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by Wang, Linghua and Zimmermann, Michael T and Gao, Galen F and Fan, Huihui and Shen, Hui and Way, Gregory P and Greene, Casey S and Feng, Bin and Donehower, Lawrence A and Miller, Chase and Shen, Yang and Chen, Haoran and Kim, Pora and Liu, Jianfang and Bailey, Matthew H and Yau, Christina and Wolf, Denise and Zhao, Zhongming and Weinstein, John N and Li, Lei and Ding, Li and Mills, Gordon B and Laird, Peter W and Wheeler, David A and Monnat, Raymond J and Xiao, Yonghong and Wang, Chen and Caesar-Johnson, Samantha J and Demchok, John A and Ferguson, Martin L and Hutter, Carolyn M and Tarnuzzer, Roy and Wang, Zhining and Yang, Liming and Zenklusen, Jean C and Liu, Jia and Lolla, Laxmi and Naresh, Rashi and Pihl, Todd and Sun, Qiang and Cho, Juok and DeFreitas, Timothy and Frazer, Scott and Gehlenborg, Nils and Getz, Gad and Kim, Jaegil and Lawrence, Michael S and Meier, Sam and Bernard, Brady and Dhankani, Varsha and Knijnenburg, Theo and Kramer, Roger 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 Lu, Yiling and Rao, Arvind and Ryan, Michael and Zhang, Jiexin and Armenia, Joshua and Chakravarty, Debyani and de Bruijn, Ino and Gao, Jianjiong and Gross, Benjamin E and Heins, Zachary J and Ladanyi, Marc and Luna, Augustin and Nissan, Moriah G and Ochoa, Angelica and Reznik, Ed and Sanchez-Vega, Francisco and Sander, Chris and Schultz, Nikolaus and Sumer, S. Onur and Sun, Yichao and Wang, Jioajiao and Zhang, Hongxin and Anur, Pavana and Peto, Myron and Spellman, Paul and Benz, Christopher and Stuart, Joshua M and Wong, Christopher K and Hayes, D. Neil and Parker, Joel S and Wilkerson, Matthew D and Ally, Adrian 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 ... and The Cancer Genome Atlas Research Network 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 (Cambridge), ISSN 2211-1247, 04/2018, Volume 23, Issue 1, pp. 239 - 254.e6
Journal Article
by Worley, Kim C and Warren, Wesley C and Rogers, Jeffrey and Locke, Devin and Muzny, Donna M and Mardis, Elaine R and Weinstock, George M and Tardif, Suzette D and Aagaard, Kjersti M and Archidiacono, Nicoletta and Arul Rayan, Nirmala and Batzer, Mark A and Beal, Kathryn and Brejova, Brona and Capozzi, Oronzo and Capuano, Saverio B and Casola, Claudio and Chandrabose, Mimi M and Cree, Andrew and Diep Dao, Marvin and De Jong, Pieter J and Cruz-Herrera del Rosario, Ricardo and Delehaunty, Kim D and Dinh, Huyen H and Eichler, Evan E and Fitzgerald, Stephen and Flicek, Paul and Fontenot, Catherine C and Fowler, R. Gerald and Fronick, Catrina and Fulton, Lucinda A and Fulton, Robert S and Gabisi, Ramatu Ayiesha and Gerlach, Daniel and Graves, Tina A and Gunaratne, Preethi H and Hahn, Matthew W and Haig, David and Han, Yi and Harris, R. Alan and Herrero, Javier and Hillier, LaDeana W and Hubley, Robert and Hughes, Jennifer F and Hume, Jennifer and Jhangiani, Shalini N and Jorde, Lynn B and Joshi, Vandita and Karakor, Emre and Konkel, Miriam K and Kosiol, Carolin and LKovar, Christie and Kriventseva, Evgenia V and Lee, Sandra L and Lewis, Lora R and Liu, Yih-Shin and Lopez, John and Lopez-Otin, Carlos and Lorente-Galdos, Belen and Mansfield, Keith G and Marques-Bonet, Tomas and Minx, Patrick and Misceo, Doriana and Moncrieff, J. Scott and Morgan, Margaret B and Nazareth, Lynne V and Newsham, Irene and Nguyen, Ngoc Bich and Okwuonu, Geoffrey O and Prabhakar, Shyam and Perales, Lora and Pu, Ling-Ling and Puente, Xose S and Quesada, Victor and Ranck, Megan C and Raney, Brian J and Raveendran, Muthuswamy and Deiros, David Rio and Rocchi, Mariano and Rodriguez, David and Ross, Corinna and Ruffier, Magali and Ruiz, San Juana and Sajjadian, Saba and Santibanez, Jireh and Schrider, Daniel R and Searle, Steve and Skaletsky, Helen and Soibam, Benjamin and Smit, Arian F.A and Tennakoon, Jayantha B and Tomaska, Lubomir and Ullmer, Brygg and Vejnar, Charles E and Ventura, Mario and Vilella, Albert J and Vinar, Tomas and Vogel, Jan-Hinnerk and Walker, Jerilyn A and Wang, Qing and ... and The Marmoset Genome Sequencing and Analysis Consortium and Marmoset Genome Sequencing Anal Co and Marmoset Genome Sequencing and Analysis Consortium
Nature genetics, ISSN 1546-1718, 2014, Volume 46, Issue 8, pp. 850 - 857
Journal Article
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
Nature Communications, ISSN 2041-1723, 11/2010, Volume 1, Issue 8, p. 131
Accurately determining the distribution of rare variants is an important goal of human genetics, but resequencing of a sample large enough for this purpose has... 
NUCLEOTIDE | SAMPLE | MULTIDISCIPLINARY SCIENCES | SEQUENCE | SNPS | COMMON | GENOME
Journal Article
by Campbell, Joshua D and Yau, Christina and Bowlby, Reanne and Liu, Yuexin and Brennan, Kevin and Fan, Huihui and Taylor, Alison M and Wang, Chen and Walter, Vonn and Akbani, Rehan and Byers, Lauren Averett and Creighton, Chad J and Coarfa, Cristian and Cherniack, Andrew D and Gevaert, Olivier and Prunello, Marcos and Shen, Hui and Chen, Jianhong and Cheng, Hui and Hayes, D. Neil and Bullman, Susan and Pedamallu, Chandra Sekhar and Ojesina, Akinyemi I and Mungall, Karen L and Hegde, Apurva and Diao, Lixia and Ma, Wencai and Sumazin, Pavel and Chen, Ting-Wen and Zuna, Rosemary and Al-Ahmadie, Hikmat and Zhou, Jane H and Drill, Esther and Wong, Christopher K and Stuart, Joshua M and Laird, Peter W and Hoadley, Katherine A and Weinstein, John N and Peto, Myron and Pickering, Curtis R and Chen, Zhong and Van Waes, Carter and Caesar-Johnson, Samantha J and Ferguson, Martin L 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 Wan, Yunhu 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 Chambwe, Nyasha and Dhankani, Varsha and Knijnenburg, Theo and Kramer, Roger and Leinonen, Kalle and Miller, Michael and Reynolds, Sheila and Hegde, Apurva M and Ju, Zhenlin and Korkut, Anil and Li, Jun and Liang, Han and Ling, Shiyun and Lu, Yiling and Mills, Gordon B and Ng, Kwok-Shing and Rao, Arvind and Abeshouse, Adam and Armenia, Joshua and Chakravarty, Debyani 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 Sanchez-Vega, Francisco and Sander, Chris and Schultz, Nikolaus and Sumer, S. Onur and Sun, Yichao and ... and The Cancer Genome Atlas Research Network 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 (Cambridge), ISSN 2211-1247, 2018, Volume 23, Issue 1, pp. 194 - 212.e6
Journal Article
by Cao, Song and Gao, Qingsong and Wendl, Michael C and Vo, Nam Sy and Zhao, Yanyan and Climente-González, Héctor and Wang, Fang and Varghese, Rajees and Huang, Mo and Liang, Wen-Wei and Wyczalkowski, Matthew A and Li, Zhi and Payne, Samuel H and Fenyö, David and Miner, Jeffrey H and Vincent, Benjamin and Shmulevich, Ilya and Chen, Feng and Ding, Li and Caesar-Johnson, Samantha J and Demchok, John A and Kasapi, Melpomeni and Ferguson, Martin L and Tarnuzzer, Roy and Wang, Zhining and Yang, Liming and Zenklusen, Jean C 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 Saksena, Gordon and Zhang, Hailei and Chambwe, Nyasha and Dhankani, Varsha and Knijnenburg, Theo and Kramer, Roger and Leinonen, Kalle and Reynolds, Sheila and Thorsson, Vesteinn and Zhang, Wei and Akbani, Rehan and Broom, Bradley M and Kanchi, Rupa S and Korkut, Anil and Li, Jun and Liang, Han and Ling, Shiyun and Mills, Gordon B 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 Gross, Benjamin E and Nissan, Moriah G and Phillips, Sarah M and Reznik, Ed and Sanchez-Vega, Francisco and Schultz, Nikolaus and Sheridan, Robert and Sumer, S. Onur and Sun, Yichao and Taylor, Barry S and Wang, Jioajiao and Spellman, Paul and Yau, Christina and Wilkerson, Matthew D and Ally, Adrian and Brooks, Denise and Chuah, Eric and Dhalla, Noreen and Holt, Robert and Jones, Steven J.M and Lee, Darlene and Marra, Marco A and Moore, Richard A and Mungall, Andrew J and Robertson, A. Gordon and Sadeghi, Sara and Schein, Jacqueline E and Sipahimalani, Payal and Tam, Angela and Thiessen, Nina and Tse, Kane and Wong, Tina 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 (Cambridge), 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