Not logged in Proteomics and personalized PDX models identify treatment for a progressive malignancy within an actionable timeframe Barnabas, Georgina D.; Bhat, Tariq A.; Goebeler, Verena; Leclair, Pascal; Azzam, Nadine; Melong, Nicole; Anderson, Colleen; Gom, Alexis; An, Seohee; Ergin, Enes K.; Shen, Yaoqing; Conrrero, Agustina; Mungall, Andrew J.; Mungall, Karen L.; Maxwell, Christopher A.; Reid, Gregor S. D.; Hirst, Martin; Jones, Steven; Chan, Jennifer A.; Senger, Donna L.; Berman, Jason N.; Parker, Seth J.; Bush, Jonathan W.; Strahlendorf, Caron; Deyell, Rebecca J.; Lim, C. James; Lange, Philipp F. Share Save
Long-read sequencing of an advanced cancer cohort resolves rearrangements, unravels haplotypes, and reveals methylation landscapes O'Neill, Kieran; Pleasance, Erin; Fan, Jeremy; Akbari, Vahid; Chang, Glenn; Dixon, Katherine; Csizmok, Veronika; MacLennan, Signe; Porter, Vanessa; Galbraith, Andrew; Grisdale, Cameron J.; Culibrk, Luka; Dupuis, John H.; Corbett, Richard; Hopkins, James; Bowlby, Reanne; Pandoh, Pawan; Smailus, Duane E.; Cheng, Dean; Wong, Tina; Frey, Connor; Shen, Yaoqing; Lewis, Eleanor; Paulin, Luis F.; Sedlazeck, Fritz J.; Nelson, Jessica M. T.; Chuah, Eric; Mungall, Karen L.; Moore, Richard A.; Coope, Robin; Mungall, Andrew J.; McConechy, Melissa K.; Williamson, Laura M.; Schrader, Kasmintan A.; Yip, Stephen; Marra, Marco A.; Laskin, Janessa; Jones, Steven J. M. Share Save
Enhancing clinical genomic accuracy with panelGC: a novel metric and tool for quantifying and monitoring GC biases in hybridization capture panel sequencing Cheng, Xuanjin; Goktas, Murathan T.; Williamson, Laura M.; Krzywinski, Martin; Mulder, David T.; Swanson, Lucas; Slind, Jill; Sihvonen, Jelena; Chow, Cynthia R.; Carr, Amy; Bosdet, Ian; Tucker, Tracy; Young, Sean; Moore, Richard; Mungall, Karen L.; Yip, Stephen; Jones, Steven J. M. Share Save
Defining the heterogeneity of unbalanced structural variation underlying breast cancer susceptibility by nanopore genome sequencing Dixon, Katherine; Shen, Yaoqing; O'Neill, Kieran; Mungall, Karen L. L.; Chan, Simon; Bilobram, Steve; Zhang, Wei; Bezeau, Marjorie; Sharma, Alshanee; Fok, Alexandra; Mungall, Andrew J. J.; Moore, Richard; Bosdet, Ian; Thibodeau, My Linh; Sun, Sophie; Yip, Stephen; Schrader, Kasmintan A. A.; Jones, Steven J. M. Share Save
Long-read genome sequencing informs the molecular etiology of imprinting disorders Dixon, Katherine; Shen, Yaoqing; Chin, Hui-Lin; Gazzaz, Nour; Huynh, Stephanie; Chan, Simon; Zhang, Cathy; Culibrk, Luka; O'Neill, Kieran; Mungall, Karen; Mungall, Andrew; Moore, Richard; Gibson, William; Chanoine, Jean-Pierre; Boerkoel, Cornelius; Jones, Steven Share Save
Proteotranscriptomic classification and characterization of pancreatic neuroendocrine neoplasms Yang, Kevin C.; Kalloger, Steve E.; Aird, John J.; Lee, Michael K. C.; Rushton, Christopher; Mungall, Karen L.; Mungall, Andrew J.; Gao, Dongxia; Chow, Christine; Xu, Jing; Karasinska, Joanna M.; Colborne, Shane; Jones, Steven J. M.; Schrader, Joerg; Morin, Ryan D.; Loree, Jonathan M.; Marra, Marco A.; Renouf, Daniel J.; Morin, Gregg B.; Schaeffer, David F.; Gorski, Sharon M. Share Save
A clinical transcriptome approach to patient stratification and therapy selection in acute myeloid leukemia Docking, T. Roderick; Parker, Jeremy D. K.; Jadersten, Martin; Duns, Gerben; Chang, Linda; Jiang, Jihong; Pilsworth, Jessica A.; Swanson, Lucas A.; Chan, Simon K.; Chiu, Readman; Nip, Ka Ming; Mar, Samantha; Mo, Angela; Wang, Xuan; Martinez-Hoyer, Sergio; Stubbins, Ryan J.; Mungall, Karen L.; Mungall, Andrew J.; Moore, Richard A.; Jones, Steven J. M.; Birol, Inanc; Marra, Marco A.; Hogge, Donna; Karsan, Aly Share Save
The transcriptional landscape of Shh medulloblastoma Skowron, Patryk; Farooq, Hamza; Cavalli, Florence M. G.; Morrissy, A. Sorana; Ly, Michelle; Hendrikse, Liam D.; Wang, Evan Y.; Djambazian, Haig; Zhu, Helen; Mungall, Karen L.; Trinh, Quang M.; Zheng, Tina; Dai, Shizhong; Stucklin, Ana S. Guerreiro; Vladoiu, Maria C.; Fong, Vernon; Holgado, Borja L.; Nor, Carolina; Wu, Xiaochong; Abd-Rabbo, Diala; Berube, Pierre; Wang, Yu Chang; Luu, Betty; Suarez, Raul A.; Rastan, Avesta; Gillmor, Aaron H.; Lee, John J. Y.; Zhang, Xiao Yun; Daniels, Craig; Dirks, Peter; Malkin, David; Bouffet, Eric; Tabori, Uri; Loukides, James; Doz, Francois P.; Bourdeaut, Franck; Delattre, Olivier O.; Masliah-Planchon, Julien; Ayrault, Olivier; Kim, Seung-Ki; Meyronet, David; Grajkowska, Wieslawa A.; Carlotti, Carlos G.; de Torres, Carmen; Mora, Jaume; Eberhart, Charles G.; Van Meir, Erwin G.; Kumabe, Toshihiro; French, Pim J.; Kros, Johan M.; Jabado, Nada; Lach, Boleslaw; Pollack, Ian F.; Hamilton, Ronald L.; Rao, Amulya A. Nageswara; Giannini, Caterina; Olson, James M.; Bognar, Laszlo; Klekner, Almos; Zitterbart, Karel; Phillips, Joanna J.; Thompson, Reid C.; Cooper, Michael K.; Rubin, Joshua B.; Liau, Linda M.; Garami, Miklos; Hauser, Peter; Li, Kay Ka Wai; Ng, Ho-Keung; Poon, Wai Sang; Gillespie, G. Yancey; Chan, Jennifer A.; Jung, Shin; McLendon, Roger E.; Thompson, Eric M.; Zagzag, David; Vibhakar, Rajeev; Ra, Young Shin; Garre, Maria Luisa; Schueller, Ulrich; Shofuda, Tomoko; Faria, Claudia C.; Lopez-Aguilar, Enrique; Zadeh, Gelareh; Hui, Chi-Chung; Ramaswamy, Vijay; Bailey, Swneke D.; Jones, Steven J.; Mungall, Andrew J.; Moore, Richard A.; Calarco, John A.; Stein, Lincoln D.; Bader, Gary D.; Reimand, Juri; Ragoussis, Jiannis; Weiss, William A.; Marra, Marco A.; Suzuki, Hiromichi; Taylor, Michael D. Share Save
Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway Carrot-Zhang, Jian; Yao, Xiaotong; Devarakonda, Siddhartha; Deshpande, Aditya; Damrauer, Jeffrey S.; Silva, Tiago Chedraoui; Wong, Christopher K.; Choi, Hyo Young; Felau, Ina; Robertson, A. Gordon; Castro, Mauro A. A.; Bao, Lisui; Rheinbay, Esther; Liu, Eric Minwei; Trieu, Tuan; Haan, David; Yau, Christina; Hinoue, Toshinori; Liu, Yuexin; Shapira, Ofer; Kumar, Kiran; Mungall, Karen L.; Zhang, Hailei; Lee, Jake June-Koo; Berger, Ashton; Gao, Galen F.; Zhitomirsky, Binyamin; Liang, Wen-Wei; Zhou, Meng; Moorthi, Sitapriya; Berger, Alice H.; Collisson, Eric A.; Zody, Michael C.; Ding, Li; Cherniack, Andrew D.; Getz, Gad; Elemento, Olivier; Benz, Christopher C.; Stuart, Josh; Zenklusen, J. C.; Beroukhim, Rameen; Chang, Jason C.; Campbell, Joshua D.; Hayes, D. Neil; Yang, Lixing; Laird, Peter W.; Weinstein, John N.; Kwiatkowski, David J.; Tsao, Ming S.; Travis, William D.; Khurana, Ekta; Berman, Benjamin P.; Hoadley, Katherine A.; Robine, Nicolas; Meyerson, Matthew; Govindan, Ramaswamy; Imielinski, Marcin Share Save
Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway (vol 34, 108707-1.e1, 2021) Carrot-Zhang, Jian; Yao, Xiaotong; Devarakonda, Siddhartha; Deshpande, Aditya; Damrauer, Jeffrey S.; Silva, Tiago Chedraoui; Wong, Christopher K.; Choi, Hyo Young; Felau, Ina; Robertson, A. Gordon; Castro, Mauro A. A.; Bao, Lisui; Rheinbay, Esther; Liu, Eric Minwei; Trieu, Tuan; Haan, David; Yau, Christina; Hinoue, Toshinori; Liu, Yuexin; Shapira, Ofer; Kumar, Kiran; Mungall, Karen L.; Zhang, Hailei; Lee, Jake June-Koo; Berger, Ashton; Gao, Galen F.; Zhitomirsky, Binyamin; Liang, Wen-Wei; Zhou, Meng; Moorthi, Sitapriya; Berger, Alice H.; Collisson, Eric A.; Zody, Michael C.; Ding, Li; Cherniack, Andrew D.; Getz, Gad; Elemento, Olivier; Benz, Christopher C.; Stuart, Josh; Zenklusen, J. C.; Beroukhim, Rameen; Chang, Jason C.; Campbell, Joshua D.; Hayes, D. Neil; Yang, Lixing; Laird, Peter W.; Weinstein, John N.; Kwiatkowski, David J.; Tsao, Ming S.; Travis, William D.; Khurana, Ekta; Berman, Benjamin P.; Hoadley, Katherine A.; Robine, Nicolas; Meyerson, Matthew; Govindan, Ramaswamy; Imielinski, Marcin Share Save
Integrating whole genome and transcriptome analysis to inform treatment decisions in the metastatic cancer clinical setting Jones, Martin R.; Shen, Yaoqing; Pleasance, Erin; Majounie, Elisa; Williamson, Laura; Zhao, Eric; Chuah, Eric; Mungall, Karen L.; Mungall, Andrew J.; Moore, Richard A.; Ma, Yussanne; Yip, Stephen; Lim, Howard; Renouf, Daniel; Jones, Steven J.; Jaskin, Janesssa; Marra, Marco A. Share Save
Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas Campbell, Joshua D.; Yau, Christina; Bowlby, Reanne; Liu, Yuexin; Brennan, Kevin; Fan, Huihui; Taylor, Alison M.; Wang, Chen; Walter, Vonn; Akbani, Rehan; Byers, Lauren Averett; Creighton, Chad J.; Coarfa, Cristian; Shih, Juliann; Cherniack, Andrew D.; Gevaert, Olivier; Prunello, Marcos; Shen, Hui; Anur, Pavana; Chen, Jianhong; Cheng, Hui; Hayes, D. Neil; Bullman, Susan; Pedamallu, Chandra Sekhar; Ojesina, Akinyemi I.; Sadeghi, Sara; Mungall, Karen L.; Robertson, A. Gordon; Benz, Christopher; Schultz, Andre; Kanchi, Rupa S.; Gay, Carl M.; Hegde, Apurva; Diao, Lixia; Wang, Jing; Ma, Wencai; Sumazin, Pavel; Chiu, Hua-Sheng; Chen, Ting-Wen; Gunaratne, Preethi; Donehower, Larry; Rader, Janet S.; Zuna, Rosemary; Al-Ahmadie, Hikmat; Lazar, Alexander J.; Flores, Elsa R.; Tsai, Kenneth Y.; Zhou, Jane H.; Rustgi, Anil K.; Drill, Esther; Shen, Ronglei; Wong, Christopher K.; Stuart, Joshua M.; Laird, Peter W.; Hoadley, Katherine A.; Weinstein, John N.; Peto, Myron; Pickering, Curtis R.; Chen, Zhong; Van Waes, Carter Share Save
Successful targeting of the NRG1 pathway indicates novel treatment strategy for metastatic cancer Jones, M. R.; Lim, H.; Shen, Y.; Pleasance, E.; Ch'ng, C.; Reisle, C.; Leelakumari, S.; Zhao, C.; Yip, S.; Ho, J.; Zhong, E.; Ng, T.; Ionescu, D.; Schaeffer, D. F.; Mungall, A. J.; Mungall, K. L.; Zhao, Y.; Moore, R. A.; Ma, Y.; Chia, S.; Ho, C.; Renouf, D. J.; Gelmon, K.; Jones, S. J. M.; Marra, M. A.; Laskin, J. Share Save
Comprehensive whole genome sequence analyses yields novel genetic and structural insights for Intellectual Disability Zahir, Farah R.; Mwenifumbo, Jill C.; Chun, Hye-Jung E.; Lim, Emilia L.; Van Karnebeek, Clara D. M.; Couse, Madeline; Mungall, Karen L.; Lee, Leora; Makela, Nancy; Armstrong, Linlea; Boerkoel, Cornelius F.; Langlois, Sylvie L.; McGillivray, Barbara M.; Jones, Steven J. M.; Friedman, Jan M.; Marra, Marco A. Share Save
MEN1 Mutations in Hurthle Cell (Oncocytic) Thyroid Carcinoma Kasaian, Katayoon; Chindris, Ana-Maria; Wiseman, Sam M.; Mungall, Karen L.; Zeng, Thomas; Tse, Kane; Schein, Jacqueline E.; Rivera, Michael; Necela, Brian M.; Kachergus, Jennifer M.; Casler, John D.; Mungall, Andrew J.; Moore, Richard A.; Marra, Marco A.; Copland, John A.; Thompson, E. Aubrey; Smallridge, Robert C.; Jones, Steven J. M. Share Save
Identification and analysis of murine pancreatic islet enhancers Tennant, B. R.; Robertson, A. G.; Kramer, M.; Li, L.; Zhang, X.; Beach, M.; Thiessen, N.; Chiu, R.; Mungall, K.; Whiting, C. J.; Sabatini, P. V.; Kim, A.; Gottardo, R.; Marra, M. A.; Lynn, F. C.; Jones, S. J. M.; Hoodless, P. A.; Hoffman, B. G. Share Save
Whole genome and transcriptome sequencing defines the spectrum of somatic changes in high-risk neuroblastoma Morozova, Olena; Birol, Inanc; Corbett, Richard; Mungall, Karen; Attiyeh, Edward F.; Asgharzadeh, Shahab; Zhao, Yongjun; Moore, Richard A.; Hirst, Martin; Jones, Steven; Hogarty, Michael D.; Diskin, Sharon; Mosse, Yael P.; Diamond, Maura; Sposto, Richard; Ji, Lingyun; Gerhard, Daniela S.; Smith, Malcolm A.; Khan, Javed; Seeger, Robert C.; Marra, Marco A.; Maris, John M. Share Save
De novo assembly and analysis of RNA-seq data Robertson, Gordon; Schein, Jacqueline; Chiu, Readman; Corbett, Richard; Field, Matthew; Jackman, Shaun D.; Mungall, Karen; Lee, Sam; Okada, Hisanaga Mark; Qian, Jenny Q.; Griffith, Malachi; Raymond, Anthony; Thiessen, Nina; Cezard, Timothee; Butterfield, Yaron S.; Newsome, Richard; Chan, Simon K.; She, Rong; Varhol, Richard; Kamoh, Baljit; Prabhu, Anna-Liisa; Tam, Angela; Zhao, YongJun; Moore, Richard A.; Hirst, Martin; Marra, Marco A.; Jones, Steven J. M.; Hoodless, Pamela A.; Birol, Inanc Share Save
Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi Holt, Kathryn E.; Thomson, Nicholas R.; Wain, John; Langridge, Gemma C.; Hasan, Rumina; Bhutta, Zulfiqar A.; Quail, Michael A.; Norbertczak, Halina; Walker, Danielle; Simmonds, Mark; White, Brian; Bason, Nathalie; Mungall, Karen; Dougan, Gordon; Parkhill, Julian Share Save
The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081 Thomson, Nicholas R.; Howard, Sarah; Wren, Brendan W.; Holden, Matthew T. G.; Crossman, Lisa; Challis, Gregory L.; Churcher, Carol; Mungall, Karen; Brooks, Karen; Chillingworth, Tracey; Feltwell, Theresa; Abdellah, Zahra; Hauser, Heidi; Jagels, Kay; Maddison, Mark; Moule, Sharon; Sanders, Mandy; Whitehead, Sally; Quail, Michael A.; Dougan, Gordon; Parkhill, Julian; Prentice, Michael B. Share Save
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