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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A2AR Adenosine Signaling Suppresses Natural Killer Cell Maturation in the Tumor Microenvironment
Young, Arabella, Ngiow, Shin Foong, Gao, Yulong, Patch, Ann-Marie, Barkauskas, Deborah S, Messaoudene, Meriem, Lin, Gene, Coudert, Jerome D, Stannard, Kimberley A, Zitvogel, Laurence, Degli-Esposti, Mariapia A, Vivier, Eric, Waddell, Nicola, Linden, Joel, Huntington, Nicholas D, Souza-Fonseca-Guimaraes, Fernando, Smyth, Mark J
Published in Cancer research (Chicago, Ill.) (15.02.2018)
Published in Cancer research (Chicago, Ill.) (15.02.2018)
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MHC Class II Antigen Presentation by the Intestinal Epithelium Initiates Graft-versus-Host Disease and Is Influenced by the Microbiota
Koyama, Motoko, Mukhopadhyay, Pamela, Schuster, Iona S., Henden, Andrea S., Hülsdünker, Jan, Varelias, Antiopi, Vetizou, Marie, Kuns, Rachel D., Robb, Renee J., Zhang, Ping, Blazar, Bruce R., Thomas, Ranjeny, Begun, Jakob, Waddell, Nicola, Trinchieri, Giorgio, Zeiser, Robert, Clouston, Andrew D., Degli-Esposti, Mariapia A., Hill, Geoffrey R.
Published in Immunity (Cambridge, Mass.) (19.11.2019)
Published in Immunity (Cambridge, Mass.) (19.11.2019)
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Clinically significant changes in genes and variants associated with epilepsy over time: implications for re-analysis
Robertson, Alan J., Tran, Khoa A., Bennett, Carmen, Sullivan, Clair, Stark, Zornitza, Vadlamudi, Lata, Waddell, Nicola
Published in Scientific reports (02.04.2024)
Published in Scientific reports (02.04.2024)
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Tailored first-line and second-line CDK4-targeting treatment combinations in mouse models of pancreatic cancer
Chou, Angela, Froio, Danielle, Nagrial, Adnan M, Parkin, Ashleigh, Murphy, Kendelle J, Chin, Venessa T, Wohl, Dalia, Steinmann, Angela, Stark, Rhys, Drury, Alison, Walters, Stacey N, Vennin, Claire, Burgess, Andrew, Pinese, Mark, Chantrill, Lorraine A, Cowley, Mark J, Molloy, Timothy J, Waddell, Nicola, Johns, Amber, Grimmond, Sean M, Chang, David K, Biankin, Andrew V, Sansom, Owen J, Morton, Jennifer P, Grey, Shane T, Cox, Thomas R, Turchini, John, Samra, Jaswinder, Clarke, Stephen J, Timpson, Paul, Gill, Anthony J, Pajic, Marina
Published in Gut (01.12.2018)
Published in Gut (01.12.2018)
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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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Jak2V617F and Dnmt3a loss cooperate to induce myelofibrosis through activated enhancer-driven inflammation
Jacquelin, Sebastien, Straube, Jasmin, Cooper, Leanne, Vu, Therese, Song, Axia, Bywater, Megan, Baxter, Eva, Heidecker, Matthew, Wackrow, Brad, Porter, Amy, Ling, Victoria, Green, Joanne, Austin, Rebecca, Kazakoff, Stephen, Waddell, Nicola, Hesson, Luke B., Pimanda, John E., Stegelmann, Frank, Bullinger, Lars, Döhner, Konstanze, Rampal, Raajit K., Heckl, Dirk, Hill, Geoffrey R., Lane, Steven W.
Published in Blood (27.12.2018)
Published in Blood (27.12.2018)
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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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Interleukin-12 from CD103 + Batf3-Dependent Dendritic Cells Required for NK-Cell Suppression of Metastasis
Mittal, Deepak, Vijayan, Dipti, Putz, Eva M, Aguilera, Amelia R, Markey, Kate A, Straube, Jasmin, Kazakoff, Stephen, Nutt, Stephen L, Takeda, Kazuyoshi, Hill, Geoffrey R, Waddell, Nicola, Smyth, Mark J
Published in Cancer immunology research (01.12.2017)
Published in Cancer immunology research (01.12.2017)
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CEP55 is a determinant of cell fate during perturbed mitosis in breast cancer
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
Published in EMBO molecular medicine (01.09.2018)
Published in EMBO molecular medicine (01.09.2018)
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Sleeping Beauty mutagenesis reveals cooperating mutations and pathways in pancreatic adenocarcinoma
Mann, Karen M., Ward, Jerrold M., Yew, Christopher Chin Kuan, Kovochich, Anne, Dawson, David W., Black, Michael A., Brett, Benjamin T., Sheetz, Todd E., Dupuy, Adam J., Chang, David K., Biankin, Andrew V., Waddell, Nicola, Kassahn, Karin S., Grimmond, Sean M., Rust, Alistair G., Adams, David J., Jenkins, Nancy A., Copeland, Neal G.
Published in Proceedings of the National Academy of Sciences - PNAS (17.04.2012)
Published in Proceedings of the National Academy of Sciences - PNAS (17.04.2012)
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Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma
Feigin, Michael E, Garvin, Tyler, Bailey, Peter, Waddell, Nicola, Chang, David K, Kelley, David R, Shuai, Shimin, Gallinger, Steven, McPherson, John D, Grimmond, Sean M, Khurana, Ekta, Stein, Lincoln D, Biankin, Andrew V, Schatz, Michael C, Tuveson, David A
Published in Nature genetics (01.06.2017)
Published in Nature genetics (01.06.2017)
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Long Noncoding RNAs CUPID1 and CUPID2 Mediate Breast Cancer Risk at 11q13 by Modulating the Response to DNA Damage
Betts, Joshua A., Moradi Marjaneh, Mahdi, Al-Ejeh, Fares, Lim, Yi Chieh, Shi, Wei, Sivakumaran, Haran, Tropée, Romain, Patch, Ann-Marie, Clark, Michael B., Bartonicek, Nenad, Wiegmans, Adrian P., Hillman, Kristine M., Kaufmann, Susanne, Bain, Amanda L., Gloss, Brian S., Crawford, Joanna, Kazakoff, Stephen, Wani, Shivangi, Wen, Shu W., Day, Bryan, Möller, Andreas, Cloonan, Nicole, Pearson, John, Brown, Melissa A., Mercer, Timothy R., Waddell, Nicola, Khanna, Kum Kum, Dray, Eloise, Dinger, Marcel E., Edwards, Stacey L., French, Juliet D.
Published in American journal of human genetics (03.08.2017)
Published in American journal of human genetics (03.08.2017)
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Sharing genomic data from clinical testing with researchers: public survey of expectations of clinical genomic data management in Queensland, Australia
Vidgen, Miranda E, Kaladharan, Sid, Malacova, Eva, Hurst, Cameron, Waddell, Nicola
Published in BMC medical ethics (19.11.2020)
Published in BMC medical ethics (19.11.2020)
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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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EIF1AX and NRAS Mutations Co-occur and Cooperate in Low-Grade Serous Ovarian Carcinomas
Etemadmoghadam, Dariush, Azar, Walid J, Lei, Ying, Moujaber, Tania, Garsed, Dale W, Kennedy, Catherine J, Fereday, Sian, Mitchell, Chris, Chiew, Yoke-Eng, Hendley, Joy, Sharma, Raghwa, Harnett, Paul R, Li, Jason, Christie, Elizabeth L, Patch, Ann-Marie, George, Joshy, Au-Yeung, George, Mir Arnau, Gisela, Holloway, Timothy P, Semple, Timothy, Pearson, John V, Waddell, Nicola, Grimmond, Sean M, Köbel, Martin, Rizos, Helen, Lomakin, Ivan B, Bowtell, David D L, deFazio, Anna
Published in Cancer research (Chicago, Ill.) (15.08.2017)
Published in Cancer research (Chicago, Ill.) (15.08.2017)
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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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Recurrent inactivating RASA2 mutations in melanoma
Arafeh, Rand, Qutob, Nouar, Emmanuel, Rafi, Keren-Paz, Alona, Madore, Jason, Elkahloun, Abdel, Wilmott, James S, Gartner, Jared J, Di Pizio, Antonella, Winograd-Katz, Sabina, Sindiri, Sivasish, Rotkopf, Ron, Dutton-Regester, Ken, Johansson, Peter, Pritchard, Antonia L, Waddell, Nicola, Hill, Victoria K, Lin, Jimmy C, Hevroni, Yael, Rosenberg, Steven A, Khan, Javed, Ben-Dor, Shifra, Niv, Masha Y, Ulitsky, Igor, Mann, Graham J, Scolyer, Richard A, Hayward, Nicholas K, Samuels, Yardena
Published in Nature genetics (01.12.2015)
Published in Nature genetics (01.12.2015)
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Chromatin interactome mapping at 139 independent breast cancer risk signals
Beesley, Jonathan, Sivakumaran, Haran, Moradi Marjaneh, Mahdi, Lima, Luize G, Hillman, Kristine M, Kaufmann, Susanne, Tuano, Natasha, Hussein, Nehal, Ham, Sunyoung, Mukhopadhyay, Pamela, Kazakoff, Stephen, Lee, Jason S, Michailidou, Kyriaki, Barnes, Daniel R, Antoniou, Antonis C, Fachal, Laura, Dunning, Alison M, Easton, Douglas F, Waddell, Nicola, Rosenbluh, Joseph, Möller, Andreas, Chenevix-Trench, Georgia, French, Juliet D, Edwards, Stacey L
Published in Genome Biology (07.01.2020)
Published in Genome Biology (07.01.2020)
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