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by Akbani, Rehan and Akdemir, Kadir C and Aksoy, B. Arman and Albert, Monique and Ally, Adrian and Amin, Samirkumar B and Arachchi, Harindra and Arora, Arshi and Auman, J. Todd and Ayala, Brenda and Baboud, Julien and Balasundaram, Miruna and Balu, Saianand and Barnabas, Nandita and Bartlett, John and Bartlett, Pam and Bastian, Boris C and Baylin, Stephen B and Behera, Madhusmita and Belyaev, Dmitry and Benz, Christopher and Bernard, Brady and Beroukhim, Rameen and Bir, Natalie and Black, Aaron D and Bodenheimer, Tom and Boice, Lori and Boland, Genevieve M and Bono, Riccardo and Bootwalla, Moiz S and Bosenberg, Marcus and Bowen, Jay and Bowlby, Reanne and Bristow, Christopher A and Brockway-Lunardi, Laura and Brooks, Denise and Brzezinski, Jakub and Bshara, Wiam and Buda, Elizabeth and Burns, William R and Butterfield, Yaron S.N and Button, Michael and Calderone, Tiffany and Cappellini, Giancarlo Antonini and Carter, Candace and Carter, Scott L and Cherney, Lynn and Cherniack, Andrew D and Chevalier, Aaron and Chin, Lynda and Cho, Juok and Cho, Raymond J and Choi, Yoon-La and Chu, Andy and Chudamani, Sudha and Cibulskis, Kristian and Ciriello, Giovanni and Clarke, Amanda and Coons, Stephen and Cope, Leslie and Crain, Daniel and Curley, Erin and Danilova, Ludmila and D’Atri, Stefania and Davidsen, Tanja and Davies, Michael A and Delman, Keith A and Demchok, John A and Deng, Qixia A and Deribe, Yonathan Lissanu and Dhalla, Noreen and Dhir, Rajiv and DiCara, Daniel and Dinikin, Michael and Dubina, Michael and Ebrom, J. Stephen and Egea, Sophie and Eley, Greg and Engel, Jay and Eschbacher, Jennifer M and Fedosenko, Konstantin V and Felau, Ina and Fennell, Timothy and Ferguson, Martin L and Fisher, Sheila and Flaherty, Keith T and Frazer, Scott and Frick, Jessica and Fulidou, Victoria and Gabriel, Stacey B and Gao, Jianjiong and Gardner, Johanna and Garraway, Levi A and Gastier-Foster, Julie M and Gaudioso, Carmelo and Gehlenborg, Nils and Genovese, Giannicola and Gerken, Mark and Gershenwald, Jeffrey E and Getz, Gad and ... and Canc Genome Atlas Network and Cancer Genome Atlas Network
Cell, ISSN 0092-8674, 06/2015, Volume 161, Issue 7, pp. 1681 - 1696
Journal Article
by Thorsson, Vesteinn and Thorsson, Vésteinn and Gibbs, Richard A and Gibbs, David L and Brown, Scott D and Wolf, Gregory and Wolf, Denise and Bortone, Dante S and Ou Yang, Tai-Hsien and Porta-Pardo, Eduard and Gao, Galen F and Gao, Jianjiong and Plaisier, Christopher L and Eddy, James A and Ziv, Elad and Culhane, Aedin C and Paull, Evan O and Sivakumar, I.K. Ashok and Gentles, Andrew J and Malhotra, Raunaq and Farshidfar, Farshad and Colaprico, Antonio and Parker, Joel S and Mose, Lisle E and Vo, Nam Sy and Liu, Wenbin and Liu, Jianfang and Liu, Jia and Liu, Yuexin and Liu, Xiuping and Rader, Janet and Dhankani, Varsha and Reynolds, Sheila and Reynolds, Sheila M and Bowlby, Reanne and Califano, Andrea and Cherniack, Andrew D and Anastassiou, Dimitris and Bedognetti, Davide and Mokrab, Younes and Newman, Aaron M and Rao, Arvind and Chen, Amy and Chen, Chu and Chen, Ken and Krasnitz, Alexander and Hu, Jianhong and Hu, Hai and Malta, Tathiane M and Noushmehr, Houtan and Pedamallu, Chandra Sekhar and Bullman, Susan and Ojesina, Akinyemi I and Lamb, Andrew and Zhou, Wanding and Shen, Hui and Choueiri, Toni K and Weinstein, John N and Guinney, Justin and Saltz, Joel and Holt, Robert and Holt, Robert A and Rabkin, Charles S and Caesar-Johnson, Samantha J and Demchok, John A and Felau, Ina and Kasapi, Melpomeni and Ferguson, Martin L and Hutter, Carolyn M and Sofia, Heidi J and Tarnuzzer, Roy and Wang, Jioajiao and Wang, Min and Wang, Linghua and Wang, Zhining and Wang, Timothy and Wang, Jing and Yang, Ju Dong and Yang, Hannah and Yang, Liming and Yang, Ian and Zenklusen, Jean C and Zhang, Jiashan (Julia) and Zhang, Jiexin and Zhang, Lizhi and Zhang, Wei and Zhang, Hongzheng and Zhang, Hailei and Zhang, Hongxin and Chudamani, Sudha and Lolla, Laxmi and Naresh, Rashi and Pihl, Todd and Sun, Yichao and Sun, Qiang and Wan, Yunhu and Wu, Ye and Cho, Juok and DeFreitas, Timothy and Frazer, Scott and ... and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network
Immunity, ISSN 1074-7613, 04/2018, Volume 48, Issue 4, pp. 812 - 830.e14
We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled by TCGA. Across... 
tumor immunology | immunotherapy | cancer genomics | integrative network analysis | immuno-oncology | tumor microenvironment | immune subtypes | immunomodulatory | GENOMIC ANALYSES | INFORMATION | T-CELL-RECEPTOR | REGULATORY NETWORK | CLASSIFICATION | IMMUNOLOGY | SEQUENCING DATA | SOMATIC MUTATIONS | COMPREHENSIVE ANALYSIS | PREDICTION | REVEALS | Transforming Growth Factor beta - immunology | Prognosis | Humans | Middle Aged | Th1-Th2 Balance - physiology | Male | Neoplasms - classification | Wound Healing - immunology | Young Adult | Transforming Growth Factor beta - genetics | Neoplasms - genetics | Neoplasms - immunology | Interferon-gamma - immunology | Adolescent | Aged, 80 and over | Adult | Female | Aged | Interferon-gamma - genetics | Wound Healing - genetics | Genomics - methods | Child | Macrophages - immunology | Cell proliferation | Cluster analysis | Transcription | Copy number | p53 Protein | Lung cancer | Genomics | Aneuploidy | Lymphocytes T | Genomes | Cell interactions | Macrophages | Immunotherapy | DNA methylation | Deoxyribonucleic acid--DNA | Immune system | Medical research | Wound healing | Immunomodulation | MiRNA | Stockholders | Inflammation | T cell receptors | Communications networks | Gene expression | White blood cells | Inventors | Medical prognosis | γ-Interferon | Mutation | Cancer | Tumors | Index Medicus | Immune Subtypes | Integrative Network Analysis | Cancer Genomics | Immuno-oncology | Tumor immunology
Journal Article
by Shen, Hui and Shih, Juliann and Hollern, Daniel P and Hollern, Daniel and Wang, Zhining and Wang, Linghua and Bowlby, Reanne and Tickoo, Satish K and Thorsson, Vésteinn and Thorsson, Vesteinn and Mungall, Andrew J and Newton, Yulia and Hegde, Apurva M and Armenia, Joshua and Sánchez-Vega, Francisco and Pluta, John and Pyle, Louise C and Mehra, Rohit and Reuter, Victor E and Godoy, Guilherme and Jones, Jeffrey and Jones, Steven J.M and Jones, Corbin D and Shelley, Carl S and Feldman, Darren and Feldman, Darren R and Vidal, Daniel O and Lessel, Davor and Kulis, Tomislav and Cárcano, Flavio M and Leraas, Kristen M and Lichtenberg, Tara M and Brooks, Denise and Cherniack, Andrew D and Cho, Juok and Heiman, David I and Kasaian, Katayoon and Liu, Jia and Liu, Wenbin and Liu, Minwei and Noble, Michael S and Xi, Liu and Zhang, Jiashan (Julia) and Zhang, Jiashan and Zhang, Hailei and Zhou, Wanding and ZenKlusen, Jean C and Hutter, Carolyn M and Felau, Ina and Schultz, Nikolaus and Getz, Gad and Meyerson, Matthew and Stuart, Joshua M and Wheeler, David A and Wheeler, David and Hughes, Daniel and Covington, Kyle and Jayaseelan, Joy C and Korchina, Viktoriya and Lewis, Lora and Hu, Jianhong and Doddapaneni, HarshaVardhan and Muzny, Donna and Gibbs, Richard and Hoadley, Katherine A and Vincent, Benjamin G and Chai, Shengjie and Smith, Christof C and Auman, J. Todd and Shi, Yan and Meng, Shaowu and Skelly, Tara and Tan, Donghui and Veluvolu, Umadevi and Mieczkowski, Piotr A and Wilkerson, Matthew D and Balu, Saianand and Bodenheimer, Tom and Hoyle, Alan P and Jefferys, Stuart R and Mose, Lisle E and Simons, Janae V and Soloway, Matthew G and Roach, Jeffrey and Parker, Joel S and Hayes, D. Neil and Perou, Amy H and Perou, Charles M and Saksena, Gordon and Cibulskis, Carrie and Schumacher, Steven E and Beroukhim, Rameen and Gabriel, Stacey B and Ally, Adrian and Balasundaram, Miruna and Carlsen, Rebecca and Cheung, Dorothy and Chuah, Eric and Dhalla, Noreen and Holt, Robert A and ... and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network
Cell Reports, ISSN 2211-1247, 06/2018, Volume 23, Issue 11, pp. 3392 - 3406
We studied 137 primary testicular germ cell tumors (TGCTs) using high-dimensional assays of genomic, epigenomic, transcriptomic, and proteomic features. These... 
exome sequencing | miR-375 | KIT | DNA methylation | seminoma | nonseminoma | copy number | testicular germ cell tumors | The Cancer Genome Atlas | ENDOGENOUS RETROVIRUSES | KIT GENE | ADOLESCENTS | HIGH-RESOLUTION | MUTATIONS | SEMINOMA | EXPRESSION | HUMAN CANCER | GENOME | CARCINOMA IN-SITU | CELL BIOLOGY
Journal Article
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 10/2014, Volume 111, Issue 43, pp. 15544 - 15549
Journal Article
by Brennan, Cameron W and Verhaak, Roel G.W and McKenna, Aaron and Campos, Benito and Noushmehr, Houtan and Salama, Sofie R and Zheng, Siyuan and Chakravarty, Debyani and Sanborn, J. Zachary and Berman, Samuel H and Beroukhim, Rameen and Bernard, Brady and Wu, Junyuan and Wu, Chang-Jiun and Genovese, Giannicola and Shmulevich, Ilya and Barnholtz-Sloan, Jill and Zou, Lihua and Vegesna, Rahulsimham and Shukla, Sachet A and Ciriello, Giovanni and Yung, W.K and Yung, W.K. Alfred and Zhang, Zhaobin and Zhang, Wei and Zhang, Jianhua and Zhang, Hailei and Sougnez, Carrie and Mikkelsen, Tom and Aldape, Kenneth and Bigner, Darell D and Bigner, Darell and Van Meir, Erwin G and Prados, Michael and Sloan, Andrew and Sloan, Andrew E and Black, Keith L and Eschbacher, Jennifer and Finocchiaro, Gaetano and Friedman, William and Andrews, David W and Guha, Abhijit and Iacocca, Mary and O’Neill, Brian P and Foltz, Greg and Myers, Jerome and Weisenberger, Daniel J and Penny, Robert and Kucherlapati, Raju and Perou, Charles M and Hayes, D. Neil and Gibbs, Richard and Marra, Marco and Mills, Gordon and Mills, Gordon B and Lander, Eric S and Lander, Eric and Spellman, Paul and Wilson, Richard K and Wilson, Richard and Sander, Chris and Weinstein, John N and Weinstein, John and Meyerson, Matthew and Gabriel, Stacey B and Gabriel, Stacey and Laird, Peter W and Haussler, David and Getz, Gad and Chin, Lynda and Benz, Christopher and Barrett, Wendi and Ostrom, Quinn and Wolinsky, Yingli and Bose, Bikash and Boulos, Madgy and Boulos, Paul T and Brown, Jenn and Czerinski, Christine and Eppley, Matthew and Kempista, Thelma and Kitko, Teresa and Koyfman, Yakov and Rabeno, Brenda and Rastogi, Pawan and Sugarman, Michael and Swanson, Patricia and Yalamanchii, Kennedy and Otey, Ilana P and Liu, Yuexin and Liu, Yingchun Spring and Liu, Wenbin and Xiao, Yonghong and Auman, J.Todd and Chen, Qing-Rong and Chen, Peng-Chieh and Chen, Ken and Hadjipanayis, Angela and Lee, Eunjung and Lee, Semin and ... and TCGA Res Network and TCGA Research Network
Cell, ISSN 0092-8674, 10/2013, Volume 155, Issue 2, pp. 462 - 477
Journal Article