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John Paul Shen - Publications

Affiliations: 
2004-2005 Chemical Biology Broad Institute (MIT/Harvard) 
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33 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Raghav K, Shen JP, Jácome AA, Guerra JL, Scally CP, Taggart MW, Foo WC, Matamoros A, Shaw KR, Fournier K, Overman MJ, Eng C. Integrated clinico-molecular profiling of appendiceal adenocarcinoma reveals a unique grade-driven entity distinct from colorectal cancer. British Journal of Cancer. PMID 32733093 DOI: 10.1038/S41416-020-1015-3  0.361
2020 Ghafouri S, Burkenroad A, Pantuck M, Almomani B, Stefanoudakis D, Shen J, Drakaki A. VEGF inhibition in urothelial cancer: the past, present and future. World Journal of Urology. PMID 32361873 DOI: 10.1007/S00345-020-03213-Z  0.334
2020 Shen JP, Chowdhury S, Wu J, Fournier K, Kopetz S, Raghav K. Abstract A07: Transcriptional profiling confirms appendiceal adenocarcinoma is distinct from colorectal cancer, in vivo models needed Cancer Research. 80. DOI: 10.1158/1538-7445.Camodels2020-A07  0.361
2019 Licon K, Shen JP, Munson BP, Michaca M, Fassino C, Fassino L, Kreisberg JF, Ideker T. Ultrahigh-Density Screens for Genome-Wide Yeast EMAPs in a Single Plate. Methods in Molecular Biology (Clifton, N.J.). 2049: 73-85. PMID 31602605 DOI: 10.1007/978-1-4939-9736-7_4  0.335
2019 Hui G, Ghafouri SN, Shen J, Liu S, Drakaki A. Treating Penile Cancer in the Immunotherapy and Targeted Therapy Era. Case Reports in Oncological Medicine. 2019: 8349793. PMID 31019822 DOI: 10.1155/2019/8349793  0.344
2019 Murtuza A, Bulbul A, Shen JP, Keshavarzian P, Woodward BD, Lopez-Diaz FJ, Lippman SM, Husain H. Novel Third-Generation EGFR Tyrosine Kinase Inhibitors and Strategies to Overcome Therapeutic Resistance in Lung Cancer. Cancer Research. PMID 30718357 DOI: 10.1158/0008-5472.Can-18-1281  0.361
2018 Wang S, Ma J, Zhang W, Shen JP, Huang J, Peng J, Ideker T. Typing tumors using pathways selected by somatic evolution. Nature Communications. 9: 4159. PMID 30297789 DOI: 10.1038/S41467-018-06464-Y  0.409
2018 Shen JP, Ideker T. Synthetic Lethal Networks for Precision Oncology: Promises and Pitfalls. Journal of Molecular Biology. PMID 29932943 DOI: 10.1016/J.Jmb.2018.06.026  0.369
2018 Zhang W, Bojorquez-Gomez A, Velez DO, Xu G, Sanchez KS, Shen JP, Chen K, Licon K, Melton C, Olson KM, Yu MK, Huang JK, Carter H, Farley EK, Snyder M, et al. A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. Nature Genetics. PMID 29610481 DOI: 10.1038/S41588-018-0091-2  0.387
2018 Shen JP, Jacobs MT, Fuh IL, Baumgartner JM, Fanta PT, Lowy AM, Harismendy O. Somatic mutation landscape of appendiceal cancer. Journal of Clinical Oncology. 36: 671-671. DOI: 10.1200/Jco.2018.36.4_Suppl.671  0.393
2018 Shen JP, Zhao D, Munson B, Birmingham A, Sasik R, Bojorquez-Gomez A, Licon K, Klepper K, Beckett A, Sanchez KS, Mali P, Ideker T. Abstract 3299: High-throughput combinatorial CRISPR-Cas9 gene knockout reveals most genetic interactions are context dependent Cancer Research. 78: 3299-3299. DOI: 10.1158/1538-7445.Am2018-3299  0.441
2017 Du D, Roguev A, Gordon DE, Chen M, Chen SH, Shales M, Shen JP, Ideker T, Mali P, Qi LS, Krogan NJ. Genetic interaction mapping in mammalian cells using CRISPR interference. Nature Methods. PMID 28481362 DOI: 10.1038/Nmeth.4286  0.341
2017 Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Licon K, Klepper K, Pekin D, Beckett AN, Sanchez KS, Thomas A, Kuo CC, Du D, Roguev A, et al. Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions. Nature Methods. PMID 28319113 DOI: 10.1038/Nmeth.4225  0.383
2017 Shen JP, Bojorquez-Gomez A, Huang J, Hofree M, Kurnit K, Klepper K, Beckett A, Kreisberg JF, Saenz CC, Ideker T. A platinum-resistant subtype of high-grade serous ovarian cancer identified by a network of somatic mutations. Journal of Clinical Oncology. 35: 5561-5561. DOI: 10.1200/Jco.2017.35.15_Suppl.5561  0.356
2017 Shen JP, Bojorquez-Gomez A, Huang J, Hofree M, Klepper K, Beckett A, Saenz C, Kreisberg J, Ideker T. Abstract AP23: A PLATINUM–RESISTANT SUBTYPE OF HIGH–GRADE SEROUS OVARIAN CANCER IDENTIFIED BY A NETWORK OF SOMATIC MUTATIONS Clinical Cancer Research. 23. DOI: 10.1158/1557-3265.Ovcasymp16-Ap23  0.385
2017 Shen JP, Zhao D, Sasik R, Luebeck J, Birmingham A, Bojorquez-Gomez A, Kreisberg J, Ideker T, Mali P. Abstract PR08: Combinatorial CRISPR-Cas9 reveals many cancer synthetic lethal interactions are private to cell type Molecular Cancer Therapeutics. 16. DOI: 10.1158/1538-8514.Synthleth-Pr08  0.408
2017 Shen JP, Zhao D, Sasik R, Luebeck J, Bojorquez-Gomez A, Licon K, Ideker T, Mali P. Abstract 3039: Combinatorial CRISPR-Cas9 gene knockout to enable genetic interaction mapping in human cells Cancer Research. 77: 3039-3039. DOI: 10.1158/1538-7445.Am2017-3039  0.307
2016 Srivas R, Shen JP, Yang CC, Sun SM, Li J, Gross AM, Jensen J, Licon K, Bojorquez-Gomez A, Klepper K, Huang J, Pekin D, Xu JL, Yeerna H, Sivaganesh V, et al. A Network of Conserved Synthetic Lethal Interactions for Exploration of Precision Cancer Therapy. Molecular Cell. PMID 27453043 DOI: 10.1016/J.Molcel.2016.06.022  0.426
2016 Shen JP, Srivas R, Yang CC, Sun SM, Li JF, Gross A, Jensen J, Licon K, Bojoquez-Gomez A, Klepper K, Attikum Hv, Aza-Blanc P, Sobol R, Ideker T. Abstract NG02: A network of deeply conserved synthetic-lethal interactions for exploration of precision cancer therapy Cancer Research. 76. DOI: 10.1158/1538-7445.Am2016-Ng02  0.455
2015 Shen JP, Srivas R, Gross A, Li J, Jaehnig EJ, Sun SM, Bojorquez-Gomez A, Licon K, Sivaganesh V, Xu JL, Klepper K, Yeerna H, Pekin D, Qiu CP, van Attikum H, et al. Chemogenetic profiling identifies RAD17 as synthetically lethal with checkpoint kinase inhibition. Oncotarget. PMID 26437225 DOI: 10.18632/Oncotarget.5928  0.377
2015 Shen JP, Srivas R, Bojorquez-Gomez A, Licon K, Sivaganesh V, Xu JL, Yeerna H, Gross A, Li JF, Sobol R, Ideker T. Abstract 129: RAD17 loss of function is synthetically lethal with the checkpoint kinase inhibitors AZD7762 or MK-1775 Cancer Research. 75: 129-129. DOI: 10.1158/1538-7445.Am2015-129  0.386
2014 Srivas R, Shen JP, Li JF, Licon K, Wang ZZ, Bojoquez-Gomez A, Xu L, Gross A, Bean G, Sobol R, Ideker T. Abstract B34: High-throughput synthetic lethal interaction screening in model organisms as a strategy for the identification of novel therapeutic targets in cancer Molecular Cancer Research. 12. DOI: 10.1158/1557-3125.Modorg-B34  0.46
2014 Gross AM, Orosco RK, Shen JP, Egloff AM, Carter H, Hoffree M, Choueiri M, Coffey CS, Lippman SM, Hayes DN, Cohen EE, Grandis JR, Nguyen QT, Ideker T. Abstract 3821: A prognostic model of head and neck cancer ties TP53 mutation to 3p loss Cancer Research. 74: 3821-3821. DOI: 10.1158/1538-7445.Am2014-3821  0.35
2013 Hofree M, Shen JP, Carter H, Gross A, Ideker T. Network-based stratification of tumor mutations. Nature Methods. 10: 1108-15. PMID 24037242 DOI: 10.1038/Nmeth.2651  0.379
2013 Shen JP, McGee DM, Lowy AM, Fanta PT. Molecular profiles of appendiceal adenocarcinoma: The UCSD experience. Journal of Clinical Oncology. 31: 397-397. DOI: 10.1200/Jco.2013.31.4_Suppl.397  0.402
2013 McGee DM, Shen JP, Fanta PT, Lowy AM. Molecular profiles of gastric cancer: The UCSD experience. Journal of Clinical Oncology. 31: 29-29. DOI: 10.1200/Jco.2013.31.4_Suppl.29  0.316
2013 Gross A, Choueiri M, Shen JP, Randall JM, Ideker T, Hofree M. Association of methylation of genes in the taurine/hypotaurine pathway with worse prognosis in renal cell carcinoma. Journal of Clinical Oncology. 31. DOI: 10.1200/Jco.2013.31.15_Suppl.E15562  0.33
2013 Shen JP, Srivas R, Bojorquez-Gomez A, Licon K, Li JF, Sobol RW, Ideker T. Cross-species synthetic lethal interaction screening as a strategy for the identification of novel therapeutic targets in cancer. Journal of Clinical Oncology. 31: 11105-11105. DOI: 10.1200/Jco.2013.31.15_Suppl.11105  0.44
2013 Hofree M, Shen JP, Carter H, Gross A, Ideker T. Abstract A14: Network-based stratification: Combining genome-scale somatic mutation profiles with genetic interaction networks to identify clinically relevant subtypes in high grade serous ovarian carcinoma Clinical Cancer Research. 19. DOI: 10.1158/1078-0432.Ovca13-A14  0.379
2012 Fanta PT, Roeland E, Shen JP, Shimabukuro KA, Hwang M, Ramamoorthy S, Lowy AM. Molecular predictors of treatment response in colon and gastric cancer. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 30: 619. PMID 27983429 DOI: 10.1200/Jco.2012.30.4_Suppl.619  0.402
2010 Bradner JE, Mak R, Tanguturi SK, Mazitschek R, Haggarty SJ, Ross K, Chang CY, Bosco J, West N, Morse E, Lin K, Shen JP, Kwiatkowski NP, Gheldof N, Dekker J, et al. Chemical genetic strategy identifies histone deacetylase 1 (HDAC1) and HDAC2 as therapeutic targets in sickle cell disease. Proceedings of the National Academy of Sciences of the United States of America. 107: 12617-22. PMID 20616024 DOI: 10.1073/Pnas.1006774107  0.468
2006 Bradner JE, McPherson OM, Mazitschek R, Barnes-Seeman D, Shen JP, Dhaliwal J, Stevenson KE, Duffner JL, Park SB, Neuberg DS, Nghiem P, Schreiber SL, Koehler AN. A robust small-molecule microarray platform for screening cell lysates. Chemistry & Biology. 13: 493-504. PMID 16720270 DOI: 10.1016/J.Chembiol.2006.03.004  0.596
2006 Bradner JE, Shen JP, Perlstein EO, Divakaran S, Greenberg EF, Amaravadi R, Schreiber SL. Discovery and Characterization of Small Molecule Inhibitors of Autophagy for Cancer Therapy. Blood. 108: 2606-2606. DOI: 10.1182/Blood.V108.11.2606.2606  0.534
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