DJ, Penny R, Kucherlapati R, Perou CM, Hayes DN, Gibbs R, Marra M, Mills GB, Lander E, Spellman P, Wilson R, Sander C, Weinstein J, Meyerson M, Gabriel S, Laird PW, Haussler D, Getz G, Chin L; TCGA Research Network. The somatic genomic landscape of glioblastoma. Cell. 2013 Oct 10; 155(2):462-77. PMID:24120142

Ciriello G, Sinha R, Hoadley KA, Jacobsen AS, Reva B, Perou CM, Sander C, Schultz N. The molecular diversity of Luminal A breast tumors. Breast Cancer Res Treat. 2013 Oct; 141(3):409-20. PMID:24096568

Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Oct; 45(10):1113-20. PMID:24071849

Chen K, Navin NE, Wang Y, Schmidt HK, Wallis JW, Niu B, Fan X, Zhao H, McLellan MD, Hoadley KA, Mardis ER, Ley TJ, Perou CM, Wilson RK, Ding L. BreakTrans: uncovering the genomic architecture of gene fusions. Genome Biol. 2013 Aug 23; 14(8):R87. PMID:23972288

Cancer Genome Atlas Research Network. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature 2013 Jul 4; 499(7456):43-9. PMID:23792563

The Cancer Genome Atlas Research Network. Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia. Ley TJ, Miller C, Ding L, Raphael BJ, Mungall AJ, Robertson A, Hoadley K, Triche TJ Jr, Laird PW, Baty JD, Fulton LL, Fulton R, Heath SE, Kalicki-Veizer J, Kandoth C, Klco JM, Koboldt DC, Kanchi KL, Kulkarni S, Lamprecht TL, Larson DE, Lin L, Lu C, McLellan MD, McMichael JF, Payton J, Schmidt H, Spencer DH, Tomasson MH, Wallis JW, Wartman LD, Watson MA, Welch J, Wendl MC, Ally A, Balasundaram M, Birol I, Butterfield Y, Chiu R, Chu A, Chuah E, Chun HJ, Corbett R, Dhalla N, Guin R, He A, Hirst C, Hirst M, Holt RA, Jones S, Karsan A, Lee D, Li HI, Marra MA, Mayo M, Moore RA, Mungall K, Parker J, Pleasance E, Plettner P, Schein J, Stoll D, Swanson L, Tam A, Thiessen N, Varhol R, Wye N, Zhao Y, Gabriel S, Getz G, Sougnez C, Zou L, Leiserson MD, Vandin F, Wu HT, Applebaum F, Baylin SB, Akbani R, Broom BM, Chen K, Motter TC, Nguyen K, Weinstein JN, Zhang N, Ferguson ML, Adams C, Black A, Bowen J, Gastier-Foster J, Grossman T, Lichtenberg T, Wise L, Davidsen T, Demchok JA, Shaw KR, Sheth M, Sofia HJ, Yang L, Downing JR, Eley G. NEJM 2013 368(22): 2059-74. PMID:23634996

Cancer Genome Atlas Research Network, Kandoth C, Schultz N, Cherniack AD, Akbani R, Liu Y, Shen H, Robertson AG, Pashtan I, Shen R, Benz CC, Yau C, Laird PW, Ding L, Zhang W, Mills GB, Kucherlapati R, Mardis ER, Levine DA. Integrated genomic characterization of endometrial carcinoma. Nature 2013 May 2; 497(7447):67-73. PMID:23636398

Lock EF, Hoadley KA, Marron JS, Nobel AB. Joint and individual variation explained (JIVE) for integrated analysis of multiple data types. The Annals of Applied Statistics 2013 7(1):523-542. PMID:23745156

Walter V, Yin X, Wilkerson MD, Cabanski CR, Zhao N, Du Y, Ang MK, Hayward MC, Salazar AH, Hoadley KA, Fritchie K, Sailey CG, Weissler MC, Shockley WW, Zanation AM, Hackman T, Thorne LB, Funkhouser WD, Muldrew KL, Olshan AF, Randell SH, Wright FA, Shores CG, Hayes DN. Molecular subtypes in head and neck cancer exhibit distinct patterns of chromosomal gain and loss of canonical cancer genes. PLoS One 2013 8(2):e56823. PMID:23451093

Verhaak RG, Tamayo P, Yang JY, Hubbard D, Zhang H, Creighton CJ, Fereday S, Lawrence M, Carter SL, Mermel CH, Kostic AD, Etemadmoghadam D, Saksena G, Cibulskis K, Duraisamy S, Levanon K, Sougnez C, Tsherniak A, Gomez S, Onofrio R, Gabriel S, Chin L, Zhang N, Spellman PT, Zhang Y, Akbani R, Hoadley KA, Kahn A, Köbel M, Huntsman D, Soslow RA, Defazio A, Birrer MJ, Gray JW, Weinstein JN, Bowtell DD, Drapkin R, Mesirov JP, Getz G, Levine DA, Meyerson M; Cancer Genome Atlas Research Network. Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. J Clin Invest. 2013 Jan 2;123(1):517-25. PMID:23257362

Brauer HA, Makowski L, Hoadley KA, Casbas-Hernandez P, Lang LJ, Romàn-Pèrez E, D’Arcy M, Freemerman AJ, Perou CM, Troester MA. Impact of tumor microenvironment and epithelial phenotypes on metabolism in breast cancer. Clin Cancer Res. 2013 Feb 1;19(3):571-85. PMID:23236214

The Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature. 2012 Oct 4;490(7418):61-70. PMID:23000897

The Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012 Sep 27;489(7417):519-25. PMID:22960745

The Cancer Genome Atlas (TCGA) Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012 Jul 18;487(7407):330-7. PMID: 22810696

Carey LA, Rugo HS, Marcom PK, Mayer EL, Esteva FJ, Ma CX, Liu MC, Storniolo AM, Rimawi MF, Forero-Torres A, Wolff AC, Hobday TJ, Ivanova A, Chiu WK, Ferraro M, Burrows E, Bernard PS, Hoadley KA, Perou CM, Winer EP. TBCRC 001: Randomized Phase II Study of Cetuximab in Combination With Carboplatin in Stage IV Triple-Negative Breast Cancer. J Clin Oncol. 2012 Jul 20;30(21):2615-23. PMID: 22665533

Zhang W, Zhang J, Hoadley K, Kushwaha D, Ramakrishnan V, Li S, Kang C, You Y, Jiang C, Song SW, Jiang T, Chen CC. 2012. miR-181d: a predictive glioblastoma biomarker that downregulates MGMT expression. Neuro Oncol. 2012 Jun; 14(6):712-9. PMID: 22570426

Duncan JS, Whittle MC, Nakamura K, Abell AN, Midland AA, Zawistowski JS, Johnson NL, Granger DA, Jordan NV, Darr DB, Usary J, Kuan PF, Smalley DM, Major B, He X, Hoadley KA, Zhou B, Sharpless NE, Perou CM, Kim WY, Gomez SM, Chen X, Jin J, Frye SV, Earp HS, Graves LM, Johnson GL. Dynamic Reprogramming of the Kinome in Response to Targeted MEK Inhibition in Triple-Negative Breast Cancer. Cell 2012 149(2):307-21. PMID: 22500798

The Cancer Genome Atlas (TCGA) Research Network. Integrated genomic analysis of ovarian carcinoma. Nature 2011 474(7353):609-615. PMID: 21720365

Thorner AR, Parker JS, Hoadley KA, Perou CM. Potential Tumor Suppressor Role for the c-Myb Oncogene in Luminal Breast Cancer. PLoS ONE 2010 5(10): e13073. PMID: 20949095

Wilkerson MD, Yin X, Hoadley KA, Liu Y, Hayward MC, Cabanski CR, Muldrew KL, Miller CR, Randell SH, Socinski MA, Parsons AM, Funkhouser WK, Lee CB,Robert PJ, Thorne L,Bernard PS, Perou CM, and Hayes DN. Lung squamous cell carcinoma mRNA expression subtypes are reproducible, clinically-important and correspond to different normal cell types. Clinical Cancer Research 2010 16(19):4864-4875. PMID: 20643781

Nitta M, Kozono D, Kennedy R, Stommel J, Ng K, Zinn PO, Kushwaha D, Kesari S, Furnari F, Hoadley KA, Chin L, DePinho RA, Cavenee WK, D’Andrea A, Chen CC. Targeting EGFR induced oxidative stress by PARP1 inhibition in glioblastoma therapy. PLoS One 2010 5(5):e10767. PMID: 20532243

Noushmehr H, Weisenberger DJ, Diefes K, Phillips HS, Pujara K, Berman BP, Pan F, Pelloski CE, Sulman EP, Bhat KP, Verhaak RG, Hoadley KA, Hayes DN, Perou CM, Schmidt HK, Ding L, Wilson RK, Van Den Berg D, Shen H, Bengtsson H, Neuvial P, Cope LM, Buckley J, Herman JG, Baylin SB, Laird PW, Aldape K; The Cancer Genome Atlas Research Network. Identification of a CpG Island Methylator Phenotype that Defines a Distinct Subgroup of Glioma. Cancer Cell 2010 17(5):510-522. PMID: 20399149

Verhaak RGW*, Hoadley KA*, Purdom E, Wang V, Qi Y, Wilkerson MD, Miller CR, Ding L, Golub T, Mesirov JP, Alexe G, Lawrence M, O’Kelly M, Tamayo P, Weir BA, Gabriel S, Winckler W, Gupta S, Jakkula L, Feiler HS, Hodgson JG, James CD, Sarkaria JN, Brennan C, Kahn K, Spellman PT, Wilson RK, Speed TP, Gray JW, Meyerson M, Getz G, Perou CM, Hayes DN. Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 2010 17(1):98-110. PMID: 20129251 *Co-first authors, Cover article

Bild AH, Parker JS, Gustafson AM, Acharya CR, Hoadley KA, Anders C, Marcom PK, Carey LA, Potti A, Nevins JR, Perou CM. An integration of complementary strategies for gene-expression analysis to reveal novel therapeutic opportunities for breast cancer. Breast Cancer Research 2009 11(4):R55. PMID: 19638211

Thorner AR, Hoadley KA, Parker JS, Winkel S, Millikan RC, Perou CM. In vitro and in vivo analysis of B-Myb in basal-like breast cancer. Oncogene 2009 28:742-751. PMID: 19043454

The Cancer Genome Atlas (TCGA) Research Network. Comprehensive genomic characterization defines novel cancer genes and core pathways in human glioblastomas. Nature 2008 455(7216):1061-1068. PMID: 18772890

Jiang J, Parker CE, Hoadley KA, Perou CM, Boysen G, and Borchers CH. Development of an immuno tandem mass spectrometry (iMASS2) assay for EGFR diagnosis. Proteomics Clin. Appl. 2007 1:1651-1659. PMID: 21136662

Hoadley KA, Weigman VJ, Fan C, Sawyer LR, He X, Troester MA, Sartor CI, Rieger-House T, Bernard PS, Carey LA, and Perou CM. EGFR associated expression profiles vary with breast tumor subtype. BMC Genomics 2007 8(1):258. PMID: 17663798

Penland SK, Keku TO, Torrice C, He X, Krishnamurthy J, Hoadley KA, Woosley JT, Thomas N, Perou CM, Sandler R, and Sharpless NE. RNA expression analysis of formalin-fixed paraffin embedded tumors. Lab Investigation 2007 87(4):383-391. PMID: 17297435

Troester MA, Herschokowitz JI, Oh DS, He X, Hoadley KA, Barbier CS, and Perou CM. Gene expression patterns associated with p53 status in breast cancer. BMC Cancer 2006 6:276. PMID: 17150101

Troester MA*, Hoadley KA*, Parker JS, and Perou CM. Prediction of toxicant-specific gene expression signatures following chemotherapeutics treatment of breast cell lines. Environmental Health Perspectives Toxicogenomics 2004 112(16): 1607-1613. PMID: 15598611 *Co-first authors

Troester MA*, Hoadley KA*, Sørlie T, Børresen-Dale AL, Lønning PE, Herbert BS, Shay JW, Kaufmann WK, and Perou CM. Cell-type specific responses to chemotherapeutics in breast cancer. Cancer Research 2004 64: 4218-4226. PMID: 15205334 *Co-first authors