Not logged in Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets Ellrot, Kyle; Wong, Christopher K.; Yau, Christina; Castro, Mauro A. A.; Lee, Jordan A.; Karlberg, Brian J.; Grewal, Jasleen K.; Lagani, Vincenzo; Tercan, Bahar; Friedl, Verena; Hinoue, Toshinori; Uzunangelov, Vladislav; Westlake, Lindsay; Loinaz, Xavier; Felau, Ina; Wang, Peggy I.; Kemal, Anab; Caesar-Johnson, Samantha J.; Shmulevich, Ilya; Lazar, Alexander J.; Tsamardinos, Ioannis; Hoadley, Katherine A.; Robertson, A. Gordon; Knijnenburg, Theo A.; Benz, Christopher C.; Stuart, Joshua M.; Zenklusen, Jean C.; Cherniack, Andrew D.; Laird, Peter W. Share Save
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Leveraging compact feature sets for TCGA-based molecular subtype classification on new samples Ellrott, Kyle; Wong, Chris K.; Yau, Christina; Castro, Mauro A.; Lee, Jordan; Karlberg, Brian; Grewal, Jasleen K.; Lagani, Vincenzo; Tercan, Bahar; Friedl, Verena; Hinoue, Toshinori; Uzunangelov, Vladislav; Westlake, Lindsay; Loinaz, Xavier; Felau, Ina; Wang, Peggy; Kemal, Anab; Caesar-Johnson, Samantha J.; Shmulevich, Ilya; Lazar, Alexander J.; Tsamardinos, Ioannis; Hoadley, Katherine A.; Robertson, Gordon A.; Knijnenburg, Theo A.; Benz, Christopher C.; Stuart, Joshua M.; Zenklusen, Jean C.; Cherniack, Andrew D.; Laird, Peter W. Share Save
An integrated data platform to support the international alliance for cancer early detection Walsh, Brian; Beckman, Liam; Burchett, J. D.; Peterkort, Matthew; Lee, Jordan; Fitzsimons, Michael; Vassilatos, Peter; Bajracharya, Binam; Barnes, Craig; Qureshi, Jawad; Grossman, Robert; Yakura, Carrie; Lu, Yaozhi; Burge, Sarah; Kelberman, Daniel; Watson, Erin; Ellrott, Kyle Share Save
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Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis Visualization, and Informatics Lab-space Schatz, Michael C.; Philippakis, Anthony A.; Afgan, Enis; Banks, Eric; Carey, Vincent J.; Carroll, Robert J.; Culotti, Alessandro; Ellrott, Kyle; Goecks, Jeremy; Grossman, Robert L.; Hall, Ira M.; Hansen, Kasper D.; Lawson, Jonathan; Leek, Jeffrey T.; Luria, Anne O'Donnell; Mosher, Stephen; Morgan, Martin; Nekrutenko, Anton; O'Connor, Brian D.; Osborn, Kevin; Paten, Benedict; Patterson, Candace; Tan, Frederick J.; Taylor, Casey Overby; Vessio, Jennifer; Waldron, Levi; Wang, Ting; Wuichet, Kristin Share Save
GA4GH: International policies and standards for data sharing across genomic research and healthcare Rehm, Heidi L.; Page, Angela J. H.; Smith, Lindsay; Adams, Jeremy B.; Alterovitz, Gil; Babb, Lawrence J.; Barkley, Maxmillian P.; Baudis, Michael; Beauvais, Michael J. S.; Beck, Tim; Beckmann, Jacques S.; Beltran, Sergi; Bernick, David; Bernier, Alexander; Bonfield, James K.; Boughtwood, Tiffany F.; Bourque, Guillaume; Bowers, Sarion R.; Brookes, Anthony J.; Brudno, Michael; Brush, Matthew H.; Bujold, David; Burdett, Tony; Buske, Orion J.; Cabili, Moran N.; Cameron, Daniel L.; Carroll, Robert J.; Casas-Silva, Esmeralda; Chakravarty, Debyani; Chaudhari, Bimal P.; Chen, Shu Hui; Cherry, J. Michael; Chung, Justina; Cline, Melissa; Clissold, Hayley L.; Cook-Deegan, Robert M.; Courtot, Melanie; Cunningham, Fiona; Cupak, Miro; Davies, Robert M.; Denisko, Danielle; Doerr, Megan J.; Dolman, Lena I.; Dove, Edward S.; Dursi, L. Jonathan; Dyke, Stephanie O. M.; Eddy, James A.; Eilbeck, Karen; Ellrott, Kyle P.; Fairley, Susan; Fakhro, Khalid A.; Firth, Helen V.; Fitzsimons, Michael S.; Fiume, Marc; Flicek, Paul; Fore, Ian M.; Freeberg, Mallory A.; Freimuth, Robert R.; Fromont, Lauren A.; Fuerth, Jonathan; Gaff, Clara L.; Gan, Weiniu; Ghanaim, Elena M.; Glazer, David; Green, Robert C.; Griffith, Malachi; Griffith, Obi L.; Grossman, Robert L.; Groza, Tudor; Auvil, Jaime M. Guidry; Guigo, Roderic; Gupta, Dipayan; Haendel, Melissa A.; Hamosh, Ada; Hansen, David P.; Hart, Reece K.; Hartley, Dean Mitchell; Haussler, David; Hendricks-Sturrup, Rachele M.; Ho, Calvin W. L.; Hobb, Ashley E.; Hoffman, Michael M.; Hofmann, Oliver M.; Holub, Petr; Hsu, Jacob Shujui; Hubaux, Jean-Pierre; Hunt, Sarah E.; Husami, Ammar; Jacobsen, Julius O.; Jamuar, Saumya S.; Janes, Elizabeth L.; Jeanson, Francis; Jene, Aina; Johns, Amber L.; Joly, Yann; Jones, Steven J. M.; Kanitz, Alexander; Kato, Kazuto; Keane, Thomas M.; Kekesi-Lafrance, Kristina; Kelleher, Jerome; Kerry, Giselle; Khor, Seik-Soon; Knoppers, Bartha M.; Konopko, Melissa A.; Kosaki, Kenjiro; Kuba, Martin; Lawson, Jonathan; Leinonen, Rasko; Li, Stephanie; Lin, Michael F.; Linden, Mikael; Liu, Xianglin; Liyanage, Isuru Udara; Lopez, Javier; Lucassen, Anneke M.; Lukowski, Michael; Mann, Alice L.; Marshall, John; Mattioni, Michele; Metke-Jimenez, Alejandro; Middleton, Anna; Milne, Richard J.; Molnar-Gabor, Fruzsina; Mulder, Nicola; Munoz-Torres, Monica C.; Nag, Rishi; Nakagawa, Hidewaki; Nasir, Jamal; Navarro, Arcadi; Nelson, Tristan H.; Niewielska, Ania; Nisselle, Amy; Niu, Jeffrey; Nyronen, Tommi H.; O'Connor, Brian D.; Oesterle, Sabine; Ogishima, Soichi; Wang, Vivian Ota; Paglione, Laura A. D.; Palumbo, Emilio; Parkinson, Helen E.; Philippakis, Anthony A.; Pizarro, Angel D.; Prlic, Andreas; Rambla, Jordi; Rendon, Augusto; Rider, Renee A.; Robinson, Peter N.; Rodarmer, Kurt W.; Rodriguez, Laura Lyman; Rubin, Alan F.; Rueda, Manuel; Rushton, Gregory A.; Ryan, Rosalyn S.; Saunders, Gary I.; Schuilenburg, Helen; Schwede, Torsten; Scollen, Serena; Senf, Alexander; Sheffield, Nathan C.; Skantharajah, Neerjah; Smith, Albert V.; Sofia, Heidi J.; Spalding, Dylan; Spurdle, Amanda B.; Stark, Zornitza; Stein, Lincoln D.; Suematsu, Makoto; Tan, Patrick; Tedds, Jonathan A.; Thomson, Alastair A.; Thorogood, Adrian; Tickle, Timothy L.; Tokunaga, Katsushi; Tomroos, Juha; Torrents, David; Upchurch, Sean; Valencia, Alfonso; Guimera, Roman Valls; Vamathevan, Jessica; Varma, Susheel; Vears, Danya F.; Viner, Coby; Voisin, Craig; Wagner, Alex H.; Wallace, Susan E.; Walsh, Brian P.; Williams, Marc S.; Winkler, Eva C.; Wold, Barbara J.; Wood, Grant M.; Woolley, J. Patrick; Yamasaki, Chisato; Yates, Andrew D.; Yung, Christina K.; Zass, Lyndon J.; Zaytseva, Ksenia; Zhang, Junjun; Goodhand, Peter; North, Kathryn; Birney, Ewan Share Save
A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery Creason, Allison; Haan, David; Dang, Kristen; Chiotti, Kami E.; Inkman, Matthew; Lamb, Andrew; Yu, Thomas; Hu, Yin; Norman, Thea C.; Buchanan, Alex; van Baren, Marijke J.; Spangler, Ryan; Rollins, M. Rick; Spellman, Paul T.; Rozanov, Dmitri; Zhang, Jin; Maher, Christopher A.; Caloian, Cristian; Watson, John D.; Uhrig, Sebastian; Haas, Brian J.; Jain, Miten; Akeson, Mark; Ahsen, Mehmet Eren; Stolovitzky, Gustavo; Guinney, Justin; Boutros, Paul C.; Stuart, Joshua M.; Ellrott, Kyle Share Save
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Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples Bailey, Matthew H.; Meyerson, William U.; Dursi, Lewis Jonathan; Wang, Liang-Bo; Dong, Guanlan; Liang, Wen-Wei; Weerasinghe, Amila; Li, Shantao; Li, Yize; Kelso, Sean; Saksena, Gordon; Ellrott, Kyle; Wendl, Michael C.; Wheeler, David A.; Getz, Gad; Simpson, Jared T.; Gerstein, Mark B.; Ding, Li Share Save
A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer Wagner, Alex H.; Walsh, Brian; Mayfield, Georgia; Tamborero, David; Sonkin, Dmitriy; Krysiak, Kilannin; Deu-Pons, Jordi; Duren, Ryan P.; Gao, Jianjiong; McMurry, Julie; Patterson, Sara; Fitz, Catherine; Pitel, Beth A.; Sezerman, Ozman U.; Ellrott, Kyle; Warner, Jeremy L.; Rieke, Damian T.; Aittokallio, Tero; Cerami, Ethan; Ritter, Deborah I.; Schriml, Lynn M.; Freimuth, Robert R.; Haendel, Melissa; Raca, Gordana; Madhavan, Subha; Baudis, Michael; Beckmann, Jacques S.; Dienstmann, Rodrigo; Chakravarty, Debyani; Li, Xuan Shirley; Mockus, Susan; Elemento, Olivier; Schultz, Nikolaus; Lopez-Bigas, Nuria; Lawler, Mark; Goecks, Jeremy; Griffith, Malachi; Griffith, Obi L.; Margolin, Adam A. Share Save
Butler enables rapid cloud-based analysis of thousands of human genomes (vol 79, pg 134, 2019) Yakneen, Sergei; Waszak, Sebastian M.; Gertz, Michael; Korbel, Jan O.; Aminou, Brice; Bartolome, Javier; Boroevich, Keith A.; Boyce, Rich; Brooks, Angela N.; Buchanan, Alex; Buchhalter, Ivo; Butler, Adam P.; Byrne, Niall J.; Cafferkey, Andy; Campbell, Peter J.; Chen, Zhaohong; Cho, Sunghoon; Choi, Wan; Clapham, Peter; Davis-Dusenbery, Brandi N.; De La Vega, Francisco M.; Demeulemeester, Jonas; Dow, Michelle T.; Dursi, Lewis Jonathan; Eils, Juergen; Eils, Roland; Ellrott, Kyle; Farcas, Claudiu; Favero, Francesco; Fayzullaev, Nodirjon; Ferretti, Vincent; Flicek, Paul; Fonseca, Nuno A.; Gelpi, Josep Ll.; Getz, Gad; Gibson, Bob; Grossman, Robert L.; Harismendy, Olivier; Heath, Allison P.; Heinold, Michael C.; Hess, Julian M.; Hofmann, Oliver; Hong, Jongwhi H.; Hudson, Thomas J.; Hutter, Barbara; Hutter, Carolyn M.; Hubschmann, Daniel; Imoto, Seiya; Ivkovic, Sinisa; Jeon, Seung-Hyup; Jiao, Wei; Jung, Jongsun; Kabbe, Rolf; Kahles, Andre; Kerssemakers, Jules N. A.; Kim, Hyung-Lae; Kim, Hyunghwan; Kim, Jihoon; Kim, Youngwook; Kleinheinz, Kortine; Koscher, Michael; Koures, Antonios; Kovacevic, Milena; Lawerenz, Chris; Leshchiner, Ignaty; Liu, Jia; Livitz, Dimitri; Mihaiescu, George L.; Mijalkovic, Sanja; Lazic, Ana Mijalkovic; Miyano, Satoru; Miyoshi, Naoki; Nahal-Bose, Hardeep K.; Nakagawa, Hidewaki; Nastic, Mia; Newhouse, Steven J.; Nicholson, Jonathan; O'Connor, Brian D.; Ocana, David; Ohi, Kazuhiro; Ohno-Machado, Lucila; Omberg, Larsson; Ouellette, B. F. Francis; Paramasivam, Nagarajan; Perry, Marc D.; Pihl, Todd D.; Prinz, Manuel; Puiggros, Montserrat; Radovic, Petar; Raine, Keiran M.; Rheinbay, Esther; Rosenberg, Mara; Royo, Romina; Ratsch, Gunnar; Saksena, Gordon; Schlesner, Matthias; Shorser, Solomon I.; Short, Charles; Sofia, Heidi J.; Spring, Jonathan; Stein, Lincoln D.; Struck, Adam J.; Tiao, Grace; Tijanic, Nebojsa; Torrents, David; Van Loo, Peter; Vazquez, Miguel; Vicente, David; Wala, Jeremiah A.; Wang, Zhining; Waszak, Sebastian M.; Weischenfeldt, Joachim; Werner, Johannes; Williams, Ashley; Woo, Youngchoon; Wright, Adam J.; Xiang, Qian; Yang, Liming; Yuen, Denis; Yung, Christina K.; Zhang, Junjun; Korbel, Jan O. Share Save
A community effort to create standards for evaluating tumor subclonal reconstruction Salcedo, Adriana; Tarabichi, Maxime; Espiritu, Shadrielle Melijah G.; Deshwar, Amit G.; David, Matei; Wilson, Nathan M.; Dentro, Stefan; Wintersinger, Jeff A.; Liu, Lydia Y.; Ko, Minjeong; Sivanandan, Srinivasan; Zhang, Hongjiu; Zhu, Kaiyi; Ou Yang, Tai-Hsien; Chilton, John M.; Buchanan, Alex; Lalansingh, Christopher M.; P'ng, Christine; Anghel, Catalina V.; Umar, Imaad; Lo, Bryan; Zou, William; Simpson, Jared T.; Stuart, Joshua M.; Anastassiou, Dimitris; Guan, Yuanfang; Ewing, Adam D.; Ellrott, Kyle; Wedge, David C.; Morris, Quaid; Van Loo, Peter; Boutros, Paul C.; Jha, Alokkumar; Huang, Tanxiao; Yang, Tsun-Po; Peifer, Martin; Sahinalp, Cenk; Malikic, Salem; Vazquez-Garcia, Ignacio; Mustonen, Ville; Yang, Hsih-Te; Lee, Ken-Ray; Ji, Yuan; Sengupta, Subhajit; Rudewicz, Justine; Nikolski, Macha; Schaeverbeke, Quentin; Yuan, Ke; Markowetz, Florian; Macintyre, Geoff; Cmero, Marek; Chaudhary, Belal; Leshchiner, Ignaty; Livitz, Dimitri; Getz, Gad; Loher, Phillipe; Yu, Kaixian; Wang, Wenyi; Zhu, Hongtu Share Save
Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges Ellrott, Kyle; Buchanan, Alex; Creason, Allison; Mason, Michael; Schaffter, Thomas; Hoff, Bruce; Eddy, James; Chilton, John M.; Yu, Thomas; Stuart, Joshua M.; Saez-Rodriguez, Julio; Stolovitzky, Gustavo; Boutros, Paul C.; Guinney, Justin Share Save
Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection Lee, Anna Y.; Ewing, Adam D.; Ellrott, Kyle; Hu, Yin; Houlahan, Kathleen E.; Bare, J. Christopher; Espiritu, Shadrielle Melijah G.; Huang, Vincent; Dang, Kristen; Chong, Zechen; Caloian, Cristian; Yamaguchi, Takafumi N.; Kellen, Michael R.; Chen, Ken; Norman, Thea C.; Friend, Stephen H.; Guinney, Justin; Stolovitzky, Gustavo; Haussler, David; Margolin, Adam A.; Stuart, Joshua M.; Boutros, Paul C. Share Save
Multi-Center Mutation Calling in Multiple Cancers: The MC3 Project Ellrott, Kyle; Bailey, Mathew; Saksena, Gordon; Covington, Kyle; Kandoth, Cyriac; Stewart, Chip; McLellan, Michael; Sofia, Heidi; Hutter, Carolyn; Getz, Gad; Wheeler, David; Ding, Li Share Save
SMMART: Serial measurements of molecular and architectural responses to therapy Johnson, Brett; Keck, Jamie; Morris, Max; Siex, Kiara; Kolodzie, Annette; Parmar, Swapnil; Riesterer, Jessica; Chin, Koei; Gibbs, Summer; Heiser, Laura; Spellman, Paul; Ellrott, Kyle; Babur, Ozgun; Demir, Emek; Margolin, Adam; Goecks, Jeremy; Coussens, Lisa; Bergan, Raymond; Gray, Joe Share Save
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