Deep learning in cancer diagnosis, prognosis and treatment selection

by Khoa A. Tran, Olga Kondrashova, Andrew Bradley, Elizabeth D. Williams, John V. Pearson, Nicola Waddell
Published 2021-09-01

Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays.

by Nils Homer, Szabolcs Szelinger, Margot Redman, David Duggan, Waibhav Tembe, Jill Muehling, John V Pearson, Dietrich A Stephan, Stanley F Nelson, David W Craig
Published 2008-08-01

Whole exome sequencing of an asbestos-induced wild-type murine model of malignant mesothelioma

by Sophie Sneddon, Ann-Marie Patch, Ian M. Dick, Stephen Kazakoff, John V. Pearson, Nicola Waddell, Richard J. N. Allcock, Robert A. Holt, Bruce W. S. Robinson, Jenette Creaney
Published 2017-06-01

Verifying explainability of a deep learning tissue classifier trained on RNA-seq data

by Melvyn Yap, Rebecca L. Johnston, Helena Foley, Samual MacDonald, Olga Kondrashova, Khoa A. Tran, Katia Nones, Lambros T. Koufariotis, Cameron Bean, John V. Pearson, Maciej Trzaskowski, Nicola Waddell
Published 2021-01-01

Tumor Signature Analysis Implicates Hereditary Cancer Genes in Endometrial Cancer Development

by Olga Kondrashova, Jannah Shamsani, Tracy A. O’Mara, Felicity Newell, Amy E. McCart Reed, Sunil R. Lakhani, Judy Kirk, John V. Pearson, Nicola Waddell, Amanda B. Spurdle
Published 2021-04-01

Intratumoural Heterogeneity Underlies Distinct Therapy Responses and Treatment Resistance in Glioblastoma

by Seçkin Akgül, Ann-Marie Patch, Rochelle C.J. D’Souza, Pamela Mukhopadhyay, Katia Nones, Sarah Kempe, Stephen H. Kazakoff, Rosalind L. Jeffree, Brett W. Stringer, John V. Pearson, Nicola Waddell, Bryan W. Day
Published 2019-02-01

<em>APC</em> Mutation Marks an Aggressive Subtype of <em>BRAF </em>Mutant Colorectal Cancers

by Lochlan J. Fennell, Alexandra Kane, Cheng Liu, Diane McKeone, Winnie Fernando, Chang Su, Catherine Bond, Saara Jamieson, Troy Dumenil, Ann-Marie Patch, Stephen H. Kazakoff, John V. Pearson, Nicola Waddell, Barbara Leggett, Vicki L. J Whitehall
Published 2020-05-01

Next-Generation Sequencing of Coccidioides immitis Isolated during Cluster Investigation

by David M. Engelthaler, Tom M. Chiller, James A. Schupp, Joshua Colvin, Stephen M. Beckstrom-Sternberg, Elizabeth M. Driebe, Tracy Moses, Waibhav Tembe, Shripad Sinari, James S. Beckstrom-Sternberg, Alexis Christoforides, John V. Pearson, John Carpten, Paul Keim, Ashley Peterson, Dawn Terashita, S. Arunmozhi Balajee
Published 2011-02-01

Complete genomic characterization of a pathogenic A.II strain of Francisella tularensis subspecies tularensis.

by Stephen M Beckstrom-Sternberg, Raymond K Auerbach, Shubhada Godbole, John V Pearson, James S Beckstrom-Sternberg, Zuoming Deng, Christine Munk, Kristy Kubota, Yan Zhou, David Bruce, Jyothi Noronha, Richard H Scheuermann, Aihui Wang, Xianying Wei, Jianjun Wang, Jicheng Hao, David M Wagner, Thomas S Brettin, Nancy Brown, Paul Gilna, Paul S Keim
Published 2007-09-01

Complex structural rearrangements are present in high-grade dysplastic Barrett’s oesophagus samples

by Felicity Newell, Kalpana Patel, Michael Gartside, Lutz Krause, Sandra Brosda, Lauren G. Aoude, Kelly A. Loffler, Vanessa F. Bonazzi, Ann-Marie Patch, Stephen H. Kazakoff, Oliver Holmes, Qinying Xu, Scott Wood, Conrad Leonard, Guy Lampe, Reginald V. Lord, David C. Whiteman, John V. Pearson, Katia Nones, Nicola Waddell, Andrew P. Barbour
Published 2019-02-01

qpure: A tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles.

by Sarah Song, Katia Nones, David Miller, Ivon Harliwong, Karin S Kassahn, Mark Pinese, Marina Pajic, Anthony J Gill, Amber L Johns, Matthew Anderson, Oliver Holmes, Conrad Leonard, Darrin Taylor, Scott Wood, Qinying Xu, Felicity Newell, Mark J Cowley, Jianmin Wu, Peter Wilson, Lynn Fink, Andrew V Biankin, Nic Waddell, Sean M Grimmond, John V Pearson
Published 2012-01-01

Germline and somatic variant identification using BGISEQ-500 and HiSeq X Ten whole genome sequencing.

by Ann-Marie Patch, Katia Nones, Stephen H Kazakoff, Felicity Newell, Scott Wood, Conrad Leonard, Oliver Holmes, Qinying Xu, Venkateswar Addala, Jenette Creaney, Bruce W Robinson, Shujin Fu, Chunyu Geng, Tong Li, Wenwei Zhang, Xinming Liang, Junhua Rao, Jiahao Wang, Mingyu Tian, Yonggang Zhao, Fei Teng, Honglan Gou, Bicheng Yang, Hui Jiang, Feng Mu, John V Pearson, Nicola Waddell
Published 2018-01-01

Lost in translation: returning germline genetic results in genome-scale cancer research

by Amber L. Johns, Skye H. McKay, Jeremy L. Humphris, Mark Pinese, Lorraine A. Chantrill, R. Scott Mead, Katherine Tucker, Lesley Andrews, Annabel Goodwin, Conrad Leonard, Hilda A. High, Katia Nones, Ann-Marie Patch, Neil D. Merrett, Nick Pavlakis, Karin S. Kassahn, Jaswinder S. Samra, David K. Miller, David K. Chang, Marina Pajic, Australian Pancreatic Cancer Genome Initiative, John V. Pearson, Sean M. Grimmond, Nicola Waddell, Nikolajs Zeps, Anthony J. Gill, Andrew V. Biankin
Published 2017-04-01

Somatic point mutation calling in low cellularity tumors.

by Karin S Kassahn, Oliver Holmes, Katia Nones, Ann-Marie Patch, David K Miller, Angelika N Christ, Ivon Harliwong, Timothy J Bruxner, Qinying Xu, Matthew Anderson, Scott Wood, Conrad Leonard, Darrin Taylor, Felicity Newell, Sarah Song, Senel Idrisoglu, Craig Nourse, Ehsan Nourbakhsh, Suzanne Manning, Shivangi Wani, Anita Steptoe, Marina Pajic, Mark J Cowley, Mark Pinese, David K Chang, Anthony J Gill, Amber L Johns, Jianmin Wu, Peter J Wilson, Lynn Fink, Andrew V Biankin, Nicola Waddell, Sean M Grimmond, John V Pearson
Published 2013-01-01

DNA methylation patterns identify subgroups of pancreatic neuroendocrine tumors with clinical association

by Vanessa Lakis, Rita T. Lawlor, Felicity Newell, Ann-Marie Patch, Andrea Mafficini, Anguraj Sadanandam, Lambros T. Koufariotis, Rebecca L. Johnston, Conrad Leonard, Scott Wood, Borislav Rusev, Vincenzo Corbo, Claudio Luchini, Sara Cingarlini, Luca Landoni, Roberto Salvia, Michele Milella, David Chang, Peter Bailey, Nigel B. Jamieson, Fraser Duthie, Marie-Claude Gingras, Donna M. Muzny, David A. Wheeler, Richard A. Gibbs, Massimo Milione, APGI, ARC-Net, Paolo Pederzoli, Jaswinder S. Samra, Anthony J. Gill, Amber L. Johns, John V. Pearson, Andrew V. Biankin, Sean M. Grimmond, Nicola Waddell, Katia Nones, Aldo Scarpa
Published 2021-02-01

Whole-genome sequencing of acral melanoma reveals genomic complexity and diversity

by Felicity Newell, James S. Wilmott, Peter A. Johansson, Katia Nones, Venkateswar Addala, Pamela Mukhopadhyay, Natasa Broit, Carol M. Amato, Robert Van Gulick, Stephen H. Kazakoff, Ann-Marie Patch, Lambros T. Koufariotis, Vanessa Lakis, Conrad Leonard, Scott Wood, Oliver Holmes, Qinying Xu, Karl Lewis, Theresa Medina, Rene Gonzalez, Robyn P. M. Saw, Andrew J. Spillane, Jonathan R. Stretch, Robert V. Rawson, Peter M. Ferguson, Tristan J. Dodds, John F. Thompson, Georgina V. Long, Mitchell P. Levesque, William A. Robinson, John V. Pearson, Graham J. Mann, Richard A. Scolyer, Nicola Waddell, Nicholas K. Hayward
Published 2020-10-01

Whole genome landscapes of uveal melanoma show an ultraviolet radiation signature in iris tumours

by Peter A. Johansson, Kelly Brooks, Felicity Newell, Jane M. Palmer, James S. Wilmott, Antonia L. Pritchard, Natasa Broit, Scott Wood, Matteo S. Carlino, Conrad Leonard, Lambros T. Koufariotis, Vaishnavi Nathan, Aaron B. Beasley, Madeleine Howlie, Rebecca Dawson, Helen Rizos, Chris W. Schmidt, Georgina V. Long, Hayley Hamilton, Jens F. Kiilgaard, Timothy Isaacs, Elin S. Gray, Olivia J. Rolfe, John J. Park, Andrew Stark, Graham J. Mann, Richard A. Scolyer, John V. Pearson, Nicolas van Baren, Nicola Waddell, Karin W. Wadt, Lindsay A. McGrath, Sunil K. Warrier, William Glasson, Nicholas K. Hayward
Published 2020-05-01

Whole-genome landscape of mucosal melanoma reveals diverse drivers and therapeutic targets

by Felicity Newell, Yan Kong, James S. Wilmott, Peter A. Johansson, Peter M. Ferguson, Chuanliang Cui, Zhongwu Li, Stephen H. Kazakoff, Hazel Burke, Tristan J. Dodds, Ann-Marie Patch, Katia Nones, Varsha Tembe, Ping Shang, Louise van der Weyden, Kim Wong, Oliver Holmes, Serigne Lo, Conrad Leonard, Scott Wood, Qinying Xu, Robert V. Rawson, Pamela Mukhopadhyay, Reinhard Dummer, Mitchell P. Levesque, Göran Jönsson, Xuan Wang, Iwei Yeh, Hong Wu, Nancy Joseph, Boris C. Bastian, Georgina V. Long, Andrew J. Spillane, Kerwin F. Shannon, John F. Thompson, Robyn P. M. Saw, David J. Adams, Lu Si, John V. Pearson, Nicholas K. Hayward, Nicola Waddell, Graham J. Mann, Jun Guo, Richard A. Scolyer
Published 2019-07-01

Ampullary Cancers Harbor ELF3 Tumor Suppressor Gene Mutations and Exhibit Frequent WNT Dysregulation

by Marie-Claude Gingras, Kyle R. Covington, David K. Chang, Lawrence A. Donehower, Anthony J. Gill, Michael M. Ittmann, Chad J. Creighton, Amber L. Johns, Eve Shinbrot, Ninad Dewal, William E. Fisher, Christian Pilarsky, Robert Grützmann, Michael J. Overman, Nigel B. Jamieson, George Van Buren II, Jennifer Drummond, Kimberly Walker, Oliver A. Hampton, Liu Xi, Donna M. Muzny, Harsha Doddapaneni, Sandra L. Lee, Michelle Bellair, Jianhong Hu, Yi Han, Huyen H. Dinh, Mike Dahdouli, Jaswinder S. Samra, Peter Bailey, Nicola Waddell, John V. Pearson, Ivon Harliwong, Huamin Wang, Daniela Aust, Karin A. Oien, Ralph H. Hruban, Sally E. Hodges, Amy McElhany, Charupong Saengboonmee, Fraser R. Duthie, Sean M. Grimmond, Andrew V. Biankin, David A. Wheeler, Richard A. Gibbs
Published 2016-02-01