John N. Weinstein, MD, PhD

Peer-Reviewed Articles

1. Yuan Y, Ju YS, Kim Y, Li J, Wang Y, Yoon CJ, Yang Y, Martincorena I, Creighton CJ, Weinstein JN, Xu Y, Han L, Kim HL, Nakagawa H, Park K, Campbell PJ, Liang H, PCAWG Consortium. Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nat Genet 52(3):342-352, 2020. e-Pub 2020. PMID: 32024997.
2. ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Pan-Cancer analysis of whole genomes. Nature 578(7793):82-93, 2020. e-Pub 2020. PMID: 32025007.
3. Wang F, Zhang S, Kim TB, Lin YY, Iqbal R, Wang Z, Mohanty V, Sircar K, Karam JA, Wendl MC, Meric-Bernstam F, Weinstein JN, Ding L, Mills GB, Chen K. Integrated transcriptomic-genomic tool Texomer profiles cancer tissues. Nat Methods 16(5):401-404, 2019. e-Pub 2019. PMID: 30988467.
4. 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 362(6413), 2018. PMID: 30361341.
5. 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 174(4):1033, 2018. PMID: 30096301.
6. Malta TM, Sokolov A, Gentles AJ, Burzykowski T, Poisson L, Weinstein JN, Kaminska B, Huelsken J, Omberg L, Gevaert O, Colaprico A, Czerwinska 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 173(2):338-54, 2018. PMID: 29625051.
7. 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 33(4):690-705.e9, 2018. e-Pub 2018. PMID: 29622464.
8. 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 173(2):386-399.e12, 2018. PMID: 29625054.
9. 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 (including Weinstein JN), Hu H. An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics. Cell 173(2):400-416.e11, 2018. PMID: 29625055.
10. 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 (including Weinstein JN, 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 173(2):371-385.e18, 2018. PMID: 29625053.
11. 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 (including Weinstein JN), Van Allen EM, Cherniack AD, Ciriello G, Sander C, Schultz N. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell 173(2):321-337.e10, 2018. PMID: 29625050.
12. 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 (including Weinstein JN). Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. Cell 173(2):305-320.e10, 2018. PMID: 29625049.
13. Wang Z, Yang B, Zhang M, Guo W, Wu Z, Wang Y, Jia L, Li S, Cancer Genome Atlas Research Network (including Weinstein JN), 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 33(4):706-720.e9, 2018. e-Pub 2018. PMID: 29622465.
14. 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 (including Weinstein JN), Cherniack AD, Beroukhim R, Meyerson M. Genomic and Functional Approaches to Understanding Cancer Aneuploidy. Cancer Cell 33(4):676-689.e3, 2018. e-Pub 2018. PMID: 29622463.
15. 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 (including Weinstein JN), Thorsson V, Bass AJ, Laird PW. Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas. Cancer Cell 33(4):721-735.e8, 2018. e-Pub 2018. PMID: 29622466.
16. 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 (including Weinstein JN), 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 173(2):355-370.e14, 2018. PMID: 29625052.
17. 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 (including Weinstein JN), Stuart JM, Benz CC, Laird PW. Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell 173(2):291-304.e6, 2018. PMID: 29625048.
18. 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 33(2):244-58, 2018. PMID: 29438696.
19. Cancer Genome Atlas Research Network (including Weinstein JN). Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas. Cell 171(4):950-965.e28, 2017. PMID: 29100075.
20. 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 171(3):540-556.e25, 2017. e-Pub 2017. PMID: 28988769.
21. Cancer Genome Atlas Research Network (including Weinstein JN). Electronic address: andrew_aguirre@dfci.harvard.edu, Cancer Genome Atlas Research Network. Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma. Cancer Cell 32(2):185-203.e13, 2017. PMID: 28810144.
22. 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 (including Weinstein JN, 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 32(2):204-220.e15, 2017. PMID: 28810145.
23. Zhang Y, Kwok-Shing Ng P, Kucherlapati M, Chen F, Liu Y, Tsang YH, de Velasco G, Jeong KJ, Akbani R, Hadjipanayis A, Pantazi A, Bristow CA, Lee E, Mahadeshwar HS, Tang J, Zhang J, Yang L, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Westbrook TF, Shelley CS, Choueiri TK, Ittmann M, Van Waes C, Weinstein JN, Liang H, Henske EP, Godwin AK, Park PJ, Kucherlapati R, Scott KL, Mills GB, Kwiatkowski DJ, Creighton CJ. A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations. Cancer Cell 31(6):820-832.e3, 2017. e-Pub 2017. PMID: 28528867.
24. Cancer Genome Atlas Research Network. Electronic address: wheeler@bcm.edu, Cancer Genome Atlas Research Network (including Weinstein JN). Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma. Cell 169(7):1327-1341.e23, 2017. PMID: 28622513.
25. 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. Cancer Cell 31(3):411-23, 2017. e-Pub 2017. PMID: 28292439.
26. 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 (including Weinstein JN), Pacak K, Nathanson KL, Wilkerson MD. Comprehensive Molecular Characterization of Pheochromocytoma and Paraganglioma. Cancer Cell 31(2):181-193, 2017. e-Pub 2017. PMID: 28162975.
27. Cancer Genome Atlas Research Network (including Weinstein JN, Analysis Working Group: Asan University, BC Cancer Agency, Brigham and Women’s Hospital, Broad Institute, Brown University, Case Western Reserve University, Dana-Farber Cancer Institute, Duke University, Greater Poland Cancer Centre, Harvard Medical School, Institute for Systems Biology, KU Leuven, Mayo Clinic, Memorial Sloan Kettering Cancer Center, National Cancer Institute, Nationwide Children’s Hospital, Stanford University, University of Alabama, University of Michigan, University of North Carolina, University of Pittsburgh, University of Rochester, University of Southern California, University of Texas MD Anderson Cancer Center, University of Washington, Van Andel Research Institute, Vanderbilt University, Washington University, Genome Sequencing Center: Broad Institute, Washington University in St. Louis, Genome Characterization Centers: BC Cancer Agency, Broad Institute, Harvard Medical School, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, University of North Carolina, University of Southern California Epigenome Center, University of Texas MD Anderson Cancer Center, Van Andel Research Institute, Genome Data Analysis Centers: Broad Institute, Brown University:, Harvard Medical School, Institute for Systems Biology, Memorial Sloan Kettering Cancer Center, University of California Santa Cruz, University of Texas MD Anderson Cancer Center, Biospecimen Core Resource: International Genomics Consortium, Research Institute at Nationwide Children’s Hospital, Tissue Source Sites: Analytic Biologic Services, Asan Medical Center, Asterand Bioscience, Barretos Cancer Hospital, BioreclamationIVT, Botkin Municipal Clinic, Chonnam National University Medical School, Christiana Care Health System, Cureline, Duke University, Emory University, Erasmus University, Indiana University School of Medicine, Institute of Oncology of Moldova, International Genomics Consortium, et al.. Integrated genomic characterization of oesophageal carcinoma. Nature 541(7636):169-175, 2017. e-Pub 2017. PMID: 28052061.
28. Cancer Genome Atlas Research Network (including Weinstein JN). Integrated genomic and molecular characterization of cervical cancer. Nature, 2017. e-Pub 2017. PMID: 28112728.
29. 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 (including Weinstein JN, Hammer GD, Giordano TJ, Verhaak RG. Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. Cancer Cell 30(2):363, 2016. e-Pub 2016. PMID: 27505681.
30. 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 48(6):607-16, 2016. e-Pub 2016. PMID: 27158780.
31. 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, 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 (including Weinstein JN), Noushmehr H, Iavarone A, Verhaak RG. Molecular Profiling Reveals Biologically Discrete Subsets and Pathways of Progression in Diffuse Glioma. Cell 164(3):550-63, 2016. PMID: 26824661.
32. Cancer Genome Atlas Research Network (including Weinstein JN). The molecular taxonomy of primary prostate cancer. Cell 163(4):1011-25, 2015. PMID: 26544944.
33. Zhou W, Chen T, Chong Z, Rohrdanz MA, Melott JM, Wakefield C, Zeng J, Weinstein JN, Meric-Bernstam F, Mills GB, Chen K. TransVar: a multilevel variant annotator for precision genomics. Nat Methods 12(11):1002-3, 2015. PMID: 26513549.
34. 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 (including Weinstein JN), Perou CM. Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer. Cell 163(2):506-19, 2015. PMID: 26451490.
35. Brat DJ, The Cancer Genome Atlas (TCGA) Research Network (including Weinstein JN). Comprehensive and Integrative Genomic Characterization of Diffuse Lower Grade Gliomas. Molecular and Cellular Biology 75(15), 2015.
36. Chin L, et al (352 collaborators).. Genomic Classification of Cutaneous Melanoma. Cell 16(7):1681-96, 2015. e-Pub 2015. PMID: 26091043.
37. 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, 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. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med 372(26):2481-98, 2015. e-Pub 2015. PMID: 26061751.
38. Akbani R, Ng PK, Werner HM, Shahmoradgoli M, Zhang F, Ju Z, Liu W, Yang JY, Yoshihara K, Li J, Ling S, Seviour EG, Ram PT, Minna JD, Diao L, Tong P, Heymach JV, Hill SM, Dondelinger F, Städler N, Byers LA, Meric-Bernstam F, Weinstein JN, Broom BM, Verhaak RG, Liang H, Mukherjee S, Lu Y, Mills GB. Corrigendum: A pan-cancer proteomic perspective on The Cancer Genome Atlas. Nat Commun 6:4852, 2015. e-Pub 2015. PMID: 25629879.
39. Kim H, Zheng S, Amini S, Virk S, Brat D, Grimsby J, Sougnez C, Sloan A, Cohen M, Van Meir E, Scarpace L, Laird P, Weinstein JN, Lander E, Gabriel S, Getz G, Meryerson M, Chin L, Barnholtz-Sloan J, Verhaak R. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature 29(517(7536)):576-82, 2015.
40. Cancer Genome Atlas Research Network (including Weinstein JN). Integrated Genomic Characterization of Papillary Thyroid Carcinoma. Cell 159(3):676-90, 2014. e-Pub 2014.
41. Cancer Genome Atlas (including Weinstein J).. Comprehensive molecular characterization of gastric adenocarcinoma. Nature 11(513(7517)):202-9, 2014.
42. Cancer Genome Atlas Network (including Weinstein JN in Writing Group; invited role as scientific editor). Comprehensive Molecular Profiling of Lung Adenocarcinoma. Nature 511(7511):543-50. e-Pub 2014.
43. Davis CF, Rickets C, 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, Choueriri TK, Hakimi AA, The Cancer Genome Atlas Research Network (include Weinstein JN), Chin L, Meyerson M, Kucherlapati R, Park W-Y, Robertson AG, Laird PW, Henske EP, Kwiatkowski DJ, Park PJ, Morgan M, Shuch B, Muzny D, Wheeler DA, Lienhan WM, Gibbs RA, Rathmell WK, Creighton CJ. The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma. Cancer Cell 26(3):319-30. e-Pub 2014.
44. Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, Leiserson MD, 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, Cancer Genome Atlas Research Network, Benz CC, Perou CM, Stuart JM. Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin. Cell 158(4):929-44, 2014. e-Pub 2014. PMID: 25109877.
45. Yuan Y, Van Allen EM, Omberg L, Wagle N, Amin-Mansour A, Sokolov A, Byers LA, Xu Y, Hess KR, Diao L, Han L, Huang X, Lawrence MS, Weinstein JN, Stuart JM, Mills GB, Garraway LA, Margolin AA, Getz G, Liang H. Assessing the clinical utility of cancer genomic and proteomic data across tumor types. Nat Biotechnol 32(7):644-52, 2014. e-Pub 2014. PMID: 24952901.
46. Yao J, Caballero OL, Yung WK, Weinstein JN, Riggins GJ, Strausberg RL, Zhao Q. Tumor subtype-specific cancer-testis antigens as potential biomarkers and immunotherapeutic targets for cancers. Cancer Immunol Res 2(4):391-9, 2014. e-Pub 2013. PMID: 24764584.
47. Cancer Genome Atlas Research Network (including Weinstein JN as co-chair and lead corresponding author). Comprehensive molecular characterization of urothelial carcinoma of the bladder. Nature 507(315), 2014. e-Pub 2014.
48. Akbani R, Ng PK, Werner HM, Shahmoradgoli M, Zhang F, Ju Z, Liu W, Yang JY, Yoshihara K, Li J, Ling S, Seviour EG, Ram PT, Minna JD, Diao L, Tong P, Heymach JV, Hill SM, Dondelinger F, Städler N, Byers LA, Meric-Bernstam F, Weinstein JN, Broom BM, Verhaak RG, Liang H, Mukherjee S, Lu Y, Mills GB. A pan-cancer proteomic perspective on The Cancer Genome Atlas. Nat Commun 5(Article number: 3887):3887, 2014. e-Pub 2014. PMID: 24871328.
49. Weinstein JN, Lorenzi PL. Discrepancies in drug sensitivity. Nature 504(7480):381-3, 2013. e-Pub 2013. PMID: 24284624.
50. Li J, Lu Y, Akbani R, Ju Z, Roebuck PL, Liu W, Yang JY, Broom BM, Verhaak RG, Kane DW, Wakefield C, Weinstein JN, Mills GB, Liang H. TCPA: A Resource for Cancer Functional Proteomics Data. Nat Methods 10(11):1046-7, 2013. e-Pub 2013. PMID: 24037243.
51. 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 JN, Meyerson M, Gabriel S, Laird PW, Haussler D, Getz G, Chin L, TCGA Research Network. The somatic genomic landscape of glioblastoma. Cell 155(2):462-77, 2013. PMID: 24120142.
52. Cancer Genome Atlas Research Network, Weinstein JN, Collison EA, Mills GB, Shaw KRM, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM.. The Cancer Genome Atlas Pan-Cancer Analysis Project. Nature Genetics 45(10):1113-20, 2013. PMID: 24071849.
53. Cancer Genome Atlas Research Network (including Weinstein JN for analysis). Comprehensive Molecular characterization of clear cell renal cell carcinoma. Nature 499(7456):43-9, 2013. e-Pub 2013. PMID: 23792563.
54. Cancer Genome Atlas Research Network (include Weinstein JN). Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. NEJM 368(22):2059-74, 2013. e-Pub 2013. PMID: 23634996.
55. Cancer Genome Atlas Research Network (including Weinstein JN, 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 497(7447):67-73, 2013. PMID: 23636398.
56. Cancer Genome Atlas Network (including Weinstein JN for statistical analyses). Comprehensive molecular portraits of human breast tumours. Nature 490(7418):61-70, 2012. e-Pub 2012. PMID: 23000897.
57. Cancer Genome Atlas Research Network, Hammerman PS, Hayes DN, Wilkerson MD, Schultz N, Bose R, Chu A, Collisson EA, Cope L, Creighton CJ, Getz G, Herman JG, Johnson BE, Kucherlapati R, Ladanyi M, Maher CA, Robertson G, Sander C, Shen R, Sinha R, Sivachenko A, Thomas RK, Travis WD, Tsao MS, Weinstein JN (for statistical analyses and Writing Committee), Wigle DA, Baylin SB, Govindan R, Meyerson M. Comprehensive genomic characterization of squamous cell lung cancers. Nature 489(7417):519-25, 2012. e-Pub 2012. PMID: 22960745.
58. Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487(7407):330-7, 2012. e-Pub 2012. PMID: 22810696.
59. Weinstein JN. Drug discovery: Cell lines battle cancer. Nature 483(7391):544-5, 2012. e-Pub 2012. PMID: 22460893.
60. Bolton KL, Chenevix-Trench G, Goh C, Sadetzki S, Ramus SJ, Karlan BY, Lambrechts D, Despierre E, Barrowdale D, McGuffog L, Healey S, Easton DF, Sinilnikova O, Benitez J, Garcia MJ, Neuhausen S, Gail MH, Hartge P, Peock S, Frost D, Evans DG, Eeles R, Godwin AK, Daly MB, Kwong A, Ma ES, Lazaro C, Blanco I, Montagna M, D'Andrea E, Nicoletto MO, Johnatty SE, Kjaer, SK, Jensen A, Hogdall E, Goode EL, Fridley BL, Loud JT, Greene MH, Mai PL, Chetrit A, Lubin F, Hirsh-Yechezkel G, Glendon G, Andrulis IL, Toland AE, Senter L, Gore ME, Gourley C, Michie CO, Song H, Tyrer J, Whittemore AS, McGuire V, Sieh W, Kristoffersson U, Olsson H, Borg A, Levine DA, Steele L, Beattie MS, Chan S, Nussbaum RL, Moysich KB, Gross J, Cass I, Walsh C, Li AJ, Leuchter R, GordonO, Garcia-Closas M, Gayther SA, Chanock SJ, Antoniou AC, Pharoah PD, The Cancer Genome Atlas (including Weinstien JN. Association Between BRCA1 and BRCA2 Mutations and Survival in Women With Invasive Epithelial Ovarian Cancer. JAMA 307(4):382-90, 2012. e-Pub 2012. PMID: 22274685.
61. Agrawal N, Frederick MJ, Pickering CR, Bettegowda C, Chang K, Li RJ, Fakhry C, Xie TX, Zhang J, Wang J, Zhang N, El-Naggar AK, Jasser SA, Weinstein JN, Treviño L, Drummond JA, Muzny DM, Wu Y, Wood LD, Hruban RH, Westra WH, Koch WM, Califano JA, Gibbs RA, Sidransky D, Vogelstein B, Velculescu VE, Papadopoulos N, Wheeler DA, Kinzler KW, Myers JN. Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1. Science 333(6046):1154-7, 2011. e-Pub 2011. PMID: 21798897.
62. Cancer Genome Atlas (TCGA) Research Network (including Weinstein JN for analysis and writing). Integrated Genomic Analyses of Ovarian Carcinoma. Nature 474(7353):609-15, 2011. PMID: 21720365.
63. Weinstein JN. A postgenomic visual icon. Science 319(5871):1772-3, 2008. PMID: 18369130.
64. Cancer Genome Atlas Research Network (including Weinstein JN for pathway analyses, writing, and scientific editing). Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455(7216):1061-8, 2008. PMID: 18772890.
65. Weinstein JN, Pommier Y. Connecting genes, drugs and diseases. Nat Biotechnol 24(11):1365-6, 2006. PMID: 17093484.
66. Ludwig JA, Weinstein JN. Biomarkers in cancer staging, prognosis, and treatment selection. Nat Rev Cancer 5(11):845-56, 2005. PMID: 16239904.
67. Ule J, Ule A, Spencer J, Williams A, Hu JS, Cline M, Wang H, Clark T, Fraser C, Ruggiu M, Zeeberg BR, Kane D, Weinstein JN, Blume J, Darnell RB. Nova regulates brain-specific splicing to shape the synapse. Nat Genet 37(8):844-52, 2005. PMID: 16041372.
68. Szakacs G, Annereau JP, Lababidi S, Shankavaram U, Arciello A, Bussey KJ, Reinhold W, Guo Y, Kruh GD, Reimers M, Weinstein JN, Gottesman MM. Predicting drug sensitivity and resistance: Profiling ABC transporter genes in cancer cells. Cancer Cell 6(2):129-37, 2004. PMID: 15324696.
69. Buckner JC, Moynihan TJ, Quinn DI, Schlegel U, Ali-Osman F, Srivenugopal K, Sawaya R, Esteller M, Herman JG, Weinstein JN. The DNA-Repair Gene MGMT and the Clinical Response of Gliomas to Alkylating Agents. NEJM 344:686-88 (commentary), 2001.
70. Ross DT, Scherf U, Eisen MB, Perou CM, Rees C, Spellman P, Iyer V, Jeffrey SS, Van de Rijn M, Waltham M, Pergamenschikov A, Lee JC, Lashkari D, Shalon D, Myers TG, Weinstein JN, Botstein D, Brown PO. Systematic variation in gene expression patterns in human cancer cell lines. Nat Genet 24(3):227-35, 2000. PMID: 10700174.
71. Scherf U, Ross DT, Waltham M, Smith LH, Lee JK, Tanabe L, Kohn KW, Reinhold WC, Myers TG, Andrews DT, Scudiero DA, Eisen MB, Sausville EA, Pommier Y, Botstein D, Brown PO, Weinstein JN. A gene expression database for the molecular pharmacology of cancer. Nat Genet 24(3):236-44, 2000. PMID: 10700175.
72. Weinstein JN. Fishing expeditions. Science 282(5389):628-9, 1998. PMID: 9841413.
73. Weinstein JN, Myers TG, O'Connor PM, Friend SH, Fornace AJ, Kohn KW, Fojo T, Bates SE, Rubinstein LV, Anderson NL, Buolamwini JK, van Osdol WW, Monks AP, Scudiero DA, Sausville EA, Zaharevitz DW, Bunow B, Viswanadhan VN, Johnson GS, Wittes RE, Paull KD. An information-intensive approach to the molecular pharmacology of cancer. Science 275(5298):343-9, 1997. PMID: 8994024.
74. Lori F, Malykh A, Cara A, Sun D, Weinstein JN, Lisziewicz J, Gallo RC. Hydroxyurea as an inhibitor of human immunodeficiency virus-type 1 replication. Science 266(5186):801-5, 1994. PMID: 7973634.
75. Weinstein JN, Steller MA, Keenan AM, Covell DG, Key ME, Sieber SM, Oldham RK, Hwang KM, Parker RJ. Monoclonal antibodies in the lymphatics: selective delivery to lymph node metastases of a solid tumor. Science 222(4622):423-6, 1983. PMID: 6623082.
76. Leserman LD, Barbet J, Kourilsky F, Weinstein JN. Targeting to cells of fluorescent liposomes covalently coupled with monoclonal antibody or protein A. Nature 288(5791):602-4, 1980. PMID: 7442804.
77. Blumenthal R, Klausner RD, Weinstein JN. Voltage-dependent translocation of the asialoglycoprotein receptor across lipid membranes. Nature 288(5789):333-8, 1980. PMID: 6253830.
78. Weinstein JN, Magin RL, Yatvin MB, Zaharko DS. Liposomes and local hyperthermia: selective delivery of methotrexate to heated tumors. Science 204(4389):188-91, 1979. PMID: 432641.
79. Yatvin MB, Weinstein JN, Dennis WH, Blumenthal R. Design of liposomes for enhanced local release of drugs by hyperthermia. Science 202(4374):1290-3, 1978. PMID: 364652.
80. Weinstein JN, Yoshikami S, Henkart P, Blumenthal R, Hagins WA. Liposome-cell interaction: transfer and intracellular release of a trapped fluorescent marker. Science 195(4277):489-92, 1977. PMID: 835007.
81. Weinstein JN, Leitz FB. Electric Power from Differences in Salinity: The Dialytic Battery. Science 191(4227):557-559, 1976. PMID: 17792805.
82. Weinstein JN, Caplan SR. Charge-mosaic membranes: dialytic separation of electrolytes from nonelectrolytes and amino acids.. Science 169(942):296-8, 1970. PMID: 5450359.
83. Weinstein JN, Caplan SR. Charge-mosaic membranes: enhanced permeability and negative osmosis with a symmetrical salt.. Science 161(836):70-2, 1968. PMID: 5655268.