My Bibliography

select

Ikami K, Nuzhat N, Abbott H, Pandoy R, Haky L, Spradling AC, Tanner H, Lei L. Altered germline cyst formation and oogenesis in Tex14 mutant mice. Biol Open. 2021 Jun 15;10(6). doi: 10.1242/bio.058807. Epub 2021 Jun 22. PubMed PMID: 34156079; PubMed Central PMCID: PMC8249907.

select

Carrot-Zhang J, Yao X, Devarakonda S, Deshpande A, Damrauer JS, Silva TC, Wong CK, Choi HY, Felau I, Robertson AG, Castro MAA, Bao L, Rheinbay E, Liu EM, Trieu T, Haan D, Yau C, Hinoue T, Liu Y, Shapira O, Kumar K, Mungall KL, Zhang H, June-Koo Lee J, Berger A, Gao GF, Zhitomirsky B, Liang WW, Zhou M, Moorthi S, Berger AH, Collisson EA, Zody MC, Ding L, Cherniack AD, Getz G, Elemento O, Benz CC, Stuart J, Zenklusen JC, Beroukhim R, Chang JC, Campbell JD, Hayes DN, Yang L, Laird PW, Weinstein JN, Kwiatkowski DJ, Tsao MS, Travis WD, Khurana E, Berman BP, Hoadley KA, Robine N, Meyerson M, Govindan R, Imielinski M. Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway. Cell Rep. 2021 Feb 23;34(8):108784. doi: 10.1016/j.celrep.2021.108784. PubMed PMID: 33626341; PubMed Central PMCID: PMC8608252.

select

Hmeljak J, Sanchez-Vega F, Hoadley KA, Shih J, Stewart C, Heiman D, 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 H, Severson DT, Ravegnini G, Desmeules P, Jungbluth AA, Travis WD, Dacic S, Chirieac LR, Galateau-Sallé 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, Felau I, Zenklusen JC, Akbani R, Cherniack AD, Byers LA, Noble MS, Fletcher JA, Robertson AG, Shen R, Aburatani H, Robinson BW, Campbell P, Ladanyi M. Integrative Molecular Characterization of Malignant Pleural Mesothelioma. Cancer Discov. 2018 Dec;8(12):1548-1565. doi: 10.1158/2159-8290.CD-18-0804. Epub 2018 Oct 15. PubMed PMID: 30322867; PubMed Central PMCID: PMC6310008.

select

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.

select

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.

select

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.

select

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.

select

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 Apr 3;23(1):313-326.e5. doi: 10.1016/j.celrep.2018.03.075. PubMed PMID: 29617669; PubMed Central PMCID: PMC6075733.

select

Saltz J, Gupta R, Hou L, Kurc T, Singh P, Nguyen V, Samaras D, Shroyer KR, Zhao T, Batiste R, Van Arnam J, 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. PubMed PMID: 29617659; PubMed Central PMCID: PMC5943714.

select

Seiler M, Peng S, Agrawal AA, Palacino J, Teng T, Zhu P, Smith PG, 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. PubMed PMID: 29617667; PubMed Central PMCID: PMC5933844.

select

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 Dec 1;3(12):1654-1662. doi: 10.1001/jamaoncol.2017.0595. PubMed PMID: 28472234; PubMed Central PMCID: PMC5671371.

select

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. PubMed PMID: 29100075; PubMed Central PMCID: PMC5693358.

select

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 Nov 1;3(11):1503-1510. doi: 10.1001/jamaoncol.2017.1261. PubMed PMID: 28662222; PubMed Central PMCID: PMC5710197.

select

Scott GK, Chu D, Kaur R, Malato J, Rothschild DE, Frazier K, Eppenberger-Castori S, Hann B, Park BH, Benz CC. ERpS294 is a biomarker of ligand or mutational ERα activation and a breast cancer target for CDK2 inhibition. Oncotarget. 2017 Oct 13;8(48):83432-83445. doi: 10.18632/oncotarget.12735. eCollection 2017 Oct 13. PubMed PMID: 29137354; PubMed Central PMCID: PMC5663526.

select

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, 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. PubMed PMID: 28810145; PubMed Central PMCID: PMC5619925.

select

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, 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 Jun 27;19(13):2878-2880. doi: 10.1016/j.celrep.2017.06.008. PubMed PMID: 28658632; PubMed Central PMCID: PMC6141445.

select

Integrated genomic and molecular characterization of cervical cancer. Nature. 2017 Mar 16;543(7645):378-384. doi: 10.1038/nature21386. Epub 2017 Jan 23. PubMed PMID: 28112728; PubMed Central PMCID: PMC5354998.

select

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, Pacak K, Nathanson KL, Wilkerson MD. Comprehensive Molecular Characterization of Pheochromocytoma and Paraganglioma. Cancer Cell. 2017 Feb 13;31(2):181-193. doi: 10.1016/j.ccell.2017.01.001. Epub 2017 Feb 2. PubMed PMID: 28162975; PubMed Central PMCID: PMC5643159.

select

Huo, Hu, Rhie, Gamazon, Cherniack, Liu, Yoshimatsu, Pitt. Comprehensive comparison of breast cancer molecular portraits by African and European ancestry in The Cancer Genome Atlas. JAMA oncology. 2017 February; 77(4). doi: DOI: 10.1158/1538-7445.

select

Integrated genomic characterization of oesophageal carcinoma. Nature. 2017 Jan 12;541(7636):169-175. doi: 10.1038/nature20805. Epub 2017 Jan 4. PubMed PMID: 28052061; PubMed Central PMCID: PMC5651175.

select

Si H, Lu H, Yang X, Mattox A, Jang M, Bian Y, Sano E, Viadiu H, Yan B, Yau C, Ng S, Lee SK, Romano RA, Davis S, Walker RL, Xiao W, Sun H, Wei L, Sinha S, Benz CC, Stuart JM, Meltzer PS, Van Waes C, Chen Z. TNF-α modulates genome-wide redistribution of ΔNp63α/TAp73 and NF-κB cREL interactive binding on TP53 and AP-1 motifs to promote an oncogenic gene program in squamous cancer. Oncogene. 2016 Nov 3;35(44):5781-5794. doi: 10.1038/onc.2016.112. Epub 2016 May 2. PubMed PMID: 27132513; PubMed Central PMCID: PMC5093089.

select

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 MCBV, Cope LM, Kebebew E, Habra MA, Whitsett TG, Bussey KJ, Rainey WE, Asa SL, Bertherat J, Fassnacht M, Wheeler DA, Hammer GD, Giordano TJ, Verhaak RGW. Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. Cancer Cell. 2016 Aug 8;30(2):363. doi: 10.1016/j.ccell.2016.07.013. Epub 2016 Aug 8. PubMed PMID: 27505681.

select

Park JW, Liu MC, Yee D, Yau C, van 't Veer LJ, Symmans WF, Paoloni M, Perlmutter J, Hylton NM, Hogarth M, DeMichele A, Buxton MB, Chien AJ, Wallace AM, Boughey JC, Haddad TC, Chui SY, Kemmer KA, Kaplan HG, Isaacs C, Nanda R, Tripathy D, Albain KS, Edmiston KK, Elias AD, Northfelt DW, Pusztai L, Moulder SL, Lang JE, Viscusi RK, Euhus DM, Haley BB, Khan QJ, Wood WC, Melisko M, Schwab R, Helsten T, Lyandres J, Davis SE, Hirst GL, Sanil A, Esserman LJ, Berry DA. Adaptive Randomization of Neratinib in Early Breast Cancer. N Engl J Med. 2016 Jul 7;375(1):11-22. doi: 10.1056/NEJMoa1513750. PubMed PMID: 27406346; PubMed Central PMCID: PMC5259558.

select

Rugo HS, Olopade OI, DeMichele A, Yau C, van 't Veer LJ, Buxton MB, Hogarth M, Hylton NM, Paoloni M, Perlmutter J, Symmans WF, Yee D, Chien AJ, Wallace AM, Kaplan HG, Boughey JC, Haddad TC, Albain KS, Liu MC, Isaacs C, Khan QJ, Lang JE, Viscusi RK, Pusztai L, Moulder SL, Chui SY, Kemmer KA, Elias AD, Edmiston KK, Euhus DM, Haley BB, Nanda R, Northfelt DW, Tripathy D, Wood WC, Ewing C, Schwab R, Lyandres J, Davis SE, Hirst GL, Sanil A, Berry DA, Esserman LJ. Adaptive Randomization of Veliparib-Carboplatin Treatment in Breast Cancer. N Engl J Med. 2016 Jul 7;375(1):23-34. doi: 10.1056/NEJMoa1513749. PubMed PMID: 27406347; PubMed Central PMCID: PMC5259561.

select

Cirillo PM, Benz CC, Cohn BA. Comment on: 'Hypertensive diseases in pregnancy and breast cancer risk'. Br J Cancer. 2016 May 24;114(11):e10. doi: 10.1038/bjc.2016.81. Epub 2016 May 3. PubMed PMID: 27140311; PubMed Central PMCID: PMC4891511.

select

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. eCollection 2016. PubMed PMID: 28721375; PubMed Central PMCID: PMC5515343.

select

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, 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. doi: 10.1016/j.cell.2015.12.028. PubMed PMID: 26824661; PubMed Central PMCID: PMC4754110.

select

Linehan WM, Spellman PT, Ricketts CJ, Creighton CJ, Fei SS, Davis C, Wheeler DA, Murray BA, Schmidt L, Vocke CD, Peto M, Al Mamun AA, Shinbrot E, Sethi A, Brooks S, Rathmell WK, Brooks AN, Hoadley KA, Robertson AG, Brooks D, Bowlby R, Sadeghi S, Shen H, Weisenberger DJ, Bootwalla M, Baylin SB, Laird PW, Cherniack AD, Saksena G, Haake S, Li J, Liang H, Lu Y, Mills GB, Akbani R, Leiserson MD, Raphael BJ, Anur P, Bottaro D, Albiges L, Barnabas N, Choueiri TK, Czerniak B, Godwin AK, Hakimi AA, Ho TH, Hsieh J, Ittmann M, Kim WY, Krishnan B, Merino MJ, Mills Shaw KR, Reuter VE, Reznik E, Shelley CS, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Tickoo S, Burnett K, Crain D, Gardner J, Lau K, Mallery D, Morris S, Paulauskis JD, Penny RJ, Shelton C, Shelton WT, Sherman M, Thompson E, Yena P, Avedon MT, Bowen J, Gastier-Foster JM, Gerken M, Leraas KM, Lichtenberg TM, Ramirez NC, Santos T, Wise L, Zmuda E, Demchok JA, Felau I, Hutter CM, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Zhang J, Ayala B, Baboud J, Chudamani S, Liu J, Lolla L, Naresh R, Pihl T, Sun Q, Wan Y, Wu Y, Ally A, Balasundaram M, Balu S, Beroukhim R, Bodenheimer T, Buhay C, Butterfield YS, Carlsen R, Carter SL, Chao H, Chuah E, Clarke A, Covington KR, Dahdouli M, Dewal N, Dhalla N, Doddapaneni HV, Drummond JA, Gabriel SB, Gibbs RA, Guin R, Hale W, Hawes A, Hayes DN, Holt RA, Hoyle AP, Jefferys SR, Jones SJ, Jones CD, Kalra D, Kovar C, Lewis L, Li J, Ma Y, Marra MA, Mayo M, Meng S, Meyerson M, Mieczkowski PA, Moore RA, Morton D, Mose LE, Mungall AJ, Muzny D, Parker JS, Perou CM, Roach J, Schein JE, Schumacher SE, Shi Y, Simons JV, Sipahimalani P, Skelly T, Soloway MG, Sougnez C, Tam A, Tan D, Thiessen N, Veluvolu U, Wang M, Wilkerson MD, Wong T, Wu J, Xi L, Zhou J, Bedford J, Chen F, Fu Y, Gerstein M, Haussler D, Kasaian K, Lai P, Ling S, Radenbaugh A, Van Den Berg D, Weinstein JN, Zhu J, Albert M, Alexopoulou I, Andersen JJ, Auman JT, Bartlett J, Bastacky S, Bergsten J, Blute ML, Boice L, Bollag RJ, Boyd J, Castle E, Chen YB, Cheville JC, Curley E, Davies B, DeVolk A, Dhir R, Dike L, Eckman J, Engel J, Harr J, Hrebinko R, Huang M, Huelsenbeck-Dill L, Iacocca M, Jacobs B, Lobis M, Maranchie JK, McMeekin S, Myers J, Nelson J, Parfitt J, Parwani A, Petrelli N, Rabeno B, Roy S, Salner AL, Slaton J, Stanton M, Thompson RH, Thorne L, Tucker K, Weinberger PM, Winemiller C, Zach LA, Zuna R. Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med. 2016 Jan 14;374(2):135-45. doi: 10.1056/NEJMoa1505917. Epub 2015 Nov 4. PubMed PMID: 26536169; PubMed Central PMCID: PMC4775252.

select

The Molecular Taxonomy of Primary Prostate Cancer. Cell. 2015 Nov 5;163(4):1011-25. doi: 10.1016/j.cell.2015.10.025. PubMed PMID: 26544944; PubMed Central PMCID: PMC4695400.

select

Yau C, Meyer L, Benz S, Vaske C, Scott G, Egan B, Labhart P, Pourmand N, Benz CC. FOXM1 cistrome predicts breast cancer metastatic outcome better than FOXM1 expression levels or tumor proliferation index. Breast Cancer Res Treat. 2015 Nov;154(1):23-32. doi: 10.1007/s10549-015-3589-7. Epub 2015 Oct 12. PubMed PMID: 26456572.

select

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, Perou CM. Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer. Cell. 2015 Oct 8;163(2):506-19. doi: 10.1016/j.cell.2015.09.033. PubMed PMID: 26451490; PubMed Central PMCID: PMC4603750.

select

Laberge RM, Sun Y, Orjalo AV, Patil CK, Freund A, Zhou L, Curran SC, Davalos AR, Wilson-Edell KA, Liu S, Limbad C, Demaria M, Li P, Hubbard GB, Ikeno Y, Javors M, Desprez PY, Benz CC, Kapahi P, Nelson PS, Campisi J. MTOR regulates the pro-tumorigenic senescence-associated secretory phenotype by promoting IL1A translation. Nat Cell Biol. 2015 Aug;17(8):1049-61. doi: 10.1038/ncb3195. Epub 2015 Jul 6. PubMed PMID: 26147250; PubMed Central PMCID: PMC4691706.

select

DeMichele A, Yee D, Berry DA, Albain KS, Benz CC, Boughey J, Buxton M, Chia SK, Chien AJ, Chui SY, Clark A, Edmiston K, Elias AD, Forero-Torres A, Haddad TC, Haley B, Haluska P, Hylton NM, Isaacs C, Kaplan H, Korde L, Leyland-Jones B, Liu MC, Melisko M, Minton SE, Moulder SL, Nanda R, Olopade OI, Paoloni M, Park JW, Parker BA, Perlmutter J, Petricoin EF, Rugo H, Symmans F, Tripathy D, van't Veer LJ, Viscusi RK, Wallace A, Wolf D, Yau C, Esserman LJ. The Neoadjuvant Model Is Still the Future for Drug Development in Breast Cancer. Clin Cancer Res. 2015 Jul 1;21(13):2911-5. doi: 10.1158/1078-0432.CCR-14-1760. Epub 2015 Feb 24. PubMed PMID: 25712686; PubMed Central PMCID: PMC4490043.

select

Genomic Classification of Cutaneous Melanoma. Cell. 2015 Jun 18;161(7):1681-96. doi: 10.1016/j.cell.2015.05.044. PubMed PMID: 26091043; PubMed Central PMCID: PMC4580370.

select

Mockus M, Prebil L, Ereman R, Dollbaum C, Powell M, Yau C, Benz CC. First Pregnancy Characteristics, Postmenopausal Breast Density, and Salivary Sex Hormone Levels in a Population at High Risk for Breast Cancer. BBA Clin. 2015 Jun;3:189-195. doi: 10.1016/j.bbacli.2015.02.003. PubMed PMID: 26317068; PubMed Central PMCID: PMC4547694.

select

Jupe ER, Dalessandri KM, Mulvihill JJ, Miike R, Knowlton NS, Pugh TW, Zhao LP, DeFreese DC, Manjeshwar S, Gramling BA, Wiencke JK, Benz CC. A steroid metabolizing gene variant in a polyfactorial model improves risk prediction in a high incidence breast cancer population. BBA Clin. 2014 Dec;2:94-102. doi: 10.1016/j.bbacli.2014.11.001. eCollection 2014 Dec. PubMed PMID: 26673457; PubMed Central PMCID: PMC4633888.

select

Comprehensive molecular characterization of gastric adenocarcinoma. Nature. 2014 Sep 11;513(7517):202-9. doi: 10.1038/nature13480. Epub 2014 Jul 23. PubMed PMID: 25079317; PubMed Central PMCID: PMC4170219.

select

Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, Leiserson MDM, Niu B, McLellan MD, Uzunangelov V, Zhang J, Kandoth C, Akbani R, Shen H, Omberg L, Chu A, Margolin AA, Van't Veer LJ, Lopez-Bigas N, Laird PW, Raphael BJ, Ding L, Robertson AG, Byers LA, Mills GB, Weinstein JN, Van Waes C, Chen Z, Collisson EA, Benz CC, Perou CM, Stuart JM. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell. 2014 Aug 14;158(4):929-944. doi: 10.1016/j.cell.2014.06.049. Epub 2014 Aug 7. PubMed PMID: 25109877; PubMed Central PMCID: PMC4152462.

select

Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014 Jul 31;511(7511):543-50. doi: 10.1038/nature13385. Epub 2014 Jul 9. PubMed PMID: 25079552; PubMed Central PMCID: PMC4231481.

select

Goncalves RL, Rothschild DE, Quinlan CL, Scott GK, Benz CC, Brand MD. Sources of superoxide/H2O2 during mitochondrial proline oxidation. Redox Biol. 2014;2:901-9. doi: 10.1016/j.redox.2014.07.003. eCollection 2014. PubMed PMID: 25184115; PubMed Central PMCID: PMC4143814.

select

Wilson-Edell KA, Kehasse A, Scott GK, Yau C, Rothschild DE, Schilling B, Gabriel BS, Yevtushenko MA, Hanson IM, Held JM, Gibson BW, Benz CC. RPL24: a potential therapeutic target whose depletion or acetylation inhibits polysome assembly and cancer cell growth. Oncotarget. 2014 Jul 15;5(13):5165-76. doi: 10.18632/oncotarget.2099. PubMed PMID: 24970821; PubMed Central PMCID: PMC4148130.

select

Prebil LA, Ereman RR, Powell MJ, Jamshidian F, Kerlikowske K, Shepherd JA, Hurlbert MS, Benz CC. First pregnancy events and future breast density: modification by age at first pregnancy and specific VEGF and IGF1R gene variants. Cancer Causes Control. 2014 Jul;25(7):859-68. doi: 10.1007/s10552-014-0386-2. Epub 2014 May 7. PubMed PMID: 24801045; PubMed Central PMCID: PMC4048469.

select

Wilson-Edell KA, Yevtushenko MA, Rothschild DE, Rogers AN, Benz CC. mTORC1/C2 and pan-HDAC inhibitors synergistically impair breast cancer growth by convergent AKT and polysome inhibiting mechanisms. Breast Cancer Res Treat. 2014 Apr;144(2):287-298. doi: 10.1007/s10549-014-2877-y. Epub 2014 Feb 22. PubMed PMID: 24562770; PubMed Central PMCID: PMC4318538.

select

Zawadzka AM, Schilling B, Cusack MP, Sahu AK, Drake P, Fisher SJ, Benz CC, Gibson BW. Phosphoprotein secretome of tumor cells as a source of candidates for breast cancer biomarkers in plasma. Mol Cell Proteomics. 2014 Apr;13(4):1034-49. doi: 10.1074/mcp.M113.035485. Epub 2014 Feb 6. PubMed PMID: 24505115; PubMed Central PMCID: PMC3977182.

select

Comprehensive molecular characterization of urothelial bladder carcinoma. Nature. 2014 Mar 20;507(7492):315-22. doi: 10.1038/nature12965. Epub 2014 Jan 29. PubMed PMID: 24476821; PubMed Central PMCID: PMC3962515.

select

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. The somatic genomic landscape of glioblastoma. Cell. 2013 Oct 10;155(2):462-77. doi: 10.1016/j.cell.2013.09.034. PubMed PMID: 24120142; PubMed Central PMCID: PMC3910500.

select

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. doi: 10.1038/ng.2764. PubMed PMID: 24071849; PubMed Central PMCID: PMC3919969.

select

Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature. 2013 Jul 4;499(7456):43-9. doi: 10.1038/nature12222. Epub 2013 Jun 23. PubMed PMID: 23792563; PubMed Central PMCID: PMC3771322.

select

DeMichele A, Berry DA, Zujewski J, Hunsberger S, Rubinstein L, Tomaszewski JE, Kelloff G, Perlmutter J, Buxton M, Lyandres J, Albain KS, Benz C, Chien AJ, Haluska P, Leyland-Jones B, Liu MC, Munster P, Olopade O, Park JW, Parker BA, Pusztai L, Tripathy D, Rugo H, Yee D, Esserman L. Developing safety criteria for introducing new agents into neoadjuvant trials. Clin Cancer Res. 2013 Jun 1;19(11):2817-23. doi: 10.1158/1078-0432.CCR-12-2620. Epub 2013 Mar 7. Review. PubMed PMID: 23470967; PubMed Central PMCID: PMC4096560.

select

Lucanic M, Graham J, Scott G, Bhaumik D, Benz CC, Hubbard A, Lithgow GJ, Melov S. Age-related micro-RNA abundance in individual C. elegans. Aging (Albany NY). 2013 Jun;5(6):394-411. doi: 10.18632/aging.100564. PubMed PMID: 23793570; PubMed Central PMCID: PMC3824409.