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

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Acquired RAD51C Promoter Methylation Loss Causes PARP Inhibitor Resistance in High-Grade Serous Ovarian Carcinoma von Nesic, Ksenija, Kondrashova, Olga, Hurley, Rachel M., McGehee, Cordelia D., Vandenberg, Cassandra J., Ho, Gwo-Yaw, Lieschke, Elizabeth, Dall, Genevieve, Bound, Nirashaa, Shield-Artin, Kristy, Radke, Marc, Musafer, Ashan, Chai, Zi Qing, Ghamsari, Mohammad Reza Eftekhariyan, Harrell, Maria, Kee, Damien, Olesen, Inger, McNally, Orla, Traficante, Nadia, DeFazio, Anna, Bowtell, David D. L., Swisher, Elizabeth M., Weroha, S. John, Nones, Katia, Waddell, Nicola, Kaufmann, Scott H., Dobrovic, Alexander, Wakefield, Matthew J., Scott, Clare L.

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Phenotypic and molecular dissection of metaplastic breast cancer and the prognostic implications von 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

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Genome‐wide DNA methylation patterns in pancreatic ductal adenocarcinoma reveal epigenetic deregulation of SLIT‐ROBO, ITGA2 and MET signaling von Nones, Katia, Waddell, Nic, Song, Sarah, Patch, Ann‐Marie, Miller, David, Johns, Amber, Wu, Jianmin, Kassahn, Karin S., Wood, David, Bailey, Peter, Fink, Lynn, Manning, Suzanne, Christ, Angelika N., Nourse, Craig, Kazakoff, Stephen, Taylor, Darrin, Leonard, Conrad, Chang, David K., Jones, Marc D., Thomas, Michelle, Watson, Clare, Pinese, Mark, Cowley, Mark, Rooman, Ilse, Pajic, Marina, Butturini, Giovanni, Malpaga, Anna, Corbo, Vincenzo, Crippa, Stefano, Falconi, Massimo, Zamboni, Giuseppe, Castelli, Paola, Lawlor, Rita T., Gill, Anthony J., Scarpa, Aldo, Pearson, John V., Biankin, Andrew V., Grimmond, Sean M.

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miR-139-5p is a regulator of metastatic pathways in breast cancer von Krishnan, Keerthana, Steptoe, Anita L, Martin, Hilary C, Pattabiraman, Diwakar R, Nones, Katia, Waddell, Nic, Mariasegaram, Mythily, Simpson, Peter T, Lakhani, Sunil R, Vlassov, Alexander, Grimmond, Sean M, Cloonan, Nicole

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CEP55 is a determinant of cell fate during perturbed mitosis in breast cancer von Kalimutho, Murugan, Sinha, Debottam, Jeffery, Jessie, Nones, Katia, Srihari, Sriganesh, Fernando, Winnie C, Duijf, Pascal HG, Vennin, Claire, Raninga, Prahlad, Nanayakkara, Devathri, Mittal, Deepak, Saunus, Jodi M, Lakhani, Sunil R, López, J Alejandro, Spring, Kevin J, Timpson, Paul, Gabrielli, Brian, Waddell, Nicola, Khanna, Kum Kum

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Estimating the costs of genomic sequencing in cancer control von Gordon, Louisa G., White, Nicole M., Elliott, Thomas M., Nones, Katia, Beckhouse, Anthony G., Rodriguez-Acevedo, Astrid J., Webb, Penelope M., Lee, Xing J., Graves, Nicholas, Schofield, Deborah J.

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Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content von Ganesamoorthy, Devika, Robertson, Alan James, Chen, Wenhan, Hall, Michael B, Cao, Minh Duc, Ferguson, Kaltin, Lakhani, Sunil R, Nones, Katia, Simpson, Peter T, Coin, Lachlan J M

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MicroRNA-182-5p targets a network of genes involved in DNA repair von Krishnan, Keerthana, Steptoe, Anita L, Martin, Hilary C, Wani, Shivangi, Nones, Katia, Waddell, Nic, Mariasegaram, Mythily, Simpson, Peter T, Lakhani, Sunil R, Gabrielli, Brian, Vlassov, Alexander, Cloonan, Nicole, Grimmond, Sean M

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Performance of somatic structural variant calling in lung cancer using Oxford Nanopore sequencing technology von 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

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Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy von M. Naeini, Marjan, Newell, Felicity, Aoude, Lauren G., Bonazzi, Vanessa F., Patel, Kalpana, Lampe, Guy, Koufariotis, Lambros T., Lakis, Vanessa, Addala, Venkateswar, Kondrashova, Olga, Johnston, Rebecca L., Sharma, Sowmya, Brosda, Sandra, Holmes, Oliver, Leonard, Conrad, Wood, Scott, Xu, Qinying, Thomas, Janine, Walpole, Euan, Tao Mai, G., Ackland, Stephen P., Martin, Jarad, Burge, Matthew, Finch, Robert, Karapetis, Christos S., Shannon, Jenny, Nott, Louise, Bohmer, Robert, Wilson, Kate, Barnes, Elizabeth, Zalcberg, John R., Mark Smithers, B., Simes, John, Price, Timothy, Gebski, Val, Nones, Katia, Watson, David I., Pearson, John V., Barbour, Andrew P., Waddell, Nicola

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

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PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization von Nagaraj, Shivashankar H, Waddell, Nicola, Madugundu, Anil K, Wood, Scott, Jones, Alun, Mandyam, Ramya A, Nones, Katia, Pearson, John V, Grimmond, Sean M

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Comprehensive genomic and tumour immune profiling reveals potential therapeutic targets in malignant pleural mesothelioma von 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

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Whole Genome Sequencing in Advanced Lung Cancer can be Performed Using Diff-Quik Cytology Smears Derived from Endobronchial Ultrasound, Transbronchial Needle Aspiration (EBUS TBNA) von Fielding, David, Dalley, Andrew J., Singh, Mahendra, Nandakumar, Lakshmy, Lakis, Vanessa, Chittoory, Haarika, Fairbairn, David, Ferguson, Kaltin, Bashirzadeh, Farzad, Bint, Michael, Pahoff, Carl, Son, Jung Hwa, Hodgson, Alan, Pearson, John V., Waddell, Nicola, Lakhani, Sunil R., Hartel, Gunter, Nones, Katia, Simpson, Peter T.

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Patient-derived xenograft models capture genomic heterogeneity in endometrial cancer von 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

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

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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 Bloc... von 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.

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Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma von Krause, Lutz, Nones, Katia, Loffler, Kelly A, Nancarrow, Derek, Oey, Harald, Tang, Yue Hang, Wayte, Nicola J, Patch, Ann Marie, Patel, Kalpana, Brosda, Sandra, Manning, Suzanne, Lampe, Guy, Clouston, Andrew, Thomas, Janine, Stoye, Jens, Hussey, Damian J, Watson, David I, Lord, Reginald V, Phillips, Wayne A, Gotley, David, Smithers, B Mark, Whiteman, David C, Hayward, Nicholas K, Grimmond, Sean M, Waddell, Nicola, Barbour, Andrew P

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Next-Generation Sequencing of Endobronchial Ultrasound Transbronchial Needle Aspiration Specimens in Lung Cancer von Fielding, David, Dalley, Andrew J, Bashirzadeh, Farzad, Singh, Mahendra, Nandakumar, Lakshmy, McCart Reed, Amy E, Black, Debra, Kazakoff, Stephen, Nones, Katia, Pearson, John, Waddell, Nic, Lakhani, Sunil R, Simpson, Peter T

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