| Year |
Citation |
Score |
| 2021 |
Uzunangelov V, Wong CK, Stuart JM. Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge. Plos Computational Biology. 17: e1008878. PMID 33861732 DOI: 10.1371/journal.pcbi.1008878 |
0.375 |
|
| 2020 |
Guan X, Sun D, Lu E, Urrutia JA, Reiter RE, Rettig M, Evans CP, Lara P, Gleave M, Beer TM, Thomas GV, Huang J, Aggarwal RR, Quigley DA, Foye A, ... ... Stuart JM, et al. Copy Number Loss of 17q22 Is Associated with Enzalutamide Resistance and Poor Prognosis in Metastatic Castration-Resistant Prostate Cancer. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 32727885 DOI: 10.1158/1078-0432.Ccr-19-2303 |
0.354 |
|
| 2020 |
Rheinbay E, Nielsen MM, Abascal F, Wala JA, Shapira O, Tiao G, Hornshøj H, Hess JM, Juul RI, Lin Z, Feuerbach L, Sabarinathan R, Madsen T, Kim J, Mularoni L, ... ... Stuart JM, et al. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. Nature. 578: 102-111. PMID 32025015 DOI: 10.1038/s41586-020-1965-x |
0.329 |
|
| 2020 |
Salcedo A, Tarabichi M, Espiritu SMG, Deshwar AG, David M, Wilson NM, Dentro S, Wintersinger JA, Liu LY, Ko M, Sivanandan S, Zhang H, Zhu K, Ou Yang TH, Chilton JM, ... ... Stuart JM, et al. A community effort to create standards for evaluating tumor subclonal reconstruction. Nature Biotechnology. 38: 97-107. PMID 31919445 DOI: 10.1038/S41587-019-0364-Z |
0.343 |
|
| 2020 |
Haan D, Tao R, Friedl V, Anastopoulos IN, Wong CK, Weinstein AS, Stuart JM. Using Transcriptional Signatures to Find Cancer Drivers with LURE. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 25: 343-354. PMID 31797609 |
0.347 |
|
| 2019 |
Ding H, Blair A, Yang Y, Stuart JM. Biological process activity transformation of single cell gene expression for cross-species alignment. Nature Communications. 10: 4899. PMID 31653878 DOI: 10.1038/S41467-019-12924-W |
0.304 |
|
| 2018 |
Newton Y, Rassekh SR, Deyell RJ, Shen Y, Jones MR, Dunham C, Yip S, Leelakumari S, Zhu J, McColl D, Swatloski T, Salama SR, Ng T, Hendson G, Lee AF, ... ... Stuart JM, et al. Comparative RNA-Sequencing Analysis Benefits a Pediatric Patient With Relapsed Cancer. Jco Precision Oncology. 2. PMID 31372595 DOI: 10.1200/PO.17.00198 |
0.327 |
|
| 2018 |
Lee AY, Ewing AD, Ellrott K, Hu Y, Houlahan KE, Bare JC, Espiritu SMG, Huang V, Dang K, Chong Z, Caloian C, Yamaguchi TN, Kellen MR, Chen K, ... ... Stuart JM, et al. Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection. Genome Biology. 19: 188. PMID 30400818 DOI: 10.1186/S13059-018-1539-5 |
0.379 |
|
| 2018 |
Quigley DA, Dang HX, Zhao SG, Lloyd P, Aggarwal R, Alumkal JJ, Foye A, Kothari V, Perry MD, Bailey AM, Playdle D, Barnard TJ, Zhang L, Zhang J, Youngren JF, ... ... Stuart JM, et al. Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer. Cell. 175: 889. PMID 30340047 DOI: 10.1016/J.Cell.2018.10.019 |
0.364 |
|
| 2018 |
Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Kwok-Shing Ng P, Jeong KJ, Cao S, Wang Z, Gao J, ... ... Stuart J, et al. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 174: 1034-1035. PMID 30096302 DOI: 10.1016/J.Cell.2018.07.034 |
0.356 |
|
| 2018 |
Quigley DA, Dang HX, Zhao SG, Lloyd P, Aggarwal R, Alumkal JJ, Foye A, Kothari V, Perry MD, Bailey AM, Playdle D, Barnard TJ, Zhang L, Zhang J, Youngren JF, ... ... Stuart JM, et al. Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer. Cell. PMID 30033370 DOI: 10.1016/J.Cell.2018.06.039 |
0.418 |
|
| 2018 |
Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng PK, Jeong KJ, Cao S, Wang Z, Gao J, ... ... Stuart J, et al. Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell. 173: 371-385.e18. PMID 29625053 DOI: 10.1016/J.Cell.2018.02.060 |
0.332 |
|
| 2018 |
Malta TM, Sokolov A, Gentles AJ, Burzykowski T, Poisson L, Weinstein JN, Kamińska B, Huelsken J, Omberg L, Gevaert O, Colaprico A, Czerwińska P, Mazurek S, Mishra L, Heyn H, ... ... Stuart JM, et al. Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation. Cell. 173: 338-354.e15. PMID 29625051 DOI: 10.1016/J.Cell.2018.03.034 |
0.333 |
|
| 2018 |
Ding L, Bailey MH, Porta-Pardo E, Thorsson V, Colaprico A, Bertrand D, Gibbs DL, Weerasinghe A, Huang KL, Tokheim C, Cortés-Ciriano I, Jayasinghe R, Chen F, Yu L, Sun S, ... ... Stuart JM, et al. Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. Cell. 173: 305-320.e10. PMID 29625049 DOI: 10.1016/J.Cell.2018.03.033 |
0.417 |
|
| 2018 |
Hoadley KA, Yau C, Hinoue T, Wolf DM, Lazar AJ, Drill E, Shen R, Taylor AM, Cherniack AD, Thorsson V, Akbani R, Bowlby R, Wong CK, Wiznerowicz M, Sanchez-Vega F, ... ... Stuart JM, et al. Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell. 173: 291-304.e6. PMID 29625048 DOI: 10.1016/J.Cell.2018.03.022 |
0.393 |
|
| 2018 |
Sendorek DH, Caloian C, Ellrott K, Bare JC, Yamaguchi TN, Ewing AD, Houlahan KE, Norman TC, Margolin AA, Stuart JM, Boutros PC. Germline contamination and leakage in whole genome somatic single nucleotide variant detection. Bmc Bioinformatics. 19: 28. PMID 29385983 DOI: 10.1186/S12859-018-2046-0 |
0.383 |
|
| 2018 |
Malta TM, Sokolov A, Gentles AJ, Burzykowski T, Poisson L, Weinstein J, Kamińska B, Huelsken J, Omberg L, Gevaert O, Colaprico A, Czerwińska P, Mazurek S, Mishra L, Heyn H, ... ... Stuart JM, et al. Abstract LB-373: Comprehensive analysis of cancer stemness Cancer Research. 78. DOI: 10.1158/1538-7445.Am2018-Lb-373 |
0.395 |
|
| 2017 |
Carlin DE, Paull EO, Graim K, Wong CK, Bivol A, Ryabinin P, Ellrott K, Sokolov A, Stuart JM. Prophetic Granger Causality to infer gene regulatory networks. Plos One. 12: e0170340. PMID 29211761 DOI: 10.1371/Journal.Pone.0170340 |
0.374 |
|
| 2017 |
Newton Y, Novak AM, Swatloski T, McColl DC, Chopra S, Graim K, Weinstein AS, Baertsch R, Salama SR, Ellrott K, Chopra M, Goldstein TC, Haussler D, Morozova O, Stuart JM. TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal. Cancer Research. 77: e111-e114. PMID 29092953 DOI: 10.1158/0008-5472.Can-17-0580 |
0.392 |
|
| 2017 |
Niepel M, Hafner M, Duan Q, Wang Z, Paull EO, Chung M, Lu X, Stuart JM, Golub TR, Subramanian A, Ma'ayan A, Sorger PK. Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling. Nature Communications. 8: 1186. PMID 29084964 DOI: 10.1038/S41467-017-01383-W |
0.32 |
|
| 2017 |
Gönen M, Weir BA, Cowley GS, Vazquez F, Guan Y, Jaiswal A, Karasuyama M, Uzunangelov V, Wang T, Tsherniak A, Howell S, Marbach D, Hoff B, Norman TC, Airola A, ... ... Stuart JM, et al. A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines. Cell Systems. PMID 28988802 DOI: 10.1016/J.Cels.2017.09.004 |
0.417 |
|
| 2017 |
Farshidfar F, Zheng S, Gingras MC, Newton Y, Shih J, Robertson AG, Hinoue T, Hoadley KA, Gibb EA, Roszik J, Covington KR, Wu CC, Shinbrot E, Stransky N, Hegde A, ... ... Stuart JM, et al. Integrative Genomic Analysis of Cholangiocarcinoma Identifies Distinct IDH-Mutant Molecular Profiles. Cell Reports. 19: 2878-2880. PMID 28658632 DOI: 10.1016/J.Celrep.2017.06.008 |
0.345 |
|
| 2017 |
Graim K, Liu TT, Achrol AS, Paull EO, Newton Y, Chang SD, Harsh GR, Cordero SP, Rubin DL, Stuart JM. Revealing cancer subtypes with higher-order correlations applied to imaging and omics data. Bmc Medical Genomics. 10: 20. PMID 28359308 DOI: 10.1186/S12920-017-0256-3 |
0.385 |
|
| 2017 |
Morozova O, Newton Y, Shah AT, Beale H, Lam DL, Vivian J, Bjork I, Goldstein T, Stuart J, Salama S, Sweet-Cordero EA, Haussler D. Abstract 4890: A pan-cancer analysis framework for incorporating gene expression information into clinical interpretation of pediatric cancer genomic data Cancer Research. 77: 4890-4890. DOI: 10.1158/1538-7445.Am2017-4890 |
0.393 |
|
| 2016 |
Aggarwal R, Beer TM, Gleave M, Stuart JM, Rettig M, Evans CP, Youngren J, Alumkal JJ, Huang J, Thomas G, Witte O, Small EJ. Targeting Adaptive Pathways in Metastatic Treatment-Resistant Prostate Cancer: Update on the Stand Up 2 Cancer/Prostate Cancer Foundation-Supported West Coast Prostate Cancer Dream Team. European Urology Focus. 2: 469-471. PMID 28723508 DOI: 10.1016/J.Euf.2016.10.011 |
0.371 |
|
| 2016 |
Drake JM, Paull EO, Graham NA, Lee JK, Smith BA, Titz B, Stoyanova T, Faltermeier CM, Uzunangelov V, Carlin DE, Fleming DT, Wong CK, Newton Y, Sudha S, Vashisht AA, ... ... Stuart JM, et al. Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer. Cell. PMID 27499020 DOI: 10.1016/J.Cell.2016.07.007 |
0.438 |
|
| 2016 |
Waltman PH, Guo J, Reistetter EN, Purvine S, Ansong CK, van Baren MJ, Wong CH, Wei CL, Smith RD, Callister SJ, Stuart JM, Worden AZ. Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla. Plos One. 11: e0155839. PMID 27434306 DOI: 10.1371/Journal.Pone.0155839 |
0.322 |
|
| 2016 |
Si H, Lu H, Yang X, Mattox A, Jang M, Bian Y, Sano E, Viadiu H, Yan B, Yau C, Ng S, Lee SK, Romano RA, Davis S, Walker RL, ... ... Stuart JM, et al. TNF-α modulates genome-wide redistribution of ΔNp63α/TAp73 and NF-κB cREL interactive binding on TP53 and AP-1 motifs to promote an oncogenic gene program in squamous cancer. Oncogene. PMID 27132513 DOI: 10.1038/Onc.2016.112 |
0.396 |
|
| 2016 |
Lee JK, Phillips JW, Smith BA, Park JW, Stoyanova T, McCaffrey EF, Baertsch R, Sokolov A, Meyerowitz JG, Mathis C, Cheng D, Stuart JM, Shokat KM, Gustafson WC, Huang J, et al. N-Myc Drives Neuroendocrine Prostate Cancer Initiated from Human Prostate Epithelial Cells. Cancer Cell. 29: 536-47. PMID 27050099 DOI: 10.1016/J.Ccell.2016.03.001 |
0.308 |
|
| 2016 |
Sokolov A, Carlin DE, Paull EO, Baertsch R, Stuart JM. Pathway-Based Genomics Prediction using Generalized Elastic Net. Plos Computational Biology. 12: e1004790. PMID 26960204 DOI: 10.1371/Journal.Pcbi.1004790 |
0.42 |
|
| 2016 |
Hill SM, Heiser LM, Cokelaer T, Unger M, Nesser NK, Carlin DE, Zhang Y, Sokolov A, Paull EO, Wong CK, Graim K, Bivol A, Wang H, Zhu F, Afsari B, ... ... Stuart JM, et al. Inferring causal molecular networks: empirical assessment through a community-based effort. Nature Methods. PMID 26901648 DOI: 10.1038/Nmeth.3773 |
0.309 |
|
| 2016 |
Liu TT, Achrol AS, Mitchell LA, Du WA, Loya JJ, Rodriguez SA, Feroze A, Westbroek EM, Yeom KW, Stuart JM, Chang SD, Harsh GR, Rubin DL. Computational Identification of Tumor Anatomic Location Associated with Survival in 2 Large Cohorts of Human Primary Glioblastomas. Ajnr. American Journal of Neuroradiology. PMID 26744442 DOI: 10.3174/Ajnr.A4631 |
0.3 |
|
| 2016 |
Aggarwal RR, Youngren J, Sokolov A, Huang J, Thomas GV, True LD, Foye A, Alumkal JJ, Ryan CJ, Beer TM, Evans CP, Gleave M, Rettig M, Stuart JM, Lara P, et al. Persistence of AR signaling in small cell neuroendocrine prostate cancer (SCNC) and intermediate atypical carcinoma (IAC): Results from the SU2C/PCF/AACR West Coast Prostate Cancer Dream Team (WCDT). Journal of Clinical Oncology. 34: 5045-5045. DOI: 10.1200/Jco.2016.34.15_Suppl.5045 |
0.312 |
|
| 2016 |
Morozova O, Newton Y, Cline M, Yip S, Rao A, Stuart J, Goldstein T, Salama S, Deyell R, Rassekh SR, Haussler D. Abstract PR14: Harnessing the power of big data to advance pediatric cancer care Cancer Research. 76. DOI: 10.1158/1538-7445.Pedca15-Pr14 |
0.326 |
|
| 2016 |
Newton Y, Novak A, Swatlowski T, Chopra S, Salama S, Morozova O, Haussler D, Stuart J. Abstract LB-290: UCSC TumorMap: Exploring cancer signatures on an interactive dynamic landscape Cancer Research. 76. DOI: 10.1158/1538-7445.Am2016-Lb-290 |
0.453 |
|
| 2016 |
Drake JM, Paull EO, Graham NA, Lee JK, Smith BA, Stoyanova T, Faltermeier CM, Carlin DE, Vashisht A, Huang J, Wohlschlegel JA, Graeber TG, Witte ON, Stuart JM. Abstract 3882: Patient-specific druggable networks in lethal prostate cancer through proteome-guided multi-omic integration Cancer Research. 76: 3882-3882. DOI: 10.1158/1538-7445.Am2016-3882 |
0.432 |
|
| 2016 |
Weinstein JN, Lerner SP, Kwiatkowski DJ, Getz G, Kim J, Al-ahmadie HA, Cherniack AD, Guo G, Akbani R, Hoadley KA, Kim WY, Robertson G, Mungall AJ, Hinoue T, Laird PW, ... ... Stuart JM, et al. Abstract 128: Comprehensive molecular characterization of 412 muscle-invasive urothelial bladder carcinomas: final analysis of The Cancer Genome Atlas (TCGA) project Cancer Research. 76: 128-128. DOI: 10.1158/1538-7445.Am2016-128 |
0.441 |
|
| 2015 |
Smith BA, Sokolov A, Uzunangelov V, Baertsch R, Newton Y, Graim K, Mathis C, Cheng D, Stuart JM, Witte ON. A basal stem cell signature identifies aggressive prostate cancer phenotypes. Proceedings of the National Academy of Sciences of the United States of America. PMID 26460041 DOI: 10.1073/Pnas.1518007112 |
0.391 |
|
| 2015 |
Paten B, Diekhans M, Druker BJ, Friend S, Guinney J, Gassner N, Guttman M, James Kent W, Mantey P, Margolin AA, Massie M, Novak AM, Nothaft F, Pachter L, Patterson D, ... ... Stuart JM, et al. The NIH BD2K center for big data in translational genomics. Journal of the American Medical Informatics Association : Jamia. PMID 26174866 DOI: 10.1093/Jamia/Ocv047 |
0.333 |
|
| 2015 |
Creixell P, Reimand J, Haider S, Wu G, Shibata T, Vazquez M, Mustonen V, Gonzalez-Perez A, Pearson J, Sander C, Raphael BJ, Marks DS, Ouellette BFF, Valencia A, Bader GD, ... ... Stuart JM, et al. Pathway and network analysis of cancer genomes. Nature Methods. 12: 615-621. PMID 26125594 DOI: 10.1038/Nmeth.3440 |
0.378 |
|
| 2015 |
Ewing AD, Houlahan KE, Hu Y, Ellrott K, Caloian C, Yamaguchi TN, Bare JC, P'ng C, Waggott D, Sabelnykova VY, Kellen MR, Norman TC, Haussler D, Friend SH, ... ... Stuart JM, et al. Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Nature Methods. PMID 25984700 DOI: 10.1038/Nmeth.3407 |
0.395 |
|
| 2015 |
Youngren JF, Foye A, Thomas G, Stuart JM, Goldstein T, Robert B, Bivol A, Sokolov A, Ryan CJ, Pourmand N, Beer TM, Evans CP, Lara P, Gleave ME, Chi KN, et al. Abstract A12: Identification of pathways associated with abiraterone resistance in metastatic castration resistant prostate cancer: Preliminary results from the SU2C/AACR West Coast Prostate Cancer Dream Team Clinical Cancer Research. 21. DOI: 10.1158/1557-3265.Pms14-A12 |
0.417 |
|
| 2015 |
Lee JK, Smith BA, Phillips JW, Park J, Stoyanova TI, Baertsch R, Sokolov A, Mathis C, Cheng D, Stuart JM, Huang J, Witte ON. Abstract A28: N-Myc drives small cell neuroendocrine cancer initiated from human prostate basal cells Molecular Cancer Research. 13. DOI: 10.1158/1557-3125.Myc15-A28 |
0.35 |
|
| 2015 |
Uzunangelov V, Paull E, Chopra S, Carlin D, Bivol A, Ellrott K, Graim K, Newton Y, Ng S, Sokolov A, Stuart J. Abstract PR10: Multiple Pathway Learning accurately predicts gene essentiality in the Cancer Cell Line Encyclopedia Cancer Research. 75. DOI: 10.1158/1538-7445.Transcagen-Pr10 |
0.475 |
|
| 2015 |
Graim K, Newton Y, Bivol A, Sokolov A, Ellrott K, Baertsch R, Stuart J. Abstract A2-64: A signature catalog to classify tumor mixtures: Application to recognition of metastatic disease in prostate cancer Cancer Research. 75. DOI: 10.1158/1538-7445.Transcagen-A2-64 |
0.408 |
|
| 2015 |
Baertsch R, Wong C, Youngren J, Stuart J, Small E, Goldstein T. Abstract A1-46: Using Medbook Workbench to create evidence streams to guide medical decisions Cancer Research. 75. DOI: 10.1158/1538-7445.Transcagen-A1-46 |
0.333 |
|
| 2015 |
Uzunangelov V, Paull E, Chopra S, Carlin D, Bivol A, Ellrott K, Graim K, Newton Y, Ng S, Sokolov A, Stuart J. Abstract PR02: Multiple Pathway Learning accurately predicts gene essentiality in the Cancer Cell Line Encyclopedia Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-Pr02 |
0.469 |
|
| 2015 |
Ng S, Benz C, Haussler D, Stuart JM. Abstract B1-38: PARADIGM-SHIFT: Predicts the functional impact of ‘driver modules’ in multiple cancers using pathway impact analysis Cancer Research. 75. DOI: 10.1158/1538-7445.Compsysbio-B1-38 |
0.472 |
|
| 2015 |
Morozova O, Newton Y, Cline M, Zhu J, Learned K, Stuart J, Salama S, Arceci R, Haussler D. Abstract LB-212: Treehouse Childhood Cancer Project: a resource for sharing and multiple cohort analysis of pediatric cancer genomics data Cancer Research. 75. DOI: 10.1158/1538-7445.Am2015-Lb-212 |
0.335 |
|
| 2015 |
Woodward J, King C, Coleman D, Lisac R, Schwartzman J, Wang N, Gleave M, Gray J, Thomas G, Beer TM, Hook KV, Baertsch R, Goldstein T, Stuart J, Gao L, et al. Abstract 731: Integrative genomic analysis to identify emergent enzalutamide resistance mechanisms in castration-resistant prostate cancer Cancer Research. 75: 731-731. DOI: 10.1158/1538-7445.Am2015-731 |
0.301 |
|
| 2015 |
Weinstein JN, Kim J, Creighton CJ, Akbani R, Hoadley KA, Kim WY, Morgan MB, Hinoue T, Cherniack A, Su X, Mungall AJ, Ryan MC, Bajorin DF, Rosenberg JE, Czerniak B, ... ... Stuart JM, et al. Abstract 2969: Progress in The Cancer Genome Atlas bladder cancer project Cancer Research. 75: 2969-2969. DOI: 10.1158/1538-7445.Am2015-2969 |
0.336 |
|
| 2014 |
Small EJ, Youngren J, Alumkal J, Evans C, Ryan CJ, Lara P, Beer T, Witte O, Baertsch R, Stuart J. 760PDNEUROENDOCRINE PROSTATE CANCER (NEPC) IN PATIENTS (PTS) WITH METASTATIC CASTRATION RESISTANT PROSTATE CANCER (MCRPC) RESISTANT TO ABIRATERONE (ABI) OR ENZALUTAMIDE (ENZ): PRELIMINARY RESULTS FROM THE SU2C/PCF/AACR WEST COAST PROSTATE CANCER DREAM TEAM (WCDT). Annals of Oncology : Official Journal of the European Society For Medical Oncology. 25: iv258. PMID 28172078 DOI: 10.1093/Annonc/Mdu336.8 |
0.364 |
|
| 2014 |
Radenbaugh AJ, Ma S, Ewing A, Stuart JM, Collisson EA, Zhu J, Haussler D. RADIA: RNA and DNA integrated analysis for somatic mutation detection Plos One. 9. PMID 25405470 DOI: 10.1371/Journal.Pone.0111516 |
0.343 |
|
| 2014 |
Boutros PC, Margolin AA, Stuart JM, Califano A, Stolovitzky G. Toward better benchmarking: challenge-based methods assessment in cancer genomics. Genome Biology. 15: 462. PMID 25314947 DOI: 10.1186/S13059-014-0462-7 |
0.383 |
|
| 2014 |
Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, Leiserson MD, Niu B, McLellan MD, Uzunangelov V, Zhang J, Kandoth C, Akbani R, Shen H, Omberg L, ... ... Stuart JM, et al. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell. 158: 929-44. PMID 25109877 DOI: 10.1016/J.Cell.2014.06.049 |
0.44 |
|
| 2014 |
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, et al. Assessing the clinical utility of cancer genomic and proteomic data across tumor types. Nature Biotechnology. 32: 644-52. PMID 24952901 DOI: 10.1038/Nbt.2940 |
0.332 |
|
| 2014 |
Boutros PC, Ewing AD, Ellrott K, Norman TC, Dang KK, Hu Y, Kellen MR, Suver C, Bare JC, Stein LD, Spellman PT, Stolovitzky G, Friend SH, Margolin AA, Stuart JM. Global optimization of somatic variant identification in cancer genomes with a global community challenge. Nature Genetics. 46: 318-9. PMID 24675517 DOI: 10.1038/Ng.2932 |
0.348 |
|
| 2014 |
Small EJ, Youngren J, Beer TM, Ryan CJ, Thomas G, Pourmand N, Reiter RE, Alumkal JJ, Stuart JM, Evans CP, Gleave ME, Chi KN, Toschi A, Foye A, Lara P, et al. The molecular and pathway characterization of patients with metastatic castration resistant prostate cancer (mCRPC) refractory to therapy with abiraterone acetate or enzalutamide: Preliminary results from the SU2C/PCF/AACR West Coast Prostate Cancer Dream Team (WCDT). Journal of Clinical Oncology. 32: 79-79. DOI: 10.1200/Jco.2014.32.4_Suppl.79 |
0.375 |
|
| 2014 |
Weinstein JN, Kim J, Creighton CJ, Akbani R, Hoadley KA, Kim WY, Morgan MB, Hinoue T, Rosenberg JE, Bajorin DF, Hansel DE, Al-Ahmadie H, Gordenin D, Stuart JM, Robertson G, et al. Comprehensive molecular profiling of urothelial bladder cancer at the DNA, RNA, and protein levels: A TCGA project. Journal of Clinical Oncology. 32: 4509-4509. DOI: 10.1200/Jco.2014.32.15_Suppl.4509 |
0.438 |
|
| 2014 |
Bivol A, Baertsch R, Sokolov A, Paull E, Newton Y, Goldstein TC, Foye A, Pourmand N, Youngren J, Parulkar R, Lopez A, de Vere White R, Alumkal JJ, Toschi A, Beer TM, ... ... Stuart JM, et al. Pathway-based signature analysis of RNA-seq data to reveal new targetable avenues for metastatic castration-resistant prostate cancer (mCRPC) patients (pts): Preliminary results from the SU2C/PCF/AACR West Coast Prostate Cancer Dream Team (WCDT). Journal of Clinical Oncology. 32: 11078-11078. DOI: 10.1200/Jco.2014.32.15_Suppl.11078 |
0.344 |
|
| 2014 |
Weinstein JN, Kim J, Creighton CJ, Akbani R, Hoadley KA, Kim WY, Morgan MB, Hinoue T, Cherniack A, Su X, Mungall AJ, Ryan MC, Rosenberg JE, Bajorin DF, Czerniak B, ... ... Stuart JM, et al. Abstract 987: Comprehensive characterization of urothelial bladder cancer: a TCGA Project update Cancer Research. 74: 987-987. DOI: 10.1158/1538-7445.Am2014-987 |
0.437 |
|
| 2014 |
Bivol A, Graim K, Paull E, Carlin D, Baertsch R, Sokolov A, Stuart J. Abstract 4177: Identification of pathways relevant for metastatic site prediction in prostate cancer Cancer Research. 74: 4177-4177. DOI: 10.1158/1538-7445.Am2014-4177 |
0.309 |
|
| 2014 |
Wolf DM, Fan C, Hoadley KA, Yau C, Sokolov A, Stuart J, Perou C, Veer Lv'. Abstract 360: Thousands of published cancer signatures and pathways can be collapsed into a handful of non-redundant gene programs: a TCGA pan-cancer analysis Cancer Research. 74: 360-360. DOI: 10.1158/1538-7445.Am2014-360 |
0.334 |
|
| 2013 |
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. Nature Genetics. 45: 1113-20. PMID 24071849 DOI: 10.1038/Ng.2764 |
0.431 |
|
| 2013 |
Paull EO, Carlin DE, Niepel M, Sorger PK, Haussler D, Stuart JM. Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE). Bioinformatics (Oxford, England). 29: 2757-64. PMID 23986566 DOI: 10.1093/Bioinformatics/Btt471 |
0.455 |
|
| 2013 |
Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, ... ... Stuart JM, et al. Computational approaches to identify functional genetic variants in cancer genomes. Nature Methods. 10: 723-9. PMID 23900255 DOI: 10.1038/Nmeth.2562 |
0.313 |
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| 2013 |
Wong CK, Vaske CJ, Ng S, Sanborn JZ, Benz SC, Haussler D, Stuart JM. The UCSC Interaction Browser: multidimensional data views in pathway context. Nucleic Acids Research. 41: W218-24. PMID 23748957 DOI: 10.1093/Nar/Gkt473 |
0.385 |
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| 2013 |
Goldstein TC, Paull EO, Ellis MJ, Stuart JM. Molecular pathways: extracting medical knowledge from high-throughput genomic data. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 19: 3114-20. PMID 23430023 DOI: 10.1158/1078-0432.Ccr-12-2093 |
0.44 |
|
| 2013 |
Goldman M, Craft B, Swatloski T, Ellrott K, Cline M, Diekhans M, Ma S, Wilks C, Stuart J, Haussler D, Zhu J. The UCSC Cancer Genomics Browser: update 2013. Nucleic Acids Research. 41: D949-54. PMID 23109555 DOI: 10.1093/Nar/Gks1008 |
0.44 |
|
| 2013 |
Febbo PG, Goldstein TC, Baertsch R, Youngren J, Newton Y, Bivol A, Small EJ, Stuart JM. Identification of polo-like kinase 1 (PLK1) in aggressive prostate cancer by paradigm analysis. Journal of Clinical Oncology. 31: 5006-5006. DOI: 10.1200/Jco.2013.31.15_Suppl.5006 |
0.442 |
|
| 2013 |
Heiser LM, Shaw CA, Wang NJ, Grasso C, Anur P, Ng S, Goldstein T, Spellman PT, Stuart J, Osborne K, Gray J, Schiff R. Abstract 5238: Acquired therapeutic resistance is mediated by deregulation of multiple pathways. Cancer Research. 73: 5238-5238. DOI: 10.1158/1538-7445.Am2013-5238 |
0.361 |
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| 2012 |
Ng S, Collisson EA, Sokolov A, Goldstein T, Gonzalez-Perez A, Lopez-Bigas N, Benz C, Haussler D, Stuart JM. PARADIGM-SHIFT predicts the function of mutations in multiple cancers using pathway impact analysis. Bioinformatics (Oxford, England). 28: i640-i646. PMID 22962493 DOI: 10.1093/Bioinformatics/Bts402 |
0.45 |
|
| 2012 |
Ellis MJ, Ding L, Shen D, Luo J, Suman VJ, Wallis JW, Van Tine BA, Hoog J, Goiffon RJ, Goldstein TC, Ng S, Lin L, Crowder R, Snider J, Ballman K, ... ... Stuart JM, et al. Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature. 486: 353-60. PMID 22722193 DOI: 10.1038/Nature11143 |
0.406 |
|
| 2012 |
Heiser LM, Sadanandam A, Kuo WL, Benz SC, Goldstein TC, Ng S, Gibb WJ, Wang NJ, Ziyad S, Tong F, Bayani N, Hu Z, Billig JI, Dueregger A, Lewis S, ... ... Stuart JM, et al. Subtype and pathway specific responses to anticancer compounds in breast cancer. Proceedings of the National Academy of Sciences of the United States of America. 109: 2724-9. PMID 22003129 DOI: 10.1073/Pnas.1018854108 |
0.361 |
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| 2012 |
Ellis MJ, Ding L, Shen D, Luo J, Suman VJ, Goiffon RJ, Wallis JW, Goldstein TC, Chen K, Allred DC, Leitch AM, Olson JA, Ota DM, Watson M, Piwnica-Worms D, ... ... Stuart JM, et al. Whole genome sequencing to characterize luminal-type breast cancer. Journal of Clinical Oncology. 30: 503-503. DOI: 10.1200/Jco.2012.30.15_Suppl.503 |
0.388 |
|
| 2012 |
Stuart J. Pathway-based analysis of mutation impact Bmc Proceedings. 6: 1-1. DOI: 10.1186/1753-6561-6-S6-O3 |
0.412 |
|
| 2012 |
Szeto CW, Sokolov A, Benz S, Stuart J, Haussler D. Abstract 5085: TopModel: An online resource for predictive models in cancer Cancer Research. 72: 5085-5085. DOI: 10.1158/1538-7445.Am2012-5085 |
0.432 |
|
| 2012 |
Ng S, Thusberg J, Benz S, Vaske C, Ellrott K, Zhu J, Yau C, Collisson E, Mooney S, Benz C, Haussler D, Stuart J. Abstract 2985: Predicting the impact of mutations in cancer using an integrated pathway approach Cancer Research. 72: 2985-2985. DOI: 10.1158/1538-7445.Am2012-2985 |
0.403 |
|
| 2011 |
Koeva M, Forsberg EC, Stuart JM. Computational integration of homolog and pathway gene module expression reveals general stemness signatures. Plos One. 6: e18968. PMID 21559491 DOI: 10.1371/Journal.Pone.0018968 |
0.332 |
|
| 2011 |
Tamble CM, St. Onge RP, Giaever G, Nislow C, Williams AG, Stuart JM, Lokey RS. The synthetic genetic interaction network reveals small molecules that target specific pathways in Sacchromyces cerevisiae Molecular Biosystems. 7: 2019-2030. PMID 21487606 DOI: 10.1039/C0Mb00298D |
0.359 |
|
| 2011 |
Sanborn JZ, Benz SC, Craft B, Szeto C, Kober KM, Meyer L, Vaske CJ, Goldman M, Smith KE, Kuhn RM, Karolchik D, Kent WJ, Stuart JM, Haussler D, Zhu J. The UCSC Cancer Genomics Browser: update 2011. Nucleic Acids Research. 39: D951-9. PMID 21059681 DOI: 10.1093/Nar/Gkq1113 |
0.432 |
|
| 2011 |
Radenbaugh A, Sanborn JZ, Zerbino D, Wilks C, Stuart JM, Haussler D. Abstract 59: Identification of RNA editing events in cancer using high-throughput sequencing data Cancer Research. 71: 59-59. DOI: 10.1158/1538-7445.Am2011-59 |
0.379 |
|
| 2011 |
Zhu J, Sanborn JZ, Benz SC, Craft B, Szeto C, Kober KM, Goldman M, Meyer L, Vaske C, Collisson E, Stuart J, Haussler D. Abstract 4985: The UCSC Cancer Genomics Browser Cancer Research. 71: 4985-4985. DOI: 10.1158/1538-7445.Am2011-4985 |
0.441 |
|
| 2011 |
Ng S, Vaske C, Benz S, Durbin J, Szeto C, Heiser L, Wang N, Korkola J, Bayani N, Spellman P, Gray JW, Haussler D, Stuart J. Abstract 49: Constructing pathway based predictors of cancer clinical outcome Cancer Research. 71: 49-49. DOI: 10.1158/1538-7445.Am2011-49 |
0.451 |
|
| 2011 |
Szeto CW, Zhu J, Durbin J, Benz S, Vaske C, Stuart J, Haussler D. Abstract 43: Using matrix factorization to discover clinically-relevant molecular signatures across cancers Cancer Research. 71: 43-43. DOI: 10.1158/1538-7445.Am2011-43 |
0.413 |
|
| 2011 |
Stuart JM. Abstract CN07-04: Patient-specific pathway analysis using PARADIGM identifies key activities in multiple cancers. Molecular Cancer Therapeutics. 10. DOI: 10.1158/1535-7163.Targ-11-Cn07-04 |
0.451 |
|
| 2011 |
Yau C, Benz S, Sanborn J, Stuart J, Haussler D, Benz C. PD03-04: SuperPathway Analyses of Luminal and Basaloid Breast Cancers from the Cancer Genome Atlas (TCGA) Program. Cancer Research. 71. DOI: 10.1158/0008-5472.Sabcs11-Pd03-04 |
0.378 |
|
| 2011 |
Wolf D, Yau C, Benz S, Vaske C, Stuart J, Roy R, Olshen A, Boudreau A, Haussler D, Gray J, Spellman P, Davis S, Hylton N, Veer LV, Esserman L. P1-06-09: Patient-Specific Integrative Pathway Analysis Using PARADIGM Identifies Key Activities in I-SPY 1 Breast Cancer Patients (CALGB 150007/150012; ACRIN 6657). Cancer Research. 71. DOI: 10.1158/0008-5472.Sabcs11-P1-06-09 |
0.428 |
|
| 2010 |
House CD, Vaske CJ, Schwartz AM, Obias V, Frank B, Luu T, Sarvazyan N, Irby R, Strausberg RL, Hales TG, Stuart JM, Lee NH. Voltage-gated Na+ channel SCN5A is a key regulator of a gene transcriptional network that controls colon cancer invasion. Cancer Research. 70: 6957-67. PMID 20651255 DOI: 10.1158/0008-5472.Can-10-1169 |
0.413 |
|
| 2010 |
Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, Haussler D, Stuart JM. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics (Oxford, England). 26: i237-45. PMID 20529912 DOI: 10.1093/Bioinformatics/Btq182 |
0.484 |
|
| 2010 |
Wang BD, Kline CL, Pastor DM, Olson TL, Frank B, Luu T, Sharma AK, Robertson G, Weirauch MT, Patierno SR, Stuart JM, Irby RB, Lee NH. Prostate apoptosis response protein 4 sensitizes human colon cancer cells to chemotherapeutic 5-FU through mediation of an NF kappaB and microRNA network. Molecular Cancer. 9: 98. PMID 20433755 DOI: 10.1186/1476-4598-9-98 |
0.39 |
|
| 2010 |
Hudson TJ, Anderson W, Artez A, Barker AD, Bell C, Bernabé RR, Bhan MK, Calvo F, Eerola I, Gerhard DS, Guttmacher A, Guyer M, Hemsley FM, Jennings JL, ... ... Stuart JM, et al. International network of cancer genome projects. Nature. 464: 993-8. PMID 20393554 DOI: 10.1038/Nature08987 |
0.425 |
|
| 2010 |
Forsberg EC, Passegué E, Prohaska SS, Wagers AJ, Koeva M, Stuart JM, Weissman IL. Molecular signatures of quiescent, mobilized and leukemia-initiating hematopoietic stem cells. Plos One. 5: e8785. PMID 20098702 DOI: 10.1371/Journal.Pone.0008785 |
0.317 |
|
| 2010 |
Benz SC, Vaske C, Ng S, Sanborn JZ, Zhu J, Haussler D, Stuart J. Abstract 4905: Patient-specific pathway analysis using PARADIGM identifies key activities in multiple cancers Cancer Research. 71: 4905-4905. DOI: 10.1158/1538-7445.Am2011-4905 |
0.477 |
|
| 2010 |
House C, Vaske C, Schwartz A, Obias V, Sarvazyan N, Hales T, Stuart J, Lee N. Abstract 5292: Role of voltage-gated Na+ channels in the metastatic potential of colon cancer cells Cancer Research. 70: 5292-5292. DOI: 10.1158/1538-7445.Am10-5292 |
0.37 |
|
| 2010 |
Christopher S, Benz S, Vaske C, Sanborn JZ, Zhu J, Stuart J, Haussler D. Abstract 2001: Non-negative matrix factorization (NMF) as a clinical classifier: An example with chemotherapy response in ovarian cancer Cancer Research. 70: 2001-2001. DOI: 10.1158/1538-7445.Am10-2001 |
0.353 |
|
| 2009 |
Vaske CJ, House C, Luu T, Frank B, Yeang CH, Lee NH, Stuart JM. A factor graph nested effects model to identify networks from genetic perturbations. Plos Computational Biology. 5: e1000274. PMID 19180177 DOI: 10.1371/Journal.Pcbi.1000274 |
0.408 |
|
| 2009 |
Cozen AE, Weirauch MT, Pollard KS, Bernick DL, Stuart JM, Lowe TM. Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum Journal of Bacteriology. 191: 782-794. PMID 19047344 DOI: 10.1128/Jb.00965-08 |
0.374 |
|
| 2009 |
Koeva M, Forsberg EC, Stuart JM. Core stemness mechanisms revealed through homology Bmc Bioinformatics. 10: O4. DOI: 10.1186/1471-2105-10-S13-O4 |
0.332 |
|
| 2008 |
Weirauch MT, Wong CK, Byrne AB, Stuart JM. Information-based methods for predicting gene function from systematic gene knock-downs. Bmc Bioinformatics. 9: 463. PMID 18959798 DOI: 10.1186/1471-2105-9-463 |
0.411 |
|
| 2007 |
Salomonis N, Hanspers K, Zambon AC, Vranizan K, Lawlor SC, Dahlquist KD, Doniger SW, Stuart J, Conklin BR, Pico AR. GenMAPP 2: new features and resources for pathway analysis. Bmc Bioinformatics. 8: 217. PMID 17588266 DOI: 10.1186/1471-2105-8-217 |
0.38 |
|
| 2007 |
Hu Z, Ng DM, Yamada T, Chen C, Kawashima S, Mellor J, Linghu B, Kanehisa M, Stuart JM, DeLisi C. VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Research. 35: W625-32. PMID 17586824 DOI: 10.1093/Nar/Gkm295 |
0.36 |
|
| 2007 |
Hu Z, Mellor J, Wu J, Kanehisa M, Stuart JM, DeLisi C. Towards zoomable multidimensional maps of the cell. Nature Biotechnology. 25: 547-54. PMID 17483841 DOI: 10.1038/Nbt1304 |
0.332 |
|
| 2007 |
Chen C, Weirauch MT, Powell CC, Zambon AC, Stuart JM. A search engine to identify pathway genes from expression data on multiple organisms. Bmc Systems Biology. 1: 20. PMID 17477880 DOI: 10.1186/1752-0509-1-20 |
0.395 |
|
| 2006 |
Park CS, Gong R, Stuart J, Tang S. Molecular network and chromosomal clustering of genes involved in synaptic plasticity in the hippocampus. Journal of Biological Chemistry. 281: 30195-30211. PMID 16873368 DOI: 10.1074/Jbc.M605876200 |
0.32 |
|
| 2003 |
Stuart JM, Segal E, Koller D, Kim SK. A gene-coexpression network for global discovery of conserved genetic modules. Science (New York, N.Y.). 302: 249-55. PMID 12934013 DOI: 10.1126/Science.1087447 |
0.559 |
|
| 2003 |
Owen AB, Stuart J, Mach K, Villeneuve AM, Kim S. A gene recommender algorithm to identify coexpressed genes in C. elegans. Genome Research. 13: 1828-37. PMID 12902378 DOI: 10.1101/Gr.1125403 |
0.501 |
|
| 2002 |
Roy PJ, Stuart JM, Lund J, Kim SK. Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature. 418: 975-9. PMID 12214599 DOI: 10.1038/Nature01012 |
0.513 |
|
| 2001 |
Kim SK, Lund J, Kiraly M, Duke K, Jiang M, Stuart JM, Eizinger A, Wylie BN, Davidson GS. A gene expression map for Caenorhabditis elegans. Science (New York, N.Y.). 293: 2087-92. PMID 11557892 DOI: 10.1126/Science.1061603 |
0.552 |
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