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by Gibbs, David L and Brown, Scott D and Ou Yang, Tai-Hsien and Porta-Pardo, Eduard and Gao, Galen F and Plaisier, Christopher L and Ziv, Elad 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, Jianfang and Dhankani, Varsha and Reynolds, Sheila M and Cherniack, Andrew D and Anastassiou, Dimitris and Bedognetti, Davide and Mokrab, Younes and Rao, Arvind and Hu, Hai and Noushmehr, Houtan and Pedamallu, Chandra Sekhar and Bullman, Susan and Lamb, Andrew and Zhou, Wanding and Choueiri, Toni K and Weinstein, John N and Guinney, Justin and Rabkin, Charles S and Lazar, Alexander J and Serody, Jonathan S and Vincent, Benjamin G and Demchok, John A and Kasapi, Melpomeni and Hutter, Carolyn M and Sofia, Heidi J and Tarnuzzer, Roy and Wang, Zhining and Yang, Liming and Zenklusen, Jean C and Zhang, Jiashan (Julia) and Chudamani, Sudha and Naresh, Rashi and Pihl, Todd 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 Heiman, David I and Lawrence, Michael S and Meier, Sam and Noble, Michael S and Saksena, Gordon and Voet, Doug and Zhang, Hailei and Chambwe, Nyasha and Knijnenburg, Theo and Kramer, Roger and Leinonen, Kalle and Miller, Michael and Zhang, Wei and Akbani, Rehan and Broom, Bradley M and Hegde, Apurva M and Kanchi, Rupa S and Liang, Han and Ling, Shiyun and Liu, Wenbin and Lu, Yiling and Mills, Gordon B and Ng, Kwok-Shing and Ryan, Michael and Zhang, Jiexin and Abeshouse, Adam and Chakravarty, Debyani and Chatila, Walid K and de Bruijn, Ino and Gross, Benjamin E and Heins, Zachary J and La, Konnor and Ladanyi, Marc and Ochoa, Angelica and Phillips, Sarah M and Reznik, Ed and Sander, Chris and Sumer, S. Onur and Wang, Jioajiao and Zhang, Hongxin and Anur, Pavana and Stuart, Joshua M and Wong, Christopher K and Hayes, D. Neil and ... and The Cancer Genome Atlas Research Network and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network
Immunity (Cambridge, Mass.), 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 | Immunology | Infectious Diseases | Immunology and Allergy | 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 | miRNA | Deoxyribonucleic acid--DNA | Immune system | Medical research | Wound healing | Immunomodulation | Stockholders | Inflammation | T cell receptors | Communications networks | Gene expression | White blood cells | Inventors | Medical prognosis | γ-Interferon | Mutation | Cancer | Tumors | Immune Subtypes | Integrative Network Analysis | Cancer Genomics | Immuno-oncology | Tumor immunology
Journal Article
by Sanchez-Vega, Francisco and Mina, Marco and Armenia, Joshua and Chatila, Walid K and Luna, Augustin and Kantheti, Havish S and Saghafinia, Sadegh and Chakravarty, Debyani and Gao, Qingsong and Bailey, Matthew H and Liang, Wen-Wei and Foltz, Steven M and Shmulevich, Ilya and Ding, Li and Heins, Zachary and Ochoa, Angelica and Zhang, Hongxin and Kundra, Ritika and Kandoth, Cyriac and Dervishi, Leonard and Zhou, Wanding and Shen, Hui and Laird, Peter W and Way, Gregory P and Greene, Casey S and Liang, Han and Xiao, Yonghong and Wang, Chen and Bivona, Trever G and Lazar, Alexander J and Hammer, Gary D and Giordano, Thomas and Kwong, Lawrence N and McArthur, Grant and McCormick, Frank and Meyerson, Matthew and Cherniack, Andrew D and Ciriello, Giovanni 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 Yang, Liming and Zhang, Jiashan (Julia) and Chudamani, Sudha and Lolla, Laxmi and Pihl, Todd and Sun, Qiang and Wan, Yunhu and Wu, Ye and Getz, Gad and Heiman, David I and Lin, Pei and Meier, Sam and Saksena, Gordon and Zhang, Hailei and Bernard, Brady and Chambwe, Nyasha and Leinonen, Kalle and Liu, Yuexin and Miller, Michael and Zhang, Wei and Akbani, Rehan and Broom, Bradley M and Ju, Zhenlin and Kanchi, Rupa S and Korkut, Anil and Li, Jun and Liu, Wenbin and Lu, Yiling and Ng, Kwok-Shing and Ryan, Michael and Weinstein, John N and Zhang, Jiexin and Abeshouse, Adam and de Bruijn, Ino and Heins, Zachary J and Ladanyi, Marc and Nissan, Moriah G and Sheridan, Robert and Sumer, S. Onur and Sun, Yichao and Anur, Pavana and Peto, Myron and Stuart, Joshua M and Wong, Christopher K and Hayes, D. Neil and Ally, Adrian and Balasundaram, Miruna and Bowlby, Reanne and Carlsen, Rebecca and Chuah, Eric and Holt, Robert and Jones, Steven J.M and Kasaian, Katayoon and Ma, Yussanne and Mayo, Michael and ... and The Cancer Genome Atlas Research Network and Cancer Genome Atlas Res Network and Cancer Genome Atlas Research Network
Cell (Cambridge), ISSN 0092-8674, 04/2018, Volume 173, Issue 2, pp. 321 - 337.e10
Journal Article
by Bailey, Matthew H and Tokheim, Collin and Bertrand, Denis and Colaprico, Antonio and Wendl, Michael C and Jeong, Kang Jin and Cao, Song and Wang, Zixing and Gao, Qingsong and Wang, Fang and Mularoni, Loris and Rubio-Perez, Carlota and Cortés-Ciriano, Isidro and Liang, Wen-Wei and Hess, Julian M and Yellapantula, Venkata D and Tamborero, David and Gonzalez-Perez, Abel and Park, Peter J and Van Allen, Eliezer M and Liang, Han and Godzik, Adam and Lopez-Bigas, Nuria and Stuart, Josh and Getz, Gad and Chen, Ken and Lazar, Alexander J and Mills, Gordon B and Karchin, Rachel and Ding, Li and Demchok, John A and Kasapi, Melpomeni and Hutter, Carolyn M and Sofia, Heidi J and Tarnuzzer, Roy and Yang, Liming and Zenklusen, Jean C and Chudamani, Sudha and Naresh, Rashi and Pihl, Todd and Sun, Qiang and Wan, Yunhu and Wu, Ye and Cho, Juok and DeFreitas, Timothy and Frazer, Scott and Gehlenborg, Nils and Heiman, David I and Lin, Pei and Meier, Sam and Noble, Michael S and Voet, Doug and Zhang, Hailei and Bernard, Brady and Leinonen, Kalle and Liu, Yuexin and Miller, Michael and Shmulevich, Ilya and Zhang, Wei and Akbani, Rehan and Broom, Bradley M and Hegde, Apurva M and Ju, Zhenlin and Kanchi, Rupa S and Li, Jun and Liu, Wenbin and Lu, Yiling and Ng, Kwok-Shing and Ryan, Michael and Weinstein, John N and Zhang, Jiexin and Abeshouse, Adam and Armenia, Joshua and Chakravarty, Debyani and Chatila, Walid K and de Bruijn, Ino and Gross, Benjamin E and Kundra, Ritika and La, Konnor and Luna, Augustin and Ochoa, Angelica and Phillips, Sarah M and Reznik, Ed and Sanchez-Vega, Francisco and Sander, Chris and Schultz, Nikolaus and Sheridan, Robert and Sumer, S. Onur and Taylor, Barry S and Wang, Jioajiao and Wong, Christopher K and Hayes, D. Neil and Parker, Joel S and Ally, Adrian and Balasundaram, Miruna and Bowlby, Reanne and Carlsen, Rebecca and Chuah, Eric and Kasaian, Katayoon and Lee, Darlene and ... and The MC3 Working Group and The Cancer Genome Atlas Research Network and Canc Genome Atlas Res Network and MC3 Working Grp and MC3 Working Group and Cancer Genome Atlas Research Network
Cell (Cambridge), ISSN 0092-8674, 04/2018, Volume 173, Issue 2, pp. 371 - 385.e18
Journal Article
by Sokolov, Artem and Gentles, Andrew J and Burzykowski, Tomasz and Poisson, Laila and Weinstein, John N and Huelsken, Joerg and Omberg, Larsson and Colaprico, Antonio and Czerwińska, Patrycja and Mazurek, Sylwia and Krasnitz, Alex and Godwin, Andrew K and Lazar, Alexander J and Stuart, Joshua M and Hoadley, Katherine A and Laird, Peter W and Noushmehr, Houtan and Wiznerowicz, Maciej and Demchok, John A and Kasapi, Melpomeni and Hutter, Carolyn M and Sofia, Heidi J and Tarnuzzer, Roy and Wang, Zhining and Yang, Liming and Zenklusen, Jean C and Zhang, Jiashan (Julia) and Chudamani, Sudha and Liu, Jia and Naresh, Rashi and Pihl, Todd and Sun, Qiang and Wan, Yunhu and Wu, Ye and Cho, Juok and DeFreitas, Timothy and Frazer, Scott 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 Zhang, Hailei and Bernard, Brady and Chambwe, Nyasha and Dhankani, Varsha and Knijnenburg, Theo and Kramer, Roger and Liu, Yuexin and Miller, Michael and Reynolds, Sheila and Thorsson, Vesteinn and Zhang, Wei and Hegde, Apurva M and Ju, Zhenlin and Korkut, Anil and Li, Jun and Ling, Shiyun and Liu, Wenbin and Lu, Yiling and Mills, Gordon B and Abeshouse, Adam and Chakravarty, Debyani and Chatila, Walid K and de Bruijn, Ino and Gao, Jianjiong and Gross, Benjamin E and Heins, Zachary J and Kundra, Ritika and La, Konnor and Ladanyi, Marc and Luna, Augustin and Nissan, Moriah G and Ochoa, Angelica and Sander, Chris and Sun, Yichao and Zhang, Hongxin and Anur, Pavana and Peto, Myron and Spellman, Paul and Benz, Christopher and Yau, Christina and Hayes, D. Neil and Parker, Joel S and Balasundaram, Miruna and Bowlby, Reanne and Brooks, Denise and Carlsen, Rebecca and Dhalla, Noreen and Holt, Robert and Jones, Steven J.M and Kasaian, Katayoon and Lee, Darlene and Ma, Yussanne and Mayo, Michael and Mungall, Andrew J and Mungall, Karen and ... and The Cancer Genome Atlas Research Network and Cancer Genome Atlas Res Network and Cancer Genome Atlas Research Network
Cell (Cambridge), ISSN 0092-8674, 04/2018, Volume 173, Issue 2, pp. 338 - 354.e15
Journal Article
by Huang, Kuan-lin and Mashl, R. Jay and Wu, Yige and Wang, Jiayin and Oh, Clara and Wyczalkowski, Matthew A and Oak, Ninad and Scott, Adam D and Cherniack, Andrew D and Houlahan, Kathleen E and Jayasinghe, Reyka and Wang, Liang-Bo and Zhou, Daniel Cui and Cao, Song and Kim, Young Won and Koire, Amanda and McMichael, Joshua F and Hucthagowder, Vishwanathan and Kim, Tae-Beom and Hahn, Abigail and Wang, Chen and McLellan, Michael D and Al-Mulla, Fahd and Johnson, Kimberly J and Lichtarge, Olivier and Boutros, Paul C and Raphael, Benjamin and Lazar, Alexander J and Zhang, Wei and Wendl, Michael C and Jain, Sanjay and Wheeler, David and Kulkarni, Shashikant and Dipersio, John F and Chen, Ken and Plon, Sharon E and Chen, Feng and Caesar-Johnson, Samantha J and Demchok, John A and Kasapi, Melpomeni and Ferguson, Martin L and Sofia, Heidi J and Tarnuzzer, Roy and Wang, Zhining and Yang, Liming and Zenklusen, Jean C and Chudamani, Sudha and Liu, Jia and Lolla, Laxmi and Naresh, Rashi and Pihl, Todd and Wan, Yunhu and Cho, Juok and DeFreitas, Timothy and Frazer, Scott and Gehlenborg, Nils and Getz, Gad and Lawrence, Michael S and Lin, Pei and Noble, Michael S and Saksena, Gordon and Voet, Doug and Bernard, Brady and Chambwe, Nyasha and Dhankani, Varsha and Knijnenburg, Theo and Kramer, Roger and Miller, Michael and Thorsson, Vesteinn and Ju, Zhenlin and Kanchi, Rupa S and Li, Jun and Liang, Han and Ling, Shiyun and Liu, Wenbin and Lu, Yiling and Mills, Gordon B and Ng, Kwok-Shing and Rao, Arvind and Ryan, Michael and Armenia, Joshua and Chakravarty, Debyani and de Bruijn, Ino and Gao, Jianjiong and Gross, Benjamin E and Heins, Zachary J and La, Konnor and Ladanyi, Marc and Luna, Augustin and Nissan, Moriah G and Ochoa, Angelica and Reznik, Ed and Sanchez-Vega, Francisco and Schultz, Nikolaus and Sun, Yichao and Wang, Jioajiao and Zhang, Hongxin and Anur, Pavana and Peto, Myron and Spellman, Paul and ... and The Cancer Genome Atlas Research Network and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network
Cell (Cambridge), ISSN 0092-8674, 2018, Volume 173, Issue 2, pp. 355 - 370.e14
Journal Article
by Kanchi, Rupa S and Hegde, Apurva M and Lenoir, Walter and Liu, Wenbin and Liu, Yuexin and Shen, Hui and Rao, Arvind and Schultz, Andre and Li, Xubin and Sumazin, Pavel and Mestdagh, Pieter and Gunaratne, Preethi H and Yau, Christina and Bowlby, Reanne and Robertson, A. Gordon and Tiezzi, Daniel G and Godwin, Andrew K and Sood, Anil K and Adebamowo, Clement and Baggerly, Keith A and Chiu, Hua-Sheng and Liu, Liang and MacKenzie, Karen and Orsulic, Sandra and Roszik, Jason and Shelley, Carl Simon and Song, Qianqian and Vellano, Christopher P and Wentzensen, Nicolas and Weinstein, John N and Mills, Gordon B and Levine, Douglas A and Caesar-Johnson, Samantha J and Kasapi, Melpomeni and Ferguson, Martin L and Sofia, Heidi J and Tarnuzzer, Roy and Wang, Zhining and Zenklusen, Jean C and Chudamani, Sudha and Liu, Jia and Lolla, Laxmi and Naresh, Rashi and Pihl, Todd and Sun, Qiang and Wu, Ye and Cho, Juok and DeFreitas, Timothy and Frazer, Scott and Gehlenborg, Nils and Getz, Gad and Kim, Jaegil and Lawrence, Michael S and Lin, Pei and Noble, Michael S and Saksena, Gordon and Voet, Doug and Bernard, Brady and Chambwe, Nyasha and Dhankani, Varsha and Knijnenburg, Theo and Kramer, Roger and Miller, Michael and Reynolds, Sheila and Thorsson, Vesteinn and Broom, Bradley M and Ju, Zhenlin and Li, Jun and Ling, Shiyun and Lu, Yiling and Ryan, Michael and Zhang, Jiexin and Abeshouse, Adam and Armenia, Joshua and Chatila, Walid K and Gross, Benjamin E and Kundra, Ritika and La, Konnor and Luna, Augustin and Ochoa, Angelica and Phillips, Sarah M and Reznik, Ed and Sanchez-Vega, Francisco and Sander, Chris and Schultz, Nikolaus and Sheridan, Robert and Sumer, S. Onur and Taylor, Barry S and Wang, Jioajiao and