John N. Weinstein, MD, PhD

Peer-Reviewed Articles

1. Lee, OW, Karyadi, DM, Hartley, SW, Zhou, W, Machiela, MJ, Zamani, SA, Zurnadzhy, LY, Weinstein, JN, Park, YJ, Seo, JS, Thomas, GA, Bogdanova, T, Tronko, MD, Morton, LM, Chanock, SJ. Somatic copy number deletion of chromosome 22q in papillary thyroid carcinoma. European Thyroid Journal 14(1), 2025. e-Pub 2025. PMID: 39773491.
2. Guo, S, Liu, X, Cheng, X, Jiang, Y, Ji, S, Liang, Q, Koval, A, Li, Y, Owen, L, Kim, IK, Aparicio, A, Lee, S, Sood, AK, Kopetz, S, Shen, JY, Weinstein, JN, DeAngelis, MM, Chen, R, Wang, W. A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples. Genome Research 35(1):147-161, 2025. e-Pub 2025. PMID: 39586714.
3. Sundaram, L, Kumar, A, Zatzman, M, Salcedo, A, Ravindra, N, Shams, S, Louie, BH, Bagdatli, ST, Myers, MA, Sarmashghi, S, Choi, HY, Choi, WY, Yost, KE, Zhao, Y, Granja, J, Hinoue, T, Hayes, DN, Cherniack, AD, Felau, I, Choudhry, H, Zenklusen, JC, Farh, KH, McPherson, A, Curtis, C, Laird, PW, Corces, MR, Chang, HY, Greenleaf, WJ, Demchok, JA, Yang, L, Tarnuzzer, R, Caesar-Johnson, SJ, Wang, Z, Doane, AS, Khurana, E, Castro, MA, Lazar, A, Broom, BM, Weinstein, JN, Akbani, R, Kumar, SV, Raphael, BJ, Wong, C, Stuart, JM, Safavi, R, Benz, C, Johnson, BK, Kyi, C, Shen, H. Single-cell chromatin accessibility reveals malignant regulatory programs in primary human cancers. Science (New York, N.Y.) 385(6713):eadk9217, 2024. e-Pub 2024. PMID: 39236169.
4. Chen, Z, Ho, IL, Soeung, M, Yen, EY, Liu, J, Yan, L, Rose, J, Srinivasan, S, Jiang, S, Chang, Q, Feng, N, Gay, J, Wang, Q, Wang, J, Lorenzi, PL, Veillon, L, Wei, B, Weinstein, JN, Deem, AK, Gao, S, Genovese, G, Viale, A, Yao, W, Lyssiotis, CA, Marszalek, JR, Draetta, G, Ying, H. Ether phospholipids are required for mitochondrial reactive oxygen species homeostasis. Nature communications 14(1), 2023. e-Pub 2023. PMID: 37069167.
5. Liu, Y, Lawson, BC, Huang, X, Broom, BM, Weinstein, JN. Prediction of Ovarian Cancer Response to Therapy Based on Deep Learning Analysis of Histopathology Images. Cancers 15(16), 2023. e-Pub 2023. PMID: 37627071.
6. Shehwana H, Kumar SV, Melott JM, Rohrdanz MA, Wakefield C, Ju Z, Siwak DR, Lu Y, Broom BM, Weinstein JN, Mills GB, Akbani R. RPPA SPACE: an R package for normalization and quantitation of Reverse-Phase Protein Array data. Bioinformatics 38(22):5131-5133, 2022. e-Pub 2022. PMID: 36205581.
7. Bondaruk J, Jaksik R, Wang Z, Cogdell D, Lee S, Chen Y, Dinh KN, Majewski T, Zhang L, Cao S, Tian F, Yao H, Kus P, Chen H, Weinstein JN, Navai N, Dinney C, Gao J, Theodorescu D, Logothetis C, Guo CC, Wang W, McConkey D, Wei P, Kimmel M, Czerniak B. Erratum: The origin of bladder cancer from mucosal field effects. iScience 25(7):104715, 2022. e-Pub 2022. PMID: 35811851.
8. Bondaruk J, Jaksik R, Wang Z, Cogdell D, Lee S, Chen Y, Dinh KN, Majewski T, Zhang L, Cao S, Tian F, Yao H, Kus P, Chen H, Weinstein JN, Navai N, Dinney C, Gao J, Theodorescu D, Logothetis C, Guo CC, Wang W, McConkey D, Wei P, Kimmel M, Czerniak B. The origin of bladder cancer from mucosal field effects. iScience 25(7):104551, 2022. e-Pub 2022. PMID: 35747385.
9. Dai B, Augustine JJ, Kang Y, Roife D, Li X, Deng J, Tan L, Rusling LA, Weinstein JN, Lorenzi PL, Kim MP, Fleming JB. Compound NSC84167 selectively targets NRF2-activated pancreatic cancer by inhibiting asparagine synthesis pathway. Cell Death Dis 12(7):693, 2021. e-Pub 2021. PMID: 34247201.
10. 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, Network TR, Meyerson M, Govindan R, Imielinski M. Whole-genome Characterization of Lung Adenocarcinomas Lacking Alterations in the RTK/RAS/RAF Pathway. Cell Rep 34(8):108784, 2021. e-Pub 2021. PMID: 33626341.
11. 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, Lee JJ, 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, Network TR, Meyerson M, Govindan R, Imielinski M. Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway. Cell Rep 34(5):108707, 2021. e-Pub 2021. PMID: 33535033.
12. Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S, Group MW, working group PNSMCM, Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L, Consortium P. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun 11(1):4748, 2020. e-Pub 2020. PMID: 32958763.
13. Li CH, Prokopec SD, Sun RX, Yousif F, Schmitz N, Clinical Translation PTSA, Boutros PC, Consortium P. Sex differences in oncogenic mutational processes. Nat Commun 11(1):4330, 2020. e-Pub 2020. PMID: 32859912.
14. Goldman MJ, Zhang J, Fonseca NA, Cortés-Ciriano I, Xiang Q, Craft B, Piñeiro-Yáñez E, O'Connor BD, Bazant W, Barrera E, Muñoz-Pomer A, Petryszak R, Füllgrabe A, Al-Shahrour F, Keays M, Haussler D, Weinstein JN, Huber W, Valencia A, Park PJ, Papatheodorou I, Zhu J, Ferretti V, Vazquez M. A user guide for the online exploration and visualization of PCAWG data. Nat Commun 11(1):3400, 2020. e-Pub 2020. PMID: 32636365.
15. Yang G, Bondaruk J, Cogdell D, Wang Z, Lee S, Lee JG, Zhang S, Choi W, Wang Y, Liang Y, Wang G, Wang Y, Yao H, Dadhania V, Gao J, Logothetis C, Siefker-Radtke A, Kamat A, Dinney C, Theodorescu D, Kimmel M, Wei P, Guo CC, Weinstein JN, McConkey DJ, Czerniak B. Urothelial-to-Neural Plasticity Drives Progression to Small Cell Bladder Cancer. iScience 23(6):101201, 2020. e-Pub 2020. PMID: 32521509.
16. Guo CC, Bondaruk J, Yao H, Wang Z, Zhang L, Lee S, Lee JG, Cogdell D, Zhang M, Yang G, Dadhania V, Choi W, Wei P, Gao J, Theodorescu D, Logothetis C, Dinney C, Kimmel M, Weinstein JN, McConkey DJ, Czerniak B. Assessment of Luminal and Basal Phenotypes in Bladder Cancer. Sci Rep 10(1):9743, 2020. e-Pub 2020. PMID: 32546765.
17. Lubkowski J, Vanegas J, Chan WK, Lorenzi PL, Weinstein JN, Sukharev S, Fushman D, Rempe S, Anishkin A, Wlodawer A. Mechanism of Catalysis by l-Asparaginase. Biochemistry 59(20):1927-1945, 2020. e-Pub 2020. PMID: 32364696.
18. Kamoun A, de 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, Aine M, Bernard-Pierrot I, Czerniak B, Gibb EA, Kim J, Kwiatkowski DJ, Lebret T, Liedberg F, Siefker-Radtke AA, Sirab N, Taber A, Weinstein JN. Reply To Kenneth B. Yatai, Mark J. Dunning, Dennis Wang. Consensus Genomic Subtypes of Muscle-invasive Bladder Cancer: A Step in the Right Direction but Still a Long Way To Go. Eur Urol 2020;77:434-5. Eur Urol 77(4):436-438, 2020. e-Pub 2020. PMID: 32037144.
19. Ryan MC, Stucky M, Wakefield C, Melott JM, Akbani R, Weinstein JN, Broom BM. Interactive Clustered Heat Map Builder: An easy web-based tool for creating sophisticated clustered heat maps. F1000Research. e-Pub 2020.
20. 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, Consortium P. Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nat Genet 52(3):342-352, 2020. e-Pub 2020. PMID: 32024997.
21. Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC, Working Group PDAFI, Reimand J, Consortium P. Integrative pathway enrichment analysis of multivariate omics data. Nat Commun 11(1):735, 2020. e-Pub 2020. PMID: 32024846.
22. Sieverling L, Hong C, Koser SD, Ginsbach P, Kleinheinz K, Hutter B, Braun DM, Cortés-Ciriano I, Xi R, Kabbe R, Park PJ, Eils R, Schlesner M, Working Group PV, Brors B, Rippe K, Jones DTW, Feuerbach L, Consortium P. Genomic footprints of activated telomere maintenance mechanisms in cancer. Nat Commun 11(1):733, 2020. e-Pub 2020. PMID: 32024817.
23. Shuai S, Working Group PDAFI, Gallinger S, Stein LD, Consortium P. Combined burden and functional impact tests for cancer driver discovery using DriverPower. Nat Commun 11(1):734, 2020. e-Pub 2020. PMID: 32024818.
24. Bhandari V, Li CH, Bristow RG, Boutros PC, Consortium P. Divergent mutational processes distinguish hypoxic and normoxic tumours. Nat Commun 11(1):737, 2020. e-Pub 2020. PMID: 32024819.
25. Cmero M, Yuan K, Ong CS, Schröder J, Working Group PEAH, Corcoran NM, Papenfuss T, Hovens CM, Markowetz F, Macintyre G, Consortium P. Inferring structural variant cancer cell fraction. Nat Commun 11(1):730, 2020. e-Pub 2020. PMID: 32024845.
26. Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A, Working Group PT, Working Group PSV, Creighton CJ, Consortium P. High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations. Nat Commun 11(1):736, 2020. e-Pub 2020. PMID: 32024823.
27. Rubanova Y, Shi R, Harrigan CF, Li R, Wintersinger J, Sahin N, Deshwar AG, Working Group PEAH, Morris QD, Consortium P. Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig. Nat Commun 11(1):731, 2020. e-Pub 2020. PMID: 32024834.
28. Carlevaro-Fita J, Lanzós A, Feuerbach L, Hong C, Mas-Ponte D, Pedersen JS, Interpretation Group PDAF, Johnson R, Consortium P. Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis. Commun Biol 3(1):56, 2020. e-Pub 2020. PMID: 32024996.
29. Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, Wheeler DA, Brunak S, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, Sahinalp SC, Valencia A, Working Group PDAFI, Reimand J, Stuart JM, Raphael BJ, Consortium P. Pathway and network analysis of more than 2500 whole cancer genomes. Nat Commun 11(1):729, 2020. e-Pub 2020. PMID: 32024854.
30. Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, Shuai S, Lanzós A, Herrmann C, Maruvka YE, Shen C, Amin SB, Bandopadhayay P, Bertl J, Boroevich KA, Busanovich J, Carlevaro-Fita J, Chakravarty D, Chan CWY, Craft D, Dhingra P, Diamanti K, Fonseca NA, Gonzalez-Perez A, Guo Q, Hamilton MP, Haradhvala NJ, Hong C, Isaev K, Johnson TA, Juul M, Kahles A, Kahraman A, Kim Y, Komorowski J, Kumar K, Kumar S, Lee D, Lehmann KV, Li Y, Liu EM, Lochovsky L, Park K, Pich O, Roberts ND, Saksena G, Schumacher SE, Sidiropoulos N, Sieverling L, Sinnott-Armstrong N, Stewart C, Tamborero D, Tubio JMC, Umer HM, Uusküla-Reimand L, Wadelius C, Wadi L, Yao X, Zhang CZ, Zhang J, Haber JE, Hobolth A, Imielinski M, Kellis M, Lawrence MS, von Mering C, Nakagawa H, Raphael BJ, Rubin MA, Sander C, Stein LD, Stuart JM, Tsunoda T, Wheeler DA, Johnson R, Reimand J, Gerstein M, Khurana E, Campbell PJ, López-Bigas N, Working Group PDAFI, Working Group PSV, Weischenfeldt J, Beroukhim R, Martincorena I, Pedersen JS, Getz G, Consortium P. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature 578(7793):102-111, 2020. e-Pub 2020. PMID: 32025015.
31. Genomes Consortium IPAOW. Pan-Cancer analysis of whole genomes. Nature 578(7793):82-93, 2020. e-Pub 2020. PMID: 32025007.
32. Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, Mitchell TJ, Rubanova Y, Anur P, Yu K, Tarabichi M, Deshwar A, Wintersinger J, Kleinheinz K, Vázquez-García I, Haase K, Jerman L, Sengupta S, Macintyre G, Malikic S, Donmez N, Livitz DG, Cmero M, Demeulemeester J, Schumacher S, Fan Y, Yao X, Lee J, Schlesner M, Boutros PC, Bowtell DD, Zhu H, Getz G, Imielinski M, Beroukhim R, Sahinalp SC, Ji Y, Peifer M, Markowetz F, Mustonen V, Yuan K, Wang W, Morris QD, Working Group PE&H, Spellman PT, Wedge DC, Van Loo P, Consortium P. The evolutionary history of 2,658 cancers. Nature 578(7793):122-128, 2020. e-Pub 2020. PMID: 32025013.
33. Li Y, Roberts ND, Wala JA, Shapira O, Schumacher SE, Kumar K, Khurana E, Waszak S, Korbel JO, Haber JE, Imielinski M, Working Group PSV, Weischenfeldt J, Beroukhim R, Campbell PJ, Consortium P. Patterns of somatic structural variation in human cancer genomes. Nature 578(7793):112-121, 2020. e-Pub 2020. PMID: 32025012.
34. Core Group PT, Calabrese C, Davidson NR, Demircioglu 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, Working Group PT, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, Consortium P. Genomic basis for RNA alterations in cancer. Nature 578(7793):129-136, 2020. e-Pub 2020. PMID: 32025019.
35. Alexandrov LB, Kim J, Haradhvala NJ, Huang MN, Tian Ng AW, Wu Y, Boot A, Covington KR, Gordenin DA, Bergstrom EN, Islam SMA, Lopez-Bigas N, Klimczak LJ, McPherson JR, Morganella S, Sabarinathan R, Wheeler DA, Mustonen V, Working Group PMS, Getz G, Rozen SG, Stratton MR, Consortium P. The repertoire of mutational signatures in human cancer. Nature 578(7793):94-101, 2020. e-Pub 2020. PMID: 32025018.
36. Du D, Chang CH, Wang Y, Tong P, Chan WK, Chiu Y, Peng B, Tan L, Weinstein JN, Lorenzi PL. Response Envelope Analysis for Quantitative Evaluation of Drug Combinations. Bioinformatics 35(19):3761-3770, 2019. e-Pub 2019. PMID: 30851108.
37. Donehower LA, Soussi T, Korkut A, Liu Y, Schultz A, Cardenas M, Li X, Babur O, Hsu TK, Lichtarge O, Weinstein JN, Akbani R, Wheeler DA. Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas. Cell Rep 28(11):3010, 2019. e-Pub 2019. PMID: 31509758.
38. Chan WK, Horvath TD, Tan L, Link T, Harutyunyan KG, Pontikos MA, Anishkin A, Du D, Martin LA, Yin E, Rempe SB, Sukharev S, Konopleva M, Weinstein JN, Lorenzi PL. Glutaminase activity of L-asparaginase contributes to durable preclinical activity against acute lymphoblastic leukemia. Mol Cancer Ther 18(9):1587-1592, 2019. e-Pub 2019. PMID: 31209181.
39. Donehower LA, Soussi T, Korkut A, Liu Y, Schultz A, Cardenas M, Li X, Babur O, Hsu TK, Lichtarge O, Weinstein JN, Akbani R, Wheeler DA. Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas. Cell Rep 28(5):1370-1384.e5, 2019. e-Pub 2019. PMID: 31365877.
40. 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.
41. Chen T, Du D, Chen J, Zhou P, Weinstein JN, Yao L, Liu Y. ZC3H12A Expression in Different Stages of Colorectal Cancer. Oncoscience 6(3):301-11, 2019. e-Pub 2019. PMID: 31106233.
42. Majewski T, Yao H, Bondaruk J, Chung W, Lee S, Lee JG, Zhang S, Cogdell D, Yang G, Choi W, Dinney C, Grossman HB, Logothetis C, Scherer SE, Guo CC, Zhang L, Wei P, Weinstein JN, Issa JP, Baggerly K, McConkey DJ, Czerniak B. Whole-Organ Genomic Characterization of Mucosal Field Effects Initiating Bladder Carcinogenesis. Cell Rep 26(8):2241-2256.e4, 2019. e-Pub 2019. PMID: 30784602.
43. Peng B, Wang G, Ma J, Leong MC, Wakefield C, Melott J, Chiu Y, Du D, Weinstein JN. SoS Notebook: An Interactive Multi-Language Data Analysis Environment. Bioinformatics 34(21):3768-70, 2018. e-Pub 2018. PMID: 29790910.
44. 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, Analysis Network CGA, Greenleaf WJ, Chang HY. The chromatin accessibility landscape of primary human cancers. Science 362(6413), 2018. e-Pub 2018. PMID: 30361341.
45. j H, al E. Integrative Molecular Characterization of Malignant Pleural Mesothelioma. Cancer Discovery:1548-65, 2018. e-Pub 2018.
46. 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, Research Network RLCGA, 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 System 7(4):422-37, 2018. e-Pub 2018. PMID: 30268436.
47. Kahles A, Lehmann KV, Toussaint NC, Hüser M, Stark SG, Sachsenberg T, Stegle O, Kohlbacher O, Sander C, Research Network CGA, Rätsch G. Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients. Cancer Cell 34(2):211-224.e6, 2018. e-Pub 2018. PMID: 30078747.
48. 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, Network TR, Weinstein JN, Kwiatkowski DJ, Lerner SP. Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer. Cell 174(4):1033, 2018. e-Pub 2018. PMID: 30096301.
49. Du D, Yuan J, Ma W, Ning J, Weinstein JN, Yuan X, Fuller GN, Liu Y. Clinical Significance of FBXO17 Gene Expression in High-Grade Glioma. BMC Cancer 18(773):1-10, 2018. e-Pub 2018. PMID: 30064493.
50. 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, Research Network CGA, Akbani R, Wheeler DA, Laird PW, Nathanson KL, Cortessis VK, Hoadley KA. Integrated Molecular Characterization of Testicular Germ Cell Tumors. Cell Rep 23(11):3392-3406, 2018. e-Pub 2018. PMID: 29898407.
51. 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, Research Network CGA, Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich L. The Immune Landscape of Cancer. Immunity 48(4):812-830.e14, 2018. e-Pub 2018. PMID: 29628290.
52. Du D, Ma W, Yates MS, Chen T, Lu KH, Lu Y, Weinstein JN, Broaddus RR, Mills GB, Liu Y. Predicting high-risk endometrioid carcinomas using proteins. Oncotarget 9(28):19704-15, 2018. e-Pub 2018. PMID: 29731976.
53. 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, Research Network CGA, Bathe OF, Liang H. Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers. Cell Rep 23(1):255-269.e4, 2018. e-Pub 2018. PMID: 29617665.
54. 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, Research Network CGA, Monnat RJ, Xiao Y, Wang C. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Rep 23(1):239-254.e6, 2018. e-Pub 2018. PMID: 29617664.
55. 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, Research Network CGA, 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 23(1):194-212.e6, 2018. e-Pub 2018. PMID: 29617660.
56. Saltz J, Gupta R, Hou L, Kurc T, Singh P, Nguyen V, Samaras D, Shroyer KR, Zhao T, Batiste R, Van Arnam J, Weinstein JN) CGARN(, 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 23(1):181-193.e7, 2018. e-Pub 2018. PMID: 29617659.
57. Wang Z, Yang B, Zhang M, Guo W, Wu Z, Wang Y, Jia L, Li S, Weinstein JN) CGARN(, 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.
58. 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, Research Network CGA, 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.
59. Taylor AM, Shih J, Ha G, Gao GF, Zhang X, Berger AC, Schumacher SE, Wang C, Hu H, Liu J, Lazar AJ, Weinstein JN) CGARN(, 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.
60. Gao Q, Liang WW, Foltz SM, Mutharasu G, Jayasinghe RG, Cao S, Liao WW, Reynolds SM, Wyczalkowski MA, Yao L, Yu L, Sun SQ, Working Group FA, Weinstein JN) CGARN(, 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 23(1):227-238.e3, 2018. e-Pub 2018. PMID: 29617662.
61. 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, Weinstein JN) CGARN(, Vincent B, Eyras E, Chen K, Shmulevich I, Chen F, Ding L. Systematic Analysis of Splice-Site-Creating Mutations in Cancer. Cell Rep 23(1):270-281.e3, 2018. e-Pub 2018. PMID: 29617666.
62. 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, Weinstein JN) CGARN(. Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. Cell 173(2):305-320.e10, 2018. e-Pub 2018. PMID: 29625049.
63. Chen H, Li C, Peng X, Zhou Z, Weinstein JN, Research Network CGA, Liang H. A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples. Cell 173(2):386-399.e12, 2018. e-Pub 2018. PMID: 29625054.
64. 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, Weinstein JN) CGARN(, Hu H. An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics. Cell 173(2):400-416.e11, 2018. e-Pub 2018. PMID: 29625055.
65. 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, Group MW, 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. e-Pub 2018. PMID: 29625053.
66. 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, Weinstein JN) CGARN(, 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. e-Pub 2018. PMID: 29625050.
67. Chiu HS, Somvanshi S, Patel E, Chen TW, Singh VP, Zorman B, Patil SL, Pan Y, Chatterjee SS, Weinstein JN) CGARN(, Sood AK, Gunaratne PH, Sumazin P. Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context. Cell Rep 23(1):297-312.e12, 2018. e-Pub 2018. PMID: 29617668.
68. 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, Weinstein JN) CGARN(, Piwnica-Worms H, Ma L, Liang H. Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types. Cell Rep 23(1):213-226.e3, 2018. e-Pub 2018. PMID: 29617661.
69. 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, Research Network CGA, 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. e-Pub 2018. PMID: 29625051.
70. Seiler M, Peng S, Agrawal AA, Palacino J, Teng T, Zhu P, Smith PG, Weinstein JN) CGARN(, Buonamici S, Yu L. Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types. Cell Rep 23(1):282-296.e4, 2018. e-Pub 2018. PMID: 29617667.
71. 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, Weinstein JN) CGARN(, Spellman PT, Rathmell WK, Linehan WM. The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Rep 23(1):313-326.e5, 2018. e-Pub 2018. PMID: 29617669.
72. 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, Weinstein JN) CGAN(, 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. e-Pub 2018. PMID: 29625048.
73. 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, Weinstein JN) CGARN(, 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. e-Pub 2018. PMID: 29625052.
74. 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, Weinstein JN) CGARN(, 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.
75. Way GP, Sanchez-Vega F, La K, Armenia J, Chatila WK, Luna A, Sander C, Cherniack AD, Mina M, Ciriello G, Schultz N, Weinstein JN) CGARN(, Sanchez Y, Greene CS. Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. Cell Rep 23(1):172-180.e3, 2018. e-Pub 2018. PMID: 29617658.
76. 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, Weinstein JN) CGAN(. Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas. Cell Syst 6(3):282-300.e2, 2018. e-Pub 2018. PMID: 29596783.
77. 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, Group MW, Weinstein JN) CGARN(. Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Cell Syst 6(3):271-281.e7, 2018. e-Pub 2018. PMID: 29596782.
78. 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, Atlas Network CG, 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. e-Pub 2018. PMID: 29438696.
79. Li J, Akbani R, Zhao W, Lu Y, Weinstein JN, Mills GB, Liang H. Explore, Visualize and Analyze Functional Cancer Proteomic Data Using The Cancer Proteome Atlas. Cancer Res 77(21):e51-4, 2017. e-Pub 2017. PMID: 29092939.
80. Broom BM, Ryan MC, Brown RE, Ikeda F, Stucky M, Kane DW, Melott J, Wakefield C, Casasent TD, Akbani R, Weinstein JN. A Galaxy implementation of next-generation clustered heat maps for interactive exploration of molecular profiling data. Cancer Res 77(21):e23-26, 2017. e-Pub 2017. PMID: 29092932.
81. Weinstein JN) CGARN(. Comprehensive and Integrated Genomic Characterization of Adult Soft Tissue Sarcomas. Cell 171(4):950-965.e28, 2017. e-Pub 2017. PMID: 29100075.
82. 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, Network TR, 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.
83. Su X, Zhang J, Mouawad R, Compérat E, Rouprêt M, Allanic F, Parra J, Bitker MO, Thompson EJ, Gowrishankar B, Houldsworth J, Weinstein JN, Tost J, Broom BM, Khayat D, Spano JP, Tannir NM, Malouf GG. NSD1 inactivation and SETD2 mutation drive a convergence toward loss-of-function of H3K36 writers in clear-cell renal cell carcinomas. Cancer Res 77(18):4835-4845, 2017. e-Pub 2017. PMID: 28754676.
84. 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. e-Pub 2017. PMID: 28810145.
85. address: andrew_aguirre@dfciharvardedu CGARN(WJE, Research Network CGA. Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma. Cancer Cell 32(2):185-203.e13, 2017. e-Pub 2017. PMID: 28810144.
86. 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, Weinstein JN) CGAN(, 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 19(13):2878-2880, 2017. e-Pub 2017. PMID: 28658632.
87. address: wheeler@bcmedu CGARNE, Weinstein JN) CGARN(. Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma. Cell 169(7):1327-1341.e23, 2017. e-Pub 2017. PMID: 28622513.
88. 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.
89. 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, Research Network CGA, 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.
90. 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, Weinstein JN) CGARN(, 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.
91. Johnanning GL, Malouf GG, Zheng X Esteva F, Weinstein JN, Wang-Johanning F, Su, X. Expression of human endogenous retrovirus-K is strongly associated with a basal-like breast cancer phenotype. Scientific Reports, 2017. e-Pub 2017.
92. Weinstein JN) CGARN(. Integrated genomic and molecular characterization of cervical cancer. Nature, 2017. e-Pub 2017. PMID: 28112728.
93. Cancer Genome Atlas Research Network (including Weinstein JN, Asan University AWG, BC Cancer Agency BC, Women’s Hospital BA, Institute B, University B, Reserve University CW, Institute DC, University D, Cancer Centre GP, School HM, Systems Biology IF, KU Leuven KU, Clinic M, Cancer Center MSK, Institute NC, Hospital NC, University S, Alabama UO, Michigan UO, North Carolina UO, Pittsburgh UO, Rochester UO, Southern California UO, Cancer Center UOTMA, Washington UO, Research Institute VA, University V, University W, Broad Institute GSC, St Louis WUI, Cancer Agency GCCB, Institute B, School HM, Hopkins University SKCCCAJ, North Carolina UO, Epigenome Center UOSC, Cancer Center UOTMA, Research Institute VA, Broad Institute GDAC, University: B, School HM, Systems Biology IF, Cancer Center MSK, Santa Cruz UOC, Cancer Center UOTMA, Genomics Consortium BCRI, Children’s Hospital RIAN, Biologic Services TSSA, Center AM, Bioscience A, Hospital BC, BioreclamationIVT, Clinic BM, Medical School CNU, Health System CC, Cureline, University D, University E, University E, of Medicine IUS, of Moldova IOO, Consortium IG, al E. Integrated genomic characterization of oesophageal carcinoma. Nature 541(7636):169-175, 2017. e-Pub 2017. PMID: 28052061.
94. Dadhania V, Zhang M, Zhang L, Bondaruk J, Majewski T, Siefker-Radtke A, Guo CC, Dinney C, Cogdell DE, Zhang S, Lee S, Lee JG, Weinstein JN, Baggerly K, McConkey D, Czerniak B. Meta-analysis of the luminal and basal subtypes of bladder cancer and the identification of signature immunohistochemical markers for clinical use. EBioMedicine 12:105-117, 2016. e-Pub 2016. PMID: 27612592.
95. Guo CC, Dadhania V, Zhang L, Majewski T, Bondaruk J, Sykulski M, Wronowska W, Gambin A, Wang Y, Zhang S, Fuentes-Mattei E, Kamat AM, Dinney C, Siefker-Radtke A, Choi W, Baggerly KA, McConkey D, Weinstein JN, Czerniak B. Gene Expression Profile of the Clinically Aggressive Micropapillary Variant of Bladder Cancer. Eur Urol 70(4):611-20, 2016. e-Pub 2016. PMID: 26988609.
96. 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.
97. Yao J, Caballero OL, Huang Y, Lin C, Rimoldi D, Behren A, Cebon JS, Hung MC, Weinstein JN, Strausberg RL, Zhao Q. Altered Expression and Splicing of ESRP1 in Malignant Melanoma Correlates with Epithelial-Mesenchymal Status and Tumor-Associated Immune Cytolytic Activity. Cancer Immunol Res 4(6):552-61, 2016. e-Pub 2016. PMID: 27045022.
98. 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, Research Network CGA, 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.
99. Mak MP, Tong P, Diao L, Cardnell RJ, Gibbons DL, William WN, Skoulidis F, Parra ER, Rodriguez-Canales J, Wistuba II, Heymach JV, Weinstein JN, Coombes KR, Wang J, Byers LA. A patient-derived, pan-cancer EMT signature identifies global molecular alterations and immune target enrichment following epithelial to mesenchymal transition. Clin Cancer Res 22(3):609-20, 2016. e-Pub 2016. PMID: 26420858.
100. Research Network CGA, 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, al E. Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med 374(2):135-45, 2016. e-Pub 2016. PMID: 26536169.
101. Melott JM, Weinstein JN, Broom BM. PathwaysWeb: A Gene Pathways API with Directional Interactions, Expanded Gene Ontology, and Versioning. Bioinformatics 32(2):312-4, 2016. e-Pub 2016. PMID: 26400039.
102. 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, Weinstein JN) TRN(, 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. e-Pub 2016. PMID: 26824661.
103. Ryan M, Wong WC, Brown R, Akbani R, Su X, Melott J, Broom BM, Weinstein J. TCGA SpliceSeq - Alternative mRNA Splicing Cancer Analysis. Nucleic Acids Research 4(44):D1018-22, 2016. e-Pub 2016. PMID: 26602693.
104. Chen J, Raju GS, Jogunoori W, Menon V, Majumdar A, Chen JS, Gi YJ, Jeong YS, Phan L, Belkin M, Gu S, Kundra S, Mistry NA, Zhang J, Su X, Li S, Lin SH, Javle M, McMurray JS, Rahlfs TF, Mishra B, White J, Rashid A, Beauchemin N, Weston BR, Shafi MA, Stroehlein JR, Davila M, Akbani R, Weinstein JN, Wu X, Mishra L. Mutational profiles reveal an aberrant TGF-β-CEA regulated pathway in colon adenomas. PLoS One 11(4):e0153933, 2016. e-Pub 2016. PMID: 27100181.
105. Weinstein JN) CGARN(. The molecular taxonomy of primary prostate cancer. Cell 163(4):1011-25, 2015. e-Pub 2015. PMID: 26544944.
106. Jiang Y, Malouf GG, Zhang J, Zheng X, Chen Y, Thompson EJ, Weinstein JN, Yuan Y, Spano JP, Broaddus R, Tannir NM, Khayat D, Lu KH, Su X. Long non-coding RNA profiling links subgroup classification of endometrioid endometrial carcinomas with trithorax and polycomb complex aberrations. Oncotarget 6(37):39865-76, 2015. e-Pub 2015. PMID: 26431491.
107. 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. e-Pub 2015. PMID: 26513549.
108. 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, Weinstein JN) TRN(, Perou CM. Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer. Cell 163(2):506-19, 2015. e-Pub 2015. PMID: 26451490.
109. Li J, Han L, Roebuck P, Diao L, Liu L, Yuan Y, Weinstein JN, Liang H. TANRIC: An Interactive Open Platform to Explore the Function of lncRNAs in Cancer. Cancer Res 75(18):3728-37, 2015. e-Pub 2015. PMID: 26208906.
110. Anishkin A, Vanegas JM, Rogers DM, Lorenzi PL, Chan WK, Purwaha P, Weinstein JN, Sukharev S, Rempe SB. Catalytic Role of the Substrate Defines Specificity of Therapeutic l-Asparaginase. J Mol Biol 427(17):2867-85, 2015. e-Pub 2015. PMID: 26142822.
111. Skoulidis F, Byers LA, Diao L, Papadimitrakopoulou VA, Tong P, Izzo J, Behrens C, Kadara H, Parra ER, Canales JR, Zhang J, Giri U, Gudikote J, Cortez MA, Yang C, Fan Y, Peyton M, Girard L, Coombes KR, Toniatti C, Heffernan TP, Choi M, Frampton GM, Miller V, Weinstein JN, Herbst RS, Wong KK, Zhang J, Sharma P, Mills GB, Hong WK, Minna JD, Allison JP, Futreal A, Wang J, Wistuba II, Heymach JV. Co-occurring genomic alterations define major subsets of KRAS - mutant lung adenocarcinoma with distinct biology, immune profiles, and therapeutic vulnerabilities. Cancer Discov 5(8):860-77, 2015. e-Pub 2015. PMID: 26069186.
112. Brat DJ, Weinstein JN) TCGA(RN(. Comprehensive and Integrative Genomic Characterization of Diffuse Lower Grade Gliomas. Molecular and Cellular Biology 75(15), 2015. e-Pub 2015.
113. Research Network CGA, 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.
114. Chin L, (352 collaborators) EA. Genomic Classification of Cutaneous Melanoma. Cell 16(7):1681-96, 2015. e-Pub 2015. PMID: 26091043.
115. Kim H, Zheng S, Amini SS, Virk SM, Mikkelsen T, Brat DJ, Grimsby J, Sougnez C, Muller F, Hu J, Sloan AE, Cohen ML, Van Meir EG, Scarpace L, Laird PW, Weinstein JN, Lander ES, Gabriel S, Getz G, Meyerson M, Chin L, Barnholtz-Sloan JS, Verhaak RG. Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution. Genome Res 25(3):316-27, 2015. e-Pub 2015. PMID: 25650244.
116. Ju Z, Liu W, Roebuck PL, Siwak DR, Zhang N, Lu Y, Davies MA, Akbani R, Weinstein JN, Mills GB, Coombes KR. Development of a robust classifier for quality control of reversephase protein arrays. Bioinformatics 31(6):912-8, 2015. e-Pub 2015. PMID: 25380958.
117. Malouf GG, Zhang J, Yuan Y, Compérat E, Rouprêt M, Cussenot O, Chen Y, Thompson EJ, Tannir NM, Weinstein JN, Valero V, Khayat D, Spano JP, Su X. Characterization of long-non coding RNA transcriptome in clear-cell renal cell carcinoma by next-generation deep sequencing. Mol Oncol 9(1):32-43, 2015. e-Pub 2015. PMID: 25126716.
118. 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. e-Pub 2015.
119. 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.
120. Weinstein JN) CGARN(. Integrated Genomic Characterization of Papillary Thyroid Carcinoma. Cell 159(3):676-90, 2014. e-Pub 2014.
121. Su X, Malouf G, Chen Y, Zhang J, Yao H, Valero V, Weinstein JN, J-P S, Meric-Bernstam F, DK??, Esteva F. Comprehensive analysis of long non-coding RNAs in human breast cancer clinical subtypes. Oncotarget 5(20):9864-76, 2014. e-Pub 2014.
122. Weinstein J) CGA(. Comprehensive molecular characterization of gastric adenocarcinoma. Nature 11(513(7517)):202-9, 2014. e-Pub 2014.
123. Torres-García W, Zheng S, Sivachenko A, Vegesna R, Wang Q, Yao R, Berger MF, Weinstein JN, Getz G, Verhaak RG. PRADA: Pipeline for RNA sequencing Data Analysis",. Bioinformatics 30(15):2224-6, 2014. e-Pub 2014. PMID: 24695405.
124. scientific editor) CGAN(WJIWGIRA. Comprehensive Molecular Profiling of Lung Adenocarcinoma. Nature 511(7511):543-50. e-Pub 2014.
125. 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, Weinstein JN) TCGARN(, Chin L, Meyerson M, Kucherlapati R, W-Y P, 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.
126. 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, Research Network CGA, 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.
127. Malouf GG, Su X, Yao H, Gao J, Xiong L, He Q, Compérat E, Couturier J, Molinié V, Escudier B, Camparo P, Doss DJ, Thompson EJ, Khayat D, Wood CG, Yu W, Teh BT, Weinstein J, Tannir NM. Next generation sequencing of translocation renal cell carcinomas reveals novel RNA splicing partners and frequent mutations of chromatin remodeling genes. Clin Cancer Res 20(15):4129-40, 2014. e-Pub 2014. PMID: 24899691.
128. Lorenzi PL, Claerhout S, Mills GB, Weinstein JN. A curated census of autophagy-modulating proteins and small molecules. Autophagy 10(7):1-11, 2014. e-Pub 2014. PMID: 24906121.
129. 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.
130. Pickering CR, Zhang J, Neskey DM, Zhao M, Jasser SA, Wang J, Ward A, Tsai CJ, Ortega Alves MV, Zhou JH, Drummond J, El-Naggar AK, Gibbs R, Weinstein JN, Wheeler DA, Wang J, Frederick MJ, Myers JN. Squamous cell carcinoma of the oral tongue in young non-smokers is genomically similar to tumors in older smokers. Clin Cancer Res doi:10.1158/1078-0432.CCR-14-0565(14):3842-8, 2014. e-Pub 2014. PMID: 24874835.
131. Purwaha P, Silva LP, Hawke DH, Weinstein JN, Lorenzi PL. An artifact in LC-MS/MS measurement of glutamine and glutamic acid: in-source cyclization to pyroglutamic acid. Anal Chem Epub ahead of print(12):5633-7, 2014. e-Pub 2014. PMID: 24892977.
132. Chan WK, Lorenzi PL, Anishkin A, Purwaha P, Rogers DM, Sukharev S, Rempe SB, Weinstein JN. The glutaminase activity of L-asparaginase is not required for anticancer activity against ASNS-negative cells. Blood 123(23):3596-606, 2014. e-Pub 2014. PMID: 24659632.
133. 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 2014. PMID: 24764584.
134. Preeti P, Lorenzi P, Silva L, Hawke D, Weinstein JN. Targeted metabolomic analysis of amino acid response to L-asparaginase in adherent cells. Metabolomics 10(5):909-19, 2014. e-Pub 2014.
135. corresponding author) CGARN(WJACAL. Comprehensive molecular characterization of urothelial carcinoma of the bladder. Nature 507(315), 2014. e-Pub 2014.
136. Varma S, Pommier Y, Sunshine M, Weinstein JN, Reinhold WC. High Resolution Copy Number Variation Data in the NCI-60 Cancer Cell Lines from Whole Genome Microarrays Accessible through CellMiner. PLoS One 9(3):e92047, 2014. e-Pub 2014. PMID: 24670534.
137. 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.
138. Lin SH, Wang J, Saintigny P, Wu CC, Giri U, Zhang J, Menju T, Diao L, Byers L, Weinstein JN, Coombes KR, Girard L, Komaki R, Wistuba II, Date H, Minna JD, Heymach JV. Genes suppressed by DNA methylation in non-small cell lung cancer reveal the epigenetics of epithelial-mesenchymal transition. BMC Genomics 15(1079):1-15, 2014. e-Pub 2014. PMID: 25486910.
139. Weinstein JN, Lorenzi PL. Discrepancies in drug sensitivity. Nature 504(7480):381-3, 2013. e-Pub 2013. PMID: 24284624.
140. 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.
141. Desai S, Ding M, Wang B, Lu Z, Zhao Q, (TCGA) SK, Yung WK, Weinstein JN, Tan M, Yao J. Tissue-specific isoform switch and DNA hypomethylation of the pyruvate kinase PKM gene in human cancers. Oncotarget 5(18):8202-10. e-Pub 2013.
142. Research Network CGA, 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. e-Pub 2013. PMID: 24071849.
143. Silva LP, Lorenzi PL, Purwaha P, Yong V, Hawke DH, Weinstein JN. Measurement of DNA concentration as a normalization strategy for metabolomic data from adherent cell lines. Anal Chem Epub ahead of print(20):9536-42, 2013. e-Pub 2013. PMID: 24011029.
144. 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, Network TR. The somatic genomic landscape of glioblastoma. Cell 155(2):462-77, 2013. e-Pub 2013. PMID: 24120142.
145. Khoury J, Tannir N, Williams M, Chen Y, Yao H, Zhang J, Thompson E, Network TT, Meric-Bernstam F, Medeiros LJ, Weinstein JN, Su, Xiaoping. The Landscape of DNA Virus Associations Across Human Malignant Cancers Using RNA-Seq: An Analysis of 3775 Cases. J VIROL 87(16):1-11, 2013. e-Pub 2013.
146. Pickering CR, Zhang J, Yoo SY, Bengtsson L, Moorthy S, Neskey DM, Zhao M, Ortega Alves MV, Chang K, Drummond J, Cortez E, Xie TX, Zhang D, Chung W, Issa JP, Zweidler-McKay PA, Wu X, El-Naggar AK, Weinstein JN, Wang J, Muzny DM, Gibbs RA, Wheeler DA, Myers JN, Frederick MJ. Integrative genomic characterization of oral squamous cell carcinoma identifies frequent somatic drivers. Cancer Discov 3(7):770-81, 2013. e-Pub 2013. PMID: 23619168.
147. Zheng S, Fu J, Vegesna R, Mao Y, Heathcock LE, Torres-Garcia W, Ezhilarasan R, Wang S, McKenna A, Chin L, Brennan CW, Yung WK, Weinstein JN, Aldape KD, Sulman EP, Chen K, Koul D, Verhaak RG. A survey of intragenic breakpoints in glioblastoma identifies a distinct subset associated with poor survival. Genes Dev 27(13):1462-72, 2013. e-Pub 2013. PMID: 23796897.
148. for analysis) CGARN(WJ. Comprehensive Molecular characterization of clear cell renal cell carcinoma. Nature 499(7456):43-9, 2013. e-Pub 2013. PMID: 23792563.
149. Weinstein JN) CGARN(. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. NEJM 368(22):2059-74, 2013. e-Pub 2013. PMID: 23634996.
150. Zhao Q, Caballero OL, Davis ID, Jonasch E, Tamboli P, Yung WK, Weinstein JN, research network KSFTT, Strausberg RL, Yao J. Tumor-Specific Isoform Switch of the Fibroblast Growth Factor Receptor 2 Underlies the Mesenchymal and Malignant Phenotypes of Clear Cell Renal Cell Carcinomas. Clin Cancer Res 19(9):2460-2472, 2013. e-Pub 2013. PMID: 23444225.
151. 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. e-Pub 2013. PMID: 23636398.
152. Chen Y, Yao H, Thompson EJ, Tannir NM, Weinstein JN, Su X. VirusSeq: Software to identify viruses and their integration sites using nextgeneration sequencing of human cancer tissue. Bioinformatics 29(2):266-7, 2013. e-Pub 2013. PMID: 23162058.
153. Byers LA, Diao L, Wang J, Saintigny P, Girard L, Peyton M, Shen L, Fan Y, Giri U, Tumula PK, Nilsson MB, Gudikote J, Tran H, Cardnell RJ, Bearss DJ, Warner SL, Foulks JM, Kanner SB, Gandhi V, Krett N, Rosen ST, Kim ES, Herbst RS, Blumenschein GR, Lee JJ, Lippman SM, Ang KK, Mills GB, Hong WK, Weinstein JN, Wistuba II, Coombes KR, Minna JD, Heymach JV. An epithelial-mesenchymal transition gene signature predicts resistance to EGFR and PI3K inhibitors and identifies Axl as a therapeutic target for overcoming EGFR inhibitor resistance. Clin Cancer Res 19(1):279-90, 2013. e-Pub 2013. PMID: 23091115.
154. Verhaak RG, Tamayo P, Creighton CJ, J-Y Y, Hubbard D, Zhang H, Fereday S, Lawrence M, Carter SL, Mermel CH, Kostic AD, Etemadmoghadam D, Saksena G, Cibulski 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, Kobel 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, Genome Atlas TC. Prognostically relevant gene expression signatures of high grade serous ovarian carcinoma. J Clin Investig 123(1):517-25, 2013. e-Pub 2013.
155. Claerhout S, Lorenzi PL, Weinstein JN, Mills GB. Modulation of Autophagy and its Potential for Cancer Therapy. Drugs of the Future 36(12):919-25, 2012. e-Pub 2012.
156. statistical analyses) CGAN(WJF. Comprehensive molecular portraits of human breast tumours. Nature 490(7418):61-70, 2012. e-Pub 2012. PMID: 23000897.
157. Research Network CGA, 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, Writing Committee) WJ(SAA, 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.
158. Byers LA, Wang J, Nilsson MB, Fujimoto J, Saintigny P, Yordy J, Giri U, Peyton M, Fan YH, Diao L, Masrorpour F, Shen L, Liu W, Duchemann B, Tumula P, Bhardwaj V, Welsh J, Weber S, Glisson BS, Kalhor N, Wistuba II, Girard L, Lippman SM, Mills GB, Coombes KR, Weinstein JN, Minna JD, Heymach JV. Proteomic profiling identifies dysregulated pathways in small cell lung cancer and novel therapeutic targets including PARP1. Cancer Discov 2(9):798-811, 2012. e-Pub 2012. PMID: 22961666.
159. Su X, Zhang L, Zhang J, Meric-Bernstam F, Weinstein JN. PurityEst: estimating purity of human tumor samples using next-generation sequencing data. Bioinformatics 28(17):2265-6, 2012. e-Pub 2012. PMID: 22743227.
160. Ryan MC, Cleland J, Kim R, Wong WC, Weinstein JN. SpliceSeq: A resource for analysis and visualization of RNA-seq data on alternative splicing and its functional impacts. Bioinformatics 28(18):2385-7, 2012. e-Pub 2012. PMID: 22820202.
161. Atlas Network CG. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487(7407):330-7, 2012. e-Pub 2012. PMID: 22810696.
162. Chen K, Wallis JW, Kandoth C, Kalicki-Veizer JM, Mungall KL, Mungall AJ, Jones SJ, Marra MA, Ley TJ, Mardis ER, Wilson RK, Weinstein JN, Ding L. BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data. Bioinformatics 28(14):1923-4, 2012. e-Pub 2012. PMID: 22563071.
163. Kim YH, Liang H, Liu X, Lee JS, Cho JY, Cheong JH, Kim H, Li M, Downey TJ, Dyer MD, Sun Y, Sun J, Beasley EM, Chung HC, Noh SH, Weinstein JN, Liu CG, Powis G. AMPKα modulation in cancer progression: multilayer integrative analysis of the whole transcriptome in Asian gastric cancer. Cancer Res 72(10):2512-21, 2012. e-Pub 2012. PMID: 22434430.
164. Weinstein JN. Drug discovery: Cell lines battle cancer. Nature 483(7391):544-5, 2012. e-Pub 2012. PMID: 22460893.
165. 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.
166. Zeeberg BR, Kohn KW, Kahn A, Larionov V, Weinstein JN, Reinhold W, Pommier Y. Concordance of gene expression and functional correlation patterns across the NCI-60 cell lines and the Cancer Genome Atlas glioblastoma samples. PLoS One 7(7):e40062, 2012. e-Pub 2012. PMID: 22848369.
167. Zeeberg BR, Reinhold W, Snajder R, Thallinger GG, Weinstein JN, Kohn KW, Pommier Y. Functional Categories Associated with Clusters of Genes That Are Co-Expressed across the NCI-60 Cancer Cell Lines. PLoS One 7(1):e30317, 2012. e-Pub 2012. PMID: 22291933.
168. Yao J, Zhao Q, Yuan Y, Zhang L, Liu X, Yung WK, Weinstein JN. Identification of common prognostic gene expression signatures with biological meanings from microarray gene expression datasets. PLoS One 7(9):e45894, 2012. e-Pub 2012. PMID: 23029298.
169. Weinstein JN. MicroRNAs in cancer pharmacology and therapeutics: exploiting a natural synergy between '-omic' and hypothesis-driven research. Mol Cancer Ther 10(11):2021. e-Pub 2011.
170. 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.
171. and writing) CGA(RN(WJFA. Integrated Genomic Analyses of Ovarian Carcinoma. Nature 474(7353):609-15, 2011. e-Pub 2011. PMID: 21720365.
172. Patterson AD, Bonzo JA, Li F, Krausz KW, Eichler GS, Aslam S, Tigno X, Weinstein JN, Hansen BC, Idle JR, Gonzalez FJ. Metabolomics reveals attenuation of the SLC6A20 kidney transporter in nonhuman primate and mouse models of type 2 diabetes mellitus. J Biol Chem 286(22):19511-22, 2011. e-Pub 2011. PMID: 21487016.
173. Zeeberg BR, Liu H, Kahn AB, Ehler M, Rajapakse VN, Bonner RF, Brown JD, Brooks BP, Larionov VL, Reinhold W, Weinstein JN, Pommier YG. RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis. BMC Bioinformatics 12:52, 2011. e-Pub 2011. PMID: 21310028.
174. Deus HF, Veiga DF, Freire PR, Weinstein JN, Mills GB, Almeida JS. Exposing The Cancer Genome Atlas as a SPARQL endpoint. J Biomed Inform 43(6):998-1008, 2010. e-Pub 2010. PMID: 20851208.
175. Solier S, Barb J, Zeeberg BR, Varma S, Ryan MC, Kohn KW, Weinstein JN, Munson PJ, Pommier Y. Genome-wide analysis of novel splice variants induced by topoisomerase I poisoning shows preferential occurrence in genes encoding splicing factors. Cancer Res 70(20):8055-65, 2010. e-Pub 2010. PMID: 20817775.
176. Kahn AB, Zeeberg BR, Ryan MC, Jamison DC, Rockoff DM, Pommier Y, Weinstein JN. Ontogenomic study of the relationship between number of gene splice variants and GO categorization. Bioinformatics 26(16):1945-9, 2010. e-Pub 2010. PMID: 20616384.
177. Lu JJ, Meng LH, Shankavaram UT, Zhu CH, Tong LJ, Chen G, Lin LP, Weinstein JN, Ding J. Dihydroartemisinin accelerates c-MYC oncoprotein degradation and induces apoptosis in c-MYC-overexpressing tumor cells. Biochem Pharmacol 80(1):22-30, 2010. e-Pub 2010. PMID: 20206143.
178. Liu H, D'Andrade P, Fulmer-Smentek S, Lorenzi P, Kohn KW, Weinstein JN, Pommier Y, Reinhold WC. mRNA and microRNA expression profiles of the NCI-60 integrated with drug activities. Mol Cancer Ther 9(5):1080-91, 2010. e-Pub 2010. PMID: 20442302.
179. Reinhold WC, Mergny JL, Liu H, Ryan M, Pfister TD, Kinders R, Parchment R, Doroshow J, Weinstein JN, Pommier Y. Exon array analyses across the NCI-60 reveal potential regulation of TOP1 by transcription pausing at guanosine quartets in the first intron. Cancer Res 70(6):2191-203, 2010. e-Pub 2010. PMID: 20215517.
180. Hanczar B, Hua J, Sima C, Weinstein JN, Bittner M, Dougherty ER. Small-sample precision of ROC-related estimates. Bioinformatics 26(6):822-30, 2010. e-Pub 2010. PMID: 20130029.
181. Park ES, Rabinovsky R, Carey M, Hennessy BT, Agarwal R, Liu W, Ju Z, Deng W, Lu Y, Woo HG, Kim SB, Cheong JH, Garraway LA, Weinstein JN, Mills GB, Lee JS, Davies MA. Integrative analysis of proteomic signatures, mutations, and drug responsiveness in the NCI 60 cancer cell line set. Mol Cancer Ther 9(2):257-67, 2010. e-Pub 2010. PMID: 20124458.
182. Reinhold WC, Reimers MA, Lorenzi P, Ho J, Shankavaram UT, Ziegler MS, Bussey KJ, Nishizuka S, Ikediobi O, Pommier YG, Weinstein JN. Multifactorial regulation of E-cadherin expression: an integrative study. Mol Cancer Ther 9(1):1-16, 2010. e-Pub 2010. PMID: 20053763.
183. Orina JN, Calcagno AM, Wu CP, Varma S, Shih J, Lin M, Eichler G, Weinstein JN, Pommier Y, Ambudkar SV, Gottesman MM, Gillet JP. Evaluation of current methods used to analyze the expression profiles of ATP-binding cassette transporters yields an improved drug-discovery database. Mol Cancer Ther 8(7):2057-66, 2009. e-Pub 2009. PMID: 19584229.
184. Kohn KW, Aladjem MI, Weinstein JN, Pommier Y. Network architecture of signaling from uncoupled helicase-polymerase to cell cycle checkpoints and trans-lesion DNA synthesis. Cell Cycle 8(14):1-18, 2009. e-Pub 2009. PMID: 19556879.
185. Lorenzi PL, Reinhold WC, Varma S, Hutchinson AA, Pommier Y, Chanock SJ, Weinstein JN. DNA fingerprinting of the NCI-60 cell line panel. Mol Cancer Ther 8(4):713-24, 2009. e-Pub 2009. PMID: 19372543.
186. Lorenzi PL, Weinstein JN. Asparagine Synthetase: a new potential biomarker in ovarian cancer. Drug News Perspect 22(1):61, 2009. e-Pub 2009. PMID: 19209300.
187. Shankavaram UT, Varma S, Kane D, Sunshine M, Chary KK, Reinhold WC, Pommier Y, Weinstein JN. CellMiner: a relational database and query tool for the NCI-60 cancer cell lines. BMC Genomics 10:277, 2009. e-Pub 2009. PMID: 19549304.
188. Roschke AV, Glebov OK, Lababidi S, Gehlhaus KS, Weinstein JN, Kirsch IR. Chromosomal instability is associated with higher expression of genes implicated in epithelial-mesenchymal transition, cancer invasiveness, and metastasis and with lower expression of genes involved in cell cycle checkpoints, DNA repair, and chromatin maintenance. Neoplasia 10(11):1222-30, 2008. e-Pub 2008. PMID: 18953431.
189. Lorenzi PL, Llamas J, Gunsior M, Ozbun L, Reinhold WC, Varma S, Ji H, Kim H, Hutchinson AA, Kohn EC, Goldsmith PK, Birrer MJ, Weinstein JN. Asparagine synthetase is a predictive biomarker of L-asparaginase activity in ovarian cancer cell lines. Mol Cancer Ther 7(10):3123-8, 2008. e-Pub 2008. PMID: 18852115.
190. Okabe M, Szakacs G, Reimers MA, Suzuki T, Hall MD, Abe T, Weinstein JN, Gottesman MM. Profiling SLCO and SLC22 genes in the NCI-60 cancer cell lines to identify drug uptake transporters. Mol Cancer Ther 7(9):3081-91, 2008. e-Pub 2008. PMID: 18790787.
191. Ruden DM, Jamison DC, Zeeberg BR, Garfinkel MD, Weinstein JN, Rasouli P, Lu X. The EDGE hypothesis: epigenetically directed genetic errors in repeat-containing proteins (RCPs) involved in evolution, neuroendocrine signaling, and cancer. Frontiers in Neuroendocrinology 29(3):428-44, 2008. e-Pub 2008. PMID: 18295320.
192. Ikediobi ON, Reimers M, Durinck S, Blower PE, Futreal AP, Stratton MR, Weinstein JN. In vitro differential sensitivity of melanomas to phenothiazines is based on the presence of codon 600 BRAF mutation. Mol Cancer Ther 7(6):1337-46, 2008. e-Pub 2008. PMID: 18524847.
193. Ashworth A, Balkwill F, Bast RC, Berek JS, Kaye A, Boyd JA, Mills G, Weinstein JN, Woolley K, Workman P. Opportunities and challenges in ovarian cancer research, a perspective from the 11th Ovarian cancer action/HHMT Forum, Lake Como, March 2007. Gynecol Oncol 108(3):652-7, 2008. e-Pub 2008. PMID: 18096210.
194. Weinstein JN. A postgenomic visual icon. Science 319(5871):1772-3, 2008. e-Pub 2008. PMID: 18369130.
195. Boersma BJ, Reimers M, Yi M, Ludwig JA, Luke BT, Stephens RM, Yfantis HG, Lee DH, Weinstein JN, Ambs S. A stromal gene signature associated with inflammatory breast cancer. Int J Cancer 122(6):1324-32, 2008. e-Pub 2008. PMID: 17999412.
196. Patterson AD, Li H, Eichler GS, Krausz KW, Weinstein JN, Jr FA, Gonzalez FJ, Idle JR. UPLC-ESI-TOFMS-based metabolomics and gene expression dynamics inspector self-organizing metabolomic maps as tools for understanding the cellular response to ionizing radiation. Anal Chem 80(3):665-74, 2008. e-Pub 2008. PMID: 18173289.
197. Blower PE, Chung JH, Verducci JS, Lin S, Park JK, Dai Z, Liu CG, Schmittgen TD, Reinhold WC, Croce CM, Weinstein JN, Sadee W. MicroRNAs modulate the chemosensitivity of tumor cells. Mol Cancer Ther 7(1):1-9, 2008. e-Pub 2008. PMID: 18187804.
198. Sheehan KM, Gulmann C, Eichler GS, Weinstein JN, Barrett HL, Kay EW, Conroy RM, Liotta LA, 3rd PE. Signal pathway profiling of epithelial and stromal compartments of colonic carcinoma reveals epithelial-mesenchymal transition. Oncogene 27(3):323-31, 2008. e-Pub 2008. PMID: 17621268.
199. Kohn KW, Aladjem MI, Weinstein JN, Pommier Y. Chromatin challenges during DNA replication: a systems representation. Mol Biol Cell 19(1):1-7, 2008. e-Pub 2008. PMID: 17959828.
200. Amundson SA, Do KT, Vinikoor LC, Lee RA, Koch-Paiz CA, Ahn J, Reimers M, Chen Y, Scudiero DA, Weinstein JN, Trent JM, Bittner ML, Meltzer PS, Jr FA. Integrating global gene expression and radiation survival parameters across the 60 cell lines of the National Cancer Institute Anticancer Drug Screen. Cancer Res 68(2):415-24, 2008. e-Pub 2008. PMID: 18199535.
201. Stevens EV, Nishizuka S, Antony S, Reimers M, Varma S, Young L, Munson PJ, Weinstein JN, Kohn EC, Pommier Y. Predicting cisplatin and trabectedin drug sensitivity in ovarian and colon cancers. Mol Cancer Ther 7(1):10-8, 2008. e-Pub 2008. PMID: 18187810.
202. Kestler HA, Muller A, Buchholz M, Gress TM, Liu H, Kane DW, Zeeberg BR, Weinstein JN. VennMaster: area-proportional Euler diagrams for functional GO analysis of microarrays. BMC Bioinformatics 9:67, 2008. e-Pub 2008. PMID: 18230172.
203. Sheehan KM, Gulmann C, Eichler GS, Weinstein JN, Barrett HL, Kay EW, Conroy RM, Liotta LA, Petricoin EF III. Signal pathway profiling of epithelial and stromal compartments of colonic carcinoma reveals epithelial-mesenchymal transition. Oncogene 27(3):323-31, 2008. e-Pub 2008. PMID: 17621268.
204. Ryan MC, Zeeberg BR, Caplen NJ, Cleland JA, Kahn AB, Liu H, Weinstein JN. SpliceCenter: a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies. BMC Bioinformatics 9:313, 2008. e-Pub 2008. PMID: 18638396.
205. pathway analyses CGARN(WJF, writing, editing) AS. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455(7216):1061-8, 2008. e-Pub 2008. PMID: 18772890.
206. Miao ZH, Player A, Shankavaram U, Wang YH, Zimonjic DB, Lorenzi PL, Liao ZY, Liu H, Shimura T, Zhang HL, Meng LH, Zhang YW, Kawasaki ES, Popescu NC, Aladjem MI, Goldstein DJ, Weinstein JN, Pommier Y. Nonclassical functions of human topoisomerase I: genome-wide and pharmacologic analyses. Cancer Res 67(18):8752-61, 2007. e-Pub 2007. PMID: 17875716.
207. Reinhold WC, Reimers MA, Maunakea AK, Kim S, Lababidi S, Scherf U, Shankavaram UT, Ziegler MS, Stewart C, Kouros-Mehr H, Cui H, Dolginow D, Scudiero DA, Pommier YG, Munroe DJ, Feinberg AP, Weinstein JN. Detailed DNA methylation profiles of the E-cadherin promoter in the NCI-60 cancer cells. Mol Cancer Ther 6(2):391-403, 2007. e-Pub 2007. PMID: 17272646.
208. Martin SE, Jones TL, Thomas CL, Lorenzi PL, Nguyen DA, Runfola T, Gunsior M, Weinstein JN, Goldsmith PK, Lader E, Huppi K, Caplen NJ. Multiplexing siRNAs to compress RNAi-based screen size in human cells. Nucleic Acids Res 35(8):e57, 2007. e-Pub 2007. PMID: 17392344.
209. Eichler GS, Reimers M, Kane D, Weinstein JN. The LeFE algorithm: Embracing the complexity of gene expression in the interpretation of microarray data. Genome Biol 8(9):R187, 2007. e-Pub 2007. PMID: 17845722.
210. Blower PE, Verducci JS, Lin S, Zhou J, Chung JH, Dai Z, Liu CG, Reinhold W, Lorenzi PL, Kaldjian EP, Croce CM, Weinstein JN, Sadee W. MicroRNA expression profiles for the NCI-60 cancer cell panel. Mol Cancer Ther 6(5):1483-91, 2007. e-Pub 2007. PMID: 17483436.
211. Liu H, Zeeberg BR, Qu G, Koru AG, Ferrucci A, Kahn A, Ryan MC, Nuhanovic A, Munson PJ, Reinhold WC, Kane DW, Weinstein JN. AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets. Bioinformatics 23(18):2385-90, 2007. e-Pub 2007. PMID: 17660211.
212. Shankavaram UT, Reinhold WC, Nishizuka S, Major S, Morita D, Chary KK, Reimers MA, Scherf U, Kahn A, Dolginow D, Cossman J, Kaldjian EP, Scudiero DA, Petricoin E, Liotta L, Lee JK, Weinstein JN. Transcript and protein expression profiles of the NCI-60 cancer cell panel: An integromic microarray study. Mol Cancer Ther 6(3):820-3, 2007. e-Pub 2007. PMID: 17339364.
213. Kahn AB, Ryan MC, Liu H, Zeeberg BR, Jamison DC, Weinstein JN. SpliceMiner: A High-Throughput Database Implementation of the NCBI Evidence Viewer for Microarray Splice Variant Analysis. BMC Bioinformatics 8:75, 2007. e-Pub 2007. PMID: 17338820.
214. Lee JK, Havaleshko DM, Cho HJ, Weinstein JN, Karpovich J, Grimshaw A, Theodorescu D. A new strategy for predicting the chemosensitivity of human cancers and its application to drug discovery. Proc. Natl. Acad. Sci. U.S.A. 2007 104:13086-91, 2007. e-Pub 2007.
215. Weinstein JN. Spotlight on molecular profiling: "Integromic" analysis of the NCI-60 cancer cell lines. Mol Cancer Ther 5(11):2601-5, 2006. e-Pub 2006. PMID: 17088435.
216. Weinstein JN, Pommier Y. Connecting genes, drugs and diseases. Nat Biotechnol 24(11):1365-6, 2006. e-Pub 2006. PMID: 17093484.
217. Riss J, Khanna C, Koo S, Chandramouli GV, Yang HH, Hu Y, Kleiner DE, Rosenwald A, Schaefer CF, Ben-Sasson SA, Yang L, Powell J, Kane DW, Star RA, Aprelikova O, Bauer K, Vasselli JR, Maranchie JK, Kohn KW, Buetow KH, Linehan WM, Weinstein JN, Lee MP, Klausner RD, Barrett JC. Cancers as wounds that do not heal: differences and similarities between renal regeneration/repair and renal cell carcinoma. Cancer Res 66(14):7216-24, 2006. e-Pub 2006. PMID: 16849569.
218. Pommier Y, Weinstein JN, Aladjem MI, Kohn KW. Chk2 molecular interaction map and rationale for Chk2 inhibitors. Clin Cancer Res 12(9):2657-61, 2006. e-Pub 2006. PMID: 16675556.
219. Ludwig JA, Szakács G, Martin SE, Chu BF, Cardarelli C, Sauna ZE, Caplen NJ, Fales HM, Ambudkar SV, Weinstein JN, Gottesman MM. Selective toxicity of NSC73306 in MDR1-positive cells as a new strategy to circumvent multidrug resistance in cancer. Cancer Res 66(9):4808-15, 2006. e-Pub 2006. PMID: 16651436.
220. Lorenzi PL, Reinhold WC, Rudelius M, Gunsior M, Shankavaram U, Bussey KJ, Scherf U, Eichler GS, Martin SE, Chin K, Gray JW, Kohn EC, Horak ID, Von Hoff DD, Raffeld M, Goldsmith PK, Caplen NJ, Weinstein JN. Asparagine synthetase as a causal, predictive biomarker for L-asparaginase activity in ovarian cancer cells. Mol Cancer Ther 5(11):2613-23, 2006. e-Pub 2006. PMID: 17088436.
221. Major SM, Nishizuka S, Morita D, Rowland R, Sunshine M, Shankavaram U, Washburn F, Asin D, Kouros-Mehr H, Kane D, Weinstein JN. AbMiner: a bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies. BMC Bioinformatics 7:192, 2006. e-Pub 2006. PMID: 16600027.
222. Bussey KJ, Chin K, Lababidi S, Reimers M, Reinhold WC, Kuo WL, Gwadry F, Ajay F, Kouros-Mehr H, Fridlyand J, Jain A, Collins C, Nishizuka S, Tonon G, Roschke A, Gehlhaus K, Kirsch I, Scudiero DA, Gray JW, Weinstein JN. Integrating data on DNA copy number with gene expression levels and drug sensitivities in the NCI-60 cell line panel. Mol Cancer Ther 5(4):853-67, 2006. e-Pub 2006. PMID: 16648555.
223. Blower PE, Cross KP, Eichler GS, Myatt GJ, Weinstein JN, Yang C. Comparison of methods for sequential screening of large compound sets. Comb Chem High Throughput Screen 9(2):115-22, 2006. e-Pub 2006. PMID: 16475969.
224. Morin RD, Chang E, Petrescu A, Liao N, Griffith M, Chow W, Kirkpatrick R, Butterfield YS, Young AC, Stott J, Barber S, Babakaiff R, Dickson MC, Matsuo C, Wong D, Yang GS, Smailus DE, Wetherby KD, Kwong PN, Grimwood J, Brinkley CP, Brown-John M, Reddix-Dugue ND, Mayo M, Schmutz J, Beland J, Park M, Gibson S, Olson T, Bouffard GG, Tsai M, Featherstone R, Chand S, Siddiqui AS, Jang W, Lee E, Klein SL, Blakesley RW, Zeeberg BR, Narasimhan S, Weinstein JN, Pennacchio CP, Myers RM, Green ED, Wagner L, Gerhard DS, Marra MA, Jones SJ, Holt RA. Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling. Genome Res 16(6):796-803, 2006. e-Pub 2006. PMID: 16672307.
225. Kohn KW, Aladjem MI, Weinstein JN, Pommier Y. Molecular interaction maps of bioregulatory networks: a general rubric for systems biology. Mol Biol Cell 17(1):1-13, 2006. e-Pub 2006. PMID: 16267266.
226. Ikediobi ON, Davies H, Bignell G, Edkins S, Stevens C, O'Meara S, Santarius T, Avis T, Barthorpe S, Brackenbury L, Buck G, Butler A, Clements J, Cole J, Dicks E, Forbes S, Gray K, Halliday K, Harrison R, Hills K, Hinton J, Hunter C, Jenkinson A, Jones D, Kosmidou V, Lugg R, Menzies A, Mironenko T, Parker A, Perry J, Raine K, Richardson D, Shepherd R, Small A, Smith R, Solomon H, Stephens P, Teague J, Tofts C, Varian J, Webb T, West S, Widaa S, Yates A, Reinhold W, Weinstein JN, Stratton MR, Futreal PA, Wooster R. Mutation analysis of 24 known cancer genes in the NCI-60 cell line set. Mol Cancer Ther 5(11):2606-12, 2006. e-Pub 2006. PMID: 17088437.
227. L-H M, Shankavaram U, Chen C, Agama K, H-Q F, Gonzalez FJ, Weinstein JN, Pommier Y. Activation of aminoflavone (NSC 686288) by a sulfotransferase is required for the antiproliferative effect of the drug and for induction of histone gamma-H2AX. Cancer Res 66(19):9656-64, 2006. e-Pub 2006. PMID: 17018623.
228. Lotze MT, Wang E, Marincola F, Hanna N, Panelli MC, Weinstein JN, Perricone MA, Shivers SC, Bugelski J, Sauter G, Burns CA, Howell M, Damle N, Taylor L, Godfrey T, Petricoin E, Scheibenbogen C, Whiteside TL, Coukos G. Workshop on cancer biometrics: identifying biomarkers and surrogates of cancer in patients: a meeting held at the Masur Auditorium, National Institutes of Health. J Immunother 28(2):79-119, 2005. e-Pub 2005. PMID: 15725954.
229. Roschke AV, Lababidi S, Tonon G, Gehlhaus KS, Bussey K, Weinstein JN, Kirsch IR. Karyotypic "state" as a potential determinant for anticancer drug discovery. Proc Natl Acad Sci U S A 102(8):2964-9, 2005. e-Pub 2005. PMID: 15703300.
230. 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. e-Pub 2005. PMID: 16041372.
231. Reimers M, Weinstein JN. Quality assessment of microarrays: visualization of spatial artifacts and quantitation of regional biases. BMC Bioinformatics 6:166, 2005. e-Pub 2005. PMID: 15992406.
232. Reimers M, Weinstein JN. Visualization of spatial artifacts and quantitation of regional biases. BMC Bioinformatics 6:166, 2005. e-Pub 2005. PMID: 15992406.
233. Zeeberg BR, Qin H, Narasimhan S, Sunshine M, Cao H, Kane DW, Reimers M, Stephens RM, Bryant D, Burt SK, Elnekave E, Hari DM, Wynn TA, Cunningham-Rundles C, Stewart DM, Nelson D, Weinstein JN. High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID). BMC Bioinformatics 6:168, 2005. e-Pub 2005. PMID: 15998470.
234. Petersen D, Gadisetti C, Geoghegan J, Hilburn J, Paarlberg J, Kim CH, Munroe D, Gangi L, Han J, Puri R, Staudt L, Weinstein JN, Barrett JC, Green J, Kawasaki ES. Three microarray platforms: an analysis of their concordance in profiling gene expression. BMC Genomics 6(1):63, 2005. e-Pub 2005. PMID: 15876355.
235. Staib F, Robles AI, Varticovski L, Wang XW, Zeeberg BR, Sirotin M, Zhurkin VB, Hofseth LJ, Hussain SP, Weinstein JN, Galle PR, Harris CC. The p53 tumor suppressor network is a key responder to microenvironmental components of chronic inflammatory stress. Cancer Res 65(22):10255-64, 2005. e-Pub 2005. PMID: 16288013.
236. Annereau JP, Szakács G, Tucker CJ, Arciello A, Cardarelli C, Collins J, Grissom S, Zeeberg BR, Reinhold W, Weinstein JN, Pommier Y, Paules RS, Gottesman MM. Analysis of ATP-binding cassette transporter expression in drug-selected cell lines by a microarray dedicated to multidrug resistance. Mol Pharmacol 66(6):1397-405, 2004. e-Pub 2004. PMID: 15342794.
237. Mulshine JL, Weinstein JN. Is the gene expression pattern of lung cancer detected by screening with spiral computed tomography different from that of symptom-detected lung cancer?. Clin Cancer Res 10(18 Pt 1):5973-4, 2004. e-Pub 2004. PMID: 15447979.
238. 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. e-Pub 2004. PMID: 15324696.
239. Huang Y, Anderle P, Bussey KJ, Barbacioru C, Shankavaram U, Dai Z, Reinhold WC, Papp A, Weinstein JN, Sadée W. Membrane transporters and channels: role of the transportome in cancer chemosensitivity and chemoresistance. Cancer Res 64(12):4294-301, 2004. e-Pub 2004. PMID: 15205344.
240. Kohn KW, Riss J, Aprelikova O, Weinstein JN, Pommier Y, Barrett JC. Properties of switch-like bioregulatory networks studied by simulation of the hypoxia response control system. Mol Biol Cell 15(7):3042-52, 2004. e-Pub 2004. PMID: 15107465.
241. Zeeberg BR, Riss J, Kane DW, Bussey KJ, Uchio E, Linehan WM, Barrett JC, Weinstein JN. Mistaken identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics. BMC Bioinformatics 5:80, 2004. e-Pub 2004. PMID: 15214961.
242. Weinstein JN. Integromic analysis of the NCI-60 cancer cell lines. Breast Dis 19:11-22, 2004. e-Pub 2004. PMID: 15687693.
243. Weinstein JN, Nishizuka S, Reinhold WC, Bussey K, Kim S, Major S, Lababidi S, Feng W, Wang G, Raffeld M, Sunshine M, Narasimhan S, Zeeberg B, Wang M, Lee JK, Kane D. Cancer drug discovery: Genomics, Proteomics, and Bioinformatics. Molecular Target Therapy of Cancer 1, 2004. e-Pub 2004.
244. Roschke AV, Tonon G, Gehlhaus KS, McTyre N, Bussey KJ, Lababidi S, Scudiero DA, Weinstein JN, Kirsch IR. Karyotypic complexity of the NCI-60 drug-screening panel. Cancer Res 63(24):8634-47, 2003. e-Pub 2003. PMID: 14695175.
245. Nishizuka S, Charboneau L, Young L, Major S, Reinhold WC, Waltham M, Kouros-Mehr H, Bussey KJ, Lee JK, Espina V, Munson PJ, Petricoin E, Liotta LA, Weinstein JN. Proteomic profiling of the NCI-60 cancer cell lines using new high-density reverse-phase lysate microarrays. Proc Natl Acad Sci U S A 100(24):14229-34, 2003. e-Pub 2003. PMID: 14623978.
246. Nishizuka S, Chen ST, Gwadry FG, Alexander J, Major SM, Scherf U, Reinhold WC, Waltham M, Charboneau L, Young L, Bussey KJ, Kim S, Lababidi S, Lee JK, Pittaluga S, Scudiero DA, Sausville EA, Munson PJ, Petricoin EF, Liotta LA, Hewitt SM, Raffeld M, Weinstein JN. Diagnostic markers that distinguish colon and ovarian adenocarcinomas: identification by genomic, proteomic, and tissue array profiling. Cancer Res 63(17):5243-50, 2003. e-Pub 2003. PMID: 14500354.
247. Yoshida A, Urasaki Y, Waltham M, Bergman AC, Pourquier P, Rothwell DG, Inuzuka M, Weinstein JN, Ueda T, Appella E, Hickson ID, Pommier Y. Human apurinic/apyrimidinic endonuclease (Ape1) and its N-terminal truncated form (AN34) are involved in DNA fragmentation during apoptosis. J Biol Chem 278(39):37768-76, 2003. e-Pub 2003. PMID: 12842873.
248. Daoud SS, Munson PJ, Reinhold W, Young L, Prabhu VV, Yu Q, LaRose J, Kohn KW, Weinstein JN, Pommier Y. Impact of p53 knockout and topotecan treatment on gene expression profiles in human colon carcinoma cells: a pharmacogenomic study. Cancer Res 63(11):2782-93, 2003. e-Pub 2003. PMID: 12782583.
249. Reinhold WC, Kouros-Mehr H, Kohn KW, Maunakea AK, Lababidi S, Roschke A, Stover K, Alexander J, Pantazis P, Miller L, Liu E, Kirsch IR, Urasaki Y, Pommier Y, Weinstein JN. Apoptotic susceptibility of cancer cells selected for camptothecin resistance: gene expression profiling, functional analysis, and molecular interaction mapping. Cancer Res 63(5):1000-11, 2003. e-Pub 2003. PMID: 12615715.
250. Bussey KJ, Kane D, Sunshine M, Narasimhan S, Nishizuka S, Reinhold WC, Zeeberg B, Ajay W, Weinstein JN. MatchMiner: a tool for batch navigation among gene and gene product identifiers. Genome Biol 4(4):R27, 2003. e-Pub 2003. PMID: 12702208.
251. Lee JK, Bussey KJ, Gwadry FG, Reinhold W, Riddick G, Pelletier SL, Nishizuka S, Szakacs G, Annereau JP, Shankavaram U, Lababidi S, Smith LH, Gottesman MM, Weinstein JN. Comparing cDNA and oligonucleotide array data: concordance of gene expression across platforms for the NCI-60 cancer cells. Genome Biol 4(12):R82, 2003. e-Pub 2003. PMID: 14659019.
252. Zeeberg BR, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M, Narasimhan S, Kane DW, Reinhold WC, Lababidi S, Bussey KJ, Riss J, Barrett JC, Weinstein JN. GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol 4(4):R28, 2003. e-Pub 2003. PMID: 12702209.
253. Kim S, Weinstein JN, Grefenstette JJ. Inference of large-scale topology of gene regulation networks by neural nets. Proc. IEEE International Conference of Systems, Man, and Cybernetics:3969-75, 2003. e-Pub 2003.
254. Feng W, Wang G, Zeeberg BR, Guo K, Fojo AT, Kane DW, Reinhold WC, Lababidi S, Weinstein JN, Wang MD. Development of gene ontology tool for biological interpretation of genomic and proteomic data. AMIA Annu Symp Proc:839, 2003. e-Pub 2003. PMID: 14728344.
255. Zhou Y, Gwadry FG, Reinhold WC, Miller LD, Smith LH, Scherf U, Liu ET, Kohn KW, Pommier Y, Weinstein JN. Transcriptional regulation of mitotic genes by camptothecin-induced DNA damage: microarray analysis of dose- and time-dependent effects. Cancer Res 62(6):1688-95, 2002. e-Pub 2002. PMID: 11912141.
256. Blower PE, Yang C, Fligner MA, Verducci JS, Yu L, Richman S, Weinstein JN. Pharmacogenomic analysis: correlating molecular substructure classes with microarray gene expression data. Pharmacogenomics J 2(4):259-71, 2002. e-Pub 2002. PMID: 12196914.
257. Staunton JE, Slonim DK, Coller HA, Tamayo P, Angelo MJ, Park J, Scherf U, Lee JK, Reinhold WO, Weinstein JN, Mesirov JP, Lander ES, Golub TR. Chemosensitivity prediction by transcriptional profiling. Proc Natl Acad Sci U S A 98(19):10787-92, 2001. e-Pub 2001. PMID: 11553813.
258. Fan Y, Shi LM, Kohn KW, Pommier Y, Weinstein JN. Quantitative structure-antitumor activity relationships of camptothecin analogues: cluster analysis and genetic algorithm-based studies. J Med Chem 44(20):3254-63, 2001. e-Pub 2001. PMID: 11563924.
259. Viswanadhan VN, Mueller GA, Basak SC, Weinstein JN. Comparison of a neural net-based QSAR algorithm (PCANN) with Hologram- and multiple linear regression-based QSAR approaches: application to 1,4-dihydropyridine-based calcium channel antagonists. J Chem Inf Comput Sci 41(3):505-11, 2001. e-Pub 2001. PMID: 11410024.
260. 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. e-Pub 2001.
261. Lisziewicz J, Zeng G, Gratas C, Weinstein JN, Lori F. Combination gene therapy: synergistic inhibition of human immunodeficiency virus Tat and Rev functions by a single RNA molecule. Hum Gene Ther 11(6):807-15, 2000. e-Pub 2000. PMID: 10779158.
262. 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. e-Pub 2000. PMID: 10700174.
263. 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. e-Pub 2000. PMID: 10700175.
264. Shi LM, Fan Y, Lee JK, Waltham M, Andrews DT, Scherf U, Paull KD, Weinstein JN. Mining and visualizing large anticancer drug discovery databases. J Chem Inf Comput Sci 40(2):367-79, 2000. e-Pub 2000. PMID: 10761142.
265. Rindflesch TC, Tanabe L, Weinstein JN, Hunter L. EDGAR: extraction of drugs, genes and relations from the biomedical literature. Pac Symp Biocomput:517-28, 2000. e-Pub 2000. PMID: 10902199.
266. van Osdol WW, Myers TG, Weinstein JN. Neural network techniques for informatics of cancer drug discovery. Methods Enzymol 321:369-95, 2000. e-Pub 2000. PMID: 10909067.
267. Tanabe L, Scherf U, Smith LH, Lee JK, Hunter L, Weinstein JN. MedMiner: an Internet text-mining tool for biomedical information, with application to gene expression profiling. Biotechniques 27(6):1210-4, 1216-7, 1999. e-Pub 1999. PMID: 10631500.
268. Carrier F, Georgel PT, Pourquier P, Blake M, Kontny HU, Antinore MJ, Gariboldi M, Myers TG, Weinstein JN, Pommier Y, Fornace AJ. Gadd45, a p53-responsive stress protein, modifies DNA accessibility on damaged chromatin. Mol Cell Biol 19(3):1673-85, 1999. e-Pub 1999. PMID: 10022855.
269. Fornace Jr AJ, Amundson SA, Bittner M, Myers TG, Meltzer P, Weinstein JN, Trent J. The complexity of radiation stress responses: Analysis by informatics and functional genomics approaches. Gene Expression 7:387-400, 1999. e-Pub 1999.
270. Weinstein JN. Fishing expeditions. Science 282(5389):628-9, 1998. e-Pub 1998. PMID: 9841413.
271. Fan Y, Weinstein JN, Kohn KW, Shi LM, Pommier Y. Molecular modeling studies of the DNA-topoisomerase I ternary cleavable complex with camptothecin. J Med Chem 41(13):2216-26, 1998. e-Pub 1998. PMID: 9632354.
272. Shi LM, Fan Y, Myers TG, O'Connor PM, Paull KD, Friend SH, Weinstein JN. Mining the NCI anticancer drug discovery databases: genetic function approximation for the QSAR study of anticancer ellipticine analogues. J Chem Inf Comput Sci 38(2):189-99, 1998. e-Pub 1998. PMID: 9538518.
273. Shi LM, Myers TG, Fan Y, O'Connor PM, Paull KD, Friend SH, Weinstein JN. Mining the National Cancer Institute Anticancer Drug Discovery Database: cluster analysis of ellipticine analogs with p53-inverse and central nervous system-selective patterns of activity. Mol Pharmacol 53(2):241-51, 1998. e-Pub 1998. PMID: 9463482.
274. O'Connor PM, Jackman J, Bae I, Myers TG, Fan S, Mutoh M, Scudiero DA, Monks A, Sausville EA, Weinstein JN, Friend S, Fornace AJ, Kohn KW. Characterization of the p53 tumor suppressor pathway in cell lines of the National Cancer Institute anticancer drug screen and correlations with the growth-inhibitory potency of 123 anticancer agents. Cancer Res 57(19):4285-300, 1997. e-Pub 1997. PMID: 9331090.
275. Wosikowski K, Schuurhuis D, Johnson K, Paull KD, Myers TG, Weinstein JN, Bates SE. Identification of epidermal growth factor receptor and c-erbB2 pathway inhibitors by correlation with gene expression patterns. J Natl Cancer Inst 89(20):1505-15, 1997. e-Pub 1997. PMID: 9337347.
276. Li G, Waltham M, Anderson NL, Unsworth E, Treston A, Weinstein JN. Rapid mass spectrometric identification of proteins from two-dimensional polyacrylamide gels after in gel proteolytic digestion. Electrophoresis 18(3-4):391-402, 1997. e-Pub 1997. PMID: 9150917.
277. Myers TG, Anderson NL, Waltham M, Li G, Buolamwini JK, Scudiero DA, Paull KD, Sausville EA, Weinstein JN. A protein expression database for the molecular pharmacology of cancer. Electrophoresis 18(3-4):647-53, 1997. e-Pub 1997. PMID: 9150955.
278. Burke HB, Goodman PH, Rosen DB, Henson DE, Weinstein JN, Harrell FE, Marks JR, Winchester DP, Bostwick DG. Artificial neural networks improve the accuracy of cancer survival prediction. Cancer 79(4):857-62, 1997. e-Pub 1997. PMID: 9024725.
279. 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. e-Pub 1997. PMID: 8994024.
280. Myers TG, Waltham M, Li G, Buolamwini JK, Scudiero DA, Rubinstein LV, Paull KD, Sausville EA, Anderson NL, Weinstein JN. A protein expression database for the molecular pharmacology of cancer. Electrophoresis 18:647-53, 1997. e-Pub 1997.
281. Shi LM, Fan Y, Myers TG, Weinstein JN. Genetic function approximation in the molecular pharmacology of cancer. Symp. Intl. Congress on Neural Networks 1, 1997. e-Pub 1997.
282. Buolamwini JK, Raghavan K, Fesen MR, Pommier Y, Kohn KW, Weinstein JN. Application of the electrotopological state index to QSAR analysis of flavone derivatives as HIV-1 integrase inhibitors. Pharm Res 13(12):1892-5, 1996. e-Pub 1996. PMID: 8987091.
283. Dearing MP, Englee-Miller MJ, Kratzke RA, Kramer BS, Chu E, Weinstein JN, Anderson M, Venzon D, Mulshine JL, Gazdar AF. Dipyridamole mediated enhanced antiproliferative activity of 10-ethyl-10-deazaaminopterin (10-EDAM) against human lung cancer cell lines. J Cell Biochem 24:165-72, 1996. e-Pub 1996.
284. Weinstein JN, Waltham MC, Myers TG. Neural networks in drug discovery. Symp. World Congress on Neural Networks 1, 1996. e-Pub 1996.
285. Viswanadhan VN, Mueller GA, Basak SC, Weinstein JN. A new QSAR algorithm combining principal component analysis with a neural network: Application to calcium channel antagonists. NetSci:http://www.netsci.org/Science/Compchem/feature07.html, 1996. e-Pub 1996.
286. Chokekijchai S, Shirasaka T, Weinstein JN, Mitsuya H. In vitro anti-HIV-1 activity of HIV protease inhibitor KNI-272 in resting and activated cells: implications for its combined use with AZT or ddI. Antiviral Res 28(1):25-38, 1995. e-Pub 1995. PMID: 8585758.
287. Saga T, Neumann RD, Heya T, Sato J, Kinuya S, Le N, Paik CH, Weinstein JN. Targeting cancer micrometastases with monoclonal antibodies: a binding-site barrier. Proc Natl Acad Sci U S A 92(19):8999-9003, 1995. e-Pub 1995. PMID: 7568060.
288. Raghavan K, Buolamwini JK, Fesen MR, Pommier Y, Kohn KW, Weinstein JN. Three-dimensional quantitative structure-activity relationship (QSAR) of HIV integrase inhibitors: a comparative molecular field analysis (CoMFA) study. J Med Chem 38(6):890-7, 1995. e-Pub 1995. PMID: 7699704.
289. Weinstein JN, Myers TG, Fan Y, Paull KD, Zaharevitz DW, Kohn KW, van Osdol WW. An "information-intensive" strategy for drug discovery at the National Cancer institute: The role of neural networks. Symp. World Congress on Neural Networks 11:750-3, 1995. e-Pub 1995.
290. Alvarez M, Paull K, Hose C, J-S L, Weinstein JN, Grever M, Bates S, Fojo T. Generation of a drug resistance profile by quantitation of mdr-1/P-glycoprotein expression in the cell lines of the NCI anticancer drug screen. J Clinical Investig 95:2205-14, 1995. e-Pub 1995.
291. Mazumder A, Raghavan K, Weinstein JN, Kohn KW, Pommier Y. Inhibition of human immunodeficiency virus type-1 integrase by curcumin. Biochem Pharmacol 49:1165-70, 1995. e-Pub 1995.
292. Weinstein JN, Myers TG. Information resources for liposome research: The drug discovery program of the U.S. National Cancer Institute. J Liposome Research 5:837-44, 1995. e-Pub 1995.
293. van Osdol WW, Myers TG, Paull KD, Kohn KW, Weinstein JN. Use of the Kohonen self-organizing map to study the mechanisms of action of chemotherapeutic agents. J Natl Cancer Inst 86(24):1853-9, 1994. e-Pub 1994. PMID: 7990160.
294. Casciari JJ, Hollingshead MG, Alley MC, Mayo JG, Malspeis L, Miyauchi S, Grever MR, Weinstein JN. Growth and chemotherapeutic response of cells in a hollow-fiber in vitro solid tumor model. J Natl Cancer Inst 86(24):1846-52, 1994. e-Pub 1994. PMID: 7990159.
295. Chung KN, Paik TH, Roberts S, Kim CH, Kirassova M, Weinstein JN, Trepel JB, Elwood PC. Site-directed mutagenesis of tryptophan residues to conserved hydrophobic residues inhibits the processing of human KB cell folate receptor. Arch Biochem Biophys 315(2):407-14, 1994. e-Pub 1994. PMID: 7986085.
296. 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. e-Pub 1994. PMID: 7973634.
297. Hendrix CW, Flexner C, Szebeni J, Kuwahara S, Pennypacker S, Weinstein JN, Lietman PS. Effect of dipyridamole on zidovudine pharmacokinetics and short-term tolerance in asymptomatic human immunodeficiency virus-infected subjects. Antimicrob Agents Chemother 38(5):1036-40, 1994. e-Pub 1994. PMID: 8067734.
298. Sung C, van Osdol WW, Saga T, Neumann RD, Dedrick RL, Weinstein JN. Streptavidin distribution in metastatic tumors pretargeted with a biotinylated monoclonal antibody: theoretical and experimental pharmacokinetics. Cancer Res 54(8):2166-75, 1994. e-Pub 1994. PMID: 8174124.
299. Saga T, Weinstein JN, Jeong JM, Heya T, Lee JT, Le N, Paik CH, Sung C, Neumann RD. Two-step targeting of experimental lung metastases with biotinylated antibody and radiolabeled streptavidin. Cancer Res 54(8):2160-5, 1994. e-Pub 1994. PMID: 8174123.
300. Koutsoukos AD, Rubinstein LV, Faraggi D, Simon RM, Kalyandrug S, Weinstein JN, Kohn KW, Paull KD. Discrimination techniques applied to the NCI in vitro anti-tumour drug screen: predicting biochemical mechanism of action. Stat Med 13(5-7):719-30, 1994. e-Pub 1994. PMID: 8023045.
301. Weinstein JN, Myers T, Buolamwini J, Raghavan K, van Osdol W, Licht J, Viswanadhan VN, Kohn KW, Rubinstein LV, Koutsoukos AD. Predictive statistics and artificial intelligence in the U.S. National Cancer Institute's Drug Discovery Program for Cancer and AIDS. Stem Cells 12(1):13-22, 1994. e-Pub 1994. PMID: 8142917.
302. Weinstein JN, Casciari JJ, Raghavan K, Buolamwini J, Myers TG. Neural networks in the biomedical sciences: A survey of 386 publications since the beginning of 1991. Symp. World Congress on Neural Networks 1:121-6, 1994. e-Pub 1994.
303. van Osdol WW, Sung C, Dedrick RL, Weinstein JN. A distributed pharmacokinetic model of two-step imaging and treatment protocols: application to streptavidin-conjugated monoclonal antibodies and radiolabeled biotin. J Nucl Med 34(9):1552-64, 1993. e-Pub 1993. PMID: 8355076.
304. Juweid M, Sato J, Paik C, Onay-Basaran S, Weinstein JN, Neumann RD. A simple method for affinity purification of radiolabeled monoclonal antibodies. Nucl Med Biol 20(3):311-5, 1993. e-Pub 1993. PMID: 8485490.
305. Betageri GV, Black CD, Szebeni J, Wahl LM, Weinstein JN. Fc-receptor-mediated targeting of antibody-bearing liposomes containing dideoxycytidine triphosphate to human monocyte/macrophages. J Pharm Pharmacol 45(1):48-53, 1993. e-Pub 1993. PMID: 8094446.
306. Weinstein JN, Rubinstein LV, Koutsoukos AD, Kohn KW, Grever MR, Monks A, Scudiero DA, Welch L, Chiausa AJ, Fojo AT, Viswanadhan VN, Paull, KD. Neural networks in the discovery of new treatments for cancer and AIDS. Symp. World Congress on Neural Networks 1:111-6, 1993. e-Pub 1993.
307. Juweid M, Neumann R, Paik C, Perez-Bacete MJ, Sato J, van Osdol W, Weinstein JN. Micropharmacology of monoclonal antibodies in solid tumors: direct experimental evidence for a binding site barrier. Cancer Res 52(19):5144-53, 1992. e-Pub 1992. PMID: 1327501.
308. Weinstein JN, Kohn KW, Grever MR, Viswanadhan VN, Rubinstein LV, Monks AP, Scudiero DA, Welch L, Koutsoukos AD, Chiausa AJ. Neural computing in cancer drug development: predicting mechanism of action. Science 258(5081):447-51, 1992. e-Pub 1992. PMID: 1411538.
309. Kageyama S, Weinstein JN, Shirasaka T, Kempf DJ, Norbeck DW, Plattner JJ, Erickson J, Mitsuya H. In vitro inhibition of human immunodeficiency virus (HIV) type 1 replication by C2 symmetry-based HIV protease inhibitors as single agents or in combinations. Antimicrob Agents Chemother 36(5):926-33, 1992. e-Pub 1992. PMID: 1510415.
310. Hui TE, Fisher DR, Press OW, Eary JF, Weinstein JN, Badger CC, Bernstein ID. Localized beta dosimetry of 131I-labeled antibodies in follicular lymphoma. Med Phys 19(1):97-104, 1992. e-Pub 1992. PMID: 1620064.
311. Reddy MR, Viswanadhan VN, Weinstein JN. Relative differences in the binding free energies of human immunodeficiency virus 1 protease inhibitors: a thermodynamic cycle-perturbation approach. Proc Natl Acad Sci U S A 88(22):10287-91, 1991. e-Pub 1991. PMID: 1946447.
312. Fujimori K, Fisher DR, Weinstein JN. Integrated microscopic-macroscopic pharmacology of monoclonal antibody radioconjugates: the radiation dose distribution. Cancer Res 51(18):4821-7, 1991. e-Pub 1991. PMID: 1893374.
313. van Osdol W, Fujimori K, Weinstein JN. An analysis of monoclonal antibody distribution in microscopic tumor nodules: consequences of a "binding site barrier". Cancer Res 51(18):4776-84, 1991. e-Pub 1991. PMID: 1893370.
314. Szebeni J, Weinstein JN. Dipyridamole binding to proteins in human plasma and tissue culture media. J Lab Clin Med 117(6):485-92, 1991. e-Pub 1991. PMID: 2045716.
315. Patel SS, Szebeni J, Wahl LM, Weinstein JN. Differential inhibition of 2'-deoxycytidine salvage as a possible mechanism for potentiation of the anti-human immunodeficiency virus activity of 2',3'-dideoxycytidine by dipyridamole. Antimicrob Agents Chemother 35(6):1250-3, 1991. e-Pub 1991. PMID: 1656858.
316. Szebeni J, Patel SS, Hung K, Wahl LM, Weinstein JN. Effects of thymidine and uridine on the phosphorylation of 3'-azido-3'-deoxythymidine (zidovudine) in human mononuclear cells. Antimicrob Agents Chemother 35(1):198-200, 1991. e-Pub 1991. PMID: 2014977.
317. Mulshine JL, Carrasquillo JA, Weinstein JN, Keenan AM, Reynolds JC, Herdt J, Bunn PA, Sausville E, Eddy J, Cotelingam JD. Direct intralymphatic injection of radiolabeled 111In-T101 in patients with cutaneous T-cell lymphoma. Cancer Res 51(2):688-95, 1991. e-Pub 1991. PMID: 1985786.
318. Szebeni J, Dieffenbach C, Wahl SM, Venkateshan CN, Yeh A, Popovic M, Gartner S, Wahl LM, Peterfy M, Friedman RM, Weinstein JN. Induction of interferon-α by human immunodeficiency virus type-1 in human monocyte-macrophage cultures. Journal of Virology 65:6362-4, 1991. e-Pub 1991.
319. Ashorn P, Moss B, Weinstein JN, Chaudhary VK, FitzGerald DJ, Pastan I, Berger EA. Elimination of infectious human immunodeficiency virus from human T-cell cultures by synergistic action of CD4-Pseudomonas exotoxin and reverse transcriptase inhibitors. Proc Natl Acad Sci U S A 87(22):8889-93, 1990. e-Pub 1990. PMID: 1701055.
320. Betageri GV, Szebeni J, Hung K, Patel SS, Wahl LM, Corcoran M, Weinstein JN. Effect of dipyridamole on transport and phosphorylation of thymidine and 3'-azido-3'-deoxythymidine in human monocyte/macrophages. Biochem Pharmacol 40(4):867-70, 1990. e-Pub 1990. PMID: 2386551.
321. Fujimori K, Covell DG, Fletcher JE, Weinstein JN. A modeling analysis of monoclonal antibody percolation through tumors: a binding-site barrier. J Nucl Med 31(7):1191-8, 1990. e-Pub 1990. PMID: 2362198.
322. Viswanadhan VN, Ghose AK, Weinstein JN. Mapping the binding site of the nucleoside transporter protein: a 3D-OSAR study. Biochim Biophys Acta 1039(3):356-66, 1990. e-Pub 1990. PMID: 2378893.
323. Szebeni J, Wahl SM, Betageri GV, Wahl LM, Gartner S, Popovic M, Parker RJ, Black CD, Weinstein JN. Inhibition of HIV-1 in monocyte/macrophage cultures by 2',3'-dideoxycytidine-5'-triphosphate, free and in liposomes. AIDS Res Hum Retroviruses 6(5):691-702, 1990. e-Pub 1990. PMID: 2163269.
324. Szebeni J, Wahl SM, Schinazi RF, Popovic M, Gartner S, Wahl LM, Weislow OS, Betageri G, Fine RL, Dahlberg JE, Hunter E, Weinstein JN. Dipyridamole potentiates the aactivity of zidovudine and other dideoxynucleosides against HIV-1 in cultured cells. Annals NY Acad Sci 616:613-6, 1990. e-Pub 1990.
325. Bunow B, Weinstein, JN. Combo: A new approach to the analysis of drug combinations in vitro. Annals NY Acad Sci 616:490-4, 1990. e-Pub 1990.
326. Weinstein JN, Schinazi RF, Wahl SM, Bunow B, Garner S, Popovic M, Wahl LM, Weislow OS, Szebeni J. Synergistic drug combinations in AIDS therapy: Dipyridamole-zidovudine in particular and principles of analysis in general. Annals NY Acad Sci 616:367-84, 1990. e-Pub 1990.
327. Fujimori K, Covell DG, Fletcher JE, Weinstein JN. Modeling analysis of the global and microscopic distribution of immunoglobulin G, F(ab')2, and Fab in tumors. Cancer Res 49(20):5656-63, 1989. e-Pub 1989. PMID: 2790783.
328. Szebeni J, Wahl SM, Popovic M, Wahl LM, Gartner S, Fine RL, Skaleric U, Friedmann RM, Weinstein JN. Dipyridamole potentiates the inhibition by 3'-azido-3'-deoxythymidine and other dideoxynucleosides of human immunodeficiency virus replication in monocyte-macrophages. Proc Natl Acad Sci U S A 86(10):3842-6, 1989. e-Pub 1989. PMID: 2542948.
329. Fujimori K, Weinstein JN. Pharmacokinetics and organ targeting of monoclonal antibodies. Advances in Immunopharmacology 4:127-9, 1989. e-Pub 1989.
330. Weinstein JN, Oster DM, Park JB, Park SH, Loening S. The effect of the extracorporeal shock wave lithotriptor on the bone-cement interface in dogs. Clin Orthop Relat Res(235):261-7, 1988. e-Pub 1988. PMID: 3416532.
331. Black CD, Kroczek RA, Barbet J, Weinstein JN, Shevach EM. Induction of IL-2 receptor expression in vivo: response to concanavalin A. Cell Immunol 111(2):420-32, 1988. e-Pub 1988. PMID: 3123074.
332. Borden EC, Bradley EC, Evans CH, Fox CF, Metzgar RS, Mitchell MS, Weinstein JN. Biotechnology products in cancer therapy: a colloquium. Cancer Res 48(1):223-5, 1988. e-Pub 1988. PMID: 3275492.
333. Barbet J, Black CDV, Holton III OD, Weinstein JN. Specific toxicity to activated T and B lymphocytes of a ricin A immunotoxin directed against the class I MHC antigen H-2 K. J Antibody, Immunoconjugates and Radiopharmaceuticals 1:169-80, 1988. e-Pub 1988.
334. Glusa E, Markwardt F. Studies on thrombin-induced endothelium-dependent vascular effects. Biomed Biochim Acta 47(7):623-30, 1988. e-Pub 1988. PMID: 3202849.
335. Black CDV, Atcher RW, Barbet J, Brechbiel MW, Holton III OD, Hines JJ, Gansow OA, Weinstein JN. Selective ablation of B Lymphocytes in vivo by an alpha emitter, 212bismuth, chelated to a monocloncal antibody. J Antibody, Immunoconjugtes and Radiopharmaceuticals 1:43-53, 1988. e-Pub 1988.
336. Keenan AM, Weinstein JN, Carrasquillo JA, Bunn PA, Reynolds JC, Foon KA, Smarte NC, Ghosh B, Fejka RM, Larson SM. Immunolymphoscintigraphy and the dose dependence of 111In-labeled T101 monoclonal antibody in patients with cutaneous T-cell lymphoma. Cancer Res 47(22):6093-9, 1987. e-Pub 1987. PMID: 3499222.
337. Holton OD, Black CD, Parker RJ, Covell DG, Barbet J, Sieber SM, Talley MJ, Weinstein JN. Biodistribution of monoclonal IgG1, F(ab')2, and Fab' in mice after intravenous injection. Comparison between anti-B cell (anti-Lyb8.2) and irrelevant (MOPC-21) antibodies. J Immunol 139(9):3041-9, 1987. e-Pub 1987. PMID: 3499463.
338. Mulshine JL, Keenan AM, Carrasquillo JA, Walsh T, Linnoila RI, Holton OD, Harwell J, Larson SM, Bunn PA, Weinstein JN. Immunolymphoscintigraphy of pulmonary and mediastinal lymph nodes in dogs: a new approach to lung cancer imaging. Cancer Res 47(13):3572-6, 1987. e-Pub 1987. PMID: 3472655.
339. Eger RR, Covell DG, Carrasquillo JA, Abrams PG, Foon KA, Reynolds JC, Schroff RW, Morgan AC, Larson SM, Weinstein JN. Kinetic model for the biodistribution of an 111In-labeled monoclonal antibody in humans. Cancer Res 47(12):3328-36, 1987. e-Pub 1987. PMID: 3581071.
340. Parker RJ, Keenan AM, Dower SK, Steller MA, Holton OD, Sieber SM, Weinstein JN. Targeting of murine radiolabeled monoclonal antibodies in the lymphatics. Cancer Res 47(8):2073-6, 1987. e-Pub 1987. PMID: 3828997.
341. Quill H, Carlson L, Fox BS, Weinstein JN, Schwartz RH. Optimization of antigen presentation to T cell hybridomas by purified Ia molecules in planar membranes. Ia molecule polymorphism determines the antigenic fine specificity of the response to cytochrome c peptides. J Immunol Methods 98(1):29-41, 1987. e-Pub 1987. PMID: 2435810.
342. Keenan AM, Weinstein JN, Mulshine JL, Carrasquillo JA, Bunn PA, Reynolds JC, Larson SM. Immunolymphoscintigraphy in patients with lymphoma after subcutaneous injection of indium-111-labeled T101 monoclonal antibody. J Nucl Med 28(1):42-6, 1987. e-Pub 1987. PMID: 3794811.
343. Lotze MT, Carrasquillo JA, Weinstein JN, Bryant GJ, Perentesis P, Reynolds JC, Matis LA, Eger RR, Keenan AM, Hellström I. Monoclonal antibody imaging of human melanoma. Radioimmunodetection by subcutaneous or systemic injection. Ann Surg 204(3):223-35, 1986. e-Pub 1986. PMID: 3753057.
344. Covell DG, Barbet J, Holton OD, Black CD, Parker RJ, Weinstein JN. Pharmacokinetics of monoclonal immunoglobulin G1, F(ab')2, and Fab' in mice. Cancer Res 46(8):3969-78, 1986. e-Pub 1986. PMID: 3731067.
345. Weinstein JN, Lehmann TR, Hejna W, McNeill T, Spratt K. Chemonucleolysis versus open discectomy. A ten-year follow-up study. Clin Orthop Relat Res(206):50-5, 1986. e-Pub 1986. PMID: 3708992.
346. Steller MA, Parker RJ, Covell DG, Holton OD, Keenan AM, Sieber SM, Weinstein JN. Optimization of monoclonal antibody delivery via the lymphatics: the dose dependence. Cancer Res 46(4 Pt 1):1830-4, 1986. e-Pub 1986. PMID: 3948166.
347. Weinstein JN, Blumenthal R, Klausner RD. Carboxyfluorescein leakage assay for lipoprotein-liposome interaction. Methods Enzymol 128:657-68, 1986. e-Pub 1986. PMID: 3724529.
348. Covell DG, Barbet J, Holton III OD, Black CVD, Keenan AM, Sieber SM, Weinstein JN. Global and local factors in the pharmacology of monoclonal antibodies. American Statistical Society Symposium, 1986. e-Pub 1986.
349. Weinstein JN, Holton OD, Black CD, Keenan AM, Covell DG, Spaulding GF, Barbet J, Steller MA, Sieber SM, Talley MJ. Regional delivery of monoclonal antitumor antibodies: detection and possible treatment of lymph node metastases. Prog Clin Biol Res 212:169-81, 1986. e-Pub 1986. PMID: 3714728.
350. Klausner RD, Blumenthal R, Innerarity T, Weinstein JN. The interaction of apolipoprotein A-I with small unilamellar vesicles of L-alpha-dipalmitoylphosphatidylcholine. J Biol Chem 260(25):13719-27, 1985. e-Pub 1985. PMID: 3932344.
351. Covell DG, Steller MA, Parker RJ, Weinstein JN. Delivery of monoclonal antibodies through the lymphatics. Computer Applications in Medical Care 10:884-8, 1985. e-Pub 1985.
352. Weinstein JN, Parker RJ, Holton OD, Keenan AM, Covell DG, Black CD, Sieber SM. Lymphatic delivery of monoclonal antibodies: potential for detection and treatment of lymph node metastases. Cancer Invest 3(1):85-95, 1985. e-Pub 1985. PMID: 3971201.
353. Weinstein JN. Liposomes as drug carriers in cancer therapy. Cancer Treat Rep 68(1):127-35, 1984. e-Pub 1984. PMID: 6692424.
354. Weinstein JN, Steller MA, Covell DG, Holton OD, Keenan AM, Sieber SM, Parker RJ. Monoclonal antitumor antibodies in the lymphatics. Cancer Treat Rep 68(1):257-64, 1984. e-Pub 1984. PMID: 6692428.
355. Weinstein JN, Stellar MA, Covell DG, Dower SK, Segal DM, Keenan AM, Sieber SM, Parker RJ. Use of monoclonal antibodies for diagnosis and therapy of tumor metastases in lymph nodes. Affinity Chromatography and Biological Recognition:33-42, 1984. e-Pub 1984.
356. 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. e-Pub 1983. PMID: 6623082.
357. Klausner RD, Kempf C, Weinstein JN, Blumenthal R, Van Renswoude J. The folding of ovalbumin. Renaturation in vitro versus biosynthesis in vitro. Biochem J 212(3):801-10, 1983. e-Pub 1983. PMID: 6882395.
358. Miller M, Weinstein JN, Wlodawer A. Preliminary x-ray analysis of single crystals of ovalbumin and plakalbumin. J Biol Chem 258(9):5864-6, 1983. e-Pub 1983. PMID: 6853552.
359. Blumenthal R, Kempf C, Van Renswoude J, Weinstein JN, Klausner RD. Voltage-dependent orientation of membrane proteins. J Cell Biochem 22(1):55-67, 1983. e-Pub 1983. PMID: 6321525.
360. Weinstein JN, Parker RJ, Keenan AM, Dower SK, Morse HC, Sieber SM. Monoclonal anitbodies in the lymphatics: toward the diagnosis and therapy of tumor metastases. Science 218(4579):1334-7, 1982. e-Pub 1982. PMID: 7146917.
361. Kumar N, Blumenthal R, Henkart M, Weinstein JN, Klausner RD. Aggregation and calcium-induced fusion of phosphatidylcholine vesicle-tubulin complexes. J Biol Chem 257(24):15137-44, 1982. e-Pub 1982. PMID: 6897406.
362. Klausner RD, Berman M, Blumenthal R, Weinstein JN, Caplan SR. Compartmental analysis of light-induced proton movement in reconstituted bacteriorhodopsin vesicles. Biochemistry 21(15):3643-50, 1982. e-Pub 1982. PMID: 7115689.
363. Kempf C, Klausner RD, Weinstein JN, Van Renswoude J, Pincus M, Blumenthal R. Voltage-dependent trans-bilayer orientation of melittin. J Biol Chem 257(5):2469-76, 1982. e-Pub 1982. PMID: 7061434.
364. Blumenthal R, Ralston E, Dragsten P, Leserman LD, Weinstein JN. Lipid vesicle-cell interactions: analysis of a model for transfer of contents from adsorbed vesicles to cells. Membr Biochem 4(4):283-303, 1982. e-Pub 1982. PMID: 6897439.
365. Blumenthal R, Klausner RD, Weinstein JN. Voltage-dependent changes in a membrane protein: Studies with the asialoglycoprotein receptor. Biophysical Journal 37:122-4, 1982. e-Pub 1982.
366. Weinstein JN, Blumenthal R, van Renswoude J, Kempf C, Klausner RD. Charge clusters and the orientation of membrane proteins. J Membr Biol 66(3):203-12, 1982. e-Pub 1982. PMID: 6808138.
367. Weinstein JN, Klausner RD, Innerarity T, Ralston E, Blumenthal R. Phase transition release, a new approach to the interaction of proteins with lipid vesicles. Application to lipoproteins. Biochim Biophys Acta 647(2):270-84, 1981. e-Pub 1981. PMID: 6895324.
368. Kumar N, Klausner RD, Weinstein JN, Blumenthal R, Flavin M. Interaction of tubulin with phospholipid vesicles. II. Physical changes of the protein. J Biol Chem 256(11):5886-9, 1981. e-Pub 1981. PMID: 6894594.
369. Klausner RD, Kumar N, Weinstein JN, Blumenthal R, Flavin M. Interaction of tubulin with phospholipid vesicles. I. Association with vesicles at the phase transition. J Biol Chem 256(11):5879-85, 1981. e-Pub 1981. PMID: 6894593.
370. Pitas RE, Innerarity TL, Weinstein JN, Mahley RW. Acetoacetylated lipoproteins used to distinguish fibroblasts from macrophages in vitro by fluorescence microscopy. Arteriosclerosis 1(3):177-85, 1981. e-Pub 1981. PMID: 6895305.
371. Yatvin MB, Mühlensiepen H, Porschen W, Weinstein JN, Feinendegen LE. Selective delivery of liposome-associated cis-dichlorodiammineplatinum(II) by heat and its influence on tumor drug uptake and growth. Cancer Res 41(5):1602-7, 1981. e-Pub 1981. PMID: 7194141.
372. Weinstein JN. Liposomes as "targeted" drug carriers. A physical chemical perspective. Pure and Applied Chemistry 53:2241-54, 1981. e-Pub 1981.
373. Ralston E, Hjelmeland LM, Klausner RD, Weinstein JN, Blumental R. Carboxyfluorescein as a probe for liposome-cell interactions: Effect of impurities and purification of the dye. Biochem Biophys Acta 649:133-7, 1981. e-Pub 1981.
374. Parker RJ, Sieber SM, Weinstein JN. Effect of liposome encapsulation of a fluorescent dye on its uptake by the lymphatics of the rat. Pharmacology 23(3):128-36, 1981. e-Pub 1981. PMID: 7280007.
375. Leserman LD, Weinstein JN, Moore JJ, Terry WD. Specific interaction of myeloma tumor cells with hapten-bearing liposomes containing methotrexate and carboxyfluorescein. Cancer Res 40(12):4768-74, 1980. e-Pub 1980. PMID: 7438109.
376. 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. e-Pub 1980. PMID: 7442804.
377. Blumenthal R, Klausner RD, Weinstein JN. Voltage-dependent translocation of the asialoglycoprotein receptor across lipid membranes. Nature 288(5789):333-8, 1980. e-Pub 1980. PMID: 6253830.
378. Guo LS, Hamilton RL, Goerke J, Weinstein JN, Havel RJ. Interaction of unilamellar liposomes with serum lipoproteins and apolipoproteins. J Lipid Res 21(8):993-1003, 1980. e-Pub 1980. PMID: 6780646.
379. Klausner RD, Bridges K, Tsunoo H, Blumenthal R, Weinstein JN, Ashwell G. Reconstitution of the hepatic asialoglycoprotein receptor with phospholipid vesicles. Proc Natl Acad Sci U S A 77(9):5087-91, 1980. e-Pub 1980. PMID: 6254057.
380. Leserman LD, Weinstein JN, Blumenthal R, Terry WD. Receptor-mediated endocytosis of antibody-opsonized liposomes by tumor cells. Proc Natl Acad Sci U S A 77(7):4089-93, 1980. e-Pub 1980. PMID: 7001454.
381. Weinstein JN, Magin RL, Cysyk RL, Zaharko DS. Treatment of solid L1210 murine tumors with local hyperthermia and temperature-sensitive liposomes containing methotrexate. Cancer Res 40(5):1388-95, 1980. e-Pub 1980. PMID: 6892792.
382. Ralston E, Blumenthal R, Weinstein JN, Sharrow SO, Henkart P. Lysophosphatidylcholine in liposomal membranes: enhanced permeability but little effect on transfer of a water-soluble fluorescent marker into human lymphocytes. Biochim Biophys Acta 597(3):543-51, 1980. e-Pub 1980. PMID: 7378402.
383. Blumenthal R, Klausner RD, Weinstein JN, Bridges K, Tsunoo H, Ashwell G. Voltage-dependent translocation of hepatic binding protein. Ann N Y Acad Sci 358:368-9, 1980. e-Pub 1980. PMID: 6938158.
384. Van Renswoude AJ, Blumenthal R, Weinstein JN. Thin-layer chromatography with agarose gels. A quick, simple method for evaluating liposome size. Biochim Biophys Acta 595(1):151-6, 1980. e-Pub 1980. PMID: 7349878.
385. Wlodawer A, Segrest JP, Chung BH, Chiovetti R, Weinstein JN. High-density lipoprotein recombinants: evidence for a bicycle tire micelle structure obtained by neutron scattering and electron microscopy. FEBS Lett 104(2):231-5, 1979. e-Pub 1979. PMID: 225206.
386. 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. e-Pub 1979. PMID: 432641.
387. Leserman LD, Weinstein JN, Blumenthal R, Sharrow SO, Terry WD. Binding of antigen-bearing fluorescent liposomes to the murine myeloma tumor MOPC 315. J Immunol 122(2):585-91, 1979. e-Pub 1979. PMID: 368242.
388. Dragsten PR, Henkart P, Blumental R, Weinstein JN, Schlessinger J. Lateral diffusion of surface immunoglobulin, Thy-I antigen, and a lipid probe in lymphocyte plasma membranes. Proceedings of the National Academy of Science 76:5163-7, 1979. e-Pub 1979.
389. 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. e-Pub 1978. PMID: 364652.
390. Weinstein JN, Blumenthal R, Sharrow SO, Henkart PA. Antibody-mediated targeting of liposomes. Binding to lymphocytes does not ensure incorporation of vesicle contents into the cells. Biochim Biophys Acta 509(2):272-88, 1978. e-Pub 1978. PMID: 656414.
391. Blumenthal R, Weinstein JN, Sharrow SO, Henkart P. Liposome--lymphocyte interaction: saturable sites for transfer and intracellular release of liposome contents. Proc Natl Acad Sci U S A 74(12):5603-7, 1977. e-Pub 1977. PMID: 271988.
392. 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. e-Pub 1977. PMID: 835007.
393. Blumenthal R, Weinstein JN, Henkart P. Lipid model membrane studies on immune cytotoxic mechanisms. Adv Exp Med Biol 84:495-507, 1977. e-Pub 1977. PMID: 302636.
394. Weinstein JN, Leitz FB. Electric Power from Differences in Salinity: The Dialytic Battery. Science 191(4227):557-559, 1976. e-Pub 1976. PMID: 17792805.
395. Weinstein JN, Leitz FB. Piezodialysis: A comparison of theoretical treatments. Desalination 16:245-7, 1975. e-Pub 1975.
396. Gardner C, Weinstein JN, Caplan SR. Transport properties of charge-mosaic membranes III. Piezodialysis. Desalination 12:19-33, 1973. e-Pub 1973.
397. Weinstein JN, Caplan SR. The definition of volume flow in the Kedem-Katchalsky description of membrane transport. J Phys Chem 77:2710-1, 1973. e-Pub 1973.
398. Weinstein JN, Kalif D, Caplan SR. Transport properties of charge-mosaic membranes II. Experimental studies. Desalination 12:1-17, 1973. e-Pub 1973.
399. Weinstein JN, Bunow B, Caplan SR. Transport properties of charge-mosaic membranes I. Theoretical considerations. Desalination 11:341-77, 1972. e-Pub 1972.
400. Weinstein JN, Caplan SR. Charge-mosaic membranes: dialytic separation of electrolytes from nonelectrolytes and amino acids. Science 169(942):296-8, 1970. e-Pub 1970. PMID: 5450359.
401. Weinstein JN, Caplan SR. Charge-mosaic membranes: enhanced permeability and negative osmosis with a symmetrical salt. Science 161(836):70-2, 1968. e-Pub 1968. PMID: 5655268.

Review Articles

1. Kim J, Akbani R, Creighton CJ, Lerner SP, Weinstein JN, Getz G, Kwiatkowski DJ. Invasive Bladder Cancer: Genomic Insights and Therapeutic Promise. Clin Cancer Res 21(20):4514-24, 2015. e-Pub 2015. PMID: 26473186.
2. Kohn KW, Aladjem MI, Kim S, Weinstein JN, Pommier Y. Depicting combinatorial complexity with the molecular interaction map notation. Mol Syst Biol 2:51, 2006. e-Pub 2006. PMID: 17016517.
3. Ludwig JA, Weinstein JN. Biomarkers in cancer staging, prognosis, and treatment selection. Nat Rev Cancer 5(11):845-56, 2005. e-Pub 2005. PMID: 16239904.
4. Fojo T, Farrell N, Ortuzar W, Tanimura H, Weinstein JN, Myers TG. Identification of non-cross-resistant platinum compounds with novel cytotoxicity profiles using the NCI anticancer drug screen and clustered image map visualizations. Crit Rev Oncol Hematol 53(1):25-34, 2005. e-Pub 2005. PMID: 15607933.
5. Aladjem MI, Pasa S, Parodi S, Weinstein JN, Pommier Y, Kohn KW. Molecular interaction maps--a diagrammatic graphical language for bioregulatory networks. Sci STKE 222:pe8, 2004. e-Pub 2004. PMID: 14997004.
6. Weinstein JN, Pommier Y. Transcriptomic analysis of the NCI-60 cancer cell lines. C R Biol 326(10-11):909-20, 2003. e-Pub 2003. PMID: 14744097.
7. Weinstein JN. 'Omic' and hypothesis-driven research in the molecular pharmacology of cancer. Curr Opin Pharmacol 2(4):361-5, 2002. e-Pub 2002. PMID: 12127867.
8. Weinstein JN, Scherf U, Lee JK, Nishizuka S, Gwadry F, Bussey AK, Kim S, Smith LH, Tanabe L, Richman S, Alexander J, Kouros-Mehr H, Maunakea A, Reinhold WC. The bioinformatics of microarray gene expression profiling. Cytometry 47(1):46-9, 2002. e-Pub 2002. PMID: 11774349.
9. Weinstein JN. Searching for pharmacogenomic markers: the synergy between omic and hypothesis-driven research. Dis Markers 17(2):77-88, 2001. e-Pub 2001. PMID: 11673654.
10. Weinstein JN, Buolamwini JK. Molecular targets in cancer drug discovery: cell-based profiling. Curr Pharm Des 6(4):473-83, 2000. e-Pub 2000. PMID: 10788592.
11. Casciari JJ, Sato H, Durum SK, Fiege J, Weinstein JN. Reference databases of cytokine structure and function. Cancer Chemother Biol Response Modif 16:315-46, 1996. e-Pub 1996. PMID: 8639389.
12. Bates SE, Fojo AT, Weinstein JN, Myers TG, Alvarez M, Pauli KD, Chabner BA. Molecular targets in the National Cancer Institute drug screen. J Cancer Res Clin Oncol 121(9-10):495-500, 1995. e-Pub 1995. PMID: 7559726.
13. Weinstein JN, van Osdol W. Early intervention in cancer using monoclonal antibodies and other biological ligands: micropharmacology and the "binding site barrier". Cancer Res 52(9 Suppl):2747s-2751s, 1992. e-Pub 1992. PMID: 1563006.
14. Weinstein JN, van Osdol W. The macroscopic and microscopic pharmacology of monoclonal antibodies. Int J Immunopharmacol 14(3):457-63, 1992. e-Pub 1992. PMID: 1618598.
15. Viswanadhan VN, Denckla B, Weinstein JN. New joint prediction algorithm (Q7-JASEP) improves the prediction of protein secondary structure. Biochemistry 30(46):11164-72, 1991. e-Pub 1991. PMID: 1932036.
16. Weinstein JN. Antibody lymphoscintigraphy. Cancer Treat Res 51:365-85, 1990. e-Pub 1990. PMID: 1977456.
17. Weinstein JN, Eger RR, Covell DG, Black CD, Mulshine J, Carrasquillo JA, Larson SM, Keenan AM. The pharmacology of monoclonal antibodies. Ann N Y Acad Sci 507:199-210, 1987. e-Pub 1987. PMID: 3327413.
18. Weinstein JN, Leserman LD. Liposomes as drug carriers in cancer chemotherapy. Pharmacol Ther 24(2):207-33, 1984. e-Pub 1984. PMID: 6379684.
19. Pagano RE, Weinstein JN. Interactions of liposomes with mammalian cells. Annu Rev Biophys Bioeng 7:435-68, 1978. e-Pub 1978. PMID: 352245.

Other Articles

1. Liu, Y, Lawson, BC, Huang, X, Broom, BM, Weinstein, JN RETRACTED. Cancers 16(3), 2024. PMID: 38339431.
2. 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, Aaltonen, LA, Abascal, F, Abeshouse, A, Aburatani, H, Adams, DJ, Agrawal, N, Ahn, KS, Ahn, SM, Aikata, H, Akbani, R, Akdemir, KC, Aldape, KD, Cao, S, Chakravarty, D, Chen, Y, Czerniak, BA, Eils, R, El-Naggar, AK, Fan, Y, Gershenwald, JE, Han, L, Huse, J, von Kalle, C, Krishnamurthy, S, Langerod, A, Lazar, A, Lichter, P, Mills, GB, Myklebost, O, Sood, AK, Thompson, A, Van Loo, P, Wang, L Author Correction. Nature Genetics 55(6):1078, 2023. PMID: 36944732.
3. Cortés-Ciriano, I, Lee, JK, Xi, R, Jain, D, Jung, YL, Yang, L, Gordenin, D, Klimczak, LJ, Zhang, CZ, Pellman, D, Akdemir, KC, Alvarez, EG, Baez-Ortega, A, Beroukhim, R, Boutros, PC, Bowtell, DD, Brors, B, Burns, KH, Campbell, PJ, Chan, K, Chen, K, Cortés-Ciriano, I, Dueso-Barroso, A, Akbani, R, Akdemir, KC, Aldape, KD, Cao, S, Chakravarty, D, Chen, Y, Czerniak, BA, Eils, R, El-Naggar, AK, Fan, Y, Gershenwald, JE, Han, L, Huse, J, von Kalle, C, Krishnamurthy, S, Langerod, A, Lazar, A, Lichter, P, Mills, GB, Myklebost, O, Sood, AK, Thompson, A, Van Loo, P, Wang, L, Weinstein, JN, Yuan, Y, Zhu, H Author Correction. Nature Genetics 55(6):1076, 2023. PMID: 36944733.
4. Akdemir, KC, Le, VT, Chandran, S, Li, Y, Verhaak, R, Beroukhim, R, Campbell, PJ, Chin, L, Dixon, JR, Futreal, A, Akdemir, KC, Alvarez, EG, Baez-Ortega, A, Boutros, PC, Bowtell, DD, Brors, B, Burns, KH, Campbell, PJ, Chan, K, Chen, KS, Cortés-Ciriano, I, Dueso-Barroso, A, Dunford, AJ, Akbani, R, Aldape, KD, Cao, S, Chakravarty, D, Chen, Y, Czerniak, BA, Eils, R, El-Naggar, AK, Fan, Y, Gershenwald, JE, Han, L, Huse, J, von Kalle, C, Krishnamurthy, S, Langerod, A, Lazar, A, Li, J, Lichter, P, Mills, GB, Myklebost, O, Sood, AK, Thompson, A, Van Loo, P, Wang, L, Weinstein, JN, Yuan, Y, Zhu, H Author Correction. Nature Genetics 55(6):1079, 2023. PMID: 36944735.
5. 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 Publisher Correction. Nature Genetics 55(5):893, 2023. PMID: 32047324.
6. .
7. Prediction of Ovarian Cancer Response to Therapy Based on Deep Learning Analysis of Histopathology Images.

Abstracts

1. Robertson G, Kim J, Cherniack A, Guo G, Akbani R, Kanchi RS, Hoadley KA, Hinoue T, Laird PW, Al-Ahmadie H, Bellmunt J, Castro M, Gordenin D, Mills GB, Sanchez-Vega F, Shukla SA, Gibb EA, Weinstein &N, Kwiatkowski DJ, Lerner SP. Comprehensive molecular characterization and analysis of muscle-invasive urothelial carcinomas. 2017 ASCO Annual Meeting, 2017. e-Pub 2017.
2. Li J, Han L, Roebuck P, Weinstein JN, Liang H. TANRIC: A User-friendly, Interactive, Open Platform for Exploring the Function of LncRNAs in Cancer. TCGA Network Face-to-Face Meeting, Bethesda MD, 2016. e-Pub 2016.
3. Horvath T, Tan L, Pontikos M, Du D, Chiu Y, Weinstein JN Hawke D, Lorenzi PL. Comparison of metabolite quantitation by a triple quadrupole vs. an Orbitrap-class mass spectrometer. 2016 American Society of Mass Spectrometry National meeting, 2016. e-Pub 2016.
4. Cherniack A, Shen H, Walter VA, Stewart C, Murray B, Bowlby R, Hu X, Ling S, Robertson G Kucherlapati R, Mills GB, Research Network TCGA, Weinstein JN, Zhang J, Akbani R, Levine DA. Integrated Molecular Characterisation of Uterine Carcinosarcoma. Nature, 2016. e-Pub 2016.
5. 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 trans-level variant annotator for precision genomics. TCGA Network Face-to-Face Meeting, Bethesda MD, 2015. e-Pub 2015.

Book Chapters

1. Weinstein, JN. Cancer Bioinformatics. In: Cancer Medicine. 10th Edition. John Wiley, 2023.
2. Weinstein JN, Ralston E, Leserman LD, Klausner RD, Dragsten P, Blumenthal R. Self-quenching of carboxyfluorescein Fluorescence: Uses in studying lioposome stability and liposome-cell interaction. In: Liposome Technology. CRC Press, 183-204, 2018.
3. Weinstein JN. Cancer Bioinformatics. In: Cancer Medicine, 9th Edition. John Wiley, 2017.
4. Ben-Dor A, Lipson D, Tsalenko A, Baumbusch L, Barrett MM, Weinstein JN, Reimers M, A-L B, Yakhini Z. Framework for Identifying Common Aberrations in DNA Copy Number Data. In: RECOMB 2007. Springer Berlin, 122-36, 2007.
5. Weinstein JN. Linking drugs and genes: Pharmacogenomics, pharmacoproteomics, bioinformatics, and the NCI-60. In: Oncogenomics: Molecular Approaches to Cancer. John Wiley & Sons, 117-37, 2004.
6. Viswanadhan VN, Ghose AK, Kiselyov A, Weinstein JN, Wendeloski JJ. Knowledge-based approaches for the design of small molecule libraries for drug discovery. In: Combinatorial library design and evaluation: Principles, software tools, and Applications in Drug Discovery. Marcel-Dekker, 8888, 2001.
7. Weinstein JN, Waltham M, Reinhold W, Lee JK, Smith LH, Andrews D, Tanabe L, Zhou Y, Myers TG, Buolamwini JK, Scherf U. The current revolution in cancer drug discovery: Genomics, proteomics, and bioinformatics. In: Fighting against Cancer: Progress and New Hopes, 21-36, 2000.
8. Casciari J, Sato H, Durum, SK, Fiege J, Weinstein JN. Tabular lexicon of cytokine structure and function. In: Cancer Chemotherapy and Biotherapy: Principles and Practice. Lippincott-Raven, 787-810, 1996.
9. Casciari J, Sato H, Durum SK, Fiege J, Weinstein JN. Reference databases of cytokine structure and function. In: Chemotherapy and Biological Response Modifiers Annual 16. Elsevier, 315-46, 1996.
10. Chabner BA, Weinstein JN, Paull KD, Grever MR. Cell line-based screening for new anticancer drugs. In: Cancer Treatment an Update. Springer-Verlag France, 10-6, 1994.
11. Weinstein JN. Neural networks and predictive statistics in drug discovery. In: Handbook for the International Forum on Advances in Screening Technology and Data Management, 79-83, 1994.
12. Weinstein JN, Bunow, B. COMBO: New concepts and methods for designing and analyzing experiments on combination therapy. In: Combination Therapies: Biological Response Modifiers in the Treatment of Cancer and Infectious Diseases. Plenum Press, 29-38, 1992.
13. Weinstein JN, Fujimore K. Antibody-mediated drug delivery. In: Protein Design and the Development of New Therapeutics and Vaccines. Plenum Press, 359-70, 1990.
14. Weinstein JN, Fujimori K. The pharmacokinetics of monoclonal antibodies and derived peptides. In: Preclinical Evaluation of Peptides and Recombinant Proteins. Skogs Grafiska AB, 35-41, 1990.
15. Weinstein JN, Fujimori K. Predictive Pharmacology of monoclonal antibodies. In: Cancer Therapy: New Trends. Springer-Verlag, 197-9, 1989.
16. Weinstein JN. Immunolymphoscintigraphy and other regional applications of monoclonal antibodies. In: Antibodies in Radiodiagnosis and Therapy. CRC Press, 153-67, 1988.
17. Weinstein JN, Black CDV, Holton III OD, Covell DG, Parker RJ, Mulshine JL, Lotze MT, Carrasquillo J, Eger RR, Lewis A, Sm L, Keenan AM. Delivery of monoclonal antibodies to lymph nodes via the lymphatics. In: The Pharmacology and Toxicology of Proteins. Alar R. Liss, 75-89, 1987.
18. Weinstein JN. Liposomes in the diagnosis and treatment of cancer. In: Liposomes. Marcel Dekker, 277-338, 1987.
19. Weinstein JN, Covell DG, Barbet J, Eger RR, Holton III OD, Talley MJ, Parker RJ, black CDV. The pharmacology of monoclonal antibodies. In: Membrane-mediated Cytotoxicity. Alan R. Liss, 279-89, 1987.
20. Weinstein JN, Blumenthal R, Klausner RD. Carboxyfluorescein leakage assay for lipoprotein-liposome interaction. In: Methods in Enzymol. A. Academic Press, 657-68, 1986.
21. Weinstein JN, Leserman LD. Liposomes as drug carriers in cancer chemotherapy. In: The International Encyclopedia of Pharmacology and Therapeutics: Membrane Transport of Anti-neoplastic Agents. Pergamon Press, 169-94, 1986.
22. Weinstein JN, Black CDV, Keenan AM, Holton III OD, Larson SM, Sieber SM, Covell DG, Carrasquillo J, Barbet J, Parker RJ. Use of monoclonal antibodies for detection of lymph node metastases. In: Monoclonal Antibodies in Cancer Therapy. Alan R. Liss, 473-88, 1986.
23. Weinstein JN, Black CDV, Barbet J, Eger RR, Parker RJ, Holton III OD, Mulshine JL, Keenan AM, Larson SM, Carrasquillo JA, Sieber SM, Covell DG. Selected issues in the pharmacology of monoclonal antibodies. In: Site-specific Drug Delivery: Cell Biology, Medicinal and Pharmaceutical Aspects. John Wiley, 81-91, 1986.
24. Weinstein JN, Keenan AM, Holton III OD, Covell DG, Sieber SM, Black CDV, Barbet J, Parker RJ. Use of monoclonal antibodies to detect metastases of solid tumors in lumph nodes. In: Monoclonal Antibodies and Breast Cancer. Martinus Nijhof, 218-32, 1985.
25. Weinstein JN, Holton OD, Black CDV, Keenan AM, Covell DG, Spaulding GF, Barbet J, Steller MA, Sieber SM, Talley MJ, Parker RJ. Monoclonal Antitumor antibodies in the lumphatics. In: 1985 Year Book of Cancer. Year Book Medical Publishers, 264-6, 1985.
26. Blumenthal R, Kempf C, Renswoude JV, Weinstein JN, Klausner RD. Voltage-dependent orientation of membrane proteins. In: Protein Transport and Secretion. Alan R. Liss, 1-13, 1984.
27. Weinstein JN, Leserman LD, Henkart PA, Blumental R. Antibody-mediated targeting of liposomes. In: Targeting of Drugs. Plenum, 185-202, 1982.
28. Magin RL, Weinstein JN. Delivery of drugs in temperature-sensitive liposomes. In: Targeting of Drugs. Plenum, 203-21, 1982.
29. Magin RL, Weinstein JN. Selective delivery of drugs in "temperature-sensitive" liposomes. In: Liposomes and Immunobiology. Elsevier, 315-25, 1980.
30. Leserman LD, Weinstein JN. Receptor mediated binding and endocytosis of drug-containing liposomes by tumor cells. In: Liposomes and Immunobiology. Elsevier, 241-51, 1980.
31. Yatvin MB, Weinstein JN, Dennis WH, Blumenthal R. Use of hyperthermia to promote selective local release of drugs from liposomes. In: Proceedings of the Conference on Clinical Prospects for Hypoxic Cell Sensitizers and Hyperthermia. Madison Printing and Publishing Company, 105-12, 1978.

Patents

1. Treatment of Diagnosis by Endoscopic Administration into the Lymphatics. Patent Number: 9999.
2. Therapeutic Asparaginases. Patent Number: 14/917,934.
3. Materials and Methods Directed to Asparagine Synthetase and Asparaginease Therapies. Patent Number: Patent #9181552.
4. Restriction Display (RD-PCR) of Differentially Expressed mRNAs. Patent Number: 9999.