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JOHN N WEINSTEIN

TitleProfessor
InstitutionMD Anderson
DepartmentBioinformatics & Computational Biology
Address1400 Pressler St
Houston TX 77030-4008
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Mahmud I, Wei B, Veillon L, Tan L, Martinez S, Tran B, Raskind A, de Jong F, Akbani R, Weinstein JN, Beecher C, Lorenzi PL, Mahmud I, Wei B, Veillon L, Tan L, Martinez S, Tran B, Raskind A, de Jong F, Akbani R, Weinstein JN, Beecher C, Lorenzi PL. An IROA Workflow for correction and normalization of ion suppression in mass spectrometry-based metabolomic profiling data. Res Sq. 2024 Feb 01. PMID: 38352620; PMCID: PMC10862963.
      Citations:    
    2. Liu Y, Lawson BC, Huang X, Broom BM, Weinstein JN. RETRACTED: Liu et al. Prediction of Ovarian Cancer Response to Therapy Based on Deep Learning Analysis of Histopathology Images. Cancers 2023, 15, 4044. Cancers (Basel). 2024 Jan 24; 16(3). PMID: 38339431; PMCID: PMC10854773.
      Citations:    
    3. Zhang N, Casasent TD, Casasent AK, Kumar SV, Wakefield C, Broom BM, Weinstein JN, Akbani R, Zhang N, Casasent TD, Casasent AK, Kumar SV, Wakefield C, Broom BM, Weinstein JN, Akbani R. PCA-Plus: Enhanced principal component analysis with illustrative applications to batch effects and their quantitation. bioRxiv. 2024 Jan 03. PMID: 38260566; PMCID: PMC10802324.
      Citations:    
    4. Guo S, Liu X, Cheng X, Jiang Y, Ji S, Liang Q, Koval A, Li Y, Owen LA, Kim IK, Aparicio A, Shen JP, Kopetz S, Weinstein JN, DeAngelis MM, Chen R, Wang W, Wang W. DeMixSC: a deconvolution framework that uses single-cell sequencing plus a small benchmark dataset for improved analysis of cell-type ratios in complex tissue samples. bioRxiv. 2023 Nov 11. PMID: 37873318; PMCID: PMC10592762.
      Citations:    
    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 (Basel). 2023 Aug 10; 15(16). PMID: 37627071; PMCID: PMC10452505.
      Citations: 1     
    6. Yuan Y, Ju YS, Kim Y, Li J, Wang Y, Yoon CJ, Yang Y, Martincorena I, Creighton CJ, Weinstein JN, Xu Y, Han L, Kim HL, Nakagawa H, Park K, Campbell PJ, Liang H, PCAWG Consortium. Author Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nat Genet. 2023 Jun; 55(6):1078. PMID: 36944732; PMCID: PMC10260393.
      Citations:    Fields:    
    7. Yuan Y, Ju YS, Kim Y, Li J, Wang Y, Yoon CJ, Yang Y, Martincorena I, Creighton CJ, Weinstein JN, Xu Y, Han L, Kim HL, Nakagawa H, Park K, Campbell PJ, Liang H, PCAWG Consortium. Publisher Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nat Genet. 2023 May; 55(5):893. PMID: 32047324; PMCID: PMC10300644.
      Citations:    Fields:    
    8. Yuan Y, Ju YS, Kim Y, Li J, Wang Y, Yoon CJ, Yang Y, Martincorena I, Creighton CJ, Weinstein JN, Xu Y, Han L, Kim HL, Nakagawa H, Park K, Campbell PJ, Liang H, PCAWG Consortium. Author Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nat Genet. 2023 May; 55(5):892. PMID: 32341528; PMCID: PMC10300646.
      Citations:    Fields:    
    9. Chen Z, Ho IL, Soeung M, Yen EY, Liu J, Yan L, Rose JL, Srinivasan S, Jiang S, Edward Chang Q, Feng N, Gay JP, Wang Q, Wang J, Lorenzi PL, Veillon LJ, Wei B, Weinstein JN, Deem AK, Gao S, Genovese G, Viale A, Yao W, Lyssiotis CA, Marszalek JR, Draetta GF, Ying H. Ether phospholipids are required for mitochondrial reactive oxygen species homeostasis. Nat Commun. 2023 04 17; 14(1):2194. PMID: 37069167; PMCID: PMC10110566.
      Citations: 1     Fields:    Translation:HumansCells
    10. 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. 2022 11 15; 38(22):5131-5133. PMID: 36205581; PMCID: PMC9665860.
      Citations:    Fields:    
    11. 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. 2022 Jul 15; 25(7):104715. PMID: 35811851; PMCID: PMC9263966.
      Citations:    
    12. 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. 2022 Jul 15; 25(7):104551. PMID: 35747385; PMCID: PMC9209726.
      Citations:    
    13. 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. 2021 07 10; 12(7):693. PMID: 34247201; PMCID: PMC8272721.
      Citations: 2     Fields:    Translation:HumansAnimalsCells
    14. 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, TCGA Research Network, Meyerson M, Govindan R, Imielinski M. Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway. Cell Rep. 2021 Feb 23; 34(8):108784. PMID: 33626341; PMCID: PMC8608252.
      Citations: 1     Fields:    
    15. Carrot-Zhang J, Yao X, Devarakonda S, Deshpande A, Damrauer JS, Silva TC, Wong CK, Choi HY, Felau I, Robertson AG, 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, TCGA Research Network, Meyerson M, Govindan R, Imielinski M, Castro MAA. Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway. Cell Rep. 2021 02 02; 34(5):108707. PMID: 33535033; PMCID: PMC8009291.
      Citations: 3     Fields:    Translation:Humans
    16. Goldman MJ, Zhang J, Fonseca NA, Xiang Q, Craft B, O'Connor BD, Bazant W, Barrera E, Petryszak R, Al-Shahrour F, Keays M, Haussler D, Weinstein JN, Huber W, Valencia A, Park PJ, Papatheodorou I, Zhu J, Ferretti V, Vazquez M, Cort?s-Ciriano I, Pi?eiro-Y??ez E, Mu?oz-Pomer A, F?llgrabe A. A user guide for the online exploration and visualization of PCAWG data. Nat Commun. 2020 07 07; 11(1):3400. PMID: 32636365; PMCID: PMC7340791.
      Citations: 8     Fields:    Translation:Humans
    17. 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. 2020 06 16; 10(1):9743. PMID: 32546765; PMCID: PMC7298008.
      Citations: 29     Fields:    Translation:Humans
    18. 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. 2020 Jun 26; 23(6):101201. PMID: 32521509; PMCID: PMC7286965.
      Citations: 5     
    19. 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. 2020 05 26; 59(20):1927-1945. PMID: 32364696.
      Citations: 10     Fields:    Translation:Cells
    20. Robertson AG, Seiler R, Hoadley KA, Al-Ahmadie H, Choi W, Eriksson P, Mo Q, Kardos J, Zlotta A, Dinney CP, Bellmunt J, Powles T, Chan KS, Kim WY, McConkey DJ, Black PC, Lerner SP, Real FX, Aine M, Czerniak B, Gibb EA, Kim J, Kwiatkowski DJ, Lebret T, Siefker-Radtke AA, Sirab N, Taber A, Weinstein JN, Kamoun A, de Reyni?s A, Allory Y, Sj?dahl G, Groeneveld CS, Castro MAA, Fontugne J, Hartmann A, Malats N, Dyrskj?t L, H?glund M, Radvanyi F, Bernard-Pierrot I, Liedberg F. 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. 2020 04; 77(4):436-438. PMID: 32037144.
      Citations:    Fields:    Translation:Humans
    21. Yuan Y, Ju YS, Kim Y, Li J, Wang Y, Yoon CJ, Yang Y, Martincorena I, Creighton CJ, Weinstein JN, Xu Y, Han L, Kim HL, Nakagawa H, Park K, Campbell PJ, Liang H, PCAWG Consortium. Comprehensive molecular characterization of mitochondrial genomes in human cancers. Nat Genet. 2020 03; 52(3):342-352. PMID: 32024997; PMCID: PMC7058535.
      Citations: 76     Fields:    Translation:HumansCells
    22. 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. F1000Res. 2019; 8. PMID: 32269754; PMCID: PMC7111501.
      Citations: 12     Fields:    
    23. 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. 2019 10 01; 35(19):3761-3770. PMID: 30851108; PMCID: PMC7963081.
      Citations:    Fields:    
    24. 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. 2019 Sep 10; 28(11):3010. PMID: 31509758.
      Citations: 24     Fields:    
    25. Donehower LA, Korkut A, Liu Y, Schultz A, Cardenas M, Li X, Babur O, Hsu TK, Lichtarge O, Weinstein JN, Akbani R, Wheeler DA, Soussi T. Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas. Cell Rep. 2019 07 30; 28(5):1370-1384.e5. PMID: 31365877; PMCID: PMC7546539.
      Citations: 123     Fields:    Translation:Humans
    26. 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. 2019 09; 18(9):1587-1592. PMID: 31209181; PMCID: PMC6726508.
      Citations: 20     Fields:    Translation:HumansAnimalsCells
    27. Guo CC, Majewski T, Zhang L, Yao H, Bondaruk J, Wang Y, Zhang S, Wang Z, Lee JG, Lee S, Cogdell D, Zhang M, Wei P, Grossman HB, Kamat A, Duplisea JJ, Ferguson JE, Huang H, Dadhania V, Gao J, Dinney C, Weinstein JN, Baggerly K, McConkey D, Czerniak B. Dysregulation of EMT Drives the Progression to Clinically Aggressive Sarcomatoid Bladder Cancer. Cell Rep. 2019 05 07; 27(6):1781-1793.e4. PMID: 31067463; PMCID: PMC6546434.
      Citations: 31     Fields:    Translation:HumansCells
    28. 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. 2019 05; 16(5):401-404. PMID: 30988467; PMCID: PMC7337246.
      Citations: 4     Fields:    Translation:HumansCells
    29. Chen T, Du D, Chen J, Zhou P, Weinstein JN, Yao L, Liu Y. ZC3H12A Expression in Different Stages of Colorectal Cancer. Oncoscience. 2019 Mar; 6(3-4):301-311. PMID: 31106233; PMCID: PMC6508193.
      Citations: 3     
    30. Du D, Tan L, Wang Y, Peng B, Weinstein JN, Wondisford FE, Su X, Lorenzi PL. ElemCor: accurate data analysis and enrichment calculation for high-resolution LC-MS stable isotope labeling experiments. BMC Bioinformatics. 2019 Feb 19; 20(1):89. PMID: 30782135; PMCID: PMC6381631.
      Citations: 4     Fields:    Translation:Animals
    31. 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. 2019 02 19; 26(8):2241-2256.e4. PMID: 30784602.
      Citations: 11     Fields:    Translation:HumansCells
    32. Horvath TD, Chan WK, Pontikos MA, Martin LA, Du D, Tan L, Konopleva M, Weinstein JN, Lorenzi PL. Assessment of l-Asparaginase Pharmacodynamics in Mouse Models of Cancer. Metabolites. 2019 Jan 09; 9(1). PMID: 30634463; PMCID: PMC6359345.
      Citations: 3     
    33. Zhang Z, Ye Y, Gong J, Ruan H, Liu CJ, Xiang Y, Cai C, Guo AY, Ling J, Diao L, Weinstein JN, Han L. Global analysis of tRNA and translation factor expression reveals a dynamic landscape of translational regulation in human cancers. Commun Biol. 2018; 1:234. PMID: 30588513; PMCID: PMC6303286.
      Citations: 34     
    34. 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. 2018 11 01; 34(21):3768-3770. PMID: 29790910; PMCID: PMC6198852.
      Citations: 3     Fields:    
    35. Korkut A, Zaidi S, Kanchi RS, Rao S, Gough NR, Schultz A, Li X, Lorenzi PL, Berger AC, Robertson G, Kwong LN, Datto M, Roszik J, Ling S, Ravikumar V, Manyam G, Rao A, Shelley S, Liu Y, Ju Z, Hansel D, de Velasco G, Pennathur A, Andersen JB, O'Rourke CJ, Ohshiro K, Jogunoori W, Nguyen BN, Li S, Osmanbeyoglu HU, Ajani JA, Mani SA, Houseman A, Wiznerowicz M, Chen J, Gu S, Ma W, Zhang J, Tong P, Cherniack AD, Deng C, Resar L, Cancer Genome Atlas Research Network, Weinstein JN, Mishra L, Akbani R. A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-? Superfamily. Cell Syst. 2018 10 24; 7(4):422-437.e7. PMID: 30268436; PMCID: PMC6370347.
      Citations: 63     Fields:    Translation:HumansCells
    36. Robertson AG, Kim J, Al-Ahmadie H, Bellmunt J, Guo G, Cherniack AD, Hinoue T, Laird PW, Hoadley KA, Akbani R, Castro MAA, Gibb EA, Kanchi RS, Gordenin DA, Shukla SA, Sanchez-Vega F, Hansel DE, Czerniak BA, Reuter VE, Su X, de Sa Carvalho B, Chagas VS, Mungall KL, Sadeghi S, Pedamallu CS, Lu Y, Klimczak LJ, Zhang J, Choo C, Ojesina AI, Bullman S, Leraas KM, Lichtenberg TM, Wu CJ, Schultz N, Getz G, Meyerson M, Mills GB, McConkey DJ, TCGA Research Network, Weinstein JN, Kwiatkowski DJ, Lerner SP. Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer. Cell. 2018 08 09; 174(4):1033. PMID: 30096301; PMCID: PMC6297116.
      Citations: 111     Fields:    
    37. 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. 2018 Jul 31; 18(1):773. PMID: 30064493; PMCID: PMC6069786.
      Citations: 5     Fields:    Translation:HumansCells
    38. 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. 2018 Apr 13; 9(28):19704-19715. PMID: 29731976; PMCID: PMC5929419.
      Citations: 4     Fields:    
    39. Sokolov A, Gentles AJ, Burzykowski T, Poisson L, Weinstein JN, Kaminska B, Huelsken J, Omberg L, Gevaert O, Czerwinska P, Mazurek S, Mishra L, Heyn H, Krasnitz A, Godwin AK, Lazar AJ, Cancer Genome Atlas Research Network, Stuart JM, Hoadley KA, Laird PW, Wiznerowicz M, Malta TM, Colaprico A, Noushmehr H. Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation. Cell. 2018 04 05; 173(2):338-354.e15. PMID: 29625051; PMCID: PMC5902191.
      Citations: 467     Fields:    Translation:HumansCells
    40. Chen H, Li C, Peng X, Zhou Z, Weinstein JN, Cancer Genome Atlas Research Network, Liang H. A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples. Cell. 2018 04 05; 173(2):386-399.e12. PMID: 29625054; PMCID: PMC5890960.
      Citations: 104     Fields:    Translation:HumansCells
    41. Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Mokrab Y, Newman AM, Rao A, Chen K, Krasnitz A, Hu H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CS, Cancer Genome Atlas Research Network, Lazar AJ, Serody JS, Disis ML, Vincent BG, Shmulevich I, Thorsson V, Malta TM, Noushmehr H, Demicco EG. The Immune Landscape of Cancer. Immunity. 2018 04 17; 48(4):812-830.e14. PMID: 29628290; PMCID: PMC5982584.
      Citations: 1407     Fields:    Translation:HumansCells
    42. Peng X, Chen Z, Farshidfar F, Xu X, Lorenzi PL, Wang Y, Cheng F, Tan L, Mojumdar K, Du D, Ge Z, Li J, Thomas GV, Birsoy K, Liu L, Zhang H, Zhao Z, Marchand C, Weinstein JN, Cancer Genome Atlas Research Network, Bathe OF, Liang H. Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers. Cell Rep. 2018 04 03; 23(1):255-269.e4. PMID: 29617665; PMCID: PMC5916795.
      Citations: 94     Fields:    Translation:HumansCells
    43. Knijnenburg TA, Wang L, Zimmermann MT, Chambwe N, Gao GF, Cherniack AD, Fan H, Shen H, Way GP, Greene CS, Liu Y, Akbani R, Feng B, Donehower LA, Miller C, Shen Y, Karimi M, Chen H, Kim P, Jia P, Shinbrot E, Zhang S, Liu J, Hu H, Bailey MH, Yau C, Wolf D, Zhao Z, Weinstein JN, Li L, Ding L, Mills GB, Laird PW, Wheeler DA, Shmulevich I, Cancer Genome Atlas Research Network, Monnat RJ, Xiao Y, Wang C. Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell Rep. 2018 04 03; 23(1):239-254.e6. PMID: 29617664; PMCID: PMC5961503.
      Citations: 310     Fields:    Translation:HumansCells
    44. Campbell JD, Yau C, Bowlby R, Liu Y, Brennan K, Fan H, Taylor AM, Wang C, Walter V, Akbani R, Byers LA, Creighton CJ, Coarfa C, Shih J, Cherniack AD, Gevaert O, Prunello M, Shen H, Anur P, Chen J, Cheng H, Hayes DN, Bullman S, Pedamallu CS, Ojesina AI, Sadeghi S, Mungall KL, Robertson AG, Benz C, Schultz A, Kanchi RS, Gay CM, Hegde A, Diao L, Wang J, Ma W, Sumazin P, Chiu HS, Chen TW, Gunaratne P, Donehower L, Rader JS, Zuna R, Al-Ahmadie H, Lazar AJ, Flores ER, Tsai KY, Zhou JH, Rustgi AK, Drill E, Shen R, Wong CK, Cancer Genome Atlas Research Network, Stuart JM, Laird PW, Hoadley KA, Weinstein JN, Peto M, Pickering CR, Chen Z, Van Waes C. Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell Rep. 2018 04 03; 23(1):194-212.e6. PMID: 29617660; PMCID: PMC6002769.
      Citations: 107     Fields:    Translation:HumansCells
    45. 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, Mestdagh P, Gunaratne PH, Yau C, Bowlby R, Robertson AG, Wang C, Cherniack AD, Godwin AK, Kuderer NM, Rader JS, Zuna RE, Sood AK, Lazar AJ, Ojesina AI, Adebamowo C, Adebamowo SN, Baggerly KA, Chen TW, Chiu HS, Lefever S, Liu L, MacKenzie K, Orsulic S, Roszik J, Shelley CS, Song Q, Vellano CP, Wentzensen N, Cancer Genome Atlas Research Network, Weinstein JN, Mills GB, Levine DA, Akbani R, Williams C, Tiezzi DG. A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. Cancer Cell. 2018 04 09; 33(4):690-705.e9. PMID: 29622464; PMCID: PMC5959730.
      Citations: 207     Fields:    Translation:Humans
    46. Radovich M, Pickering CR, Felau I, Ha G, Zhang H, Jo H, Hoadley KA, Anur P, Zhang J, McLellan M, Bowlby R, Matthew T, Danilova L, Hegde AM, Kim J, Leiserson MDM, Sethi G, Lu C, Ryan M, Su X, Cherniack AD, Robertson G, Akbani R, Spellman P, Weinstein JN, Hayes DN, Raphael B, Lichtenberg T, Leraas K, Zenklusen JC, Cancer Genome Atlas Network, Fujimoto J, Scapulatempo-Neto C, Moreira AL, Hwang D, Huang J, Marino M, Korst R, Giaccone G, Gokmen-Polar Y, Badve S, Rajan A, Girard N, Tsao MS, Marx A, Tsao AS, Loehrer PJ, Str?bel P. The Integrated Genomic Landscape of Thymic Epithelial Tumors. Cancer Cell. 2018 02 12; 33(2):244-258.e10. PMID: 29438696; PMCID: PMC5994906.
      Citations: 97     Fields:    Translation:Humans
    47. 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 Heatmaps for Interactive Exploration of Molecular Profiling Data. Cancer Res. 2017 11 01; 77(21):e23-e26. PMID: 29092932; PMCID: PMC5715806.
      Citations: 16     Fields:    Translation:HumansCells
    48. 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. 2017 11 01; 77(21):e51-e54. PMID: 29092939; PMCID: PMC5679242.
      Citations: 44     Fields:    Translation:Humans
    49. Robertson AG, Kim J, Al-Ahmadie H, Bellmunt J, Guo G, Cherniack AD, Hinoue T, Laird PW, Hoadley KA, Akbani R, Gibb EA, Kanchi RS, Gordenin DA, Shukla SA, Sanchez-Vega F, Hansel DE, Czerniak BA, Reuter VE, Su X, Mungall KL, Sadeghi S, Pedamallu CS, Lu Y, Klimczak LJ, Zhang J, Choo C, Ojesina AI, Bullman S, Leraas KM, Lichtenberg TM, Wu CJ, Schultz N, Getz G, Meyerson M, Mills GB, McConkey DJ, TCGA Research Network, Kwiatkowski DJ, Lerner SP, Castro MAA, de Sa Carvalho B, Chagas VS, Weinstein JN. Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer. Cell. 2017 Oct 19; 171(3):540-556.e25. PMID: 28988769; PMCID: PMC5687509.
      Citations: 661     Fields:    Translation:HumansCells
    50. Su X, Zhang J, Thompson EJ, Gowrishankar B, Houldsworth J, Weinstein JN, Tost J, Broom BM, Tannir NM, Mouawad R, Comp?rat E, Roupr?t M, Allanic F, Parra J, Bitker MO, Khayat D, Spano JP, 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. 2017 09 15; 77(18):4835-4845. PMID: 28754676; PMCID: PMC6211291.
      Citations: 17     Fields:    Translation:HumansCells
    51. Zhang Y, Kwok-Shing Ng P, Kucherlapati M, Chen F, Liu Y, Tsang YH, de Velasco G, Jeong KJ, Akbani R, Hadjipanayis A, Pantazi A, Bristow CA, Lee E, Mahadeshwar HS, Tang J, Zhang J, Yang L, Seth S, Lee S, Ren X, Song X, Sun H, Seidman J, Luquette LJ, Xi R, Chin L, Protopopov A, Westbrook TF, Shelley CS, Choueiri TK, Ittmann M, Van Waes C, Weinstein JN, Liang H, Henske EP, Godwin AK, Park PJ, Kucherlapati R, Scott KL, Mills GB, Kwiatkowski DJ, Creighton CJ. A Pan-Cancer Proteogenomic Atlas of PI3K/AKT/mTOR Pathway Alterations. Cancer Cell. 2017 06 12; 31(6):820-832.e3. PMID: 28528867; PMCID: PMC5502825.
      Citations: 189     Fields:    Translation:HumansCells
    52. Cherniack AD, Shen H, Walter V, Stewart C, Murray BA, Bowlby R, Hu X, Ling S, Soslow RA, Broaddus RR, Zuna RE, Robertson G, Laird PW, Kucherlapati R, Mills GB, Cancer Genome Atlas Research Network, Weinstein JN, Zhang J, Akbani R, Levine DA. Integrated Molecular Characterization of Uterine Carcinosarcoma. Cancer Cell. 2017 03 13; 31(3):411-423. PMID: 28292439; PMCID: PMC5599133.
      Citations: 137     Fields:    Translation:Humans
    53. Johanning GL, Zheng X, Esteva FJ, Weinstein JN, Wang-Johanning F, Su X, Malouf GG. Expression of human endogenous retrovirus-K is strongly associated with the basal-like breast cancer phenotype. Sci Rep. 2017 02 06; 7:41960. PMID: 28165048; PMCID: PMC5292751.
      Citations: 36     Fields:    Translation:HumansCells
    54. 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. 2016 Oct; 12:105-117. PMID: 27612592; PMCID: PMC5078592.
      Citations: 116     Fields:    Translation:Humans
    55. Campbell JD, Alexandrov A, Kim J, Wala J, Berger AH, Pedamallu CS, Shukla SA, Guo G, Brooks AN, Murray BA, Imielinski M, Hu X, Ling S, Akbani R, Rosenberg M, Cibulskis C, Ramachandran A, Collisson EA, Kwiatkowski DJ, Lawrence MS, Weinstein JN, Verhaak RG, Wu CJ, Hammerman PS, Cherniack AD, Getz G, Cancer Genome Atlas Research Network, Artyomov MN, Schreiber R, Govindan R, Meyerson M. Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas. Nat Genet. 2016 06; 48(6):607-16. PMID: 27158780; PMCID: PMC4884143.
      Citations: 440     Fields:    Translation:Humans
    56. 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-?-CEA Regulated Pathway in Colon Adenomas. PLoS One. 2016; 11(4):e0153933. PMID: 27100181; PMCID: PMC4839765.
      Citations: 10     Fields:    Translation:HumansCells
    57. Yao J, Huang Y, Lin C, Rimoldi D, Behren A, Cebon JS, Hung MC, Weinstein JN, Strausberg RL, Zhao Q, Caballero OL. Altered Expression and Splicing of ESRP1 in Malignant Melanoma Correlates with Epithelial-Mesenchymal Status and Tumor-Associated Immune Cytolytic Activity. Cancer Immunol Res. 2016 06; 4(6):552-61. PMID: 27045022.
      Citations: 33     Fields:    Translation:HumansCells
    58. 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. 2016 10; 70(4):611-620. PMID: 26988609; PMCID: PMC5804336.
      Citations: 52     Fields:    Translation:HumansCells
    59. Jiang Y, Zhang J, Zheng X, Chen Y, Thompson EJ, Weinstein JN, Yuan Y, Broaddus R, Tannir NM, Lu KH, Su X, Malouf GG, Spano JP, Khayat D. Long non-coding RNA profiling links subgroup classification of endometrioid endometrial carcinomas with trithorax and polycomb complex aberrations. Oncotarget. 2015 Nov 24; 6(37):39865-76. PMID: 26431491; PMCID: PMC4741866.
      Citations: 10     Fields:    Translation:HumansCells
    60. Ryan M, Wong WC, Brown R, Akbani R, Su X, Broom B, Melott J, Weinstein J. TCGASpliceSeq a compendium of alternative mRNA splicing in cancer. Nucleic Acids Res. 2016 Jan 04; 44(D1):D1018-22. PMID: 26602693; PMCID: PMC4702910.
      Citations: 163     Fields:    Translation:Cells
    61. Cancer Genome Atlas Research Network, Linehan WM, Spellman PT, Ricketts CJ, Creighton CJ, Fei SS, Davis C, Wheeler DA, Murray BA, Schmidt L, Vocke CD, Peto M, Al Mamun AA, Shinbrot E, Sethi A, Brooks S, Rathmell WK, Brooks AN, Hoadley KA, Robertson AG, Brooks D, Bowlby R, Sadeghi S, Shen H, Weisenberger DJ, Bootwalla M, Baylin SB, Laird PW, Cherniack AD, Saksena G, Haake S, Li J, Liang H, Lu Y, Mills GB, Akbani R, Leiserson MD, Raphael BJ, Anur P, Bottaro D, Albiges L, Barnabas N, Choueiri TK, Czerniak B, Godwin AK, Hakimi AA, Ho TH, Hsieh J, Ittmann M, Kim WY, Krishnan B, Merino MJ, Mills Shaw KR, Reuter VE, Reznik E, Shelley CS, Shuch B, Signoretti S, Srinivasan R, Tamboli P, Thomas G, Tickoo S, Burnett K, Crain D, Gardner J, Lau K, Mallery D, Morris S, Paulauskis JD, Penny RJ, Shelton C, Shelton WT, Sherman M, Thompson E, Yena P, Avedon MT, Bowen J, Gastier-Foster JM, Gerken M, Leraas KM, Lichtenberg TM, Ramirez NC, Santos T, Wise L, Zmuda E, Demchok JA, Felau I, Hutter CM, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Zhang J, Ayala B, Baboud J, Chudamani S, Liu J, Lolla L, Naresh R, Pihl T, Sun Q, Wan Y, Wu Y, Ally A, Balasundaram M, Balu S, Beroukhim R, Bodenheimer T, Buhay C, Butterfield YS, Carlsen R, Carter SL, Chao H, Chuah E, Clarke A, Covington KR, Dahdouli M, Dewal N, Dhalla N, Doddapaneni HV, Drummond JA, Gabriel SB, Gibbs RA, Guin R, Hale W, Hawes A, Hayes DN, Holt RA, Hoyle AP, Jefferys SR, Jones SJ, Jones CD, Kalra D, Kovar C, Lewis L, Li J, Ma Y, Marra MA, Mayo M, Meng S, Meyerson M, Mieczkowski PA, Moore RA, Morton D, Mose LE, Mungall AJ, Muzny D, Parker JS, Perou CM, Roach J, Schein JE, Schumacher SE, Shi Y, Simons JV, Sipahimalani P, Skelly T, Soloway MG, Sougnez C, Tam A, Tan D, Thiessen N, Veluvolu U, Wang M, Wilkerson MD, Wong T, Wu J, Xi L, Zhou J, Bedford J, Chen F, Fu Y, Gerstein M, Haussler D, Kasaian K, Lai P, Ling S, Radenbaugh A, Van Den Berg D, Weinstein JN, Zhu J, Albert M, Alexopoulou I, Andersen JJ, Auman JT, Bartlett J, Bastacky S, Bergsten J, Blute ML, Boice L, Bollag RJ, Boyd J, Castle E, Chen YB, Cheville JC, Curley E, Davies B, DeVolk A, Dhir R, Dike L, Eckman J, Engel J, Harr J, Hrebinko R, Huang M, Huelsenbeck-Dill L, Iacocca M, Jacobs B, Lobis M, Maranchie JK, McMeekin S, Myers J, Nelson J, Parfitt J, Parwani A, Petrelli N, Rabeno B, Roy S, Salner AL, Slaton J, Stanton M, Thompson RH, Thorne L, Tucker K, Weinberger PM, Winemiller C, Zach LA, Zuna R. Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med. 2016 Jan 14; 374(2):135-45. PMID: 26536169; PMCID: PMC4775252.
      Citations: 414     Fields:    Translation:HumansCells
    62. 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. 2015 Nov; 12(11):1002-3. PMID: 26513549; PMCID: PMC4772859.
      Citations: 31     Fields:    Translation:Humans
    63. 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. 2015 Oct 15; 21(20):4514-24. PMID: 26473186; PMCID: PMC4610178.
      Citations: 51     Fields:    Translation:HumansAnimalsCells
    64. 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. 2016 Feb 01; 22(3):609-20. PMID: 26420858; PMCID: PMC4737991.
      Citations: 203     Fields:    Translation:HumansCells
    65. Melott JM, Weinstein JN, Broom BM. PathwaysWeb: a gene pathways API with directional interactions, expanded gene ontology, and versioning. Bioinformatics. 2016 Jan 15; 32(2):312-4. PMID: 26400039; PMCID: PMC4907393.
      Citations: 3     Fields:    Translation:HumansAnimalsCells
    66. 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. 2015 Sep 15; 75(18):3728-37. PMID: 26208906; PMCID: PMC4573884.
      Citations: 262     Fields:    Translation:HumansCells
    67. 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. 2015 Aug 28; 427(17):2867-85. PMID: 26142822.
      Citations: 10     Fields:    Translation:Cells
    68. 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. 2015 Aug; 5(8):860-77. PMID: 26069186; PMCID: PMC4527963.
      Citations: 330     Fields:    Translation:HumansCells
    69. Cancer Genome Atlas Research Network, Brat DJ, Verhaak RG, Aldape KD, Yung WK, Salama SR, Cooper LA, Rheinbay E, Miller CR, Vitucci M, Morozova O, Robertson AG, Noushmehr H, Laird PW, Cherniack AD, Akbani R, Huse JT, Ciriello G, Poisson LM, Barnholtz-Sloan JS, Berger MS, Brennan C, Colen RR, Colman H, Flanders AE, Giannini C, Grifford M, Iavarone A, Jain R, Joseph I, Kim J, Kasaian K, Mikkelsen T, Murray BA, O'Neill BP, Pachter L, Parsons DW, Sougnez C, Sulman EP, Vandenberg SR, Van Meir EG, von Deimling A, Zhang H, Crain D, Lau K, Mallery D, Morris S, Paulauskis J, Penny R, Shelton T, Sherman M, Yena P, Black A, Bowen J, Dicostanzo K, Gastier-Foster J, Leraas KM, Lichtenberg TM, Pierson CR, Ramirez NC, Taylor C, Weaver S, Wise L, Zmuda E, Davidsen T, Demchok JA, Eley G, Ferguson ML, Hutter CM, Mills Shaw KR, Ozenberger BA, Sheth M, Sofia HJ, Tarnuzzer R, Wang Z, Yang L, Zenklusen JC, Ayala B, Baboud J, Chudamani S, Jensen MA, Liu J, Pihl T, Raman R, Wan Y, Wu Y, Ally A, Auman JT, Balasundaram M, Balu S, Baylin SB, Beroukhim R, Bootwalla MS, Bowlby R, Bristow CA, Brooks D, Butterfield Y, Carlsen R, Carter S, Chin L, Chu A, Chuah E, Cibulskis K, Clarke A, Coetzee SG, Dhalla N, Fennell T, Fisher S, Gabriel S, Getz G, Gibbs R, Guin R, Hadjipanayis A, Hayes DN, Hinoue T, Hoadley K, Holt RA, Hoyle AP, Jefferys SR, Jones S, Jones CD, Kucherlapati R, Lai PH, Lander E, Lee S, Lichtenstein L, Ma Y, Maglinte DT, Mahadeshwar HS, Marra MA, Mayo M, Meng S, Meyerson ML, Mieczkowski PA, Moore RA, Mose LE, Mungall AJ, Pantazi A, Parfenov M, Park PJ, Parker JS, Perou CM, Protopopov A, Ren X, Roach J, 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, Gehlenborg N, Haussler D, Heiman DI, Iype L, Jacobsen A, Ju Z, Katzman S, Kim H, Knijnenburg T, Kreisberg RB, Lawrence MS, Lee W, Leinonen K, Lin P, Ling S, Liu W, Liu Y, Liu Y, Lu Y, Mills G, Ng S, Noble MS, Paull E, Rao A, Reynolds S, Saksena G, Sanborn Z, Sander C, Schultz N, Senbabaoglu Y, Shen R, Shmulevich I, Sinha R, Stuart J, Sumer SO, Sun Y, Tasman N, Taylor BS, Voet D, Weinhold N, Weinstein JN, Yang D, Yoshihara K, Zheng S, Zhang W, Zou L, Abel T, Sadeghi S, Cohen ML, Eschbacher J, Hattab EM, Raghunathan A, Schniederjan MJ, Aziz D, Barnett G, Barrett W, Bigner DD, Boice L, Brewer C, Calatozzolo C, Campos B, Carlotti CG, Chan TA, Cuppini L, Curley E, Cuzzubbo S, Devine K, DiMeco F, Duell R, Elder JB, Fehrenbach A, Finocchiaro G, Friedman W, Fulop J, Gardner J, Hermes B, Herold-Mende C, Jungk C, Kendler A, Lehman NL, Lipp E, Liu O, Mandt R, McGraw M, Mclendon R, McPherson C, Neder L, Nguyen P, Noss A, Nunziata R, Ostrom QT, Palmer C, Perin A, Pollo B, Potapov A, Potapova O, Rathmell WK, Rotin D, Scarpace L, Schilero C, Senecal K, Shimmel K, Shurkhay V, Sifri S, Singh R, Sloan AE, Smolenski K, Staugaitis SM, Steele R, Thorne L, Tirapelli DP, Unterberg A, Vallurupalli M, Wang Y, Warnick R, Williams F, Wolinsky Y, Bell S, Rosenberg M, Stewart C, Huang F, et al. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med. 2015 Jun 25; 372(26):2481-98. PMID: 26061751; PMCID: PMC4530011.
      Citations: 1192     Fields:    Translation:HumansCells
    70. Lerner SP, Weinstein J, Kwiatkowski D, Kim J, Robertson G, Hoadley KA, Akbani R, Creighton C, TCGA Muscle Invasive Bladder Cancer Analysis Working Group. The Cancer Genome Atlas Project on Muscle-invasive Bladder Cancer. Eur Urol Focus. 2015 Aug; 1(1):94-95. PMID: 28723366.
      Citations: 2     Fields:    
    71. 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. 2015 Mar; 25(3):316-27. PMID: 25650244; PMCID: PMC4352879.
      Citations: 174     Fields:    Translation:HumansCells
    72. 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, Byers LA, Meric-Bernstam F, Weinstein JN, Broom BM, Verhaak RG, Liang H, Mukherjee S, Lu Y, Mills GB, St?dler N. Corrigendum: A pan-cancer proteomic perspective on The Cancer Genome Atlas. Nat Commun. 2015 Jan 28; 6:4852. PMID: 25629879.
      Citations: 4     Fields:    
    73. 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. 2014 Dec 08; 15:1079. PMID: 25486910; PMCID: PMC4298954.
      Citations: 27     Fields:    Translation:HumansCells
    74. 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 reverse-phase protein arrays. Bioinformatics. 2015 Mar 15; 31(6):912-8. PMID: 25380958; PMCID: PMC4375399.
      Citations: 24     Fields:    
    75. Su X, Chen Y, Zhang J, Yao H, Valero V, Weinstein JN, Meric-Bernstam F, Esteva FJ, Malouf GG, Spano JP, Khayat D. Comprehensive analysis of long non-coding RNAs in human breast cancer clinical subtypes. Oncotarget. 2014 Oct 30; 5(20):9864-76. PMID: 25296969; PMCID: PMC4259443.
      Citations: 106     Fields:    Translation:HumansCells
    76. Desai S, Ding M, Wang B, Lu Z, Zhao Q, Shaw K, 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. 2014 Sep 30; 5(18):8202-10. PMID: 24077665; PMCID: PMC4226677.
      Citations: 81     Fields:    Translation:HumansCells
    77. Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, Leiserson MDM, Niu B, McLellan MD, Uzunangelov V, Zhang J, Kandoth C, Akbani R, Shen H, Omberg L, Chu A, Margolin AA, Van't Veer LJ, Laird PW, Raphael BJ, Ding L, Robertson AG, Byers LA, Mills GB, Weinstein JN, Van Waes C, Chen Z, Collisson EA, Cancer Genome Atlas Research Network, Benz CC, Perou CM, Stuart JM, Lopez-Bigas N. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell. 2014 Aug 14; 158(4):929-944. PMID: 25109877; PMCID: PMC4152462.
      Citations: 630     Fields:    Translation:HumansCells
    78. Zhang J, Yuan Y, Chen Y, Thompson EJ, Tannir NM, Weinstein JN, Valero V, Su X, Malouf GG, Comp?rat E, Roupr?t M, Cussenot O, Khayat D, Spano JP. Characterization of long non-coding RNA transcriptome in clear-cell renal cell carcinoma by next-generation deep sequencing. Mol Oncol. 2015 Jan; 9(1):32-43. PMID: 25126716; PMCID: PMC4516270.
      Citations: 45     Fields:    Translation:Humans
    79. Cancer Genome Atlas Research Network. Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014 Jul 31; 511(7511):543-50. PMID: 25079552; PMCID: PMC4231481.
      Citations: 2046     Fields:    Translation:HumansCells
    80. 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. 2014 Jul; 32(7):644-52. PMID: 24952901; PMCID: PMC4102885.
      Citations: 124     Fields:    Translation:Humans
    81. Silva LP, Hawke DH, Weinstein JN, Lorenzi PL, Purwaha P. An artifact in LC-MS/MS measurement of glutamine and glutamic acid: in-source cyclization to pyroglutamic acid. Anal Chem. 2014 Jun 17; 86(12):5633-7. PMID: 24892977; PMCID: PMC4063328.
      Citations: 22     Fields:    Translation:Cells
    82. Malouf GG, Su X, Yao H, Gao J, Xiong L, He Q, Escudier B, Camparo P, Doss DJ, Thompson EJ, Khayat D, Wood CG, Yu W, Teh BT, Weinstein J, Tannir NM, Comp?rat E, Couturier J, Molini? V. Next-generation sequencing of translocation renal cell carcinoma reveals novel RNA splicing partners and frequent mutations of chromatin-remodeling genes. Clin Cancer Res. 2014 Aug 01; 20(15):4129-40. PMID: 24899691; PMCID: PMC4167829.
      Citations: 45     Fields:    Translation:HumansCells
    83. 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, Byers LA, Meric-Bernstam F, Weinstein JN, Broom BM, Verhaak RG, Liang H, Mukherjee S, Lu Y, Mills GB, St?dler N. A pan-cancer proteomic perspective on The Cancer Genome Atlas. Nat Commun. 2014 May 29; 5:3887. PMID: 24871328; PMCID: PMC4109726.
      Citations: 248     Fields:    Translation:HumansCells
    84. 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. 2014 Jul 15; 20(14):3842-8. PMID: 24874835; PMCID: PMC4102633.
      Citations: 56     Fields:    Translation:Humans
    85. Lorenzi PL, Claerhout S, Mills GB, Weinstein JN. A curated census of autophagy-modulating proteins and small molecules: candidate targets for cancer therapy. Autophagy. 2014 Jul; 10(7):1316-26. PMID: 24906121; PMCID: PMC4203555.
      Citations: 18     Fields:    Translation:HumansCells
    86. Zheng S, Sivachenko A, Vegesna R, Wang Q, Yao R, Berger MF, Weinstein JN, Getz G, Verhaak RG, Torres-Garc?a W. PRADA: pipeline for RNA sequencing data analysis. Bioinformatics. 2014 Aug 01; 30(15):2224-6. PMID: 24695405; PMCID: PMC4103589.
      Citations: 86     Fields:    Translation:HumansCells
    87. 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. 2014; 9(3):e92047. PMID: 24670534; PMCID: PMC3966786.
      Citations: 21     Fields:    Translation:HumansCells
    88. 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. 2014 Jun 05; 123(23):3596-606. PMID: 24659632; PMCID: PMC4047499.
      Citations: 68     Fields:    Translation:HumansCells
    89. Purwaha P, Lorenzi PL, Silva LP, Hawke DH, Weinstein JN. Targeted metabolomic analysis of amino acid response to L-asparaginase in adherent cells. Metabolomics. 2014; 10(5):909-919. PMID: 25177232; PMCID: PMC4145215.
      Citations: 14     Fields:    
    90. Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature. 2014 Mar 20; 507(7492):315-22. PMID: 24476821; PMCID: PMC3962515.
      Citations: 1166     Fields:    Translation:HumansCells
    91. Weinstein JN, Lorenzi PL. Cancer: Discrepancies in drug sensitivity. Nature. 2013 Dec 19; 504(7480):381-3. PMID: 24284624.
      Citations: 21     Fields:    Translation:Humans
    92. 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. 2014 Apr; 2(4):371-9. PMID: 24764584; PMCID: PMC4007352.
      Citations: 47     Fields:    Translation:HumansCells
    93. Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, Barnholtz-Sloan J, Zou L, Vegesna R, Shukla SA, Ciriello G, Yung WK, Zhang W, Sougnez C, Mikkelsen T, Aldape K, Bigner DD, Van Meir EG, Prados M, Sloan A, Black KL, Eschbacher J, Finocchiaro G, Friedman W, Andrews DW, Guha A, Iacocca M, O'Neill BP, Foltz G, Myers J, Weisenberger DJ, Penny R, Kucherlapati R, Perou CM, Hayes DN, Gibbs R, Marra M, Mills GB, Lander E, Spellman P, Wilson R, Sander C, Weinstein J, Meyerson M, Gabriel S, Laird PW, Haussler D, Getz G, Chin L, TCGA Research Network. The somatic genomic landscape of glioblastoma. Cell. 2013 Oct 10; 155(2):462-77. PMID: 24120142; PMCID: PMC3910500.
      Citations: 2110     Fields:    Translation:HumansCells
    94. 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. 2013 Oct 15; 85(20):9536-42. PMID: 24011029; PMCID: PMC3868625.
      Citations: 33     Fields:    Translation:HumansCells
    95. Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013 Oct; 45(10):1113-20. PMID: 24071849; PMCID: PMC3919969.
      Citations: 2555     Fields:    Translation:Humans
    96. 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. 2013 Nov; 10(11):1046-7. PMID: 24037243; PMCID: PMC4076789.
      Citations: 221     Fields:    Translation:Humans
    97. 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. 2013 Jul 01; 27(13):1462-72. PMID: 23796897; PMCID: PMC3713427.
      Citations: 43     Fields:    Translation:Animals
    98. Cancer Genome Atlas Research Network. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature. 2013 Jul 04; 499(7456):43-9. PMID: 23792563; PMCID: PMC3771322.
      Citations: 1409     Fields:    Translation:HumansCells
    99. Khoury JD, Tannir NM, Williams MD, Chen Y, Yao H, Zhang J, Thompson EJ, TCGA Network, Meric-Bernstam F, Medeiros LJ, Weinstein JN, Su X. Landscape of DNA virus associations across human malignant cancers: analysis of 3,775 cases using RNA-Seq. J Virol. 2013 Aug; 87(16):8916-26. PMID: 23740984; PMCID: PMC3754044.
      Citations: 94     Fields:    Translation:HumansCells
    100. Cancer Genome Atlas Research Network, Kandoth C, Schultz N, Cherniack AD, Akbani R, Liu Y, Shen H, Robertson AG, Pashtan I, Shen R, Benz CC, Yau C, Laird PW, Ding L, Zhang W, Mills GB, Kucherlapati R, Mardis ER, Levine DA. Integrated genomic characterization of endometrial carcinoma. Nature. 2013 May 02; 497(7447):67-73. PMID: 23636398; PMCID: PMC3704730.
      Citations: 1657     Fields:    Translation:HumansCells
    101. Cancer Genome Atlas Research Network, Ley TJ, Miller C, Ding L, Raphael BJ, Mungall AJ, Robertson A, Hoadley K, Triche TJ, Laird PW, Baty JD, Fulton LL, Fulton R, Heath SE, Kalicki-Veizer J, Kandoth C, Klco JM, Koboldt DC, Kanchi KL, Kulkarni S, Lamprecht TL, Larson DE, Lin L, Lu C, McLellan MD, McMichael JF, Payton J, Schmidt H, Spencer DH, Tomasson MH, Wallis JW, Wartman LD, Watson MA, Welch J, Wendl MC, Ally A, Balasundaram M, Birol I, Butterfield Y, Chiu R, Chu A, Chuah E, Chun HJ, Corbett R, Dhalla N, Guin R, He A, Hirst C, Hirst M, Holt RA, Jones S, Karsan A, Lee D, Li HI, Marra MA, Mayo M, Moore RA, Mungall K, Parker J, Pleasance E, Plettner P, Schein J, Stoll D, Swanson L, Tam A, Thiessen N, Varhol R, Wye N, Zhao Y, Gabriel S, Getz G, Sougnez C, Zou L, Leiserson MD, Vandin F, Wu HT, Applebaum F, Baylin SB, Akbani R, Broom BM, Chen K, Motter TC, Nguyen K, Weinstein JN, Zhang N, Ferguson ML, Adams C, Black A, Bowen J, Gastier-Foster J, Grossman T, Lichtenberg T, Wise L, Davidsen T, Demchok JA, Shaw KR, Sheth M, Sofia HJ, Yang L, Downing JR, Eley G. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med. 2013 05 30; 368(22):2059-74. PMID: 23634996; PMCID: PMC3767041.
      Citations: 2081     Fields:    Translation:HumansCells
    102. 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. 2013 Jul; 3(7):770-81. PMID: 23619168; PMCID: PMC3858325.
      Citations: 241     Fields:    Translation:HumansCells
    103. Zhao Q, Caballero OL, Davis ID, Jonasch E, Tamboli P, Yung WK, Weinstein JN, Kenna Shaw for TCGA research network, 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. 2013 May 01; 19(9):2460-72. PMID: 23444225; PMCID: PMC3644028.
      Citations: 39     Fields:    Translation:HumansCells
    104. Verhaak RG, Tamayo P, Yang JY, Hubbard D, Zhang H, Creighton CJ, Fereday S, Lawrence M, Carter SL, Mermel CH, Kostic AD, Etemadmoghadam D, Saksena G, Cibulskis K, Duraisamy S, Levanon K, Sougnez C, Tsherniak A, Gomez S, Onofrio R, Gabriel S, Chin L, Zhang N, Spellman PT, Zhang Y, Akbani R, Hoadley KA, Kahn A, Huntsman D, Soslow RA, Defazio A, Birrer MJ, Gray JW, Weinstein JN, Bowtell DD, Drapkin R, Mesirov JP, Getz G, Levine DA, Meyerson M, Cancer Genome Atlas Research Network, K?bel M. Prognostically relevant gene signatures of high-grade serous ovarian carcinoma. J Clin Invest. 2013 Jan; 123(1):517-25. PMID: 23257362; PMCID: PMC3533304.
      Citations: 277     Fields:    Translation:HumansCTClinical Trials
    105. Chen Y, Yao H, Thompson EJ, Tannir NM, Weinstein JN, Su X. VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue. Bioinformatics. 2013 Jan 15; 29(2):266-7. PMID: 23162058; PMCID: PMC3546792.
      Citations: 85     Fields:    Translation:HumansCells
    106. 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. 2013 Jan 01; 19(1):279-90. PMID: 23091115; PMCID: PMC3567921.
      Citations: 463     Fields:    Translation:HumansAnimalsCells
    107. 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. 2012; 7(9):e45894. PMID: 23029298; PMCID: PMC3448701.
      Citations: 9     Fields:    Translation:HumansCells
    108. Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012 Sep 27; 489(7417):519-25. PMID: 22960745; PMCID: PMC3466113.
      Citations: 1742     Fields:    Translation:HumansCells
    109. 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. 2012 Sep; 2(9):798-811. PMID: 22961666; PMCID: PMC3567922.
      Citations: 217     Fields:    Translation:HumansCells
    110. 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. 2012; 7(7):e40062. PMID: 22848369; PMCID: PMC3406063.
      Citations: 9     Fields:    Translation:HumansCells
    111. 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. 2012 Sep 15; 28(18):2385-7. PMID: 22820202; PMCID: PMC3436850.
      Citations: 112     Fields:    Translation:Cells
    112. Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012 Jul 18; 487(7407):330-7. PMID: 22810696; PMCID: PMC3401966.
      Citations: 3605     Fields:    Translation:HumansCells
    113. Su X, Zhang L, Zhang J, Meric-Bernstam F, Weinstein JN. PurityEst: estimating purity of human tumor samples using next-generation sequencing data. Bioinformatics. 2012 Sep 01; 28(17):2265-6. PMID: 22743227; PMCID: PMC3426843.
      Citations: 35     Fields:    Translation:HumansCells
    114. 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. 2012 Jul 15; 28(14):1923-4. PMID: 22563071; PMCID: PMC3389765.
      Citations: 38     Fields:    Translation:HumansCells
    115. Weinstein JN. Drug discovery: Cell lines battle cancer. Nature. 2012 Mar 28; 483(7391):544-5. PMID: 22460893.
      Citations: 43     Fields:    Translation:Humans
    116. 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. AMPKa modulation in cancer progression: multilayer integrative analysis of the whole transcriptome in Asian gastric cancer. Cancer Res. 2012 May 15; 72(10):2512-21. PMID: 22434430; PMCID: PMC3872998.
      Citations: 54     Fields:    Translation:HumansCells
    117. Zeeberg BR, Reinhold W, Thallinger GG, Weinstein JN, Kohn KW, Pommier Y, Snajder R. Functional categories associated with clusters of genes that are co-expressed across the NCI-60 cancer cell lines. PLoS One. 2012; 7(1):e30317. PMID: 22291933; PMCID: PMC3265467.
      Citations: 10     Fields:    Translation:HumansCells
    118. Weinstein JN. MicroRNAs in cancer pharmacology and therapeutics: exploiting a natural synergy between '-omic' and hypothesis-driven research. Mol Cancer Ther. 2011 Nov; 10(11):2021. PMID: 22072806.
      Citations: 1     Fields:    Translation:Humans
    119. 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, 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, Trevi?o L. Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1. Science. 2011 Aug 26; 333(6046):1154-7. PMID: 21798897; PMCID: PMC3162986.
      Citations: 840     Fields:    Translation:HumansAnimalsCells
    120. Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature. 2011 Jun 29; 474(7353):609-15. PMID: 21720365; PMCID: PMC3163504.
      Citations: 3238     Fields:    Translation:HumansCells
    121. 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. 2011 Jun 03; 286(22):19511-22. PMID: 21487016; PMCID: PMC3103330.
      Citations: 31     Fields:    Translation:HumansAnimals
    122. 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. 2011 Feb 10; 12:52. PMID: 21310028; PMCID: PMC3223614.
      Citations: 4     Fields:    Translation:Animals
    123. Claerhout S, Lorenzi PL, Weinstein JN, Mills GB. MODULATION OF AUTOPHAGY AND ITS POTENTIAL FOR CANCER THERAPY. Drugs Future. 2011; 36(12). PMID: 25419038; PMCID: PMC4239665.
      Citations: 1     
    124. Deus HF, Veiga DF, Freire PR, Weinstein JN, Mills GB, Almeida JS. Exposing the cancer genome atlas as a SPARQL endpoint. J Biomed Inform. 2010 Dec; 43(6):998-1008. PMID: 20851208; PMCID: PMC3071752.
      Citations: 12     Fields:    
    125. Barb J, Zeeberg BR, Varma S, Ryan MC, Kohn KW, Weinstein JN, Munson PJ, Pommier Y, Solier S. Genome-wide analysis of novel splice variants induced by topoisomerase I poisoning shows preferential occurrence in genes encoding splicing factors. Cancer Res. 2010 Oct 15; 70(20):8055-65. PMID: 20817775; PMCID: PMC2992871.
      Citations: 34     Fields:    Translation:HumansCells
    126. 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. 2010 Aug 15; 26(16):1945-9. PMID: 20616384; PMCID: PMC2916722.
      Citations:    Fields:    Translation:HumansCells
    127. 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. 2010 May; 9(5):1080-91. PMID: 20442302; PMCID: PMC2879615.
      Citations: 78     Fields:    Translation:HumansCells
    128. 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. 2010 Mar 15; 70(6):2191-203. PMID: 20215517; PMCID: PMC2922994.
      Citations: 35     Fields:    Translation:HumansCells
    129. 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. 2010 Jul 01; 80(1):22-30. PMID: 20206143.
      Citations: 32     Fields:    Translation:HumansAnimalsCells
    130. Hanczar B, Hua J, Sima C, Weinstein J, Bittner M, Dougherty ER. Small-sample precision of ROC-related estimates. Bioinformatics. 2010 Mar 15; 26(6):822-30. PMID: 20130029.
      Citations: 57     Fields:    
    131. 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. 2010 Feb; 9(2):257-67. PMID: 20124458; PMCID: PMC4085051.
      Citations: 49     Fields:    Translation:HumansCells
    132. 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. 2010 Jan; 9(1):1-16. PMID: 20053763; PMCID: PMC2821037.
      Citations: 21     Fields:    Translation:HumansCells
    133. 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. 2009 Jul 15; 8(14):2281-99. PMID: 19556879; PMCID: PMC4018747.
      Citations: 4     Fields:    Translation:HumansCells
    134. 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. 2009 Jul; 8(7):2057-66. PMID: 19584229; PMCID: PMC2736804.
      Citations: 22     Fields:    Translation:HumansCells
    135. 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. 2009 Jun 23; 10:277. PMID: 19549304; PMCID: PMC2709662.
      Citations: 131     Fields:    Translation:HumansCells
    136. 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. 2009 Apr; 8(4):713-24. PMID: 19372543; PMCID: PMC4020356.
      Citations: 91     Fields:    Translation:HumansCells
    137. Lorenzi PL, Weinstein JN. Asparagine synthetase: a new potential biomarker in ovarian cancer. Drug News Perspect. 2009 Jan-Feb; 22(1):61-4. PMID: 19209300; PMCID: PMC4096155.
      Citations: 7     Fields:    Translation:HumansCells
    138. Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Butte A, Califano A, Celis J, Cufer T, Ferrell J, Galas D, Gallahan D, Gatenby R, Goldbeter A, Hace N, Henney A, Hood L, Iyengar R, Jackson V, Kallioniemi O, Kolar P, Kolch W, Kyriakopoulou C, Laplace F, Lehrach H, Marcus F, Matrisian L, Nolan G, Pelkmans L, Potti A, Sander C, Seljak M, Singer D, Sorger P, Stunnenberg H, Superti-Furga G, Uhlen M, Vidal M, Weinstein J, Wigle D, Williams M, Wolkenhauer O, Zhivotovsky B, Zinovyev A, Zupan B, Brunak S, Klingm?ller U. Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Mol Oncol. 2009 Feb; 3(1):9-17. PMID: 19383362; PMCID: PMC2930781.
      Citations: 11     Fields:    Translation:Humans
    139. 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. 2008 Nov; 10(11):1222-30. PMID: 18953431; PMCID: PMC2570598.
      Citations: 23     Fields:    Translation:HumansCells
    140. 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. 2008 Oct; 7(10):3123-8. PMID: 18852115; PMCID: PMC4123961.
      Citations: 39     Fields:    Translation:HumansCells
    141. Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008 Oct 23; 455(7216):1061-8. PMID: 18772890; PMCID: PMC2671642.
      Citations: 3574     Fields:    Translation:HumansCells
    142. Okabe M, Reimers MA, Suzuki T, Hall MD, Abe T, Weinstein JN, Gottesman MM, Szak?cs G. Profiling SLCO and SLC22 genes in the NCI-60 cancer cell lines to identify drug uptake transporters. Mol Cancer Ther. 2008 Sep; 7(9):3081-91. PMID: 18790787; PMCID: PMC2597359.
      Citations: 56     Fields:    Translation:HumansCells
    143. 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. 2008 Jul 18; 9:313. PMID: 18638396; PMCID: PMC2491637.
      Citations: 26     Fields:    Translation:Cells
    144. 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. 2008 Jun; 7(6):1337-46. PMID: 18524847; PMCID: PMC2705835.
      Citations: 7     Fields:    Translation:HumansCells
    145. Weinstein JN. Biochemistry. A postgenomic visual icon. Science. 2008 Mar 28; 319(5871):1772-3. PMID: 18369130.
      Citations: 22     Fields:    Translation:Cells
    146. 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. 2008 Mar 15; 122(6):1324-32. PMID: 17999412.
      Citations: 97     Fields:    Translation:HumansCells
    147. Kestler HA, Kraus JM, Buchholz M, Gress TM, Liu H, Kane DW, Zeeberg BR, Weinstein JN, M?ller A. VennMaster: area-proportional Euler diagrams for functional GO analysis of microarrays. BMC Bioinformatics. 2008 Jan 29; 9:67. PMID: 18230172; PMCID: PMC2335321.
      Citations: 33     Fields:    
    148. 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, Fornace AJ. Integrating global gene expression and radiation survival parameters across the 60 cell lines of the National Cancer Institute Anticancer Drug Screen. Cancer Res. 2008 Jan 15; 68(2):415-24. PMID: 18199535.
      Citations: 123     Fields:    Translation:HumansCells
    149. 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. 2008 Jan; 7(1):10-8. PMID: 18187810.
      Citations: 24     Fields:    Translation:HumansCells
    150. 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. 2008 Jan; 7(1):1-9. PMID: 18187804.
      Citations: 154     Fields:    Translation:HumansCells
    151. 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. Front Neuroendocrinol. 2008 Jun; 29(3):428-44. PMID: 18295320; PMCID: PMC2716011.
      Citations: 11     Fields:    Translation:HumansAnimalsCells
    152. Patterson AD, Li H, Eichler GS, Krausz KW, Weinstein JN, Fornace AJ, 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. 2008 Feb 01; 80(3):665-74. PMID: 18173289; PMCID: PMC2254319.
      Citations: 59     Fields:    Translation:HumansCells
    153. 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. 2008 Mar; 108(3):652-7. PMID: 18096210.
      Citations: 10     Fields:    Translation:Humans
    154. Kohn KW, Aladjem MI, Weinstein JN, Pommier Y. Chromatin challenges during DNA replication: a systems representation. Mol Biol Cell. 2008 Jan; 19(1):1-7. PMID: 17959828; PMCID: PMC2174177.
      Citations: 12     Fields:    Translation:AnimalsCells
    155. 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. Nonclassic functions of human topoisomerase I: genome-wide and pharmacologic analyses. Cancer Res. 2007 Sep 15; 67(18):8752-61. PMID: 17875716.
      Citations: 52     Fields:    Translation:HumansCells
    156. Lee JK, Havaleshko DM, Cho H, Weinstein JN, Kaldjian EP, Karpovich J, Grimshaw A, Theodorescu D. A strategy for predicting the chemosensitivity of human cancers and its application to drug discovery. Proc Natl Acad Sci U S A. 2007 Aug 07; 104(32):13086-91. PMID: 17666531; PMCID: PMC1941805.
      Citations: 153     Fields:    Translation:HumansCells
    157. 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. 2007 Sep 15; 23(18):2385-90. PMID: 17660211.
      Citations: 50     Fields:    Translation:Cells
    158. 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. 2007 May; 6(5):1483-91. PMID: 17483436.
      Citations: 106     Fields:    Translation:HumansCells
    159. 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. 2007; 35(8):e57. PMID: 17392344; PMCID: PMC1885663.
      Citations: 14     Fields:    Translation:HumansCells
    160. 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. 2007 Mar; 6(3):820-32. PMID: 17339364.
      Citations: 164     Fields:    Translation:HumansCells
    161. 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. 2007 Mar 05; 8:75. PMID: 17338820; PMCID: PMC1839109.
      Citations: 16     Fields:    Translation:HumansCells
    162. 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. 2007 Feb; 6(2):391-403. PMID: 17272646.
      Citations: 26     Fields:    Translation:HumansCells
    163. 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. 2007; 8(9):R187. PMID: 17845722; PMCID: PMC2375025.
      Citations: 11     Fields:    Translation:HumansCells
    164. Weinstein JN. Spotlight on molecular profiling: "Integromic" analysis of the NCI-60 cancer cell lines. Mol Cancer Ther. 2006 Nov; 5(11):2601-5. PMID: 17088435.
      Citations: 39     Fields:    Translation:HumansCells
    165. 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. 2006 Nov; 5(11):2606-12. PMID: 17088437; PMCID: PMC2705832.
      Citations: 216     Fields:    Translation:HumansCells
    166. 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. 2006 Nov; 5(11):2613-23. PMID: 17088436.
      Citations: 42     Fields:    Translation:HumansCells
    167. Weinstein JN, Pommier Y. Connecting genes, drugs and diseases. Nat Biotechnol. 2006 Nov; 24(11):1365-6. PMID: 17093484.
      Citations: 5     Fields:    
    168. Kohn KW, Aladjem MI, Kim S, Weinstein JN, Pommier Y. Depicting combinatorial complexity with the molecular interaction map notation. Mol Syst Biol. 2006; 2:51. PMID: 17016517; PMCID: PMC1681518.
      Citations: 22     Fields:    Translation:HumansCells
    169. Meng LH, Shankavaram U, Chen C, Agama K, Fu HQ, Gonzalez FJ, Weinstein J, 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. 2006 Oct 01; 66(19):9656-64. PMID: 17018623.
      Citations: 21     Fields:    Translation:HumansCells
    170. 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. 2006 Jul 15; 66(14):7216-24. PMID: 16849569.
      Citations: 48     Fields:    Translation:Animals
    171. 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. 2006 Jun; 16(6):796-803. PMID: 16672307; PMCID: PMC1479861.
      Citations: 42     Fields:    Translation:AnimalsCells
    172. Pommier Y, Weinstein JN, Aladjem MI, Kohn KW. Chk2 molecular interaction map and rationale for Chk2 inhibitors. Clin Cancer Res. 2006 May 01; 12(9):2657-61. PMID: 16675556.
      Citations: 40     Fields:    Translation:HumansCells
    173. Ludwig JA, Martin SE, Chu BF, Cardarelli C, Sauna ZE, Caplen NJ, Fales HM, Ambudkar SV, Weinstein JN, Gottesman MM, Szak?cs G. Selective toxicity of NSC73306 in MDR1-positive cells as a new strategy to circumvent multidrug resistance in cancer. Cancer Res. 2006 May 01; 66(9):4808-15. PMID: 16651436; PMCID: PMC1474781.
      Citations: 55     Fields:    Translation:HumansCells
    174. 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. 2006 Apr 06; 7:192. PMID: 16600027; PMCID: PMC1524995.
      Citations: 9     Fields:    
    175. Bussey KJ, Chin K, Lababidi S, Reimers M, Reinhold WC, Kuo WL, Gwadry 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. 2006 Apr; 5(4):853-67. PMID: 16648555; PMCID: PMC2733874.
      Citations: 80     Fields:    Translation:HumansCells
    176. 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. 2005 Nov 15; 65(22):10255-64. PMID: 16288013; PMCID: PMC1421332.
      Citations: 47     Fields:    Translation:HumansCells
    177. Kohn KW, Aladjem MI, Weinstein JN, Pommier Y. Molecular interaction maps of bioregulatory networks: a general rubric for systems biology. Mol Biol Cell. 2006 Jan; 17(1):1-13. PMID: 16267266; PMCID: PMC1345641.
      Citations: 50     Fields:    Translation:HumansAnimalsCells
    178. Ludwig JA, Weinstein JN. Biomarkers in cancer staging, prognosis and treatment selection. Nat Rev Cancer. 2005 Nov; 5(11):845-56. PMID: 16239904.
      Citations: 521     Fields:    Translation:HumansAnimals
    179. 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. 2005 Aug; 37(8):844-52. PMID: 16041372.
      Citations: 256     Fields:    Translation:AnimalsCells
    180. 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. 2005 Jul 05; 6:168. PMID: 15998470; PMCID: PMC1190154.
      Citations: 152     Fields:    Translation:HumansCells
    181. Reimers M, Weinstein JN. Quality assessment of microarrays: visualization of spatial artifacts and quantitation of regional biases. BMC Bioinformatics. 2005 Jul 01; 6:166. PMID: 15992406; PMCID: PMC1189079.
      Citations: 23     Fields:    
    182. Petersen D, Chandramouli GV, Geoghegan J, Hilburn J, Paarlberg J, Kim CH, Munroe D, Gangi L, Han J, Puri R, Staudt L, Weinstein J, Barrett JC, Green J, Kawasaki ES. Three microarray platforms: an analysis of their concordance in profiling gene expression. BMC Genomics. 2005 May 05; 6:63. PMID: 15876355; PMCID: PMC1140753.
      Citations: 41     Fields:    Translation:HumansCells
    183. Lotze MT, Wang E, Marincola FM, Hanna N, Bugelski PJ, Burns CA, Coukos G, Damle N, Godfrey TE, Howell WM, Panelli MC, Perricone MA, Petricoin EF, Sauter G, Scheibenbogen C, Shivers SC, Taylor DL, Weinstein JN, Whiteside TL. 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. 2005 Mar-Apr; 28(2):79-119. PMID: 15725954.
      Citations: 10     Fields:    Translation:HumansCells
    184. 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. 2005 Feb 22; 102(8):2964-9. PMID: 15703300; PMCID: PMC549443.
      Citations: 12     Fields:    
    185. Fojo T, Farrell N, Ortuzar W, Tanimura H, Weinstein J, 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. 2005 Jan; 53(1):25-34. PMID: 15607933.
      Citations: 13     Fields:    Translation:HumansCells
    186. 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. 2004 Sep 15; 10(18 Pt 1):5973-4. PMID: 15447979.
      Citations:    Fields:    Translation:HumansPHPublic Health
    187. Annereau JP, Tucker CJ, Arciello A, Cardarelli C, Collins J, Grissom S, Zeeberg BR, Reinhold W, Weinstein JN, Pommier Y, Paules RS, Gottesman MM, Szak?cs G. Analysis of ATP-binding cassette transporter expression in drug-selected cell lines by a microarray dedicated to multidrug resistance. Mol Pharmacol. 2004 Dec; 66(6):1397-405. PMID: 15342794.
      Citations: 24     Fields:    Translation:HumansCells
    188. Annereau JP, Lababidi S, Shankavaram U, Arciello A, Bussey KJ, Reinhold W, Guo Y, Kruh GD, Reimers M, Weinstein JN, Gottesman MM, Szak?cs G. Predicting drug sensitivity and resistance: profiling ABC transporter genes in cancer cells. Cancer Cell. 2004 Aug; 6(2):129-37. PMID: 15324696.
      Citations: 205     Fields:    Translation:HumansCells
    189. 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. 2004 Jun 23; 5:80. PMID: 15214961; PMCID: PMC459209.
      Citations: 43     Fields:    Translation:HumansAnimals
    190. Huang Y, Anderle P, Bussey KJ, Barbacioru C, Shankavaram U, Dai Z, Reinhold WC, Papp A, Weinstein JN, Sad?e W. Membrane transporters and channels: role of the transportome in cancer chemosensitivity and chemoresistance. Cancer Res. 2004 Jun 15; 64(12):4294-301. PMID: 15205344.
      Citations: 109     Fields:    Translation:HumansCells
    191. 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. 2004 Jul; 15(7):3042-52. PMID: 15107465; PMCID: PMC452562.
      Citations: 34     Fields:    Translation:HumansAnimals
    192. Aladjem MI, Pasa S, Parodi S, Weinstein JN, Pommier Y, Kohn KW. Molecular interaction maps--a diagrammatic graphical language for bioregulatory networks. Sci STKE. 2004 Feb 24; 2004(222):pe8. PMID: 14997004.
      Citations: 11     Fields:    Translation:AnimalsCells
    193. Weinstein JN. Integromic analysis of the NCI-60 cancer cell lines. Breast Dis. 2004; 19:11-22. PMID: 15687693.
      Citations: 19     Fields:    
    194. 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. 2003 Dec 15; 63(24):8634-47. PMID: 14695175.
      Citations: 150     Fields:    Translation:HumansCells
    195. 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. 2003; 4(12):R82. PMID: 14659019; PMCID: PMC329421.
      Citations: 47     Fields:    Translation:HumansCells
    196. 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. 2003 Nov 25; 100(24):14229-34. PMID: 14623978; PMCID: PMC283574.
      Citations: 158     Fields:    Translation:HumansCells
    197. Weinstein JN, Pommier Y. Transcriptomic analysis of the NCI-60 cancer cell lines. C R Biol. 2003 Oct-Nov; 326(10-11):909-20. PMID: 14744097.
      Citations: 23     Fields:    Translation:HumansCells
    198. 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. 2003 Sep 01; 63(17):5243-50. PMID: 14500354.
      Citations: 43     Fields:    Translation:HumansCells
    199. 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. 2003 Sep 26; 278(39):37768-76. PMID: 12842873.
      Citations: 24     Fields:    Translation:Cells
    200. 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. 2003 Jun 01; 63(11):2782-93. PMID: 12782583.
      Citations: 26     Fields:    Translation:HumansCells
    201. 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. 2003; 4(4):R28. PMID: 12702209; PMCID: PMC154579.
      Citations: 481     Fields:    Translation:Humans
    202. 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. 2003; 4(4):R27. PMID: 12702208; PMCID: PMC154578.
      Citations: 75     Fields:    Translation:HumansCells
    203. 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. 2003 Mar 01; 63(5):1000-11. PMID: 12615715.
      Citations: 19     Fields:    Translation:HumansCells
    204. 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. 2003; 839. PMID: 14728344; PMCID: PMC1479940.
      Citations: 8     Fields:    Translation:Humans
    205. Weinstein JN. 'Omic' and hypothesis-driven research in the molecular pharmacology of cancer. Curr Opin Pharmacol. 2002 Aug; 2(4):361-5. PMID: 12127867.
      Citations: 18     Fields:    Translation:HumansAnimals
    206. 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. 2002 Mar 15; 62(6):1688-95. PMID: 11912141.
      Citations: 26     Fields:    Translation:HumansCells
    207. 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. 2002 Jan 01; 47(1):46-9. PMID: 11774349.
      Citations: 6     Fields:    Translation:Humans
    208. Buckner JC, Moynihan TJ. The DNA-repair gene MGMT and the clinical response of gliomas to alkylating agents. N Engl J Med. 2001 Mar 01; 344(9):686; author reply 687-8. PMID: 11229337.
      Citations:    Fields:    Translation:HumansCells
    209. Brien P, Brien M. Clinical crossroads: a 45-year-old man with low back pain. JAMA. 1999 Mar 10; 281(10):893; author reply 895. PMID: 10078473.
      Citations:    Fields:    Translation:Humans
    210. Fornace AJ, Amundson SA, Bittner M, Myers TG, Meltzer P, Weinsten JN, Trent J. The complexity of radiation stress responses: analysis by informatics and functional genomics approaches. Gene Expr. 1999; 7(4-6):387-400. PMID: 10440239; PMCID: PMC6174659.
      Citations: 20     Fields:    Translation:HumansAnimals
    211. Szebeni J, Dieffenbach C, Wahl SM, Venkateshan CN, Yeh A, Popovic M, Gartner S, Wahl LM, Peterfy M, Friedman RM, et al. Induction of alpha interferon by human immunodeficiency virus type 1 in human monocyte-macrophage cultures. J Virol. 1991 Nov; 65(11):6362-4. PMID: 1920639; PMCID: PMC250359.
      Citations: 20     Fields:    Translation:HumansCells
    212. Weinstein JN. Antibody lymphoscintigraphy. Cancer Treat Res. 1990; 51:365-85. PMID: 1977456.
      Citations: 1     Fields:    Translation:HumansAnimals
    213. Weinstein JN, Leserman LD. Liposomes as drug carriers in cancer chemotherapy. Pharmacol Ther. 1984; 24(2):207-33. PMID: 6379684.
      Citations: 15     Fields:    Translation:HumansAnimals
    214. Weinstein JN. Liposomes as drug carriers in cancer therapy. Cancer Treat Rep. 1984 Jan; 68(1):127-35. PMID: 6692424.
      Citations: 14     Fields:    Translation:Humans
    215. Pitas RE, Innerarity TL, Weinstein JN, Mahley RW. Acetoacetylated lipoproteins used to distinguish fibroblasts from macrophages in vitro by fluorescence microscopy. Arteriosclerosis. 1981 May-Jun; 1(3):177-85. PMID: 6895305.
      Citations: 102     Fields:    Translation:HumansCells
    216. Parker RJ, Sieber SM, Weinstein JN. Effect of liposome encapsulation of a fluorescent dye on its uptake by the lymphatics of the rat. Pharmacology. 1981; 23(3):128-36. PMID: 7280007.
      Citations: 1     Fields:    Translation:Animals
    217. Guo LS, Hamilton RL, Goerke J, Weinstein JN, Havel RJ. Interaction of unilamellar liposomes with serum lipoproteins and apolipoproteins. J Lipid Res. 1980 Nov; 21(8):993-1003. PMID: 6780646.
      Citations: 18     Fields:    Translation:HumansAnimals
    218. 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. 1980 Apr 24; 597(3):543-51. PMID: 7378402.
      Citations: 6     Fields:    Translation:HumansCells
    219. Van Renswoude AJ, Blumenthal R, Weinstein JN. Thin-layer chromatography with agarose gels. A quick, simple method for evaluating liposome size. Biochim Biophys Acta. 1980; 595(1):151-6. PMID: 7349878.
      Citations: 1     Fields:    
    220. 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. 1979 Feb; 122(2):585-91. PMID: 368242.
      Citations: 4     Fields:    Translation:AnimalsCells
    221. 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. 1978 May 18; 509(2):272-88. PMID: 656414.
      Citations: 7     Fields:    Translation:Cells
    222. Pagano RE, Weinstein JN. Interactions of liposomes with mammalian cells. Annu Rev Biophys Bioeng. 1978; 7:435-68. PMID: 352245.
      Citations: 78     Fields:    Translation:Cells
    223. Blumenthal R, Weinstein JN, Henkart P. Lipid model membrane studies on immune cytotoxic mechanisms. Adv Exp Med Biol. 1977; 84:495-507. PMID: 302636.
      Citations:    Fields:    Translation:HumansAnimalsCells
    224. Invasive bladder cancer. Clinical Cancer Research. 21:4514-4524.
    225. Modulation of autophagy and its potential for cancer therapy. Drugs of the Future. 36:919-925.
    226. Targeted metabolomic analysis of amino acid response to L-asparaginase in adherent cells. Metabolomics. 1-11.
    227. Gene Expression Profile of the Clinically Aggressive Micropapillary Variant of Bladder Cancer. European Urology.
    228. Framework for identifying common aberrations in DNA copy number data. 122-136.
    229. Detection of tumor in lymph nodes by delivery of monoclonal antibodies via the lymphatics.
    230. TCGASpliceSeq a compendium of alternative mRNA splicing in cancer. Nucleic Acids Research. 44:D1018-D1022.
    231. Genes suppressed by DNA methylation in non-small cell lung cancer reveal the epigenetics of epithelial-mesenchymal transition. BMC Genomics. 1-15.
    232. Erratum. Science. 222:566.
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