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by Abeshouse, Adam and Ahn, Jaeil and Akbani, Rehan and Ally, Adrian and Amin, Samirkumar and Andry, Christopher D and Annala, Matti and Aprikian, Armen and Armenia, Joshua and Arora, Arshi and Auman, J. Todd and Balasundaram, Miruna and Balu, Saianand and Barbieri, Christopher E and Bauer, Thomas and Benz, Christopher C and Bergeron, Alain and Beroukhim, Rameen and Berrios, Mario and Bivol, Adrian and Bodenheimer, Tom and Boice, Lori and Bootwalla, Moiz S and Borges dos Reis, Rodolfo and Boutros, Paul C and Bowen, Jay and Bowlby, Reanne and Boyd, Jeffrey and Bradley, Robert K and Breggia, Anne and Brimo, Fadi and Bristow, Christopher A and Brooks, Denise and Broom, Bradley M and Bryce, Alan H and Bubley, Glenn and Burks, Eric and Butterfield, Yaron S.N and Button, Michael and Canes, David and Carlotti, Carlos G and Carlsen, Rebecca and Carmel, Michel and Carroll, Peter R and Carter, Scott L and Cartun, Richard and Carver, Brett S and Chan, June M and Chang, Matthew T and Chen, Yu and Cherniack, Andrew D and Chevalier, Simone and Chin, Lynda and Cho, Juok and Chu, Andy and Chuah, Eric and Chudamani, Sudha and Cibulskis, Kristian and Ciriello, Giovanni and Clarke, Amanda and Cooperberg, Matthew R and Corcoran, Niall M and Costello, Anthony J and Cowan, Janet and Crain, Daniel and Curley, Erin and David, Kerstin and Demchok, John A and Demichelis, Francesca and Dhalla, Noreen and Dhir, Rajiv and Doueik, Alexandre and Drake, Bettina and Dvinge, Heidi and Dyakova, Natalya and Felau, Ina and Ferguson, Martin L and Frazer, Scott and Freedland, Stephen and Fu, Yao and Gabriel, Stacey B and Gao, Jianjiong and Gardner, Johanna and Gastier-Foster, Julie M and Gehlenborg, Nils and Gerken, Mark and Gerstein, Mark B and Getz, Gad and Godwin, Andrew K and Gopalan, Anuradha and Graefen, Markus and Graim, Kiley and Gribbin, Thomas and Guin, Ranabir and Gupta, Manaswi and Hadjipanayis, Angela and Haider, Syed and Hamel, Lucie and Hayes, D. Neil and Heiman, David I and ... and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network
Cell, ISSN 0092-8674, 11/2015, Volume 163, Issue 4, pp. 1011 - 1025
Journal Article
BMC BIOINFORMATICS, ISSN 1471-2105, 07/2019, Volume 20, Issue 1, pp. 407 - 407
BackgroundOntologies are invaluable in the life sciences, but building and maintaining ontologies often requires a challenging number of distinct tasks such as... 
Automation | Ontology development | Reasoning | Workflows | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | Ontology release | Quality control | Import management | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | Technology application | Java (Computer program language) | Software | Mechanization | Backup software | Robots | Index Medicus
Journal Article
Bioinformatics (Oxford, England), ISSN 1367-4803, 11/2017, Volume 33, Issue 21, pp. 3502 - 3504
Motivation: The Unix 'make' program is widely used in bioinformatics pipelines, but suffers from problems that limit its application to large analysis... 
Journal Article
by Ricketts, Christopher J and De Cubas, Aguirre A and Fan, Cheng and Fan, Huihui and Smith, Christof C and Smith, Jennifer and Lang, James and Lang, Martin and Reznik, Ed and Bowlby, Reanne and Gibb, Ewan A and Akbani, Rehan and Beroukhim, Rameen and Bottaro, Donald P and Choueiri, Toni K and Gibbs, Richard A and Godwin, Andrew K and Godwin, Eryn M and Haake, Scott and Hakimi, A. Ari and Henske, Elizabeth P and Hsieh, James J and Ho, Thai and Ho, Thai H and Kanchi, Rupa S and Krishnan, Bhavani and Kwiatkowski, David J and Lui, Wembin and Merino, Maria J and Mills, Gordon B and Myers, Jerome and Nickerson, Michael L and Reuter, Victor E and Reuter, Victor and Schmidt, Laura S and Schmidt, Heather K and Shelley, C. Simon and Shelley, Carl Simon and Shen, Hui and Shuch, Brian and Signoretti, Sabina and Srinivasan, Ramaprasad and Tamboli, Pheroze and Thomas, George and Vincent, Benjamin G and Vocke, Cathy D and Wheeler, David A and Yang, Lixing and Yang, Ian and Yang, Ju Dong and Yang, Hannah and Yang, Liming and Kim, Jaegil and Kim, William Y and Robertson, A. Gordon 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, Timothy and Wang, Linghua and Wang, Jioajiao and Wang, Min and Wang, Zhining and Wang, Jing and Zenklusen, Jean C and Zhang, Hailei and Zhang, Jiashan (Julia) and Zhang, Wei and Zhang, Hongxin and Zhang, Lizhi and Zhang, Jiexin and Zhang, Hongzheng and Chudamani, Sudha and Liu, Wenbin and Liu, Jia and Liu, Yuexin and Liu, Xiuping 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 ... and Canc Genome Atlas Res Network and Cancer Genome Atlas Research Network
Cell Reports, ISSN 2211-1247, 04/2018, Volume 23, Issue 1, pp. 313 - 326.e5
Renal cell carcinoma (RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and... 
clear cell renal cell carcinoma | papillary renal cell carcinoma | chromophobe renal cell carcinoma | CDKN2A | PanCanAtlas | immune signature | chromatin remodeling | DNA hypermethylation | TCGA | GENETIC-BASIS | MESSENGER-RNA | RNA-SEQ | LANDSCAPE | SOMATIC POINT MUTATIONS | SEQUENCING DATA | CLASS DISCOVERY | EXPRESSION | KIDNEY CANCER | BREAST | CELL BIOLOGY | Index Medicus
Journal Article
by Davis, Caleb F and Ricketts, Christopher and Ricketts, Christopher J and Wang, Min and Wang, Wenyi and Wang, Qiaoyan and Wang, Zhining and Yang, Liming and Yang, Lixing and Cherniack, Andrew D and Shen, Hui and Buhay, Christian and Kang, Hyojin and Kim, Jaegil and Kim, Sang Cheol and Fahey, Catherine C and Hacker, Kathryn E and Bhanot, Gyan and Gordenin, Dmitry A and Chu, Andy and Gunaratne, Preethi H and Biehl, Michael and Seth, Sahil and Kaipparettu, Benny A and Bristow, Christopher A and Donehower, Lawrence A and Wallen, Eric M and Smith, Angela B and Tickoo, Satish K and Tamboli, Pheroze and Reuter, Victor and Schmidt, Laura S and Hsieh, James J and Choueiri, Toni K and Hakimi, A. Ari and Creighton, Chad J and Creighton, Chad J and Morgan, Margaret and Wheeler, David A and Wheeler, David A and Gibbs, Richard A and Gibbs, Richard A and Signoretti, Sabina and Robertson, A. Gordon and Robertson, A. Gordon and Henske, Elizabeth P and Henske, Elizabeth P and Kwiatkowski, David J and Kwiatkowski, David J and Linehan, W. Marston and Linehan, W. Marston and Seiler, Michael and Rathmell, W. Kimryn and Rathmell, W. Kimryn and Laird, Peter W and Laird, Peter W and Shuch, Brian and Muzny, Donna and Chao, Hsu and Dahdouli, Mike and Xi, Liu and Kakkar, Nipun and Reid, Jeffrey G and Downs, Brittany and Drummond, Jennifer and Morton, Donna and Doddapaneni, Harsha and Lewis, Lora and English, Adam and Meng, Shaowu and Meng, Qingchang and Kovar, Christie and Hale, Walker and Hawes, Alicia and Kalra, Divya and Walker, Kimberly and Murray, Bradley A and Sougnez, Carrie and Saksena, Gordon and Carter, Scott L and Schumacher, Steven E and Tabak, Barbara and Zack, Travis I and Getz, Gad and Beroukhim, Rameen and Gabriel, Stacey B and Meyerson, Matthew and Ally, Adrian and Balasundaram, Miruna and Birol, Inanc and Brooks, Denise and Butterfield, Yaron S.N and Chuah, Eric and Clarke, Amanda and Dhalla, Noreen and Guin, Ranabir and Holt, Robert A and Kasaian, Katayoon and Lee, Darlene and Lee, Eunjung and ... and Canc Genome Atlas Res Network and The Cancer Genome Atlas Research Network
Cancer Cell, ISSN 1535-6108, 09/2014, Volume 26, Issue 3, pp. 319 - 330
Journal Article
by Creighton, Chad J and Morgan, Margaret and Gunaratne, Preethi H and Wheeler, David A and Gibbs, Richard A and Robertson, Gordon and Chu, Andy and Beroukhim, Rameen and Cibulskis, Kristian and Signoretti, Sabina and Vandin, Fabio and Wu, Hsin-Ta and Raphael, Benjamin J and Verhaak, Roel G.W and Tamboli, Pheroze and Torres-Garcia, Wandaliz and Akbani, Rehan and Weinstein, John N and Reuter, Victor and Hsieh, James J and Brannon, A. Rose and Hakimi, A. Ari and Jacobsen, Anders and Ciriello, Giovanni and Reva, Boris and Ricketts, Christopher J and Linehan, W. Marston and Stuart, Joshua M and Rathmell, W. Kimryn and Hui, Shen and Laird, Peter W and Muzny, Donna and Davis, Caleb and Liu, Xi and Chang, Kyle and Kakkar, Nipun and Treviño, Lisa R and Benton, Susan and Reid, Jeffrey G and Morton, Donna and Doddapaneni, Harsha and Yi, Han and Lewis, Lora and Huyen, Dinh and Kovar, Christie and Zhu, Yiming and Santibanez, Jireh and Min, Wang and Hale, Walker and Kalra, Divya and Getz, Gad and Lawrence, Michael S and Sougnez, Carrie and Carter, Scott L and Sivachenko, Andrey and Lee, Lichtenstein and Stewart, Chip and Voet, Doug and Fisher, Sheila and Gabriel, Stacey B and Lander, Eric and Schumacher, Steve E and Tabak, Barbara and Saksena, Gordon and Onofrio, Robert C and Cherniack, Andrew D and Gentry, Jeff and Ardlie, Kristin and Meyerson, Matthew and Chun, Hye-Jung E and Mungall, Andrew J and Sipahimalani, Payal and Stoll, Dominik and Ally, Adrian and Balasundaram, Miruna and Butterfield, Yaron S.N and Carlsen, Rebecca and Carter, Candace and Chuah, Eric and Coope, Robin J.N and Dhalla, Noreen and Gorski, Sharon and Guin, Ranabir and Hirst, Carrie and Hirst, Martin and Holt, Robert A and Lebovitz, Chandra and Lee, Darlene and Li, Haiyan I and Mayo, Michael and Moore, Richard A and Pleasance, Erin and Plettner, Patrick and Schein, Jacqueline E and Shafiei, Arash and Slobodan, Jared R and Tam, Angela and Thiessen, Nina and Varhol, Richard J and Wye, Natasja and ... and Canc Genome Atlas Res Network and Anal Working Grp
Nature, ISSN 0028-0836, 2013, Volume 499, Issue 7456, pp. 43 - 49
Genetic changes underlying clear cell renal cell carcinoma(ccRCC) include alterations in genes controlling cellular oxygen sensing (for example, VHL) and the... 
Journal Article
by Andersson, Robin and Gebhard, Claudia and Miguel-Escalada, Irene and Hoof, Ilka and Bornholdt, Jette and Boyd, Mette and Chen, Yun and Zhao, Xiaobei and Schmidl, Christian and Suzuki, Takahiro and Ntini, Evgenia and Arner, Erik and Valen, Eivind and Li, Kang and Schwarzfischer, Lucia and Glatz, Dagmar and Raithel, Johanna and Lilje, Berit and Rapin, Nicolas and Bagger, Frederik Otzen and Jørgensen, Mette and Andersen, Peter Refsing and Bertin, Nicolas and Rackham, Owen and Burroughs, A. Maxwell and Baillie, J. Kenneth and Ishizu, Yuri and Shimizu, Yuri and Furuhata, Erina and Maeda, Shiori and Negishi, Yutaka and Mungall, Christopher J and Meehan, Terrence F and Lassmann, Timo and Itoh, Masayoshi and Kawaji, Hideya and Kondo, Naoto and Kawai, Jun and Lennartsson, Aneas and Daub, Carsten O and Heutink, Peter and Hume, David A and Jensen, Torben Heick and Suzuki, Harukazu and Hayashizaki, Yoshihide and Müller, Ferenc and Forrest, Alistair R. R and Carninci, Piero and Rehli, Michael and Sandelin, Albin and de Hoon, Michiel J. L and Haberle, Vanja and Kulakovskiy, Ivan V and Lizio, Marina and Mungall, Christoher J and Schmeier, Sebastian and Dimont, Emmanuel and Schmid, Christian and Schaefer, Ulf and Medvedeva, Yulia A and Plessy, Charles and Vitezic, Morana and Severin, James and Semple, Colin A and Young, Robert S and Francescatto, Margherita and Alam, Intikhab and Albanese, Davide and Altschuler, Gabriel M and Arakawa, Takahiro and Archer, John A. C and Arner, Peter and Babina, Magda and Rennie, Sarah and Balwierz, Piotr J and Beckhouse, Anthony G and Pradhan-Bhatt, Swati and Blake, Judith A and Blumenthal, Antje and Bodega, Beatrice and Bonetti, Alessano and Briggs, James and Brombacher, Frank and Califano, Anea and Cannistracti, Carlo V and Carbajo, Daniel and Chierici, Marco and Ciani, Yari and Clevers, Hans C and Dalla, Emiliano and Davis, Carrie A and Detmar, Michael and Diehl, Alexander D and Dohi, Taeko and bløs, Finn and Edge, Albert S. B and Edinger, Matthias and Ekwall, Karl and Endoh, Mitsuhiro and Enomoto, Hideki and ... and FANTOM Consortium and The FANTOM Consortium
Nature, ISSN 0028-0836, 2014, Volume 507, Issue 7493, pp. 455 - 461
Journal Article