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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 Rao, Arvind and Chen, Chu and Chen, Ken and Chen, Amy 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 E 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, Linghua and Wang, Zhining and Wang, Jing and Wang, Timothy and Wang, Min and Yang, Hannah and Yang, Ian and Yang, Ju Dong and Yang, Liming and Zenklusen, Jean C and Zhang, Lizhi and Zhang, Hongxin and Zhang, Jiexin and Zhang, Hongzheng and Zhang, Jiashan (Julia) and Zhang, Wei and Zhang, Hailei 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 Gehlenborg, Nils and Getz, Gad 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 Knijnenburg, Theo and Knijnenburg, Theo A and Wang, Chen and Wang, Linghua and Wang, Jing and Wang, Jioajiao and Wang, Min and Wang, Zhining and Wang, Timothy and Zimmermann, Michael T and Chambwe, Nyasha and Gao, Jianjiong and Gao, Galen F and Cherniack, Andrew D and Fan, Huihui and Fan, Cheng and Shen, Yang and Shen, Hui and Way, Gregory P and Greene, Casey S and Liu, Wenbin and Liu, Jianfang and Liu, Jia and Liu, Yuexin and Liu, Xiuping and Akbani, Rehan and Feng, Bin and Donehower, Lawrence A and Miller, Christopher A and Miller, Chase and Miller, Judy and Miller, Michael and Karimi, Mostafa and Chen, Haoran and Chen, Amy and Chen, Chu and Kim, Jaegil and Kim, Pora and Jia, Peilin and Shinbrot, Eve and Zhang, Hongxin and Zhang, Wei and Zhang, Hailei and Zhang, Jiashan (Julia) and Zhang, Lizhi and Zhang, Jiexin and Zhang, Shaojun and Zhang, Hongzheng and Hu, Jianhong and Hu, Hai and Bailey, Matthew H and Bailey, Matthew and Yau, Christina and Wolf, Denise and Wolf, Gregory and Zhao, Fengmei and Zhao, Zhongming and Weinstein, John N and Li, Lei and Li, Jun and Li, Wei and Ding, Li and Mills, Gordon B and Laird, Peter W and Wheeler, David A and Shmulevich, Ilya 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 Yang, Ian and Yang, Ju Dong and Yang, Hannah and Yang, Liming and Zenklusen, Jean C and Chudamani, Sudha and Lolla, Laxmi and Naresh, Rashi and Pihl, Todd and Sun, Qiang and Sun, Yichao and Wan, Yunhu and Wu, Ye and Cho, Juok and DeFreitas, Timothy and Frazer, Scott and Gehlenborg, Nils and Getz, Gad and Heiman, David I and Lawrence, Michael S and Lin, Pei and Meier, Sam and Noble, Michael S and Saksena, Gordon and Voet, Doug and Bernard, Brady and ... and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network and Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Cell Reports, ISSN 2211-1247, 04/2018, Volume 23, Issue 1, pp. 239 - 254.e6
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
by Bass, Adam J and Cancer Genome Atlas Research Network, Genome Atlas Research Network and Thorsson, Vesteinn and Shmulevich, Ilya and Reynolds, Sheila M and Miller, Michael and Bernard, Brady and Hinoue, Toshinori and Laird, Peter W and Curtis, Christina and Shen, Hui and Weisenberger, Daniel J and Schultz, Nikolaus and Shen, Ronglai and Weinhold, Nils and Kelsen, David P and Bowlby, Reanne and Chu, Andy and Kasaian, Katayoon and Mungall, Andrew J and Robertson, A. Gordon and Sipahimalani, Payal and Cherniack, Andrew D and Getz, Gad and Liu, Yingchun and Noble, Michael S and Pedamallu, Chandra and Sougnez, Carrie and Taylor-Weiner, Amaro and Akbani, Rehan and Lee, Ju-Seog and Liu, Wenbin and Mills, Gordon B and Yang, Da and Zhang, Wei and Pantazi, Angeliki and Parfenov, Michael and Gulley, Margaret and Piazuelo, M. Blanca and Schneider, Barbara G and Kim, Jihun and Boussioutas, Alex and Sheth, Margi and Demchok, John A and Rabkin, Charles S and Willis, Joseph E and Ng, Sam and Garman, Katherine and Beer, David G and Pennathur, Arjun and Raphael, Benjamin J and Wu, Hsin-Ta and Odze, Robert and Kim, Hark K and Bowen, Jay and Leraas, Kristen M and Lichtenberg, Tara M and Weaver, Stephanie and McLellan, Michael and Wiznerowicz, Maciej and Sakai, Ryo and Lawrence, Michael S and Cibulskis, Kristian and Lichtenstein, Lee and Fisher, Sheila and Gabriel, Stacey B and Lander, Eric S and Ding, Li and Niu, Beifang and Ally, Adrian and Balasundaram, Miruna and Birol, Inanc and Brooks, Denise and Butterfield, Yaron S. N and Carlsen, Rebecca and Chu, Justin and Chuah, Eric and Chun, Hye-Jung E and Clarke, Amanda and Dhalla, Noreen and Guin, Ranabir and Holt, Robert A and Jones, Steven J. M and Lee, Darlene and Li, Haiyan A and Lim, Emilia and Ma, Yussanne and Marra, Marco A and Mayo, Michael and Moore, Richard A and Mungall, Karen L and Nip, Ka Ming and Schein, Jacqueline E and Tam, Angela and Thiessen, Nina and Beroukhim, Rameen and Carter, Scott L and Cho, Juok and DiCara, Daniel and Frazer, Scott and ... and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network and The Cancer Genome Atlas Research Network
Nature, ISSN 0028-0836, 2014, Volume 513, Issue 7517, pp. 202 - 209
Journal Article