Modulation of the Host Cell Transcriptome and Epigenome by Fusobacterium nucleatum by Cody A. Despins, Scott D. Brown, Avery V. Robinson, Andrew J. Mungall, Emma Allen-Vercoe, Robert A. Holt

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Exploration of Germline Correlates and Risk of Immune-Related Adverse Events in Advanced Cancer Patients Treated with Immune Checkpoint Inhibitors by Emma Titmuss, Irene S. Yu, Erin D. Pleasance, Laura M. Williamson, Karen Mungall, Andrew J. Mungall, Daniel J. Renouf, Richard Moore, Steven J. M. Jones, Marco A. Marra, Janessa J. Laskin, Kerry J. Savage

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The evolution of the DLK1-DIO3 imprinted domain in mammals. by Carol A Edwards, Andrew J Mungall, Lucy Matthews, Edward Ryder, Dionne J Gray, Andrew J Pask, Geoffrey Shaw, Jennifer A M Graves, Jane Rogers, SAVOIR consortium, Ian Dunham, Marilyn B Renfree, Anne C Ferguson-Smith

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Tumor infiltrating neutrophils and gland formation predict overall survival and molecular subgroups in pancreatic ductal adenocarcinoma by Julia R. Naso, James T. Topham, Joanna M. Karasinska, Michael K.C. Lee, Steve E. Kalloger, Hui‐li Wong, Jessica Nelson, Richard A. Moore, Andrew J. Mungall, Steven J.M. Jones, Janessa Laskin, Marco A. Marra, Daniel J. Renouf, David F. Schaeffer

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A high-throughput pipeline for DNA/RNA/small RNA purification from tissue samples for sequencing by Jing Xu, Pawan K Pandoh, Richard D Corbett, Duane Smailus, Reanne Bowlby, Denise Brooks, Helen McDonald, Simon Haile, Sundeep Chahal, Steve Bilobram, Karen L Mungall, Andrew J Mungall, Robin Coope, Richard A Moore, Yongjun Zhao, Steven JM Jones, Marco A Marra

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Evaluation of protocols for rRNA depletion-based RNA sequencing of nanogram inputs of mammalian total RNA. by Simon Haile, Richard D Corbett, Steve Bilobram, Karen Mungall, Bruno M Grande, Heather Kirk, Pawan Pandoh, Tina MacLeod, Helen McDonald, Miruna Bala, Robin J Coope, Richard A Moore, Andrew J Mungall, Yongjun Zhao, Ryan D Morin, Steven J Jones, Marco A Marra

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Molecular attributes underlying central nervous system and systemic relapse in diffuse large B-cell lymphoma by Keren Isaev, Daisuke Ennishi, Laura Hilton, Brian Skinnider, Karen L. Mungall, Andrew J. Mungall, Mehran Bakhtiari, Rosemarie Tremblay-LeMay, Anjali Silva, Susana Ben-Neriah, Merrill Boyle, Diego Villa, Marco A. Marra, Christian Steidl, Randy D. Gascoyne, Ryan Morin, Kerry J. Savage, David W. Scott, Robert Kridel

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Increasing quality, throughput and speed of sample preparation for strand-specific messenger RNA sequencing by Simon Haile, Richard D. Corbett, Tina MacLeod, Steve Bilobram, Duane Smailus, Philip Tsao, Heather Kirk, Helen McDonald, Pawan Pandoh, Miruna Bala, Martin Hirst, Diane Miller, Richard A. Moore, Andrew J. Mungall, Jacquie Schein, Robin J. Coope, Yussanne Ma, Yongjun Zhao, Rob A. Holt, Steven J. Jones, Marco A. Marra

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The North American bullfrog draft genome provides insight into hormonal regulation of long noncoding RNA by S. Austin Hammond, René L. Warren, Benjamin P. Vandervalk, Erdi Kucuk, Hamza Khan, Ewan A. Gibb, Pawan Pandoh, Heather Kirk, Yongjun Zhao, Martin Jones, Andrew J. Mungall, Robin Coope, Stephen Pleasance, Richard A. Moore, Robert A. Holt, Jessica M. Round, Sara Ohora, Branden V. Walle, Nik Veldhoen, Caren C. Helbing, Inanc Birol

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A high-throughput protocol for isolating cell-free circulating tumor DNA from peripheral blood by Pawan K Pandoh, Richard D Corbett, Helen McDonald, Miguel Alcaide, Heather Kirk, Eva Trinh, Simon Haile, Tina MacLeod, Duane Smailus, Steve Bilobram, Andrew J Mungall, Yussanne Ma, Richard A Moore, Robin Coope, Yongjun Zhao, Steven JM Jones, Robert A Holt, Aly Karsan, Ryan D Morin, Marco A Marra

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Mapping the human T cell repertoire to recurrent driver mutations in MYD88 and EZH2 in lymphoma by Julie S. Nielsen, Andrew R. Chang, Darin A. Wick, Colin G. Sedgwick, Zusheng Zong, Andrew J. Mungall, Spencer D. Martin, Natalie N. Kinloch, Susann Ott-Langer, Zabrina L. Brumme, Steven P. Treon, Joseph M. Connors, Randy D. Gascoyne, John R. Webb, Brian R. Berry, Ryan D. Morin, Nicol Macpherson, Brad H. Nelson

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Single-cell decoding of drug induced transcriptomic reprogramming in triple negative breast cancers by Farhia Kabeer, Hoa Tran, Mirela Andronescu, Gurdeep Singh, Hakwoo Lee, Sohrab Salehi, Beixi Wang, Justina Biele, Jazmine Brimhall, David Gee, Viviana Cerda, Ciara O’Flanagan, Teresa Algara, Takako Kono, Sean Beatty, Elena Zaikova, Daniel Lai, Eric Lee, Richard Moore, Andrew J. Mungall, IMAXT Consortium, Marc J. Williams, Andrew Roth, Kieran R. Campbell, Sohrab P. Shah, Samuel Aparicio

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A Distributed Whole Genome Sequencing Benchmark Study by Richard D. Corbett, Robert Eveleigh, Joe Whitney, Namrata Barai, Mathieu Bourgey, Eric Chuah, Joanne Johnson, Richard A. Moore, Neda Moradin, Karen L. Mungall, Sergio Pereira, Miriam S. Reuter, Bhooma Thiruvahindrapuram, Richard F. Wintle, Jiannis Ragoussis, Lisa J. Strug, Jo-Anne Herbrick, Naveed Aziz, Steven J. M. Jones, Mark Lathrop, Stephen W. Scherer, Alfredo Staffa, Andrew J. Mungall

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Automated high throughput nucleic acid purification from formalin-fixed paraffin-embedded tissue samples for next generation sequence analysis. by Simon Haile, Pawan Pandoh, Helen McDonald, Richard D Corbett, Philip Tsao, Heather Kirk, Tina MacLeod, Martin Jones, Steve Bilobram, Denise Brooks, Duane Smailus, Christian Steidl, David W Scott, Miruna Bala, Martin Hirst, Diane Miller, Richard A Moore, Andrew J Mungall, Robin J Coope, Yussanne Ma, Yongjun Zhao, Rob A Holt, Steven J Jones, Marco A Marra

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A clinical transcriptome approach to patient stratification and therapy selection in acute myeloid leukemia by T. Roderick Docking, Jeremy D. K. Parker, Martin Jädersten, Gerben Duns, Linda Chang, Jihong Jiang, Jessica A. Pilsworth, Lucas A. Swanson, Simon K. Chan, Readman Chiu, Ka Ming Nip, Samantha Mar, Angela Mo, Xuan Wang, Sergio Martinez-Høyer, Ryan J. Stubbins, Karen L. Mungall, Andrew J. Mungall, Richard A. Moore, Steven J. M. Jones, İnanç Birol, Marco A. Marra, Donna Hogge, Aly Karsan

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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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A Scalable Strand-Specific Protocol Enabling Full-Length Total RNA Sequencing From Single Cells by Simon Haile, Richard D. Corbett, Veronique G. LeBlanc, Lisa Wei, Stephen Pleasance, Steve Bilobram, Ka Ming Nip, Kirstin Brown, Eva Trinh, Jillian Smith, Diane L. Trinh, Miruna Bala, Eric Chuah, Robin J. N. Coope, Richard A. Moore, Andrew J. Mungall, Karen L. Mungall, Yongjun Zhao, Martin Hirst, Samuel Aparicio, Inanc Birol, Inanc Birol, Steven J. M. Jones, Steven J. M. Jones, Marco A. Marra, Marco A. Marra

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Whole genome and transcriptome integrated analyses guide clinical care of pediatric poor prognosis cancers by Rebecca J. Deyell, Yaoqing Shen, Emma Titmuss, Katherine Dixon, Laura M. Williamson, Erin Pleasance, Jessica M. T. Nelson, Sanna Abbasi, Martin Krzywinski, Linlea Armstrong, Melika Bonakdar, Carolyn Ch’ng, Eric Chuah, Chris Dunham, Alexandra Fok, Martin Jones, Anna F. Lee, Yussanne Ma, Richard A. Moore, Andrew J. Mungall, Karen L. Mungall, Paul C. Rogers, Kasmintan A. Schrader, Alice Virani, Kathleen Wee, Sean S. Young, Yongjun Zhao, Steven J. M. Jones, Janessa Laskin, Marco A. Marra, Shahrad R. Rassekh

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Identification and Analyses of Extra-Cranial and Cranial Rhabdoid Tumor Molecular Subgroups Reveal Tumors with Cytotoxic T Cell Infiltration by Hye-Jung E. Chun, Pascal D. Johann, Katy Milne, Marc Zapatka, Annette Buellesbach, Naveed Ishaque, Murat Iskar, Serap Erkek, Lisa Wei, Basile Tessier-Cloutier, Jake Lever, Emma Titmuss, James T. Topham, Reanne Bowlby, Eric Chuah, Karen L. Mungall, Yussanne Ma, Andrew J. Mungall, Richard A. Moore, Michael D. Taylor, Daniela S. Gerhard, Steven J.M. Jones, Andrey Korshunov, Manfred Gessler, Kornelius Kerl, Martin Hasselblatt, Michael C. Frühwald, Elizabeth J. Perlman, Brad H. Nelson, Stefan M. Pfister, Marco A. Marra, Marcel Kool

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Identification of genetic subtypes in follicular lymphoma by Victoria Shelton, Rajesh Detroja, Ting Liu, Keren Isaev, Anjali Silva, Verena Passerini, Mehran Bakhtiari, Lourdes Calvente, Michael Hong, Michael Y. He, Saloni Modi, Samantha A. Hershenfeld, Maja Ludvigsen, Charlotte Madsen, Stephen Hamilton-Dutoit, Francesco Annibale d’Amore, Marianne Brodtkorb, Nathalie A. Johnson, Tara Baetz, David LeBrun, Josh W. D. Tobin, Maher K. Gandhi, Andrew J. Mungall, Wei Xu, Susana Ben-Neriah, Christian Steidl, Jan Delabie, Rosemarie Tremblay-LeMay, Opeyemi Jegede, Oliver Weigert, Brad Kahl, Andrew M. Evens, Robert Kridel

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