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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 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 | 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 | 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 | Immune Subtypes | Integrative Network Analysis | Cancer Genomics | Immuno-oncology | Tumor immunology
Journal Article
by Chiu, Hua-Sheng and Somvanshi, Sonal and Patel, Ektaben and Patel, Tushar and Chen, Amy and Chen, Chu and Chen, Ting-Wen and Singh, Rosy and Singh, Vivek P and Singh, Bhuvanesh and Zorman, Barry and Patil, Sagar L and Pan, Yinghong and Chatterjee, Sujash 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, Jing and Wang, Timothy and Wang, Min and Wang, Jioajiao and Wang, Zhining and Wang, Linghua and Yang, Ju Dong and Yang, Liming and Yang, Ian and Yang, Hannah and Zenklusen, Jean C and Zhang, Jiashan (Julia) and Zhang, Hailei and Zhang, Wei and Zhang, Jiexin and Zhang, Hongxin and Zhang, Lizhi and Zhang, Hongzheng and Chudamani, Sudha and Liu, Jia and Liu, Yuexin and Liu, Xiuping and Liu, Wenbin 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 Kim, Jaegil and Lawrence, Michael S and Lin, Pei and Meier, Sam 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 Leinonen, Kalle and Miller, Christopher A and Miller, Michael and Miller, Judy and Reynolds, Sheila and Shmulevich, Ilya and Thorsson, Vesteinn and Akbani, Rehan and Broom, Bradley M and Hegde, Apurva M and Ju, Zhenlin and Kanchi, Rupa S and Korkut, Anil and Li, Jun and Li, Wei and Liang, Han and Ling, Shiyun and Lu, Yiling and Mills, Gordon B and Ng, Kwok-Shing and Rao, Arvind and Ryan, Michael and Weinstein, John N and Abeshouse, Adam and Armenia, Joshua and Chakravarty, Debyani and Chatila, Walid K and de Bruijn, Ino and Gao, Galen F and Gao, Jianjiong and ... and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network
Cell Reports, ISSN 2211-1247, 04/2018, Volume 23, Issue 1, pp. 297 - 312.e12
Long noncoding RNAs (lncRNAs) are commonly dysregulated in tumors, but only a handful are known to play pathophysiological roles in cancer. We inferred lncRNAs... 
lncRNA | pan-cancer | noncoding RNA | regulation | modulation | cancer gene | microRNA | RNA-binding proteins | interactome | Biochemistry, Genetics and Molecular Biology(all) | LONG NONCODING RNAS | DATABASE | MICRORNA-TARGET | LANDSCAPE | BINDING SITES | CELL-PROLIFERATION | IDENTIFICATION | TRANSCRIPTION FACTOR | EXPRESSION | RESOURCE | CELL BIOLOGY
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