Allele-specific transcriptional effects of subclonal copy number alterations enable genotype-phenotype mapping in cancer cells by Hongyu Shi, Marc J. Williams, Gryte Satas, Adam C. Weiner, Andrew McPherson, Sohrab P. Shah

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Integrated structural variation and point mutation signatures in cancer genomes using correlated topic models. by Tyler Funnell, Allen W Zhang, Diljot Grewal, Steven McKinney, Ali Bashashati, Yi Kan Wang, Sohrab P Shah

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Correction to: ReMixT: clone-specific genomic structure estimation in cancer by Andrew W. McPherson, Andrew Roth, Gavin Ha, Cedric Chauve, Adi Steif, Camila P. E. de Souza, Peter Eirew, Alexandre Bouchard-Côté, Sam Aparicio, S. Cenk Sahinalp, Sohrab P. Shah

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ReMixT: clone-specific genomic structure estimation in cancer by Andrew W. McPherson, Andrew Roth, Gavin Ha, Cedric Chauve, Adi Steif, Camila P. E. de Souza, Peter Eirew, Alexandre Bouchard-Côté, Sam Aparicio, S. Cenk Sahinalp, Sohrab P. Shah

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Identification of transcriptional programs using dense vector representations defined by mutual information with GeneVector by Nicholas Ceglia, Zachary Sethna, Samuel S. Freeman, Florian Uhlitz, Viktoria Bojilova, Nicole Rusk, Bharat Burman, Andrew Chow, Sohrab Salehi, Farhia Kabeer, Samuel Aparicio, Benjamin D. Greenbaum, Sohrab P. Shah, Andrew McPherson

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Correction: Type-Specific Cell Line Models for Type-Specific Ovarian Cancer Research. by Michael S. Anglesio, Kimberly C. Wiegand, Nataliya Melnyk, Christine Chow, Clara Salamanca, Leah M. Prentice, Janine Senz, Winnie Yang, Monique A. Spillman, Dawn R. Cochrane, Karey Shumansky, Sohrab P. Shah, Steve E. Kalloger, David G. Huntsman

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Type-specific cell line models for type-specific ovarian cancer research. by Michael S Anglesio, Kimberly C Wiegand, Nataliya Melnyk, Christine Chow, Clara Salamanca, Leah M Prentice, Janine Senz, Winnie Yang, Monique A Spillman, Dawn R Cochrane, Karey Shumansky, Sohrab P Shah, Steve E Kalloger, David G Huntsman

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Correction: Type-Specific Cell Line Models for Type-Specific Ovarian Cancer Research. by Michael S Anglesio, Kimberly C Wiegand, Nataliya Melnyk, Christine Chow, Clara Salamanca, Leah M Prentice, Janine Senz, Winnie Yang, Monique A Spillman, Dawn R Cochrane, Karey Shumansky, Sohrab P Shah, Steve E Kalloger, David G Huntsman

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clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers by Kieran R. Campbell, Adi Steif, Emma Laks, Hans Zahn, Daniel Lai, Andrew McPherson, Hossein Farahani, Farhia Kabeer, Ciara O’Flanagan, Justina Biele, Jazmine Brimhall, Beixi Wang, Pascale Walters, IMAXT Consortium, Alexandre Bouchard-Côté, Samuel Aparicio, Sohrab P. Shah

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deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. by Andrew McPherson, Fereydoun Hormozdiari, Abdalnasser Zayed, Ryan Giuliany, Gavin Ha, Mark G F Sun, Malachi Griffith, Alireza Heravi Moussavi, Janine Senz, Nataliya Melnyk, Marina Pacheco, Marco A Marra, Martin Hirst, Torsten O Nielsen, S Cenk Sahinalp, David Huntsman, Sohrab P Shah

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Epiclomal: Probabilistic clustering of sparse single-cell DNA methylation data. by Camila P E de Souza, Mirela Andronescu, Tehmina Masud, Farhia Kabeer, Justina Biele, Emma Laks, Daniel Lai, Patricia Ye, Jazmine Brimhall, Beixi Wang, Edmund Su, Tony Hui, Qi Cao, Marcus Wong, Michelle Moksa, Richard A Moore, Martin Hirst, Samuel Aparicio, Sohrab P Shah

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Dissociation of solid tumor tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase-associated stress responses by Ciara H. O’Flanagan, Kieran R. Campbell, Allen W. Zhang, Farhia Kabeer, Jamie L. P. Lim, Justina Biele, Peter Eirew, Daniel Lai, Andrew McPherson, Esther Kong, Cherie Bates, Kelly Borkowski, Matt Wiens, Brittany Hewitson, James Hopkins, Jenifer Pham, Nicholas Ceglia, Richard Moore, Andrew J. Mungall, Jessica N. McAlpine, The CRUK IMAXT Grand Challenge Team, Sohrab P. Shah, Samuel Aparicio

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Single-cell profiling reveals a memory B cell-like subtype of follicular lymphoma with increased transformation risk by Xuehai Wang, Michael Nissen, Deanne Gracias, Manabu Kusakabe, Guillermo Simkin, Aixiang Jiang, Gerben Duns, Clementine Sarkozy, Laura Hilton, Elizabeth A. Chavez, Gabriela C. Segat, Rachel Wong, Jubin Kim, Tomohiro Aoki, Rashedul Islam, Christina May, Stacy Hung, Kate Tyshchenko, Ryan R. Brinkman, Martin Hirst, Aly Karsan, Ciara Freeman, Laurie H. Sehn, Ryan D. Morin, Andrew J. Roth, Kerry J. Savage, Jeffrey W. Craig, Sohrab P. Shah, Christian Steidl, David W. Scott, Andrew P. Weng

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Imaging and Molecular Annotation of Xenographs and Tumours (IMAXT): High throughput data and analysis infrastructure by Eduardo A. González-Solares, Ali Dariush, Carlos González-Fernández, Aybüke Küpcü Yoldaş, Alireza Molaeinezhad, Mohammad Al Sa’d, Leigh Smith, Tristan Whitmarsh, Neil Millar, Nicholas Chornay, Ilaria Falciatori, Atefeh Fatemi, Daniel Goodwin, Laura Kuett, Claire M. Mulvey, Marta Páez Ribes, Fatime Qosaj, Andrew Roth, Ignacio Vázquez-García, Spencer S. Watson, Jonas Windhager, Samuel Aparicio, Bernd Bodenmiller, Ed Boyden, Carlos Caldas, Owen Harris, Sohrab P. Shah, Simon Tavaré, CRUK IMAXT Grand Challenge Team, Dario Bressan, Gregory J. Hannon, Nicholas A. Walton

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Clonal somatic copy number altered driver events inform drug sensitivity in high-grade serous ovarian cancer by Filipe Correia Martins, Dominique-Laurent Couturier, Ines de Santiago, Carolin Margarethe Sauer, Maria Vias, Mihaela Angelova, Deborah Sanders, Anna Piskorz, James Hall, Karen Hosking, Anumithra Amirthanayagam, Sabina Cosulich, Larissa Carnevalli, Barry Davies, Thomas B. K. Watkins, Ionut G. Funingana, Helen Bolton, Krishnayan Haldar, John Latimer, Peter Baldwin, Robin Crawford, Matthew Eldridge, Bristi Basu, Mercedes Jimenez-Linan, Andrew W. Mcpherson, Nicholas McGranahan, Kevin Litchfield, Sohrab P. Shah, Iain McNeish, Carlos Caldas, Gerard Evan, Charles Swanton, James D. Brenton

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Histological Transformation and Progression in Follicular Lymphoma: A Clonal Evolution Study. by Robert Kridel, Fong Chun Chan, Anja Mottok, Merrill Boyle, Pedro Farinha, King Tan, Barbara Meissner, Ali Bashashati, Andrew McPherson, Andrew Roth, Karey Shumansky, Damian Yap, Susana Ben-Neriah, Jamie Rosner, Maia A Smith, Cydney Nielsen, Eva Giné, Adele Telenius, Daisuke Ennishi, Andrew Mungall, Richard Moore, Ryan D Morin, Nathalie A Johnson, Laurie H Sehn, Thomas Tousseyn, Ahmet Dogan, Joseph M Connors, David W Scott, Christian Steidl, Marco A Marra, Randy D Gascoyne, Sohrab P Shah

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Tumor-associated antigen PRAME exhibits dualistic functions that are targetable in diffuse large B cell lymphoma by Katsuyoshi Takata, Lauren C. Chong, Daisuke Ennishi, Tomohiro Aoki, Michael Yu Li, Avinash Thakur, Shannon Healy, Elena Viganò, Tao Dao, Daniel Kwon, Gerben Duns, Julie S. Nielsen, Susana Ben-Neriah, Ethan Tse, Stacy S. Hung, Merrill Boyle, Sung Soo Mun, Christopher M. Bourne, Bruce Woolcock, Adèle Telenius, Makoto Kishida, Shinya Rai, Allen W. Zhang, Ali Bashashati, Saeed Saberi, Gianluca D’Antonio, Brad H. Nelson, Sohrab P. Shah, Pamela A. Hoodless, Ari M. Melnick, Randy D. Gascoyne, Joseph M. Connors, David A. Scheinberg, Wendy Béguelin, David W. Scott, Christian Steidl

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CX-5461 is a DNA G-quadruplex stabilizer with selective lethality in BRCA1/2 deficient tumours by Hong Xu, Marco Di Antonio, Steven McKinney, Veena Mathew, Brandon Ho, Nigel J. O’Neil, Nancy Dos Santos, Jennifer Silvester, Vivien Wei, Jessica Garcia, Farhia Kabeer, Daniel Lai, Priscilla Soriano, Judit Banáth, Derek S. Chiu, Damian Yap, Daniel D. Le, Frank B. Ye, Anni Zhang, Kelsie Thu, John Soong, Shu-chuan Lin, Angela Hsin Chin Tsai, Tomo Osako, Teresa Algara, Darren N. Saunders, Jason Wong, Jian Xian, Marcel B. Bally, James D. Brenton, Grant W. Brown, Sohrab P. Shah, David Cescon, Tak W. Mak, Carlos Caldas, Peter C. Stirling, Phil Hieter, Shankar Balasubramanian, Samuel Aparicio

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Eleven grand challenges in single-cell data science by David Lähnemann, Johannes Köster, Ewa Szczurek, Davis J. McCarthy, Stephanie C. Hicks, Mark D. Robinson, Catalina A. Vallejos, Kieran R. Campbell, Niko Beerenwinkel, Ahmed Mahfouz, Luca Pinello, Pavel Skums, Alexandros Stamatakis, Camille Stephan-Otto Attolini, Samuel Aparicio, Jasmijn Baaijens, Marleen Balvert, Buys de Barbanson, Antonio Cappuccio, Giacomo Corleone, Bas E. Dutilh, Maria Florescu, Victor Guryev, Rens Holmer, Katharina Jahn, Thamar Jessurun Lobo, Emma M. Keizer, Indu Khatri, Szymon M. Kielbasa, Jan O. Korbel, Alexey M. Kozlov, Tzu-Hao Kuo, Boudewijn P.F. Lelieveldt, Ion I. Mandoiu, John C. Marioni, Tobias Marschall, Felix Mölder, Amir Niknejad, Alicja Rączkowska, Marcel Reinders, Jeroen de Ridder, Antoine-Emmanuel Saliba, Antonios Somarakis, Oliver Stegle, Fabian J. Theis, Huan Yang, Alex Zelikovsky, Alice C. McHardy, Benjamin J. Raphael, Sohrab P. Shah, Alexander Schönhuth

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