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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 AneuploidyView onlineSchließen
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Published in: Cancer Cell
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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 AtlasView onlineSchließen
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Published in: Cell Reports
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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 CarcinomasView onlineSchließen
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Published in: Cell Reports
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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 CancerView onlineSchließen
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Published in: Immunity
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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 TypesView onlineSchließen
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Published in: Cell Reports
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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 AnalyticsView onlineSchließen
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Published in: Cell
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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 CancerView onlineSchließen
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Published in: Cancer Cell
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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 AtlasView onlineSchließen
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Published in: Cell Reports
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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 DedifferentiationView onlineSchließen
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Published in: Cell
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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 CancersView onlineSchließen
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Published in: Cell Reports
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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 AtlasView onlineSchließen
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Published in: Cell
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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 AtlasView onlineSchließen
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Published in: Cell Systems
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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 SamplesView onlineSchließen
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Published in: Cell
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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 ContextView onlineSchließen
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Published in: Cell Reports
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Korkut, Anil; Zaidi, Sobia; Kanchi, Rupa S.; Rao, Shuyun; Gough, Nancy R.; Schultz, Andre; Li, Xubin; Lorenzi, Philip L.; Berger, Ashton C.; Robertson, Gordon; Kwong, Lawrence N.; Datto, Mike; Roszik, Jason; Ling, Shiyun; Ravikumar, Visweswaran; Manyam, Ganiraju; Rao, Arvind; Shelley, Simon; Liu, Yuexin; Ju, Zhenlin; Hansel, Donna; de Velasco, Guillermo; Pennathur, Arjun; Andersen, Jesper B.; [...]A Pan-Cancer Analysis Reveals High-Frequency Genetic Alterations in Mediators of Signaling by the TGF-β SuperfamilyView onlineSchließen
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Published in: Cell Systems
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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; Koire, Amanda; McMichael, Joshua F.; Hucthagowder, Vishwanathan; Kim, Tae-Beom; [...]Pathogenic Germline Variants in 10,389 Adult CancersView onlineSchließen
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Published in: Cell
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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; Suphavilai, Chayaporn; Nagarajan, Niranjan; Stuart, Joshua M.; Mills, Gordon B.; [...]Perspective on Oncogenic Processes at the End of the Beginning of Cancer GenomicsView onlineSchließen
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Published in: Cell
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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; Caesar-Johnson, Samantha J.; Demchok, John A.; Felau, Ina; Kasapi, Melpomeni; Ferguson, Martin L.; Hutter, Carolyn M.; Sofia, Heidi J.; Tarnuzzer, Roy; Wang, Zhining; [...]Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic PipelinesView onlineSchließen
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Published in: Cell Systems
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Seiler, Michael; Peng, Shouyong; Agrawal, Anant A.; Palacino, James; Teng, Teng; Zhu, Ping; Smith, Peter G.; Buonamici, Silvia; Yu, Lihua; 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; [...]Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer TypesView onlineSchließen
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Published in: Cell Reports
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Saltz, Joel; Gupta, Rajarsi; Hou, Le; Kurc, Tahsin; Singh, Pankaj; Nguyen, Vu; Samaras, Dimitris; Shroyer, Kenneth R.; Zhao, Tianhao; Batiste, Rebecca; Van Arnam, John; Shmulevich, Ilya; Rao, Arvind U.K.; Lazar, Alexander J.; Sharma, Ashish; Thorsson, Vésteinn; Caesar-Johnson, Samantha J.; Demchok, John A.; Felau, Ina; Kasapi, Melpomeni; Ferguson, Martin L.; Hutter, Carolyn M.; Sofia, Heidi J.; Tarnuzzer, Roy; [...]Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology ImagesView onlineSchließen
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Published in: Cell Reports