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)
Get full text
Journal Article
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
Published in PLoS genetics (01.08.2008)
Published in PLoS genetics (01.08.2008)
Get full text
Journal Article
The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional tradeoffs in an obligate symbiont
Tisserant, E., Kohler, A., Dozolme‐Seddas, P., Balestrini, R., Benabdellah, K., Colard, A., Croll, D., Da Silva, C., Gomez, S. K., Koul, R., Ferrol, N., Fiorilli, V., Formey, D., Franken, Ph, Helber, N., Hijri, M., Lanfranco, L., Lindquist, E., Liu, Y., Malbreil, M., Morin, E., Poulain, J., Shapiro, H., van Tuinen, D., Waschke, A., Azcón‐Aguilar, C., Bécard, G., Bonfante, P., Harrison, M. J., Küster, H., Lammers, P., Paszkowski, U., Requena, N., Rensing, S. A., Roux, C., Sanders, I. R., Shachar‐Hill, Y., Tuskan, G., Young, J. P. W., Gianinazzi‐Pearson, V., Martin, F.
Published in The New phytologist (01.02.2012)
Published in The New phytologist (01.02.2012)
Get full text
Journal Article
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)
Get full text
Journal Article
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)
Get full text
Journal Article
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)
Get full text
Journal Article
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)
Get full text
Journal Article
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)
Get full text
Journal Article
The identification of sulfide oxidation as a potential metabolism driving primary production on late Noachian Mars
Macey, M C, Fox-Powell, M, Ramkissoon, N K, Stephens, B P, Barton, T, Schwenzer, S P, Pearson, V K, Cousins, C R, Olsson-Francis, K
Published in Scientific reports (02.07.2020)
Published in Scientific reports (02.07.2020)
Get full text
Journal Article
Mycorrhiza-induced resistance against the root–knot nematode Meloidogyne incognita involves priming of defense gene responses in tomato
Vos, C., Schouteden, N., van Tuinen, D., Chatagnier, O., Elsen, A., De Waele, D., Panis, B., Gianinazzi-Pearson, V.
Published in Soil biology & biochemistry (01.05.2013)
Published in Soil biology & biochemistry (01.05.2013)
Get full text
Journal Article
Differential sensitivity to speech rhythms in young and older adults
Pearson, Dylan V, Shen, Yi, McAuley, J Devin, Kidd, Gary R
Published in Frontiers in psychology (12.05.2023)
Published in Frontiers in psychology (12.05.2023)
Get full text
Journal Article
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)
Get full text
Journal Article
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)
Get full text
Journal Article
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)
Get full text
Journal Article
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)
Get full text
Journal Article
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)
Get full text
Journal Article
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)
Get full text
Journal Article
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)
Get full text
Journal Article
β-1,3 Glucan Sulfate Induces Resistance in Grapevine against Plasmopara viticola Through Priming of Defense Responses, Including HR-like Cell Death
Trouvelot, S, Varnier, A.L, Allegre, M, Mercier, L, Baillieul, F, Arnould, C, Gianinazzi-Pearson, V, Klarzynski, O, Joubert, J.M, Pugin, A
Published in Molecular plant-microbe interactions (01.02.2008)
Published in Molecular plant-microbe interactions (01.02.2008)
Get full text
Journal Article