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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
Cell (Cambridge), ISSN 0092-8674, 04/2018, Volume 173, Issue 2, pp. 338 - 354.e15
Cancer progression involves the gradual loss of a differentiated phenotype and acquisition of progenitor and stem-cell-like features. Here, we provide novel... 
pan-cancer | genomic | stemness | epigenomic | dedifferentiation | cancer stem cells | machine learning | The Cancer Genome Atlas | Biochemistry, Genetics and Molecular Biology(all) | Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Science & Technology | Cell Biology | Index Medicus
Journal Article
by Wang, Zehua and Zhang, Min and Guo, Weiwei and Wu, Zhiyuan and Wang, Yue and Xie, Wen and Demchok, John A and Felau, Ina and Kasapi, Melpomeni and Hutter, Carolyn M and Sofia, Heidi J and Tarnuzzer, Roy and Yang, Liming and Zenklusen, Jean C and Zhang, Jiashan (Julia) and Chudamani, Sudha and Naresh, Rashi and Sun, Qiang and Wan, Yunhu and Wu, Ye and Frazer, Scott and Heiman, David I and Kim, Jaegil 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 Hegde, Apurva M and Ju, Zhenlin 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 Zhang, Jiexin and Abeshouse, Adam and Chakravarty, Debyani and Chatila, Walid K and Bruijn, Inode 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 Phillips, Sarah M and Sanchez-Vega, Francisco and Sander, Chris and Schultz, Nikolaus and Sumer, S. Onur and Taylor, Barry S and Zhang, Hongxin and Anur, Pavana and Peto, Myron and Spellman, Paul and Benz, Christopher and Stuart, Joshua M and Yau, Christina 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 Chuah, Eric and Dhalla, Noreen and Holt, Robert and Jones, Steven J.M and Kasaian, Katayoon and Lee, Darlene and Ma, Yussanne and Marra, Marco A and Mayo, Michael and Mungall, Andrew J and Mungall, Karen and Robertson, A. Gordon and Sipahimalani, Payal and Tam, Angela and ... and The Cancer Genome Atlas Research Network and Canc Genome Atlas Res Network
Cancer cell, ISSN 1535-6108, 04/2018, Volume 33, Issue 4, pp. 706 - 720.e9
We characterized the epigenetic landscape of genes encoding long noncoding RNAs (lncRNAs) across 6,475 tumors and 455 cancer cell lines. In stark contrast to... 
TCGA pan-cancer | MYC | CIMP | LOC284930 | long noncoding RNA | breast cancer | ENSG00000224271 | EPIC1 | P21 | Oncology | Cancer Research | Cell Biology | Life Sciences & Biomedicine | Science & Technology | Index Medicus
Journal Article
by Brennan, Cameron W and Verhaak, Roel G.W and McKenna, Aaron and Campos, Benito and Noushmehr, Houtan and Salama, Sofie R and Zheng, Siyuan and Chakravarty, Debyani and Sanborn, J. Zachary and Berman, Samuel H and Beroukhim, Rameen and Bernard, Brady and Wu, Chang-Jiun and Genovese, Giannicola and Shmulevich, Ilya and Barnholtz-Sloan, Jill and Zou, Lihua and Vegesna, Rahulsimham and Shukla, Sachet A and Ciriello, Giovanni and Yung, W.K and Zhang, Wei and Sougnez, Carrie and Mikkelsen, Tom and Aldape, Kenneth and Bigner, Darell D and Van Meir, Erwin G and Prados, Michael and Sloan, Andrew and Black, Keith L and Eschbacher, Jennifer and Finocchiaro, Gaetano and Friedman, William and Andrews, David W and Guha, Abhijit and Iacocca, Mary and O’Neill, Brian P and Foltz, Greg and Myers, Jerome and Weisenberger, Daniel J and Penny, Robert and Kucherlapati, Raju and Perou, Charles M and Hayes, D. Neil and Gibbs, Richard and Marra, Marco and Mills, Gordon B and Lander, Eric and Spellman, Paul and Wilson, Richard and Sander, Chris and Weinstein, John and Meyerson, Matthew and Gabriel, Stacey and Laird, Peter W and Haussler, David and Getz, Gad and Chin, Lynda and Benz, Christopher and Barrett, Wendi and Ostrom, Quinn and Wolinsky, Yingli and Bose, Bikash and Boulos, Paul T and Boulos, Madgy and Brown, Jenn and Czerinski, Christine and Eppley, Matthew and Kempista, Thelma and Kitko, Teresa and Koyfman, Yakov and Rabeno, Brenda and Rastogi, Pawan and Sugarman, Michael and Swanson, Patricia and Yalamanchii, Kennedy and Otey, Ilana P and Liu, Yingchun Spring and Xiao, Yonghong and Auman, J.Todd and Chen, Peng-Chieh and Hadjipanayis, Angela and Lee, Eunjung and Lee, Semin and Park, Peter J and Seidman, Jonathan and Yang, Lixing and Kalkanis, Steven and Poisson, Laila M and Raghunathan, Aditya and Scarpace, Lisa and Bressler, Ryan and Eakin, Andrea and Iype, Lisa and Kreisberg, Richard B and Leinonen, Kalle and Reynolds, Sheila and Rovira, Hector and Thorsson, Vesteinn and Annala, Matti J and ... and TCGA Research Network and TCGA Res Network
Cell (Cambridge), ISSN 0092-8674, 10/2013, Volume 155, Issue 2, pp. 462 - 477
We describe the landscape of somatic genomic alterations based on multidimensional and comprehensive characterization of more than 500 glioblastoma tumors... 
Biochemistry & Molecular Biology | Life Sciences & Biomedicine | Science & Technology | Cell Biology | Platelet-derived growth factor | RNA | Gene mutations | Analysis | Methylation | Glioblastoma multiforme | Telomerase | Index Medicus
Journal Article
by Linehan, W. Marston and Spellman, Paul T and Ricketts, Christopher J and Creighton, Chad J and Fei, Suzanne S and Davis, Caleb and Wheeler, David A and Murray, Bradley A and Schmidt, Laura and Vocke, Cathy D and Peto, Myron and Al Mamun, Abu Amar M and Shinbrot, Eve and Sethi, Anurag and Brooks, Samira and Rathmell, W. Kimryn and Brooks, Angela N and Hoadley, Katherine A and Robertson, A. Gordon and Brooks, Denise and Bowlby, Reanne and Sadeghi, Sara and Shen, Hui and Weisenberger, Daniel J and Bootwalla, Moiz and Baylin, Stephen B and Laird, Peter W and Cherniack, Andrew D and Saksena, Gordon and Haake, Scott and Li, Jun and Liang, Han and Lu, Yiling and Mills, Gordon B and Akbani, Rehan and Leiserson, Mark D.M and Raphael, Benjamin J and Anur, Pavana and Bottaro, Donald and Albiges, Laurence and Barnabas, Nandita and Choueiri, Toni K and Czerniak, Bogdan and Godwin, Andrew K and Hakimi, A. Ari and Ho, Thai H and Hsieh, James and Ittmann, Michael and Kim, William Y and Krishnan, Bhavani and Merino, Maria J and Shaw, Kenna R. Mills and Reuter, Victor E and Reznik, Ed and Shelley, Carl S and Shuch, Brian and Signoretti, Sabina and Srinivasan, Ramaprasad and Tamboli, Pheroze and Thomas, George and Tickoo, Satish and Burnett, Kenneth and Crain, Daniel and Gardner, Johanna and Lau, Kevin and Mallery, David and Morris, Scott and Paulauskis, Joseph D and Penny, Robert J and Shelton, Candace and Shelton, W. Troy and Sherman, Mark and Thompson, Eric and Yena, Peggy and Avedon, Melissa T and Bowen, Jay and Gastier-Foster, Julie M and Gerken, Mark and Leraas, Kristen M and Lichtenberg, Tara M and Ramirez, Nilsa C and Santos, Tracie and Wise, Lisa and Zmuda, Erik and Demchok, John A and Felau, Ina and Hutter, Carolyn M and Sheth, Margi and Sofia, Heidi J and Tarnuzzer, Roy and Wang, Zhining and Yang, Liming and Zenklusen, Jean C and Zhang, Jiashan and Ayala, Brenda and Baboud, Julien and Chudamani, Sudha and Liu, Jia and Lolla, Laxmi and Naresh, Rashi and ... and The Cancer Genome Atlas Research Network and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network
The New England journal of medicine, ISSN 1533-4406, 01/2016, Volume 374, Issue 2, pp. 135 - 145
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 Wong, Christopher K and Hayes, D. Neil and Parker, Joel S and Wilkerson, Matthew D and Ally, Adrian and Balasundaram, Miruna and Brooks, Denise and Chuah, Eric and Dhalla, Noreen and Lee, Darlene and Marra, Marco A 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)
Cancer cell, ISSN 1535-6108, 04/2018, Volume 33, Issue 4, pp. 690 - 705.e9
We analyzed molecular data on 2,579 tumors from The Cancer Genome Atlas (TCGA) of four gynecological types plus breast. Our aims were to identify shared and... 
omics | ovarian cancer | uterine cancer | gynecologic cancer | breast cancer | uterine carcinosarcoma | pan-gynecologic | cervical cancer | TCGA | The Cancer Genome Atlas | Oncology | Cell Biology | Cancer Research | Life Sciences & Biomedicine | Science & Technology | Index Medicus | molecular features | Pan-Gynecologic | Gynecologic cancer
Journal Article