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

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

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

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

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