Not logged in Tumor break load quantitates structural variant-associated genomic instability with biological and clinical relevance across cancers Lakbir, Soufyan; de Wit, Renske; de Bruijn, Ino; Kundra, Ritika; Madupuri, Ramyasree; Gao, Jianjiong; Schultz, Nikolaus; Meijer, Gerrit A.; Heringa, Jaap; Abeln, Sanne Share Save
cBioPortal for Cancer Genomics Mazor, Tali; de Bruijn, Ino; AlHamad, Rima; Chennault, Calla; Dubin, Corey; Easton-Marks, Jeremy; Fu, Zhaoyuan; Gross, Benjamin; Haynes, Charles; Higgins, David M.; Hwee, Jason; Jagannathan, Prasanna K.; Kalafati, Mirella; Kalletla, Karthik; Ko, James; Kuijpers, Tim; Kumar, Sowmiyaa; Kumari, Priti; Kundra, Ritika; Lai, Bryan; Li, Xiang; Lindsay, James; Lisman, Aaron; Lu, Qi-Xuan; Madupuri, Ramyasree; Ochoa, Angelica; Ozgul, Yusuf Z.; Plantalech, Oleguer; Pon, Matthijs N.; Satravada, Baby A.; Singh, Jessica; Sumer, Selcuk Onur; van Nierop, Pim; Vleugels, Floris; Wang, Avery; Wilson, Manda; Zhang, Hongxin; Zhao, Gaofei; Dogrusoz, Ugur; Heath, Allison; Resnick, Adam; Pugh, Trevor J.; Sander, Chris; Cerami, Ethan; Gao, Jianjiong; Schultz, Nikolaus Share Save
Quantifying the Expanding Landscape of Clinical Actionability for Patients with Cancer Suehnholz, Sarah P.; Nissan, Moriah H.; Zhang, Hongxin; Kundra, Ritika; Nandakumar, Subhiksha; Lu, Calvin; Carrero, Stephanie; Dhaneshwar, Amanda; Fernandez, Nicole; Xu, Benjamin W.; Arcila, Maria E.; Zehir, Ahmet; Syed, Aijazuddin; Brannon, A. Rose; Rudolph, Julia E.; Paraiso, Eder; Sabbatini, Paul J.; Levine, Ross L.; Dogan, Ahmet; Gao, Jianjiong; Ladanyi, Marc; Drilon, Alexander; Berger, Michael F.; Solit, David B.; Schultz, Nikolaus; Chakravarty, Debyani Share Save
Analysis and Visualization of Longitudinal Genomic and Clinical Data from the AACR Project GENIE Biopharma Collaborative in cBioPortal de Bruijn, Ino; Kundra, Ritika; Mastrogiacomo, Brooke; Tran, Thinh Ngoc; Sikina, Luke; Mazor, Tali; Li, Xiang; Ochoa, Angelica; Zhao, Gaofei; Lai, Bryan; Abeshouse, Adam; Baiceanu, Diana; Ciftci, Ersin; Dogrusoz, Ugur; Dufilie, Andrew; Erkoc, Ziya; Lara, Elena Garcia; Fu, Zhaoyuan; Gross, Benjamin; Haynes, Charles; Heath, Allison; Higgins, David; Jagannathan, Prasanna; Kalletla, Karthik; Kumari, Priti; Lindsay, James; Lisman, Aaron; Leenknegt, Bas; Lukasse, Pieter; Madela, Divya; Madupuri, Ramyasree; van Nierop, Pim; Plantalech, Oleguer; Quach, Joyce; Resnick, Adam C.; Rodenburg, Sander Y. A.; Satravada, Baby A.; Schaeffer, Fedde; Sheridan, Robert; Singh, Jessica; Sirohi, Rajat; Sumer, Selcuk Onur; van Hagen, Sjoerd; Wang, Avery; Wilson, Manda; Zhang, Hongxin; Zhu, Kelsey; Rusk, Nicole; Brown, Samantha; Lavery, Jessica A.; Panageas, Katherine S.; Rudolph, Julia E.; LeNoue-Newton, Michele L.; Warner, Jeremy L.; Guo, Xindi; Hunter-Zinck, Haley; Yu, Thomas V.; Pilai, Shirin; Nichols, Chelsea; Gardos, Stuart M.; Philip, John; Kehl, Kenneth L.; Riely, Gregory J.; Schrag, Deborah; Lee, Jocelyn; Fiandalo, Michael V.; Sweeney, Shawn M.; Pugh, Trevor J.; Sander, Chris; Cerami, Ethan; Gao, Jianjiong; Schultz, Nikolaus Share Save
cBioPortal for Cancer Genomics de Bruijn, Ino; Mazor, Tali; Abeshouse, Adam; Baiceanu, Diana; Carrero, Stephanie; Lara, Elena Garcia; Gross, Benjamin; Higgins, David M.; Jagannathan, Prasanna K.; Kumari, Priti; Kundra, Ritika; Lai, Bryan; Li, Xiang; Lindsay, James; Lisman, Aaron; Madala, Divya; Madupuri, Ramyasree; Ochoa, Angelica; Ozgul, Yusuf Ziya; Plantalech, Oleguer; Rodenburg, Sander; Satravada, Baby Anusha; Sheridan, Robert; Sikina, Lucas; Singh, Jessica; Sumer, S. Onur; Sun, Yichao; van Nierop, Pim; Wang, Avery; Wilson, Manda; Zhang, Hongxin; Zhao, Gaofei; van Hagen, Sjoerd; Dogrusoz, Ugur; Heath, Allison; Resnick, Adam; Pugh, Trevor J.; Sander, Chris; Cerami, Ethan; Gao, Jianjiong; Schultz, Nikolaus Share Save
Multimodal integration of radiology, pathology and genomics for prediction of response to PD-(L)1 blockade in patients with non-small cell lung cancer Vanguri, Rami S.; Luo, Jia; Aukerman, Andrew T.; Egger, Jacklynn, V; Fong, Christopher J.; Horvat, Natally; Pagano, Andrew; Araujo-Filho, Jose De Arimateia Batista; Geneslaw, Luke; Rizvi, Hira; Sosa, Ramon; Boehm, Kevin M.; Yang, Soo-Ryum; Bodd, Francis M.; Ventura, Katia; Hollmann, Travis J.; Ginsberg, Michelle S.; Gao, Jianjiong; Hellmann, Matthew D.; Sauter, Jennifer L.; Shah, Sohrab P. Share Save
Multimodal data integration using machine learning improves risk stratification of high-grade serous ovarian cancer Boehm, Kevin M.; Aherne, Emily A.; Ellenson, Lora; Nikolovski, Ines; Alghamdi, Mohammed; Vazquez-Garcia, Ignacio; Zamarin, Dmitriy; Roche, Kara Long; Liu, Ying; Patel, Druv; Aukerman, Andrew; Pasha, Arfath; Rose, Doori; Selenica, Pier; Causa Andrieu, Pamela I.; Fong, Chris; Capanu, Marinela; Reis-Filho, Jorge S.; Vanguri, Rami; Veeraraghavan, Harini; Gangai, Natalie; Sosa, Ramon; Leung, Samantha; McPherson, Andrew; Gao, JianJiong; Lakhman, Yulia; Shah, Sohrab P. Share Save
Genome Nexus: A Comprehensive Resource for the Annotation and Interpretation of Genomic Variants in Cancer de Bruijn, Ino; Li, Xiang; Sumer, Selcuk Onur; Gross, Benjamin; Sheridan, Robert; Ochoa, Angelica; Wilson, Manda; Wang, Avery; Zhang, Hongxin; Lisman, Aaron; Abeshouse, Adam; Zhang, Emily; Thum, Alice; Sadagopan, Ananthan; Heins, Zachary; Kandoth, Cyriac; Rodenburg, Sander; Tan, Sander; Lukasse, Pieter; van Hagen, Sjoerd; Fijneman, Remond J. A.; Meijer, Gerrit A.; Schultz, Nikolaus; Gao, Jianjiong Share Save
Semisupervised Training of a Brain MRI Tumor Detection Model Using Mined Annotations Swinburne, Nathaniel C.; Yadav, Vivek; Kim, Julie; Choi, Ye R.; Gutman, David C.; Yang, Jonathan T.; Moss, Nelson; Stone, Jacqueline; Tisnado, Jamie; Hatzoglou, Vaios; Haque, Sofia S.; Karimi, Sasan; Lyo, John; Juluru, Krishna; Pichotta, Karl; Gao, Jianjiong; Shah, Sohrab P.; Holodny, Andrei, I; Young, Robert J. Share Save
OncoTree: A Cancer Classification System for Precision Oncology Kundra, Ritika; Zhang, Hongxin; Sheridan, Robert; Sirintrapun, Sahussapont Joseph; Wang, Avery; Ochoa, Angelica; Wilson, Manda; Gross, Benjamin; Sun, Yichao; Madupuri, Ramyasree; Satravada, Baby A.; Reales, Dalicia; Vakiani, Efsevia; Al-Ahmadie, Hikmat A.; Dogan, Ahmet; Arcila, Maria; Zehir, Ahmet; Maron, Steven; Berger, Michael F.; Viaplana, Cristina; Janeway, Katherine; Ducar, Matthew; Sholl, Lynette; Dogan, Snjezana; Bedard, Philippe; Surrey, Lea F.; Sanchez, Iker Huerga; Syed, Aijaz; Rema, Anoop Balakrishnan; Chakravarty, Debyani; Suehnholz, Sarah; Nissan, Moriah; Iyer, Gopakumar, V; Murali, Rajmohan; Bouvier, Nancy; Soslow, Robert A.; Hyman, David; Younes, Anas; Intlekofer, Andrew; Harding, James J.; Carvajal, Richard D.; Sabbatini, Paul J.; Abou-Alfa, Ghassan K.; Morris, Luc; Janjigian, Yelena Y.; Gallagher, Meighan M.; Soumerai, Tara A.; Mellinghoff, Ingo K.; Hakimi, Abraham A.; Fury, Matthew; Huse, Jason T.; Bagrodia, Aditya; Hameed, Meera; Thomas, Stacy; Gardos, Stuart; Cerami, Ethan; Mazor, Tali; Kumari, Priti; Raman, Pichai; Shivdasani, Priyanka; MacFarland, Suzanne; Newman, Scott; Waanders, Angela; Gao, Jianjiong; Solit, David; Schultz, Nikolaus Share Save
The context-specific role of germline pathogenicity in tumorigenesis Srinivasan, Preethi; Bandlamudi, Chaitanya; Jonsson, Philip; Kemel, Yelena; Chavan, Shweta S.; Richards, Allison L.; Penson, Alexander, V; Bielski, Craig M.; Fong, Christopher; Syed, Aijazuddin; Jayakumaran, Gowtham; Prasad, Meera; Hwee, Jason; Sumer, Selcuk Onur; de Bruijn, Ino; Li, Xiang; Gao, JianJiong; Schultz, Nikolaus; Cambria, Roy; Galle, Jesse; Mukherjee, Semanti; Vijai, Joseph; Cadoo, Karen A.; Carlo, Maria, I; Walsh, Michael F.; Mandelker, Diana; Ceyhan-Birsoy, Ozge; Shia, Jinru; Zehir, Ahmet; Ladanyi, Marc; Hyman, David M.; Zhang, Liying; Offit, Kenneth; Robson, Mark E.; Solit, David B.; Stadler, Zsofia K.; Berger, Michael F.; Taylor, Barry S. Share Save
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Multiomic Integration of Public Oncology Databases in Bioconductor Ramos, Marcel; Geistlinger, Ludwig; Oh, Sehyun; Schiffer, Lucas; Azhar, Rimsha; Kodali, Hanish; de Bruijn, Ino; Gao, Jianjiong; Carey, Vincent J.; Morgan, Martin; Waldron, Levi Share Save
Leveraging Systematic Functional Analysis to Benchmark an In Silico Framework Distinguishes Driver from Passenger MEK Mutants in Cancer Hanrahan, Aphrothiti J.; Sylvester, Brooke E.; Chang, Matthew T.; Elzein, Arijh; Gao, Jianjiong; Han, Weiwei; Liu, Ye; Xu, Dong; Gao, Sizhi P.; Gorelick, Alexander N.; Jones, Alexis M.; Kiliti, Amber J.; Nissan, Moriah H.; Nimura, Clare A.; Poteshman, Abigail N.; Yao, Zhan; Gao, Yijun; Hu, Wenhuo; Wise, Hannah C.; Gavrila, Elena, I; Shoushtari, Alexander N.; Tiwari, Shakuntala; Viale, Agnes; Abdel-Wahab, Omar; Merghoub, Taha; Berger, Michael F.; Rosen, Neal; Taylor, Barry S.; Solit, David B. Share Save
Integrative analysis of clinical and genomic information identifies predictive markers of metastatic risk Fong, Christopher J.; Sanchez-Vega, Francisco; Bastien Ngyuen; Luthra, Anisha; Nandakumar, Subhiksha; Walch, Henry; Chatila, Walid; Rajanna, Arjun; Zehir, Ahmet; Berger, Michael; Gao, Jianjiong; Schultz, Nikolaus Share Save
OncoKB, a precision oncology knowledgebase Suehnholz, Sarah; Zhang, Hongxin; Nissan, Moriah; Kundra, Ritika; Su, Jing; LaFave, Lindsay; Gala, Kinisha; Vanderbilt, Chad; Arcila, Maria; Ladanyi, Marc; Berger, Michael; Zehir, Ahmet; Rudolph, Julia E.; Sabbatini, Paul; Levine, Ross; Dogan, Ahmet; Gao, Jianjiong; Solit, David B.; Schultz, Nikolaus; Chakravarty, Debyani Share Save
The cBioPortal for Cancer Genomics Gao, Jianjiong; Mazor, Tali; Abeshouse, Adam; de Bruijn, Ino; Gross, Benjamin; Kalletla, Karthik; Kumari, Priti; Kundra, Ritika; Li, Xiang; Lindsay, James; Lisman, Aaron; Lukasse, Pieter; Madupuri, Ramyasree; Ochoa, Angelica; Plantalech, Oleguer; Rodenburg, Sander; Schaeffer, Fedde; Sheridan, Robert; Sikina, Lucas; Su, Jing; Sumer, S. Onur; Sun, Yichao; van Dijk, Paul; van Hagen, Sjoerd; van Nierop, Pim; Wang, Avery; Wilson, Manda; Zhang, Hongxin; Zhao, Gaofei; Zhu, Kelsey; van Bochove, Kees; Dogrusoz, Ugur; Heath, Allison; Resnick, Adam; Pugh, Trevor J.; Sander, Chris; Cerami, Ethan; Schultz, Nikolaus Share Save
Modeling biological and genetic diversity in upper tract urothelial carcinoma with patient derived xenografts Kim, Kwanghee; Hu, Wenhuo; Audenet, Francois; Almassi, Nima; Hanrahan, Aphrothiti J.; Murray, Katie; Bagrodia, Aditya; Wong, Nathan; Clinton, Timothy N.; Dason, Shawn; Mohan, Vishnu; Jebiwott, Sylvia; Nagar, Karan; Gao, Jianjiong; Penson, Alex; Hughes, Chris; Gordon, Benjamin; Chen, Ziyu; Dong, Yiyu; Watson, Philip A.; Alvim, Ricardo; Elzein, Arijh; Gao, Sizhi P.; Cocco, Emiliano; Santin, Alessandro D.; Ostrovnaya, Irina; Hsieh, James J.; Sagi, Irit; Pietzak, Eugene J.; Hakimi, A. Ari; Rosenberg, Jonathan E.; Iyer, Gopa; Vargas, Herbert A.; Scaltriti, Maurizio; Al-Ahmadie, Hikmat; Solit, David B.; Coleman, Jonathan A. 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
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