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by Thorsson, Vésteinn and Gibbs, David L and Brown, Scott D and Wolf, Denise and Bortone, Dante S and Ou Yang, Tai-Hsien and Porta-Pardo, Eduard and Gao, Galen F 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, Jianfang and Liu, Yuexin and Rader, Janet and Dhankani, Varsha 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, Ken and Krasnitz, Alexander 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 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, Zhining and Yang, Liming and Zenklusen, Jean C and Zhang, Jiashan (Julia) and Chudamani, Sudha and Liu, Jia and Lolla, Laxmi 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 Kim, Jaegil 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 Leinonen, Kalle and Liu, Yuexin and Miller, Michael and Reynolds, Sheila and Shmulevich, Ilya and Thorsson, Vesteinn and Zhang, Wei and Akbani, Rehan and Broom, Bradley M and Hegde, Apurva M and ... and The Cancer Genome Atlas Research Network 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 | 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
Physics Reports, ISSN 0370-1573, 11/2013, Volume 532, Issue 4, pp. 119 - 244
Journal Article
by Acharya, S and Adamová, D and Adolfsson, J and Aggarwal, M M and Aglieri Rinella, G and Agnello, M and Agrawal, N and Ahammed, Z and Ahmad, N and Ahn, S U and Aiola, S and Akindinov, A and Alam, S N and Alba, J L. B and Albuquerque, D S. D and Aleksandrov, D and Alessandro, B and Alfaro Molina, R and Alici, A and Alkin, A and Alme, J and Alt, T and Altenkamper, L and Altsybeev, I and Alves Garcia Prado, C and Andrei, C and Andreou, D and Andrews, H A and Andronic, A and Anguelov, V and Anson, C and Antičić, T and Antinori, F and Antonioli, P and Anwar, R and Aphecetche, L and Appelshäuser, H and Arcelli, S and Arnaldi, R and Arnold, O W and Arsene, I C and Arslandok, M and Audurier, B and Augustinus, A and Averbeck, R and Azmi, M D and Badalà, A and Baek, Y W and Bagnasco, S and Bailhache, R and Bala, R and Baldisseri, A and Ball, M and Baral, R C and Barbano, A M and Barbera, R and Barile, F and Barioglio, L and Barnaföldi, G G and Barnby, L S and Barret, V and Bartalini, P and Barth, K and Bartsch, E and Basile, M and Bastid, N and Basu, S and Bathen, B and Batigne, G and Batyunya, B and Batzing, P C and Bearden, I G and Beck, H and Bedda, C and Behera, N K and Belikov, I and Bellini, F and Bello Martinez, H and Bellwied, R and Beltran, L G. E and Belyaev, V and Bencedi, G and Beole, S and Bercuci, A and Berdnikov, Y and Berenyi, D and Bertens, R A and Berzano, D and Betev, L and Bhasin, A and Bhat, I R and Bhati, A K and Bhattacharjee, B and Bhom, J and Bianchi, L and Bianchi, N and Bianchin, C and Bielčík, J and Bielčíková, J and Bilandzic, A and ... and ALICE Collaboration and The ALICE collaboration and Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Journal of High Energy Physics, ISSN 1126-6708, 9/2017, Volume 2017, Issue 9, pp. 1 - 33
Journal Article
by Acharya, S and Adamová, D and Aggarwal, M.M and Aglieri Rinella, G and Agnello, M and Agrawal, N and Ahammed, Z and Ahmad, N and Ahn, S.U and Aiola, S and Akindinov, A and Alam, S.N and Albuquerque, D.S.D and Aleksandrov, D and Alessandro, B and Alexandre, D and Alfaro Molina, R and Alici, A and Alkin, A and Alme, J and Alt, T and Altsybeev, I and Alves Garcia Prado, C and An, M and Andrei, C and Andrews, H.A and Andronic, A and Anguelov, V and Anson, C and Antičić, T and Antinori, F and Antonioli, P and Anwar, R and Aphecetche, L and Appelshäuser, H and Arcelli, S and Arnaldi, R and Arnold, O.W and Arsene, I.C and Arslandok, M and Audurier, B and Augustinus, A and Averbeck, R and Azmi, M.D and Badalà, A and Baek, Y.W and Bagnasco, S and Bailhache, R and Bala, R and Baldisseri, A and Ball, M and Baral, R.C and Barbano, A.M and Barbera, R and Barile, F and Barioglio, L and Barnaföldi, G.G and Barnby, L.S and Barret, V and Bartalini, P and Barth, K and Bartke, J and Bartsch, E and Basile, M and Bastid, N and Basu, S and Bathen, B and Batigne, G and Batista Camejo, A and Batyunya, B and Batzing, P.C and Bearden, I.G and Beck, H and Bedda, C and Behera, N.K and Belikov, I and Bellini, F and Bello Martinez, H and Bellwied, R and Beltran, L.G.E and Belyaev, V and Bencedi, G and Beole, S and Bercuci, A and Berdnikov, Y and Berenyi, D and Bertens, R.A and Berzano, D and Betev, L and Bhasin, A and Bhat, I.R and Bhati, A.K and Bhattacharjee, B and Bhom, J and Bianchi, L and Bianchi, N and Bianchin, C and Bielčík, J and Bielčíková, J and Bilandzic, A and ... and ALICE Collaboration and Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States) and Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Physics Letters B, ISSN 0370-2693, 01/2018, Volume 776, Issue C, pp. 249 - 264
Journal Article
Journal Article
by Jayasinghe, Reyka G and Cao, Song and Gao, Qingsong and Wendl, Michael C and Vo, Nam Sy and Reynolds, Sheila M and Zhao, Yanyan and Climente-González, Héctor and Chai, Shengjie and Wang, Fang and Varghese, Rajees and Huang, Mo and Liang, Wen-Wei and Wyczalkowski, Matthew A and Sengupta, Sohini and Li, Zhi and Payne, Samuel H and Fenyö, David and Miner, Jeffrey H and Walter, Matthew J 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, Zhining and Yang, Liming and Zenklusen, Jean C and Zhang, Jiashan (Julia) and Chudamani, Sudha and Liu, Jia and Lolla, Laxmi 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 Kim, Jaegil 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 Leinonen, Kalle and Liu, Yuexin and Miller, Michael and Reynolds, Sheila and Shmulevich, Ilya and Thorsson, Vesteinn and Zhang, Wei 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 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 Wang, Jing 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 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 Phillips, Sarah M and Reznik, Ed and ... and The Cancer Genome Atlas Research Network and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network and Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Cell Reports, ISSN 2211-1247, 04/2018, Volume 23, Issue 1, pp. 270 - 281.e3
For the past decade, cancer genomic studies have focused on mutations leading to splice-site disruption, overlooking those having splice-creating potential.... 
RNA | mutations of clinical relevance | splicing | Biochemistry, Genetics and Molecular Biology(all) | BREAST-CANCER | INACTIVATION | RETINOBLASTOMA | REPORTER MINIGENE | MESSENGER-RNA | TRANSCRIPTOME | UNCLASSIFIED VARIANTS | GENETIC-VARIANTS | ABERRANT | SYNONYMOUS MUTATIONS | CELL BIOLOGY | Splicing | Mutations of clinical relevance | BASIC BIOLOGICAL SCIENCES
Journal Article