Deep learning in cancer diagnosis, prognosis and treatment selection
Tran, Khoa A, Kondrashova, Olga, Bradley, Andrew, Williams, Elizabeth D, Pearson, John V, Waddell, Nicola
Published in Genome medicine (27.09.2021)
Published in Genome medicine (27.09.2021)
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Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays
Homer, Nils, Szelinger, Szabolcs, Redman, Margot, Duggan, David, Tembe, Waibhav, Muehling, Jill, Pearson, John V, Stephan, Dietrich A, Nelson, Stanley F, Craig, David W
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Published in PLoS genetics (01.08.2008)
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Germline and somatic variant identification using BGISEQ-500 and HiSeq X Ten whole genome sequencing
Patch, Ann-Marie, Nones, Katia, Kazakoff, Stephen H, Newell, Felicity, Wood, Scott, Leonard, Conrad, Holmes, Oliver, Xu, Qinying, Addala, Venkateswar, Creaney, Jenette, Robinson, Bruce W, Fu, Shujin, Geng, Chunyu, Li, Tong, Zhang, Wenwei, Liang, Xinming, Rao, Junhua, Wang, Jiahao, Tian, Mingyu, Zhao, Yonggang, Teng, Fei, Gou, Honglan, Yang, Bicheng, Jiang, Hui, Mu, Feng, Pearson, John V, Waddell, Nicola
Published in PloS one (10.01.2018)
Published in PloS one (10.01.2018)
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Phenotypic and molecular dissection of metaplastic breast cancer and the prognostic implications
McCart Reed, Amy Ellen, Kalaw, Emarene, Nones, Katia, Bettington, Mark, Lim, Malcolm, Bennett, James, Johnstone, Kate, Kutasovic, Jamie Rose, Saunus, Jodi Marie, Kazakoff, Stephen, Xu, Qinying, Wood, Scott, Holmes, Oliver, Leonard, Conrad, Reid, Lynne Estelle, Black, Debra, Niland, Colleen, Ferguson, Kaltin, Gresshoff, Irma, Raghavendra, Ashwini, Harvey, Kate, Cooper, Caroline, Liu, Cheng, Kalinowski, Lauren, Reid, Andrew Scott, Davidson, Morgan, Pearson, John V, Pathmanathan, Nirmala, Tse, Gary, Papadimos, David, Pathmanathan, Rajadurai, Harris, Gavin, Yamaguchi, Rin, Tan, Puay Hoon, Fox, Stephen B, O'Toole, Sandra A, Simpson, Peter Thomas, Waddell, Nicola, Lakhani, Sunil R
Published in The Journal of pathology (01.02.2019)
Published in The Journal of pathology (01.02.2019)
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Verifying explainability of a deep learning tissue classifier trained on RNA-seq data
Yap, Melvyn, Johnston, Rebecca L., Foley, Helena, MacDonald, Samual, Kondrashova, Olga, Tran, Khoa A., Nones, Katia, Koufariotis, Lambros T., Bean, Cameron, Pearson, John V., Trzaskowski, Maciej, Waddell, Nicola
Published in Scientific reports (29.01.2021)
Published in Scientific reports (29.01.2021)
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Performance of tumour microenvironment deconvolution methods in breast cancer using single-cell simulated bulk mixtures
Tran, Khoa A., Addala, Venkateswar, Johnston, Rebecca L., Lovell, David, Bradley, Andrew, Koufariotis, Lambros T., Wood, Scott, Wu, Sunny Z., Roden, Daniel, Al-Eryani, Ghamdan, Swarbrick, Alexander, Williams, Elizabeth D., Pearson, John V., Kondrashova, Olga, Waddell, Nicola
Published in Nature communications (16.09.2023)
Published in Nature communications (16.09.2023)
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qpure: A tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles
Song, Sarah, Nones, Katia, Miller, David, Harliwong, Ivon, Kassahn, Karin S, Pinese, Mark, Pajic, Marina, Gill, Anthony J, Johns, Amber L, Anderson, Matthew, Holmes, Oliver, Leonard, Conrad, Taylor, Darrin, Wood, Scott, Xu, Qinying, Newell, Felicity, Cowley, Mark J, Wu, Jianmin, Wilson, Peter, Fink, Lynn, Biankin, Andrew V, Waddell, Nic, Grimmond, Sean M, Pearson, John V
Published in PloS one (25.09.2012)
Published in PloS one (25.09.2012)
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Generalising uncertainty improves accuracy and safety of deep learning analytics applied to oncology
MacDonald, Samual, Foley, Helena, Yap, Melvyn, Johnston, Rebecca L., Steven, Kaiah, Koufariotis, Lambros T., Sharma, Sowmya, Wood, Scott, Addala, Venkateswar, Pearson, John V., Roosta, Fred, Waddell, Nicola, Kondrashova, Olga, Trzaskowski, Maciej
Published in Scientific reports (06.05.2023)
Published in Scientific reports (06.05.2023)
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Diff-Quik Cytology Smears from Endobronchial Ultrasound Transbronchial Needle Aspiration Lymph Node Specimens as a Source of DNA for Next-Generation Sequencing Instead of Cell Blocks
Fielding, David, Dalley, Andrew J., Bashirzadeh, Farzad, Singh, Mahendra, Nandakumar, Lakshmy, McCart Reed, Amy E., Black, Debra, Kazakoff, Stephen, Pearson, John V., Nones, Katia, Waddell, Nicola, Lakhani, Sunil R., Simpson, Peter T.
Published in Respiration (01.01.2019)
Published in Respiration (01.01.2019)
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A survey of genetic human cortical gene expression
Myers, Amanda J, Gibbs, J Raphael, Webster, Jennifer A, Rohrer, Kristen, Zhao, Alice, Marlowe, Lauren, Kaleem, Mona, Leung, Doris, Bryden, Leslie, Nath, Priti, Zismann, Victoria L, Joshipura, Keta, Huentelman, Matthew J, Hu-Lince, Diane, Coon, Keith D, Craig, David W, Pearson, John V, Holmans, Peter, Heward, Christopher B, Reiman, Eric M, Stephan, Dietrich, Hardy, John
Published in Nature genetics (01.12.2007)
Published in Nature genetics (01.12.2007)
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Performance of somatic structural variant calling in lung cancer using Oxford Nanopore sequencing technology
Liu, Lingchen, Zhang, Jia, Wood, Scott, Newell, Felicity, Leonard, Conrad, Koufariotis, Lambros T, Nones, Katia, Dalley, Andrew J, Chittoory, Haarika, Bashirzadeh, Farzad, Son, Jung Hwa, Steinfort, Daniel, Williamson, Jonathan P, Bint, Michael, Pahoff, Carl, Nguyen, Phan T, Twaddell, Scott, Arnold, David, Grainge, Christopher, Simpson, Peter T, Fielding, David, Waddell, Nicola, Pearson, John V
Published in BMC genomics (30.09.2024)
Published in BMC genomics (30.09.2024)
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Genetic Control of Human Brain Transcript Expression in Alzheimer Disease
Webster, Jennifer A., Gibbs, J. Raphael, Clarke, Jennifer, Ray, Monika, Zhang, Weixiong, Holmans, Peter, Rohrer, Kristen, Zhao, Alice, Marlowe, Lauren, Kaleem, Mona, McCorquodale, Donald S., Cuello, Cindy, Leung, Doris, Bryden, Leslie, Nath, Priti, Zismann, Victoria L., Joshipura, Keta, Huentelman, Matthew J., Hu-Lince, Diane, Coon, Keith D., Craig, David W., Pearson, John V., Heward, Christopher B., Reiman, Eric M., Stephan, Dietrich, Hardy, John, Myers, Amanda J.
Published in American journal of human genetics (01.04.2009)
Published in American journal of human genetics (01.04.2009)
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PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization
Nagaraj, Shivashankar H, Waddell, Nicola, Madugundu, Anil K, Wood, Scott, Jones, Alun, Mandyam, Ramya A, Nones, Katia, Pearson, John V, Grimmond, Sean M
Published in Journal of proteome research (01.05.2015)
Published in Journal of proteome research (01.05.2015)
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Comprehensive genomic and tumour immune profiling reveals potential therapeutic targets in malignant pleural mesothelioma
Creaney, Jenette, Patch, Ann-Marie, Addala, Venkateswar, Sneddon, Sophie A, Nones, Katia, Dick, Ian M, Lee, Y C Gary, Newell, Felicity, Rouse, Ebony J, Naeini, Marjan M, Kondrashova, Olga, Lakis, Vanessa, Nakas, Apostolos, Waller, David, Sharkey, Annabel, Mukhopadhyay, Pamela, Kazakoff, Stephen H, Koufariotis, Lambros T, Davidson, Aimee L, Ramarao-Milne, Priya, Holmes, Oliver, Xu, Qinying, Leonard, Conrad, Wood, Scott, Grimmond, Sean M, Bueno, Raphael, Fennell, Dean A, Pearson, John V, Robinson, Bruce W, Waddell, Nicola
Published in Genome medicine (30.05.2022)
Published in Genome medicine (30.05.2022)
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Unexpected UVR and non-UVR mutation burden in some acral and cutaneous melanomas
Rawson, Robert V, Johansson, Peter A, Hayward, Nicholas K, Waddell, Nicola, Patch, Ann-Marie, Lo, Serigne, Pearson, John V, Thompson, John F, Mann, Graham J, Scolyer, Richard A, Wilmott, James S
Published in Laboratory investigation (01.02.2017)
Published in Laboratory investigation (01.02.2017)
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Patient-derived xenograft models capture genomic heterogeneity in endometrial cancer
Bonazzi, Vanessa F, Kondrashova, Olga, Smith, Deborah, Nones, Katia, Sengal, Asmerom T, Ju, Robert, Packer, Leisl M, Koufariotis, Lambros T, Kazakoff, Stephen H, Davidson, Aimee L, Ramarao-Milne, Priya, Lakis, Vanessa, Newell, Felicity, Rogers, Rebecca, Davies, Claire, Nicklin, James, Garrett, Andrea, Chetty, Naven, Perrin, Lewis, Pearson, John V, Patch, Ann-Marie, Waddell, Nicola, Pollock, Pamela M
Published in Genome medicine (10.01.2022)
Published in Genome medicine (10.01.2022)
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Spatial intra-tumour heterogeneity and treatment-induced genomic evolution in oesophageal adenocarcinoma: implications for prognosis and therapy
Brosda, Sandra, Aoude, Lauren G, Bonazzi, Vanessa F, Patel, Kalpana, Lonie, James M, Belle, Clemence J, Newell, Felicity, Koufariotis, Lambros T, Addala, Venkateswar, Naeini, Marjan M, Pearson, John V, Krause, Lutz, Waddell, Nicola, Barbour, Andrew P
Published in Genome medicine (17.07.2024)
Published in Genome medicine (17.07.2024)
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Whole exome sequencing of an asbestos-induced wild-type murine model of malignant mesothelioma
Sneddon, Sophie, Patch, Ann-Marie, Dick, Ian M, Kazakoff, Stephen, Pearson, John V, Waddell, Nicola, Allcock, Richard J N, Holt, Robert A, Robinson, Bruce W S, Creaney, Jenette
Published in BMC cancer (02.06.2017)
Published in BMC cancer (02.06.2017)
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Identification of PVT1 as a Candidate Gene for End-Stage Renal Disease in Type 2 Diabetes Using a Pooling-Based Genome-Wide Single Nucleotide Polymorphism Association Study
HANSON, Robert L, CRAIG, David W, MILLIS, Meredith P, YEATTS, Kimberly A, KOBES, Sayuko, PEARSON, John V, LEE, Anne M, KNOWLER, William C, NELSON, Robert G, WOLFORD, Johanna K
Published in Diabetes (New York, N.Y.) (01.04.2007)
Published in Diabetes (New York, N.Y.) (01.04.2007)
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Discrepancies in tumor mutation burden reporting from sequential endobronchial ultrasound transbronchial needle aspiration samples within single lymph node stations - brief report
Fielding, David, Dalley, Andrew J., Singh, Mahendra, Nandakumar, Lakshmy, Lakis, Vanessa, Chittoory, Haarika, Fairbairn, David, Patch, Ann-Marie, Kazakoff, Stephen H., Ferguson, Kaltin, Bashirzadeh, Farzad, Bint, Michael, Pahoff, Carl, Son, Jung Hwa, Ryan, Kimberley, Hodgson, Alan, Sharma, Sowmya, Pearson, John V., Waddell, Nicola, Lakhani, Sunil R., Hartel, Gunter, Simpson, Peter T., Nones, Katia
Published in Frontiers in oncology (19.10.2023)
Published in Frontiers in oncology (19.10.2023)
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