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Beltran, Himisha; Hruszkewycz, Andrew; Scher, Howard I; Hildesheim, Jeffrey; Isaacs, Jennifer; Yu, Evan Y; Kelly, Kathleen; Lin, Daniel; Dicker, Adam; Arnold, Julia; Hecht, Toby; Wicha, Max; Sears, Rosalie; Rowley, David; White, Richard; Gulley, James L; Lee, John; Diaz Meco, Maria; Small, Eric J; Shen, Michael; ... (2019). The Role of Lineage Plasticity in Prostate Cancer Therapy Resistance. Clinical cancer research, 25(23), pp. 6916-6924. American Association for Cancer Research 10.1158/1078-0432.CCR-19-1423
Persi, Erez; Prandi, Davide; Wolf, Yuri I; Pozniak, Yair; Barnabas, Georgina D; Levanon, Keren; Barshack, Iris; Barbieri, Christopher; Gasperini, Paola; Beltran, Himisha; Faltas, Bishoy M; Rubin, Mark A.; Geiger, Tamar; Koonin, Eugene V; Demichelis, Francesca; Horn, David (2019). Proteomic and genomic signatures of repeat instability in cancer and adjacent normal tissues. Proceedings of the National Academy of Sciences of the United States of America - PNAS, 116(34), pp. 16987-16996. National Academy of Sciences NAS 10.1073/pnas.1908790116
Lou, Shaoke; Cotter, Kellie A.; Li, Tianxiao; Liang, Jin; Mohsen, Hussein; Liu, Jason; Zhang, Jing; Cohen, Sandra; Xu, Jinrui; Yu, Haiyuan; Rubin, Mark A.; Gerstein, Mark (2019). GRAM: A GeneRAlized Model to predict the molecular effect of a non-coding variant in a cell-type specific manner. PLoS genetics, 15(8), e1007860. Public Library of Science 10.1371/journal.pgen.1007860
Robinson, Brian D; Vlachostergios, Panagiotis J; Bhinder, Bhavneet; Liu, Weisi; Li, Kailyn; Moss, Tyler J; Bareja, Rohan; Park, Kyung; Tavassoli, Peyman; Cyrta, Joanna; Tagawa, Scott T; Nanus, David M; Beltran, Himisha; Molina, Ana M; Khani, Francesca; Miguel Mosquera, Juan; Xylinas, Evanguelos; Shariat, Shahrokh F; Scherr, Douglas S; Rubin, Mark A.; ... (2019). Upper tract urothelial carcinoma has a luminal-papillary T-cell depleted contexture and activated FGFR3 signaling. Nature Communications, 10(1), p. 2977. Springer Nature 10.1038/s41467-019-10873-y
Shen, Michael M; Rubin, Mark Andrew (2019). Prostate Cancer Research at the Crossroads. Cold Spring Harbor perspectives in medicine, 9(7) Cold Spring Harbor Laboratory Press 10.1101/cshperspect.a036277
Abida, Wassim; Cyrta, Joanna; Heller, Glenn; Prandi, Davide; Armenia, Joshua; Coleman, Ilsa; Cieslik, Marcin; Benelli, Matteo; Robinson, Dan; Van Allen, Eliezer M; Sboner, Andrea; Fedrizzi, Tarcisio; Mosquera, Juan Miguel; Robinson, Brian D; De Sarkar, Navonil; Kunju, Lakshmi P; Tomlins, Scott; Wu, Yi Mi; Nava Rodrigues, Daniel; Loda, Massimo; ... (2019). Genomic correlates of clinical outcome in advanced prostate cancer. Proceedings of the National Academy of Sciences of the United States of America - PNAS, 116(23), pp. 11428-11436. National Academy of Sciences NAS 10.1073/pnas.1902651116
Augello, Michael A; Liu, Deli; Deonarine, Lesa D; Robinson, Brian D; Huang, Dennis; Stelloo, Suzan; Blattner, Mirjam; Doane, Ashley S; Wong, Elissa W P; Chen, Yu; Rubin, Mark A.; Beltran, Himisha; Elemento, Olivier; Bergman, Andries M; Zwart, Wilbert; Sboner, Andrea; Dephoure, Noah; Barbieri, Christopher E (2019). CHD1 Loss Alters AR Binding at Lineage-Specific Enhancers and Modulates Distinct Transcriptional Programs to Drive Prostate Tumorigenesis. Cancer cell, 35(4), 603-617.e8. Cell Press 10.1016/j.ccell.2019.03.001
Lee, Rachel S; Zhang, Luxi; Berger, Adeline; Lawrence, Mitchell G; Song, Jiangning; Niranjan, Birunthi; Davies, Rebecca G; Lister, Natalie L; Sandhu, Shahneen K; Rubin, Mark A.; Risbridger, Gail P; Taylor, Renea A; Rickman, David S; Horvath, Lisa G; Daly, Roger J (2019). Characterization of the ERG-regulated Kinome in Prostate Cancer Identifies TNIK as a Potential Therapeutic Target. Neoplasia, 21(4), pp. 389-400. Elsevier 10.1016/j.neo.2019.02.005
Rubin, Mark A.; Demichelis, Francesca (2019). The Genomics of Prostate Cancer: A Historic Perspective. Cold Spring Harbor perspectives in medicine, 9(3) Cold Spring Harbor Laboratory Press 10.1101/cshperspect.a034942
Skvortsova, Ksenia; Masle-Farquhar, Etienne; Luu, Phuc-Loi; Song, Jenny Z; Qu, Wenjia; Zotenko, Elena; Gould, Cathryn M; Du, Qian; Peters, Timothy J; Colino-Sanguino, Yolanda; Pidsley, Ruth; Nair, Shalima S; Khoury, Amanda; Smith, Grady C; Miosge, Lisa A; Reed, Joanne H; Kench, James G; Rubin, Mark A.; Horvath, Lisa; Bogdanovic, Ozren; ... (2019). DNA Hypermethylation Encroachment at CpG Island Borders in Cancer Is Predisposed by H3K4 Monomethylation Patterns. Cancer cell, 35(2), 297-314.e8. Cell Press 10.1016/j.ccell.2019.01.004
Beltran, Himisha; Oromendia, Clara; Danila, Daniel C; Montgomery, Bruce; Hoimes, Christopher; Szmulewitz, Russell Z; Vaishampayan, Ulka; Armstrong, Andrew J; Stein, Mark; Pinski, Jacek; Mosquera, Juan M; Sailer, Verena; Bareja, Rohan; Romanel, Alessandro; Gumpeni, Naveen; Sboner, Andrea; Dardenne, Etienne; Puca, Loredana; Prandi, Davide; Rubin, Mark A.; ... (2019). A Phase II Trial of the Aurora Kinase A Inhibitor Alisertib for Patients with Castration-resistant and Neuroendocrine Prostate Cancer: Efficacy and Biomarkers. Clinical cancer research, 25(1), pp. 43-51. American Association for Cancer Research 10.1158/1078-0432.CCR-18-1912
Fernandez, Evan M; Eng, Kenneth; Beg, Shaham; Beltran, Himisha; Faltas, Bishoy M; Mosquera, Juan Miguel; Nanus, David M; Pisapia, David J; Rao, Rema A; Robinson, Brian D; Rubin, Mark A.; Elemento, Olivier; Sboner, Andrea; Shah, Manish A; Song, Wei (2019). Cancer-Specific Thresholds Adjust for Whole Exome Sequencing-based Tumor Mutational Burden Distribution. JCO precision oncology, 3 American Society of Clinical Oncology 10.1200/PO.18.00400
Karkampouna, Sofia; Grosjean, Joël; Klima, Irena; Genitsch, Vera; Sboner, A.; K. Y. Ng, C.; De Filippo, M.R.; Piscuoglio, S.; Spahn, M.; Rubin, Mark Andrew; Thalmann, G.N.; Kruithof-de Julio, Marianna (2019). Establishment of an androgen-sensitive patient derived xenograft model of prostate cancer. European Urology Supplements, 18(1), e1154. Elsevier 10.1016/S1569-9056(19)30831-0
Boysen, Gunther; Rodrigues, Daniel N; Rescigno, Pasquale; Seed, George; Dolling, David; Riisnaes, Ruth; Crespo, Mateus; Zafeiriou, Zafeiris; Sumanasuriya, Semini; Bianchini, Diletta; Hunt, Joanne; Moloney, Deirdre; Perez-Lopez, Raquel; Tunariu, Nina; Miranda, Susana; Figueiredo, Inês; Ferreira, Ana; Christova, Rossitza; Gil, Veronica; Aziz, Sara; ... (2018). SPOP-Mutated/CHD1-Deleted Lethal Prostate Cancer and Abiraterone Sensitivity. Clinical cancer research, 24(22), pp. 5585-5593. American Association for Cancer Research 10.1158/1078-0432.CCR-18-0937
Kahles, André; Lehmann, Kjong-Van; Toussaint, Nora C; Hüser, Matthias; Stark, Stefan G; Sachsenberg, Timo; Stegle, Oliver; Kohlbacher, Oliver; Sander, Chris; Rätsch, Gunnar (2018). Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients. Cancer cell, 34(2), 211-224.e6. Cell Press 10.1016/j.ccell.2018.07.001
Bailey, Matthew H; Tokheim, Collin; Porta-Pardo, Eduard; Sengupta, Sohini; Bertrand, Denis; Weerasinghe, Amila; Colaprico, Antonio; Wendl, Michael C; Kim, Jaegil; Reardon, Brendan; Kwok-Shing Ng, Patrick; Jeong, Kang Jin; Cao, Song; Wang, Zixing; Gao, Jianjiong; Gao, Qingsong; Wang, Fang; Liu, Eric Minwei; Mularoni, Loris; Rubio-Perez, Carlota; ... (2018). Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell, 174(4), pp. 1034-1035. Cell Press 10.1016/j.cell.2018.07.034
Cotter, Kellie Anne; Rubin, Mark Andrew (2018). Sequence of events in prostate cancer. Nature, 560(7720), pp. 557-559. Macmillan Journals Ltd. 10.1038/d41586-018-06029-5
Hopkins, Benjamin D; Pauli, Chantal; Du, Xing; Wang, Diana G; Li, Xiang; Wu, David; Amadiume, Solomon C; Goncalves, Marcus D; Hodakoski, Cindy; Lundquist, Mark R; Bareja, Rohan; Ma, Yan; Harris, Emily M; Sboner, Andrea; Beltran, Himisha; Rubin, Mark Andrew; Mukherjee, Siddhartha; Cantley, Lewis C (2018). Suppression of insulin feedback enhances the efficacy of PI3K inhibitors. Nature, 560(7719), pp. 499-503. Macmillan Journals Ltd. 10.1038/s41586-018-0343-4
Ricketts, Christopher J; De Cubas, Aguirre A; Fan, Huihui; Smith, Christof C; Lang, Martin; Reznik, Ed; Bowlby, Reanne; Gibb, Ewan A; Akbani, Rehan; Beroukhim, Rameen; Bottaro, Donald P; Choueiri, Toni K; Gibbs, Richard A; Godwin, Andrew K; Haake, Scott; Hakimi, A Ari; Henske, Elizabeth P; Hsieh, James J; Ho, Thai H; Kanchi, Rupa S; ... (2018). The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell reports, 23(12), p. 3698. Cell Press 10.1016/j.celrep.2018.06.032
Triscott, Joanna; Rubin, Mark A. (2018). Prostate Power Play: Does Accelerate -Deficient Cancer Progression? Cancer discovery, 8(6), pp. 682-685. American Association for Cancer Research 10.1158/2159-8290.CD-18-0369
Mateo, Joaquin; Cheng, Heather H; Beltran, Himisha; Dolling, David; Xu, Wen; Pritchard, Colin C; Mossop, Helen; Rescigno, Pasquale; Perez-Lopez, Raquel; Sailer, Verena; Kolinsky, Michael; Balasopoulou, Ada; Bertan, Claudia; Nanus, David M; Tagawa, Scott T; Thorne, Heather; Montgomery, Bruce; Carreira, Suzanne; Sandhu, Shahneen; Rubin, Mark Andrew; ... (2018). Clinical Outcome of Prostate Cancer Patients with Germline DNA Repair Mutations: Retrospective Analysis from an International Study. European urology, 73(5), pp. 687-693. Elsevier 10.1016/j.eururo.2018.01.010
Thorsson, Vésteinn; Gibbs, David L; Brown, Scott D; Wolf, Denise; Bortone, Dante S; Ou Yang, Tai-Hsien; Porta-Pardo, Eduard; Gao, Galen F; Plaisier, Christopher L; Eddy, James A; Ziv, Elad; Culhane, Aedin C; Paull, Evan O; Sivakumar, I K Ashok; Gentles, Andrew J; Malhotra, Raunaq; Farshidfar, Farshad; Colaprico, Antonio; Parker, Joel S; Mose, Lisle E; ... (2018). The Immune Landscape of Cancer. Immunity, 48(4), 812-830.e14. Cell Press 10.1016/j.immuni.2018.03.023
Liu, Yang; Sethi, Nilay S; Hinoue, Toshinori; Schneider, Barbara G; Cherniack, Andrew D; Sanchez-Vega, Francisco; Seoane, Jose A; Farshidfar, Farshad; Bowlby, Reanne; Islam, Mirazul; Kim, Jaegil; Chatila, Walid; Akbani, Rehan; Kanchi, Rupa S; Rabkin, Charles S; Willis, Joseph E; Wang, Kenneth K; McCall, Shannon J; Mishra, Lopa; Ojesina, Akinyemi I; ... (2018). Comparative Molecular Analysis of Gastrointestinal Adenocarcinomas. Cancer cell, 33(4), 721-735.e8. Cell Press 10.1016/j.ccell.2018.03.010
Wang, Zehua; Yang, Bo; Zhang, Min; Guo, Weiwei; Wu, Zhiyuan; Wang, Yue; Jia, Lin; Li, Song; Xie, Wen; Yang, Da (2018). lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer. Cancer cell, 33(4), 706-720.e9. Cell Press 10.1016/j.ccell.2018.03.006
Berger, Ashton C; Korkut, Anil; Kanchi, Rupa S; Hegde, Apurva M; Lenoir, Walter; Liu, Wenbin; Liu, Yuexin; Fan, Huihui; Shen, Hui; Ravikumar, Visweswaran; Rao, Arvind; Schultz, Andre; Li, Xubin; Sumazin, Pavel; Williams, Cecilia; Mestdagh, Pieter; Gunaratne, Preethi H; Yau, Christina; Bowlby, Reanne; Robertson, A Gordon; ... (2018). A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers. Cancer cell, 33(4), 690-705.e9. Cell Press 10.1016/j.ccell.2018.03.014
Taylor, Alison M; Shih, Juliann; Ha, Gavin; Gao, Galen F; Zhang, Xiaoyang; Berger, Ashton C; Schumacher, Steven E; Wang, Chen; Hu, Hai; Liu, Jianfang; Lazar, Alexander J; Cherniack, Andrew D; Beroukhim, Rameen; Meyerson, Matthew (2018). Genomic and Functional Approaches to Understanding Cancer Aneuploidy. Cancer cell, 33(4), 676-689.e3. Cell Press 10.1016/j.ccell.2018.03.007
Liu, Jianfang; Lichtenberg, Tara; Hoadley, Katherine A; Poisson, Laila M; Lazar, Alexander J; Cherniack, Andrew D; Kovatich, Albert J; Benz, Christopher C; Levine, Douglas A; Lee, Adrian V; Omberg, Larsson; Wolf, Denise M; Shriver, Craig D; Thorsson, Vesteinn (2018). An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics. Cell, 173(2), 400-416.e11. Cell Press 10.1016/j.cell.2018.02.052
Chen, Han; Li, Chunyan; Peng, Xinxin; Zhou, Zhicheng; Weinstein, John N; Liang, Han (2018). A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples. Cell, 173(2), 386-399.e12. Cell Press 10.1016/j.cell.2018.03.027
Bailey, Matthew H; Tokheim, Collin; Porta-Pardo, Eduard; Sengupta, Sohini; Bertrand, Denis; Weerasinghe, Amila; Colaprico, Antonio; Wendl, Michael C; Kim, Jaegil; Reardon, Brendan; Ng, Patrick Kwok-Shing; Jeong, Kang Jin; Cao, Song; Wang, Zixing; Gao, Jianjiong; Gao, Qingsong; Wang, Fang; Liu, Eric Minwei; Mularoni, Loris; Rubio-Perez, Carlota; ... (2018). Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell, 173(2), 371-385.e18. Cell Press 10.1016/j.cell.2018.02.060
Huang, Kuan-Lin; Mashl, R Jay; Wu, Yige; Ritter, Deborah I; Wang, Jiayin; Oh, Clara; Paczkowska, Marta; Reynolds, Sheila; Wyczalkowski, Matthew A; Oak, Ninad; Scott, Adam D; Krassowski, Michal; Cherniack, Andrew D; Houlahan, Kathleen E; Jayasinghe, Reyka; Wang, Liang-Bo; Zhou, Daniel Cui; Liu, Di; Cao, Song; Kim, Young Won; ... (2018). Pathogenic Germline Variants in 10,389 Adult Cancers. Cell, 173(2), 355-370.e14. Cell Press 10.1016/j.cell.2018.03.039
Malta, Tathiane M; Sokolov, Artem; Gentles, Andrew J; Burzykowski, Tomasz; Poisson, Laila; Weinstein, John N; Kamińska, Bożena; Huelsken, Joerg; Omberg, Larsson; Gevaert, Olivier; Colaprico, Antonio; Czerwińska, Patrycja; Mazurek, Sylwia; Mishra, Lopa; Heyn, Holger; Krasnitz, Alex; Godwin, Andrew K; Lazar, Alexander J; Stuart, Joshua M; Hoadley, Katherine A; ... (2018). Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation. Cell, 173(2), 338-354.e15. Cell Press 10.1016/j.cell.2018.03.034
Sanchez-Vega, Francisco; Mina, Marco; Armenia, Joshua; Chatila, Walid K; Luna, Augustin; La, Konnor C; Dimitriadoy, Sofia; Liu, David L; Kantheti, Havish S; Saghafinia, Sadegh; Chakravarty, Debyani; Daian, Foysal; Gao, Qingsong; Bailey, Matthew H; Liang, Wen-Wei; Foltz, Steven M; Shmulevich, Ilya; Ding, Li; Heins, Zachary; Ochoa, Angelica; ... (2018). Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell, 173(2), 321-337.e10. Cell Press 10.1016/j.cell.2018.03.035
Ding, Li; Bailey, Matthew H; Porta-Pardo, Eduard; Thorsson, Vesteinn; Colaprico, Antonio; Bertrand, Denis; Gibbs, David L; Weerasinghe, Amila; Huang, Kuan-Lin; Tokheim, Collin; Cortés-Ciriano, Isidro; Jayasinghe, Reyka; Chen, Feng; Yu, Lihua; Sun, Sam; Olsen, Catharina; Kim, Jaegil; Taylor, Alison M; Cherniack, Andrew D; Akbani, Rehan; ... (2018). Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics. Cell, 173(2), 305-320.e10. Cell Press 10.1016/j.cell.2018.03.033
Hoadley, Katherine A; Yau, Christina; Hinoue, Toshinori; Wolf, Denise M; Lazar, Alexander J; Drill, Esther; Shen, Ronglai; Taylor, Alison M; Cherniack, Andrew D; Thorsson, Vésteinn; Akbani, Rehan; Bowlby, Reanne; Wong, Christopher K; Wiznerowicz, Maciej; Sanchez-Vega, Francisco; Robertson, A Gordon; Schneider, Barbara G; Lawrence, Michael S; Noushmehr, Houtan; Malta, Tathiane M; ... (2018). Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer. Cell, 173(2), 291-304.e6. Cell Press 10.1016/j.cell.2018.03.022
Ricketts, Christopher J; De Cubas, Aguirre A; Fan, Huihui; Smith, Christof C; Lang, Martin; Reznik, Ed; Bowlby, Reanne; Gibb, Ewan A; Akbani, Rehan; Beroukhim, Rameen; Bottaro, Donald P; Choueiri, Toni K; Gibbs, Richard A; Godwin, Andrew K; Haake, Scott; Hakimi, A Ari; Henske, Elizabeth P; Hsieh, James J; Ho, Thai H; Kanchi, Rupa S; ... (2018). The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell reports, 23(1), 313-326.e5. Cell Press 10.1016/j.celrep.2018.03.075
Chiu, Hua-Sheng; Somvanshi, Sonal; Patel, Ektaben; Chen, Ting-Wen; Singh, Vivek P; Zorman, Barry; Patil, Sagar L; Pan, Yinghong; Chatterjee, Sujash S; Sood, Anil K; Gunaratne, Preethi H; Sumazin, Pavel (2018). Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context. Cell reports, 23(1), 297-312.e12. Cell Press 10.1016/j.celrep.2018.03.064
Seiler, Michael; Peng, Shouyong; Agrawal, Anant A; Palacino, James; Teng, Teng; Zhu, Ping; Smith, Peter G; Buonamici, Silvia; Yu, Lihua (2018). Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types. Cell reports, 23(1), 282-296.e4. Cell Press 10.1016/j.celrep.2018.01.088
Jayasinghe, Reyka G; Cao, Song; Gao, Qingsong; Wendl, Michael C; Vo, Nam Sy; Reynolds, Sheila M; Zhao, Yanyan; Climente-González, Héctor; Chai, Shengjie; Wang, Fang; Varghese, Rajees; Huang, Mo; Liang, Wen-Wei; Wyczalkowski, Matthew A; Sengupta, Sohini; Li, Zhi; Payne, Samuel H; Fenyö, David; Miner, Jeffrey H; Walter, Matthew J; ... (2018). Systematic Analysis of Splice-Site-Creating Mutations in Cancer. Cell reports, 23(1), 270-281.e3. Cell Press 10.1016/j.celrep.2018.03.052
Peng, Xinxin; Chen, Zhongyuan; Farshidfar, Farshad; Xu, Xiaoyan; Lorenzi, Philip L; Wang, Yumeng; Cheng, Feixiong; Tan, Lin; Mojumdar, Kamalika; Du, Di; Ge, Zhongqi; Li, Jun; Thomas, George V; Birsoy, Kivanc; Liu, Lingxiang; Zhang, Huiwen; Zhao, Zhongming; Marchand, Calena; Weinstein, John N; Bathe, Oliver F; ... (2018). Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers. Cell reports, 23(1), 255-269.e4. Cell Press 10.1016/j.celrep.2018.03.077
Knijnenburg, Theo A; Wang, Linghua; Zimmermann, Michael T; Chambwe, Nyasha; Gao, Galen F; Cherniack, Andrew D; Fan, Huihui; Shen, Hui; Way, Gregory P; Greene, Casey S; Liu, Yuexin; Akbani, Rehan; Feng, Bin; Donehower, Lawrence A; Miller, Chase; Shen, Yang; Karimi, Mostafa; Chen, Haoran; Kim, Pora; Jia, Peilin; ... (2018). Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas. Cell reports, 23(1), 239-254.e6. Cell Press 10.1016/j.celrep.2018.03.076
Gao, Qingsong; Liang, Wen-Wei; Foltz, Steven M; Mutharasu, Gnanavel; Jayasinghe, Reyka G; Cao, Song; Liao, Wen-Wei; Reynolds, Sheila M; Wyczalkowski, Matthew A; Yao, Lijun; Yu, Lihua; Sun, Sam Q; Chen, Ken; Lazar, Alexander J; Fields, Ryan C; Wendl, Michael C; Van Tine, Brian A; Vij, Ravi; Chen, Feng; Nykter, Matti; ... (2018). Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell reports, 23(1), 227-238.e3. Cell Press 10.1016/j.celrep.2018.03.050
Ge, Zhongqi; Leighton, Jake S; Wang, Yumeng; Peng, Xinxin; Chen, Zhongyuan; Chen, Hu; Sun, Yutong; Yao, Fan; Li, Jun; Zhang, Huiwen; Liu, Jianfang; Shriver, Craig D; Hu, Hai; Piwnica-Worms, Helen; Ma, Li; Liang, Han (2018). Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types. Cell reports, 23(1), 213-226.e3. Cell Press 10.1016/j.celrep.2018.03.047
Campbell, Joshua D; Yau, Christina; Bowlby, Reanne; Liu, Yuexin; Brennan, Kevin; Fan, Huihui; Taylor, Alison M; Wang, Chen; Walter, Vonn; Akbani, Rehan; Byers, Lauren Averett; Creighton, Chad J; Coarfa, Cristian; Shih, Juliann; Cherniack, Andrew D; Gevaert, Olivier; Prunello, Marcos; Shen, Hui; Anur, Pavana; Chen, Jianhong; ... (2018). Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell reports, 23(1), 194-212.e6. Cell Press 10.1016/j.celrep.2018.03.063
Saltz, Joel; Gupta, Rajarsi; Hou, Le; Kurc, Tahsin; Singh, Pankaj; Nguyen, Vu; Samaras, Dimitris; Shroyer, Kenneth R; Zhao, Tianhao; Batiste, Rebecca; Van Arnam, John (2018). Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images. Cell reports, 23(1), 181-193.e7. Cell Press 10.1016/j.celrep.2018.03.086
Way, Gregory P; Sanchez-Vega, Francisco; La, Konnor; Armenia, Joshua; Chatila, Walid K; Luna, Augustin; Sander, Chris; Cherniack, Andrew D; Mina, Marco; Ciriello, Giovanni; Schultz, Nikolaus (2018). Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. Cell reports, 23(1), 172-180.e3. Cell Press 10.1016/j.celrep.2018.03.046
Schaub, Franz X; Dhankani, Varsha; Berger, Ashton C; Trivedi, Mihir; Richardson, Anne B; Shaw, Reid; Zhao, Wei; Zhang, Xiaoyang; Ventura, Andrea; Liu, Yuexin; Ayer, Donald E; Hurlin, Peter J; Cherniack, Andrew D; Eisenman, Robert N; Bernard, Brady; Grandori, Carla (2018). Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas. Cell systems, 6(3), 282-300.e2. Elsevier 10.1016/j.cels.2018.03.003
Ellrott, Kyle; Bailey, Matthew H; Saksena, Gordon; Covington, Kyle R; Kandoth, Cyriac; Stewart, Chip; Hess, Julian; Ma, Singer; Chiotti, Kami E; McLellan, Michael; Sofia, Heidi J; Hutter, Carolyn; Getz, Gad; Wheeler, David; Ding, Li (2018). Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines. Cell systems, 6(3), 271-281.e7. Elsevier 10.1016/j.cels.2018.03.002
Sailer, Verena; Schiffman, Marc H; Kossai, Myriam; Cyrta, Joanna; Beg, Shaham; Sullivan, Brian; Pua, Bradley B; Lee, Kyungmouk Steve; Talenfeld, Adam D; Nanus, David M; Tagawa, Scott T; Robinson, Brian D; Rao, Rema A; Pauli, Chantal; Bareja, Rohan; Beltran, Luis S; Sigaras, Alexandros; Eng, Kenneth Wa; Elemento, Olivier; Sboner, Andrea; ... (2018). Bone biopsy protocol for advanced prostate cancer in the era of precision medicine. Cancer, 124(5), pp. 1008-1015. John Wiley & Sons 10.1002/cncr.31173
Shoag, Jonathan; Liu, Deli; Blattner, Mirjam; Sboner, Andrea; Park, Kyung; Deonarine, Lesa; Robinson, Brian D; Mosquera, Juan Miguel; Chen, Yu; Rubin, Mark Andrew; Barbieri, Christopher E (2018). SPOP mutation drives prostate neoplasia without stabilizing oncogenic transcription factor ERG. Journal of clinical investigation, 128(1), pp. 381-386. American Society for Clinical Investigation 10.1172/JCI96551
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D'Alfonso, Timothy M; Subramaniyam, Shivakumar; Ginter, Paula S; Mosquera, Juan Miguel; Croyle, Jaclyn; Liu, Yi-Fang; Rubin, Mark Andrew; Shin, Sandra J (2018). Characterization of CD34-deficient myofibroblastomas of the breast. The breast journal, 24(1), pp. 55-61. Wiley 10.1111/tbj.12835
Rubin, Mark Andrew; Demichelis, Francesca (2018). The Genomics of Prostate Cancer: emerging understanding with technologic advances. Modern pathology, 31(S1), S1-11. Nature Publishing Group 10.1038/modpathol.2017.166
Shukla, Shipra; Cyrta, Joanna; Murphy, Devan A; Walczak, Edward G; Ran, Leili; Agrawal, Praveen; Xie, Yuanyuan; Chen, Yuedan; Wang, Shangqian; Zhan, Yu; Li, Dan; Wong, Elissa W P; Sboner, Andrea; Beltran, Himisha; Mosquera, Juan Miguel; Sher, Jessica; Cao, Zhen; Wongvipat, John; Koche, Richard P; Gopalan, Anuradha; ... (2017). Aberrant Activation of a Gastrointestinal Transcriptional Circuit in Prostate Cancer Mediates Castration Resistance. Cancer cell, 32(6), 792-806.e7. Cell Press 10.1016/j.ccell.2017.10.008
Lee, D; Fontugne, J; Gumpeni, N; Park, K; MacDonald, T Y; Robinson, B D; Sboner, A; Rubin, Mark Andrew; Mosquera, J M; Barbieri, C E (2017). Molecular alterations in prostate cancer and association with MRI features. Prostate cancer and prostatic diseases, 20(4), pp. 430-435. Nature 10.1038/pcan.2017.33
Pauli, C; Moch, H; Rubin, Mark Andrew (2017). [Establishment of a living biobank : Improved guidance of precision cancer care with in vitro and in vivo cancer models]. Der Pathologe, 38(Suppl 2), pp. 160-168. Springer 10.1007/s00292-017-0346-1
Wilkes, David C; Sailer, Verena; Xue, Hui; Cheng, Hongwei; Collins, Colin C; Gleave, Martin; Wang, Yuzhuo; Demichelis, Francesca; Beltran, Himisha; Rubin, Mark Andrew; Rickman, David S (2017). A germline FANCA alteration that is associated with increased sensitivity to DNA damaging agents. Cold Spring Harbor molecular case studies, 3(5) Cold Spring Harbor Laboratory Press 10.1101/mcs.a001487
Dai, Xiangpeng; Gan, Wenjian; Li, Xiaoning; Wang, Shangqian; Zhang, Wei; Huang, Ling; Liu, Shengwu; Zhong, Qing; Guo, Jianping; Zhang, Jinfang; Chen, Ting; Shimizu, Kouhei; Beca, Francisco; Blattner, Mirjam; Vasudevan, Divya; Buckley, Dennis L; Qi, Jun; Buser, Lorenz; Liu, Pengda; Inuzuka, Hiroyuki; ... (2017). Prostate cancer-associated SPOP mutations confer resistance to BET inhibitors through stabilization of BRD4. Nature medicine, 23(9), pp. 1063-1071. Nature Publishing Group 10.1038/nm.4378
Minciacchi, V R; Zijlstra, A; Rubin, Mark Andrew; Di Vizio, D (2017). Extracellular vesicles for liquid biopsy in prostate cancer: where are we and where are we headed? Prostate cancer and prostatic diseases, 20(3), pp. 251-258. Nature 10.1038/pcan.2017.7
Huang, Franklin W; Mosquera, Juan Miguel; Garofalo, Andrea; Oh, Coyin; Baco, Maria; Amin-Mansour, Ali; Rabasha, Bokang; Bahl, Samira; Mullane, Stephanie A; Robinson, Brian D; Aldubayan, Saud; Khani, Francesca; Karir, Beerinder; Kim, Eejung; Chimene-Weiss, Jeremy; Hofree, Matan; Romanel, Alessandro; Osborne, Joseph R; Kim, Jong Wook; Azabdaftari, Gissou; ... (2017). Exome Sequencing of African-American Prostate Cancer Reveals Loss-of-Function ERF Mutations. Cancer discovery, 7(9), pp. 973-983. American Association for Cancer Research 10.1158/2159-8290.CD-16-0960
Wang, Hui; Barbieri, Christopher E; He, Jintang; Gao, Yuqian; Shi, Tujin; Wu, Chaochao; Schepmoes, Athena A; Fillmore, Thomas L; Chae, Sung-Suk; Huang, Dennis; Mosquera, Juan Miguel; Qian, Wei-Jun; Smith, Richard D; Srivastava, Sudhir; Kagan, Jacob; Camp, David G; Rodland, Karin D; Rubin, Mark Andrew; Liu, Tao (2017). Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics. Journal of translational medicine, 15(1), p. 175. BioMed Central 10.1186/s12967-017-1276-7
Sanda, Martin G; Feng, Ziding; Howard, David H; Tomlins, Scott A; Sokoll, Lori J; Chan, Daniel W; Regan, Meredith M; Groskopf, Jack; Chipman, Jonathan; Patil, Dattatraya H; Salami, Simpa S; Scherr, Douglas S; Kagan, Jacob; Srivastava, Sudhir; Thompson, Ian M; Siddiqui, Javed; Fan, Jing; Joon, Aron Y; Bantis, Leonidas E; Rubin, Mark Andrew; ... (2017). Association Between Combined TMPRSS2:ERG and PCA3 RNA Urinary Testing and Detection of Aggressive Prostate Cancer. JAMA oncology, 3(8), pp. 1085-1093. American Medical Association 10.1001/jamaoncol.2017.0177
Dhingra, Priyanka; Martinez-Fundichely, Alexander; Berger, Adeline; Huang, Franklin W; Forbes, Andre Neil; Liu, Eric Minwei; Liu, Deli; Sboner, Andrea; Tamayo, Pablo; Rickman, David S; Rubin, Mark Andrew; Khurana, Ekta (2017). Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network. Genome biology, 18(1), p. 141. BioMed Central Ltd. 10.1186/s13059-017-1266-3
Zou, Min; Toivanen, Roxanne; Mitrofanova, Antonina; Floch, Nicolas; Hayati, Sheida; Sun, Yanping; Le Magnen, Clémentine; Chester, Daniel; Mostaghel, Elahe A; Califano, Andrea; Rubin, Mark Andrew; Shen, Michael M; Abate-Shen, Cory (2017). Transdifferentiation as a Mechanism of Treatment Resistance in a Mouse Model of Castration-Resistant Prostate Cancer. Cancer discovery, 7(7), pp. 736-749. American Association for Cancer Research 10.1158/2159-8290.CD-16-1174
Romanel, Alessandro; Garritano, Sonia; Stringa, Blerta; Blattner, Mirjam; Dalfovo, Davide; Chakravarty, Dimple; Soong, David; Cotter, Kellie Anne; Petris, Gianluca; Dhingra, Priyanka; Gasperini, Paola; Cereseto, Anna; Elemento, Olivier; Sboner, Andrea; Khurana, Ekta; Inga, Alberto; Rubin, Mark Andrew; Demichelis, Francesca (2017). Inherited determinants of early recurrent somatic mutations in prostate cancer. Nature communications, 8(1), p. 48. Nature Publishing Group 10.1038/s41467-017-00046-0
Huang, Linda; Fernandes, Helen; Zia, Hamid; Tavassoli, Peyman; Rennert, Hanna; Pisapia, David; Imielinski, Marcin; Sboner, Andrea; Rubin, Mark Andrew; Kluk, Michael; Elemento, Olivier (2017). The cancer precision medicine knowledge base for structured clinical-grade mutations and interpretations. Journal of the American Medical Informatics Association, 24(3), pp. 513-519. Oxford University Press 10.1093/jamia/ocw148
Imielinski, Marcin; Rubin, Mark Andrew (2017). Prostate cancer: Clinical hallmarks in whole cancer genomes. Nature reviews - clinical oncology, 14(5), pp. 265-266. Nature Publishing Group 10.1038/nrclinonc.2017.45
Pauli, Chantal; Hopkins, Benjamin D; Prandi, Davide; Shaw, Reid; Fedrizzi, Tarcisio; Sboner, Andrea; Sailer, Verena; Augello, Michael; Puca, Loredana; Rosati, Rachele; McNary, Terra J; Churakova, Yelena; Cheung, Cynthia; Triscott, Joanna Catherine Caprio; Pisapia, David; Rao, Rema; Mosquera, Juan Miguel; Robinson, Brian; Faltas, Bishoy M; Emerling, Brooke E; ... (2017). Personalized In Vitro and In Vivo Cancer Models to Guide Precision Medicine. Cancer discovery, 7(5), pp. 462-477. American Association for Cancer Research 10.1158/2159-8290.CD-16-1154
Sailer, Verena; Pauli, Chantal; Merzier, Elyze C; Mosquera, Juan Miguel; Beltran, Himisha; Rubin, Mark Andrew; Rao, Rema A (2017). On-site Cytology for Development of Patient-Derived Three-dimensional Organoid Cultures - A Pilot Study. Anticancer research, 37(4), pp. 1569-1573. International Inst. of Anticancer Research 10.21873/anticanres.11486
Blattner, Mirjam; Liu, Deli; Robinson, Brian D; Huang, Dennis; Poliakov, Anton; Gao, Dong; Nataraj, Srilakshmi; Deonarine, Lesa D; Augello, Michael A; Sailer, Verena; Ponnala, Lalit; Ittmann, Michael; Chinnaiyan, Arul M; Sboner, Andrea; Chen, Yu; Rubin, Mark Andrew; Barbieri, Christopher E (2017). SPOP Mutation Drives Prostate Tumorigenesis In Vivo through Coordinate Regulation of PI3K/mTOR and AR Signaling. Cancer cell, 31(3), pp. 436-451. Cell Press 10.1016/j.ccell.2017.02.004
Mateo, Joaquin; Boysen, Gunther; Barbieri, Christopher E; Bryant, Helen E; Castro, Elena; Nelson, Pete S; Olmos, David; Pritchard, Colin C; Rubin, Mark Andrew; de Bono, Johann S (2017). DNA Repair in Prostate Cancer: Biology and Clinical Implications. European urology, 71(3), pp. 417-425. Elsevier 10.1016/j.eururo.2016.08.037
Barbieri, Christopher E; Chinnaiyan, Arul M; Lerner, Seth P; Swanton, Charles; Rubin, Mark Andrew (2017). The Emergence of Precision Urologic Oncology: A Collaborative Review on Biomarker-driven Therapeutics. European urology, 71(2), pp. 237-246. Elsevier 10.1016/j.eururo.2016.08.024
Villers, Arnauld; Rubin, Mark Andrew (2017). Re: Prognostic Significance of Percentage and Architectural Types of Contemporary Gleason Pattern 4 Prostate Cancer in Radical Prostatectomy. European urology, 71(2), p. 301. Elsevier 10.1016/j.eururo.2016.09.017
Mu, Ping; Zhang, Zeda; Benelli, Matteo; Karthaus, Wouter R; Hoover, Elizabeth; Chen, Chi-Chao; Wongvipat, John; Ku, Sheng-Yu; Gao, Dong; Cao, Zhen; Shah, Neel; Adams, Elizabeth J; Abida, Wassim; Watson, Philip A; Prandi, Davide; Huang, Chun-Hao; de Stanchina, Elisa; Lowe, Scott W; Ellis, Leigh; Beltran, Himisha; ... (2017). SOX2 promotes lineage plasticity and antiandrogen resistance in TP53- and RB1-deficient prostate cancer. Science, 355(6320), pp. 84-88. American Association for the Advancement of Science 10.1126/science.aah4307
Bishop, Jennifer L; Thaper, Daksh; Vahid, Sepideh; Davies, Alastair; Ketola, Kirsi; Kuruma, Hidetoshi; Jama, Randy; Nip, Ka Mun; Angeles, Arkhjamil; Johnson, Fraser; Wyatt, Alexander W; Fazli, Ladan; Gleave, Martin E; Lin, Dong; Rubin, Mark Andrew; Collins, Colin C; Wang, Yuzhuo; Beltran, Himisha; Zoubeidi, Amina (2017). The Master Neural Transcription Factor BRN2 Is an Androgen Receptor-Suppressed Driver of Neuroendocrine Differentiation in Prostate Cancer. Cancer discovery, 7(1), pp. 54-71. American Association for Cancer Research 10.1158/2159-8290.CD-15-1263
