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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
Single-cell decoding of drug induced transcriptomic reprogramming in triple negative breast cancers Kabeer, Farhia; Tran, Hoa; Andronescu, Mirela; Singh, Gurdeep; Lee, Hakwoo; Salehi, Sohrab; Wang, Beixi; Biele, Justina; Brimhall, Jazmine; Gee, David; Cerda, Viviana; O'Flanagan, Ciara; Algara, Teresa; Kono, Takako; Beatty, Sean; Zaikova, Elena; Lai, Daniel; Lee, Eric; Moore, Richard; Mungall, Andrew J.; Williams, Marc J.; Roth, Andrew; Campbell, Kieran R.; Shah, Sohrab P.; Aparicio, Samuel Share Save
Whole genome and transcriptome integrated analyses guide clinical care of pediatric poor prognosis cancers Deyell, Rebecca J.; Shen, Yaoqing; Titmuss, Emma; Dixon, Katherine; Williamson, Laura M.; Pleasance, Erin; Nelson, Jessica M. T.; Abbasi, Sanna; Krzywinski, Martin; Armstrong, Linlea; Bonakdar, Melika; Ch'ng, Carolyn; Chuah, Eric; Dunham, Chris; Fok, Alexandra; Jones, Martin; Lee, Anna F.; Ma, Yussanne; Moore, Richard A.; Mungall, Andrew J.; Mungall, Karen L.; Rogers, Paul C.; Schrader, Kasmintan A.; Virani, Alice; Wee, Kathleen; Young, Sean S.; Zhao, Yongjun; Jones, Steven J. M.; Laskin, Janessa; Marra, Marco A.; Rassekh, Shahrad R. Share Save
Integrative analysis of KRAS wildtype metastatic pancreatic ductal adenocarcinoma reveals mutation and expression-based similarities to cholangiocarcinoma Topham, James T.; Tsang, Erica S.; Karasinska, Joanna M.; Metcalfe, Andrew; Ali, Hassan; Kalloger, Steve E.; Csizmok, Veronika; Williamson, Laura M.; Titmuss, Emma; Nielsen, Karina; Negri, Gian Luca; Spencer Miko, Sandra E.; Jang, Gun Ho; Denroche, Robert E.; Wong, Hui-li; O'Kane, Grainne M.; Moore, Richard A.; Mungall, Andrew J.; Loree, Jonathan M.; Notta, Faiyaz; Wilson, Julie M.; Bathe, Oliver F.; Tang, Patricia A.; Goodwin, Rachel; Morin, Gregg B.; Knox, Jennifer J.; Gallinger, Steven; Laskin, Janessa; Marra, Marco A.; Jones, Steven J. M.; Schaeffer, David F.; Renouf, Daniel J. Share Save
Whole-genome and transcriptome analysis enhances precision cancer treatment options Pleasance, E.; Bohm, A.; Williamson, L. M.; Nelson, J. M. T.; Shen, Y.; Bonakdar, M.; Titmuss, E.; Csizmok, V; Wee, K.; Hosseinzadeh, S.; Grisdale, C. J.; Reisle, C.; Taylor, G. A.; Lewis, E.; Jones, M. R.; Bleile, D.; Sadeghi, S.; Zhang, W.; Davies, A.; Pellegrini, B.; Wong, T.; Bowlby, R.; Chan, S. K.; Mungall, K. L.; Chuah, E.; Mungall, A. J.; Moore, R. A.; Zhao, Y.; Deol, B.; Fisic, A.; Fok, A.; Regier, D. A.; Weymann, D.; Schaeffer, D. F.; Young, S.; Yip, S.; Schrader, K.; Levasseur, N.; Taylor, S. K.; Feng, X.; Tinker, A.; Savage, K. J.; Chia, S.; Gelmon, K.; Sun, S.; Lim, H.; Renouf, D. J.; Jones, S. J. M.; Marra, M. A.; Laskin, J. Share Save
Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes Gagalova, Kristina K.; Warren, Rene L.; Coombe, Lauren; Wong, Johnathan; Nip, Ka Ming; Saint Yuen, Macaire Man; Whitehill, Justin G. A.; Celedon, Jose M.; Ritland, Carol; Taylor, Greg A.; Cheng, Dean; Plettner, Patrick; Hammond, S. Austin; Mohamadi, Hamid; Zhao, Yongjun; Moore, Richard A.; Mungall, Andrew J.; Boyle, Brian; Laroche, Jerome; Cottrell, Joan; Mackay, John J.; Lamothe, Manuel; Gerardi, Sebastien; Isabel, Nathalie; Pavy, Nathalie; Jones, Steven J. M.; Bohlmann, Joerg; Bousquet, Jean; Birol, Inanc Share Save
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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
Use of Treatment-Focused Tumor Sequencing to Screen for Germline Cancer Predisposition Lau, Tammy T. Y.; May, Christina M.; Dashti, Zahra J. Sefid; Swanson, Lucas; Starks, Elizabeth R.; Parker, Jeremy D. K.; Moore, Richard A.; Tucker, Tracy; Bosdet, Ian; Young, Sean S.; Santos, Jennifer L.; Compton, Katie; Heidary, Nili; Hoang, Lien; Schrader, Kasmintan A.; Sun, Sophie; Kwon, Janice S.; V. Tinker, Anna; Karsan, Aly 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
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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
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Gradient of Developmental and Injury Response transcriptional states defines functional vulnerabilities underpinning glioblastoma heterogeneity Richards, Laura M.; Whitley, Owen K. N.; MacLeod, Graham; Cavalli, Florence M. G.; Coutinho, Fiona J.; Jaramillo, Julia E.; Svergun, Nataliia; Riverin, Mazdak; Croucher, Danielle C.; Kushida, Michelle; Yu, Kenny; Guilhamon, Paul; Rastegar, Naghmeh; Ahmadi, Moloud; Bhatti, Jasmine K.; Bozek, Danielle A.; Li, Naijin; Lee, Lilian; Che, Clare; Luis, Erika; Park, Nicole I.; Xu, Zhiyu; Ketela, Troy; Moore, Richard A.; Marra, Marco A.; Spears, Julian; Cusimano, Michael D.; Das, Sunit; Bernstein, Mark; Haibe-Kains, Benjamin; Lupien, Mathieu; Luchman, H. Artee; Weiss, Samuel; Angers, Stephane; Dirks, Peter B.; Bader, Gary D.; Pugh, Trevor J. Share Save
Improved structural variant interpretation for hereditary cancer susceptibility using long-read sequencing Thibodeau, My Linh; O'Neill, Kieran; Dixon, Katherine; Reisle, Caralyn; Mungall, Karen L.; Krzywinski, Martin; Shen, Yaoqing; Lim, Howard J.; Cheng, Dean; Tse, Kane; Wong, Tina; Chuah, Eric; Fok, Alexandra; Sun, Sophie; Renouf, Daniel; Schaeffer, David F.; Cremin, Carol; Chia, Stephen; Young, Sean; Pandoh, Pawan; Pleasance, Stephen; Pleasance, Erin; Mungall, Andrew J.; Moore, Richard; Yip, Stephen; Karsan, Aly; Laskin, Janessa; Marra, Marco A.; Schrader, Kasmintan A.; Jones, Steven J. M. Share Save
Endogenous Retrovirus Transcript Levels Are Associated with Immunogenic Signatures in Multiple Metastatic Cancer Types Topham, James T.; Titmuss, Emma; Pleasance, Erin D.; Williamson, Laura M.; Karasinska, Joanna M.; Culibrk, Luka; Lee, Michael K. C.; Mendis, Shehara; Denroche, Robert E.; Jang, Gun-Ho; Kalloger, Steve E.; Wong, Hui-Li; Moore, Richard A.; Mungall, Andrew J.; O'Kane, Grainne M.; Knox, Jennifer J.; Gallinger, Steven; Loree, Jonathan M.; Mager, Dixie L.; Laskin, Janessa; Marra, Marco A.; Jones, Steven J. M.; Schaeffer, David F.; Renouf, Daniel J. Share Save
Epigenomic programming in early fetal brain development Li, Luolan; Maire, Cecile L.; Bilenky, Misha; Carles, Annaick; Heravi-Moussavi, Alireza; Hong, Chibo; Tam, Angela; Kamoh, Baljit; Cho, Stephanie; Cheung, Dorothy; Li, Irene; Wong, Tina; Nagarajan, Raman P.; Mungall, Andrew J.; Moore, Richard; Wang, Ting; Kleinman, Claudia L.; Jabado, Nada; Jones, Steven J. M.; Marra, Marco A.; Ligon, Keith L.; Costello, Joseph F.; Hirst, Martin Share Save
Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes Pleasance, Erin; Titmuss, Emma; Williamson, Laura; Kwan, Harwood; Culibrk, Luka; Zhao, Eric Y.; Dixon, Katherine; Fan, Kevin; Bowlby, Reanne; Jones, Martin R.; Shen, Yaoqing; Grewal, Jasleen K.; Ashkani, Jahanshah; Wee, Kathleen; Grisdale, Cameron J.; Thibodeau, My Linh; Bozoky, Zoltan; Pearson, Hillary; Majounie, Elisa; Vira, Tariq; Shenwai, Reva; Mungall, Karen L.; Chuah, Eric; Davies, Anna; Warren, Mya; Reisle, Caralyn; Bonakdar, Melika; Taylor, Gregory A.; Csizmok, Veronika; Chan, Simon K.; Zong, Zusheng; Bilobram, Steve; Muhammadzadeh, Amir; D'Souza, Darryl; Corbett, Richard D.; MacMillan, Daniel; Carreira, Marcus; Choo, Caleb; Bleile, Dustin; Sadeghi, Sara; Zhang, Wei; Wong, Tina; Cheng, Dean; Brown, Scott D.; Holt, Robert A.; Moore, Richard A.; Mungall, Andrew J.; Zhao, Yongjun; Nelson, Jessica; Fok, Alexandra; Ma, Yussanne; Lee, Michael K. C.; Lavoie, Jean-Michel; Mendis, Shehara; Karasinska, Joanna M.; Deol, Balvir; Fisic, Ana; Schaeffer, David F.; Yip, Stephen; Schrader, Kasmintan; Regier, Dean A.; Weymann, Deirdre; Chia, Stephen; Gelmon, Karen; Tinker, Anna; Sun, Sophie; Lim, Howard; Renouf, Daniel J.; Laskin, Janessa; Jones, Steven J. M.; Marra, Marco A. Share Save
Single-cell analysis of breast cancer metastasis using patient-derived xenograft model reveals clonal relationship between primary tumor and its metastases Lee, Hakwoo; Kabeer, Farhia; O'Flanagan, Ciara; Brimhall, Jazmine; Biele, Justina; Wang, Biexi; Algara, Teresa Ruiz; Lee, So Ra; Lai, Daniel; Yuen, Michael; Song, Simong; Ye, Patricia; Pham, Jenifer; Moore, Richard; Mungall, Andy J.; Shah, Sohrab P.; Aparicio, Samuel Share Save
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