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  1. Kahles, André; Lehmann, Kjong-Van; Toussaint, Nora C.; Hüser, Matthias; Stark, Stefan G.; Sachsenberg, Timo; Stegle, Oliver; Kohlbacher, Oliver; Sander, Chris; Rätsch, Gunnar; Caesar-Johnson, Samantha J.; Demchok, John A.; Felau, Ina; Kasapi, Melpomeni; Ferguson, Martin L.; Hutter, Carolyn M.; Sofia, Heidi J.; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Zenklusen, Jean C.; Zhang, Jiashan (Julia); Chudamani, Sudha; Liu, Jia; [...]

    Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients

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    Elsevier BV, 2018

    Published in: Cancer Cell

  2. 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; Nagarajan, Niranjan; Cortés-Ciriano, Isidro; Zhou, Daniel Cui; Liang, Wen-Wei; [...]

    Comprehensive Characterization of Cancer Driver Genes and Mutations

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    Elsevier BV, 2018

    Published in: Cell

  3. 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; Nagarajan, Niranjan; Cortés-Ciriano, Isidro; Zhou, Daniel Cui; Liang, Wen-Wei; [...]

    Comprehensive Characterization of Cancer Driver Genes and Mutations

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    Elsevier BV, 2018

    Published in: Cell

  4. Wang, Yumeng; Xu, Xiaoyan; Maglic, Dejan; Dill, Michael T.; Mojumdar, Kamalika; Ng, Patrick Kwok-Shing; Jeong, Kang Jin; Tsang, Yiu Huen; Moreno, Daniela; Bhavana, Venkata Hemanjani; Peng, Xinxin; Ge, Zhongqi; Chen, Hu; Li, Jun; Chen, Zhongyuan; Zhang, Huiwen; Han, Leng; Du, Di; Creighton, Chad J.; Mills, Gordon B.; Camargo, Fernando; Liang, Han; Caesar-Johnson, Samantha J.; Demchok, John A.; [...]

    Comprehensive Molecular Characterization of the Hippo Signaling Pathway in Cancer

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    Elsevier BV, 2018

    Published in: Cell Reports

  5. 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; Tiezzi, Daniel G.; Wang, Chen; Cherniack, Andrew D.; Godwin, Andrew K.; [...]

    A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers

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    Elsevier BV, 2018

    Published in: Cancer Cell

  6. 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; Shmulevich, Ilya; Ding, Li; Caesar-Johnson, Samantha J.; Demchok, John A.; [...]

    Driver Fusions and Their Implications in the Development and Treatment of Human Cancers

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    Elsevier BV, 2018

    Published in: Cell Reports

  7. 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; Caesar-Johnson, Samantha J.; Demchok, John A.; Felau, Ina; Kasapi, Melpomeni; Ferguson, Martin L.; Hutter, Carolyn M.; Sofia, Heidi J.; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; [...]

    Genomic and Functional Approaches to Understanding Cancer Aneuploidy

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    Elsevier BV, 2018

    Published in: Cancer Cell

  8. 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; Shinbrot, Eve; Zhang, Shaojun; Liu, Jianfang; Hu, Hai; [...]

    Genomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas

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    Elsevier BV, 2018

    Published in: Cell Reports

  9. 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; Cheng, Hui; Hayes, D. Neil; Bullman, Susan; Pedamallu, Chandra Sekhar; [...]

    Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

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    Elsevier BV, 2018

    Published in: Cell Reports

  10. 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.; Vo, Nam Sy; Liu, Jianfang; Liu, Yuexin; Rader, Janet; [...]

    The Immune Landscape of Cancer

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    Elsevier BV, 2018

    Published in: Immunity

  11. 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; Caesar-Johnson, Samantha J.; Demchok, John A.; Felau, Ina; Kasapi, Melpomeni; Ferguson, Martin L.; Hutter, Carolyn M.; Sofia, Heidi J.; Tarnuzzer, Roy; [...]

    Integrated Genomic Analysis of the Ubiquitin Pathway across Cancer Types

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    Elsevier BV, 2018

    Published in: Cell Reports

  12. 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; Hu, Hai; Caesar-Johnson, Samantha J.; Demchok, John A.; Felau, Ina; Kasapi, Melpomeni; Ferguson, Martin L.; Hutter, Carolyn M.; Sofia, Heidi J.; Tarnuzzer, Roy; Wang, Zhining; [...]

    An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

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    Elsevier BV, 2018

    Published in: Cell

  13. Wang, Zehua; Yang, Bo; Zhang, Min; Guo, Weiwei; Wu, Zhiyuan; Wang, Yue; Jia, Lin; Li, Song; Xie, Wen; Yang, Da; Caesar-Johnson, Samantha J.; Demchok, John A.; Felau, Ina; Kasapi, Melpomeni; Ferguson, Martin L.; Hutter, Carolyn M.; Sofia, Heidi J.; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Zenklusen, Jean C.; Zhang, Jiashan (Julia); Chudamani, Sudha; Liu, Jia; [...]

    lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer

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    Elsevier BV, 2018

    Published in: Cancer Cell

  14. 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; Sanchez, Yolanda; Greene, Casey S.; Caesar-Johnson, Samantha J.; Demchok, John A.; Felau, Ina; Kasapi, Melpomeni; Ferguson, Martin L.; Hutter, Carolyn M.; Sofia, Heidi J.; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Zenklusen, Jean C.; [...]

    Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas

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    Elsevier BV, 2018

    Published in: Cell Reports

  15. 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.; Laird, Peter W.; Noushmehr, Houtan; Wiznerowicz, Maciej; Caesar-Johnson, Samantha J.; [...]

    Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

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    Elsevier BV, 2018

    Published in: Cell

  16. 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.; Liang, Han; Caesar-Johnson, Samantha J.; Demchok, John A.; Felau, Ina; [...]

    Molecular Characterization and Clinical Relevance of Metabolic Expression Subtypes in Human Cancers

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    Elsevier BV, 2018

    Published in: Cell Reports

  17. 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; Gross, Benjamin; Gao, Jianjiong; Zhang, Hongxin; Kundra, Ritika; [...]

    Oncogenic Signaling Pathways in The Cancer Genome Atlas

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    Elsevier BV, 2018

    Published in: Cell

  18. 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; Caesar-Johnson, Samantha J.; Demchok, John A.; Felau, Ina; Kasapi, Melpomeni; Ferguson, Martin L.; Hutter, Carolyn M.; Sofia, Heidi J.; Tarnuzzer, Roy; [...]

    Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

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    Elsevier BV, 2018

    Published in: Cell Systems

  19. Chen, Han; Li, Chunyan; Peng, Xinxin; Zhou, Zhicheng; Weinstein, John N.; Liang, Han; Caesar-Johnson, Samantha J.; Demchok, John A.; Felau, Ina; Kasapi, Melpomeni; Ferguson, Martin L.; Hutter, Carolyn M.; Sofia, Heidi J.; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Zenklusen, Jean C.; Zhang, Jiashan (Julia); Chudamani, Sudha; Liu, Jia; Lolla, Laxmi; Naresh, Rashi; Pihl, Todd; Sun, Qiang; [...]

    A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples

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    Elsevier BV, 2018

    Published in: Cell

  20. 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; Caesar-Johnson, Samantha J.; Demchok, John A.; Felau, Ina; Kasapi, Melpomeni; Ferguson, Martin L.; Hutter, Carolyn M.; Sofia, Heidi J.; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Zenklusen, Jean C.; Zhang, Jiashan (Julia); [...]

    Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

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    Elsevier BV, 2018

    Published in: Cell Reports