Dr Katia Nones
Honorary Associate Professor
School of Biomedical Sciences
Researcher biography
Dr Nones research program is focused in using genomics to better understand the molecular aspects of cancer development and response to treatment. Her work encompassed a series of cancer types including oesophageal, pancreatic, breast and lung cancers. Cancer genomics is impacting patient care through precision medicine. Her work is contributing to two areas: i) our understanding of tumour development and progression by identifying new genes and/or mechanisms that drive cancer progression or response to treatment; and ii) investigating steps to improve the translation of genomics into patient care to improve outcomes for cancer patients.
Book Chapter
Nones, Katia and Villas-Boas, Silas G. (2010). Evaluation of the beneficial effects of phytonutrients by metabolomics. Genomics, proteomics, and metabolomics in nutraceuticals and functional foods. (pp. 287-296) edited by Debasis Bagchi, Francis C. Lau and Manashi Bagchi. Iowa, USA: Blackwell Publishing. doi: 10.1002/9780813821474.ch19
Journal Articles
Newell, Felicity, Pires da Silva, Ines, Johansson, Peter A., Menzies, Alexander M., Wilmott, James S., Addala, Venkateswar, Carlino, Matteo S., Rizos, Helen, Nones, Katia, Edwards, Jarem J., Lakis, Vanessa, Kazakoff, Stephen H., Mukhopadhyay, Pamela, Ferguson, Peter M., Leonard, Conrad, Koufariotis, Lambros T., Wood, Scott, Blank, Christian U., Thompson, John F., Spillane, Andrew J., Saw, Robyn P.M., Shannon, Kerwin F., Pearson, John V., Mann, Graham J., Hayward, Nicholas K., Scolyer, Richard A., Waddell, Nicola and Long, Georgina V. (2025). Erratum: Multiomic profiling of checkpoint inhibitor-treated melanoma: Identifying predictors of response and resistance, and markers of biological discordance (Cancer Cell (2022) 40(1) (88–102.e7), (S1535610821006127), (10.1016/j.ccell.2021.11.012)). Cancer Cell, 43 (3), 563. doi: 10.1016/j.ccell.2025.01.011
Lakis, Vanessa, Chan, Noni L, Lyons, Ruth, Blackburn, Nicola, Nguyen, Tam Hong, Chang, Crystal, Masel, Andrew, West, Nicholas P., Boyle, Glen M., Patch, Ann-Marie, Gill, Anthony J. and Nones, Katia (2025). Spatial Transcriptomics Reveals Novel Mechanisms Involved in Perineural Invasion in Pancreatic Ductal Adenocarcinomas. Cancers, 17 (5) 852, 852-5. doi: 10.3390/cancers17050852
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 and Pearson, John V. (2024). Performance of somatic structural variant calling in lung cancer using Oxford Nanopore sequencing technology. BMC genomics, 25 (1) 898. doi: 10.1186/s12864-024-10792-3
Fielding, David, Lakis, Vanessa, Dalley, Andrew J., Chittoory, Haarika, Newell, Felicity, Koufariotis, Lambros T., Patch, Ann-Marie, Kazakoff, Stephen, Bashirzadeh, Farzad, Son, Jung Hwa, Ryan, Kimberley, Steinfort, Daniel, Williamson, Jonathan P., Bint, Michael, Pahoff, Carl, Nguyen, Phan Tien, Twaddell, Scott, Arnold, David, Grainge, Christopher, Pattison, Andrew, Fairbairn, David, Gune, Shailendra, Christie, Jemma, Holmes, Oliver, Leonard, Conrad, Wood, Scott, Pearson, John V., Lakhani, Sunil R., Waddell, Nicola ... Nones, Katia (2024). Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) samples from advanced non-small cell lung cancer for whole genome, whole exome and comprehensive panel sequencing. Cancers, 16 (4) 785. doi: 10.3390/cancers16040785
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. and Nones, Katia (2023). Discrepancies in tumor mutation burden reporting from sequential endobronchial ultrasound transbronchial needle aspiration samples within single lymph node stations - brief report. Frontiers in Oncology, 13 1259882, 1-10. doi: 10.3389/fonc.2023.1259882
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 and Simpson, Peter T. (2023). Whole genome sequencing in advanced lung cancer can be performed using diff-quik cytology smears derived from endobronchial ultrasound, transbronchial needle aspiration (EBUS TBNA). Lung, 201 (4), 407-413. doi: 10.1007/s00408-023-00631-9
Fielding, David I., 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, Hodgson, Alan, Sharma, Sowmya, Waddell, Nicola, Lakhani, Sunil R., Hartel, Gunter, Nones, Katia and Simpson, Peter T. (2023). Evaluating Diff‐Quik cytology smears for large‐panel mutation testing in lung cancer—Predicting DNA content and success with low‐malignant‐cellularity samples. Cancer Cytopathology, 131 (6), 373-382. doi: 10.1002/cncy.22690
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 ... Waddell, Nicola (2023). Multi-omic features of oesophageal adenocarcinoma in patients treated with preoperative neoadjuvant therapy. Nature Communications, 14 (1) 3155, 3155. doi: 10.1038/s41467-023-38891-x
Yuan, Yuan, Ju, Young Seok, Kim, Youngwook, Li, Jun, Wang, Yumeng, Yoon, Christopher J., Yang, Yang, Martincorena, Inigo, Creighton, Chad J., Weinstein, John N., Xu, Yanxun, Han, Leng, Kim, Hyung-Lae, Nakagawa, Hidewaki, Park, Keunchil, Campbell, Peter J., Liang, Han, Aaltonen, Lauri A., Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J., Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C., Al-Ahmadie, Hikmat ... von Mering, Christian (2023). Author Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers (Nature Genetics, (2020), 52, 3, (342-352), 10.1038/s41588-019-0557-x). Nature Genetics, 55 (5), 892-892. doi: 10.1038/s41588-020-0629-y
Yuan, Yuan, Ju, Young Seok, Kim, Youngwook, Li, Jun, Wang, Yumeng, Yoon, Christopher J., Yang, Yang, Martincorena, Inigo, Creighton, Chad J., Weinstein, John N., Xu, Yanxun, Han, Leng, Kim, Hyung-Lae, Nakagawa, Hidewaki, Park, Keunchil, Campbell, Peter J., Liang, Han, Aaltonen, Lauri A., Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J., Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C., Al-Ahmadie, Hikmat ... von Mering, Christian (2023). Publisher Correction: Comprehensive molecular characterization of mitochondrial genomes in human cancers (Nature Genetics, (2020), 52, 3, (342-352), 10.1038/s41588-019-0557-x). Nature Genetics, 55 (5), 893-893. doi: 10.1038/s41588-020-0587-4
Stark, Zornitza, Boughtwood, Tiffany, Haas, Matilda, Braithwaite, Jeffrey, Gaff, Clara L., Goranitis, Ilias, Spurdle, Amanda B., Hansen, David P., Hofmann, Oliver, Laing, Nigel, Metcalfe, Sylvia, Newson, Ainsley J., Scott, Hamish S., Thorne, Natalie, Ward, Robyn L., Dinger, Marcel E., Best, Stephanie, Long, Janet C., Grimmond, Sean M., Pearson, John, Waddell, Nicola, Barnett, Christopher P., Cook, Matthew, Field, Michael, Fielding, David, Fox, Stephen B., Gecz, Jozef, Jaffe, Adam, Leventer, Richard J. ... North, Kathryn N. (2023). Australian genomics: outcomes of a 5-year national program to accelerate the integration of genomics in healthcare. American Journal of Human Genetics, 110 (3), 419-426. doi: 10.1016/j.ajhg.2023.01.018
Aaltonen, Lauri A., Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J., Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C., Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T., Al-Shahrour, Fatima, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B., Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G., Amary, Fernanda, Amin, Samirkumar B., Aminou, Brice, Ammerpohl, Ole, Anderson, Matthew J., Ang, Yeng, Antonello, Davide, Anur, Pavana ... von Mering, Christian (2023). Author Correction: Pan-cancer analysis of whole genomes (Nature, (2020), 578, 7793, (82-93), 10.1038/s41586-020-1969-6). Nature, 614 (7948). doi: 10.1038/s41586-022-05598-w
Cmero, Marek, Yuan, Ke, Ong, Cheng Soon, Schröder, Jan, Adams, David J., Anur, Pavana, Beroukhim, Rameen, Boutros, Paul C., Bowtell, David D. L., Campbell, Peter J., Cao, Shaolong, Christie, Elizabeth L., Cun, Yupeng, Dawson, Kevin J., Demeulemeester, Jonas, Dentro, Stefan C., Deshwar, Amit G., Donmez, Nilgun, Drews, Ruben M., Eils, Roland, Fan, Yu, Fittall, Matthew W., Garsed, Dale W., Gerstung, Moritz, Getz, Gad, Gonzalez, Santiago, Ha, Gavin, Haase, Kerstin, Imielinski, Marcin ... von Mering, Christian (2022). Author Correction: Inferring structural variant cancer cell fraction (Nature Communications, (2020), 11, 1, (730), 10.1038/s41467-020-14351-8). Nature Communications, 13 (1) 7568. doi: 10.1038/s41467-022-32338-5
Bhandari, Vinayak, Li, Constance H., Bristow, Robert G., Boutros, Paul C., Aaltonen, Lauri A., Abascal, Federico, Abeshouse, Adam, Aburatani, Hiroyuki, Adams, David J., Agrawal, Nishant, Ahn, Keun Soo, Ahn, Sung-Min, Aikata, Hiroshi, Akbani, Rehan, Akdemir, Kadir C., Al-Ahmadie, Hikmat, Al-Sedairy, Sultan T., Al-Shahrour, Fatima, Alawi, Malik, Albert, Monique, Aldape, Kenneth, Alexandrov, Ludmil B., Ally, Adrian, Alsop, Kathryn, Alvarez, Eva G., Amary, Fernanda, Amin, Samirkumar B., Aminou, Brice, Ammerpohl, Ole ... von Mering, Christian (2022). Author Correction: Divergent mutational processes distinguish hypoxic and normoxic tumours (Nature Communications, (2020), 11, 1, (737), 10.1038/s41467-019-14052-x). Nature Communications, 13 (1) 7569. doi: 10.1038/s41467-022-32339-4
Tudini, Emma, Andrews, James, Lawrence, David M., King-Smith, Sarah L., Baker, Naomi, Baxter, Leanne, Beilby, John, Bennetts, Bruce, Beshay, Victoria, Black, Michael, Boughtwood, Tiffany F., Brion, Kristian, Cheong, Pak Leng, Christie, Michael, Christodoulou, John, Chong, Belinda, Cox, Kathy, Davis, Mark R., Dejong, Lucas, Dinger, Marcel E., Doig, Kenneth D., Douglas, Evelyn, Dubowsky, Andrew, Ellul, Melissa, Fellowes, Andrew, Fisk, Katrina, Fortuno, Cristina, Friend, Kathryn, Gallagher, Renee L. ... and on behalf of the Shariant Consortium (2022). Shariant platform: Enabling evidence sharing across Australian clinical genetic-testing laboratories to support variant interpretation. American Journal of Human Genetics, 109 (11), 1960-1973. doi: 10.1016/j.ajhg.2022.10.006
Kutasovic, Jamie R., Nones, Katia, Lakis, Vanessa, Koufariotis, Lambros T., Ferguson, Kaltin, McCart Reed, Amy E., Simpson, Peter T., Lakhani, Sunil R., Mar Fan, Helen, Higgins, Megan, Davies, Janene, Payton, Diane and Taege, Lucinda (2022). Comprehensive histopathologic and genomic analysis of a novel case of lipoblastoma-like tumour of the vulva demonstrating malignant behaviour. Human Pathology Reports, 30 300678, 300678-30. doi: 10.1016/j.hpr.2022.300678
Fielding, David, Dalley, Andrew J., Singh, Mahendra, Nandakumar, Lakshmy, Nones, Katia, Lakis, Vanessa, Chittoory, Haarika, Ferguson, Kaltin, Bashirzadeh, Farzad, Bint, Michael, Pahoff, Carl, Son, Jung Hwa, Hodgson, Alan, Sharma, Sowmya, Godbolt, David, Coleman, Kylie, Whitfield, Lenore, Waddell, Nicola, Lakhani, Sunil R., Hartel, Gunter and Simpson, Peter T. (2022). Prospective optimization of endobronchial ultrasound-guided transbronchial needle aspiration lymph node assessment for lung cancer: Three needle agitations are noninferior to 10 agitations for adequate tumor cell and DNA yield. JTO Clinical and Research Reports, 3 (10) 100403, 100403. doi: 10.1016/j.jtocrr.2022.100403
Newell, Felicity, Johansson, Peter A., Wilmott, James S., Nones, Katia, Lakis, Vanessa, Pritchard, Antonia L., Lo, Serigne N., Rawson, Robert V., Kazakoff, Stephen H., Colebatch, Andrew J., Koufariotis, Lambros T., Ferguson, Peter M., Wood, Scott, Leonard, Conrad, Law, Matthew H., Brooks, Kelly M., Broit, Natasa, Palmer, Jane M., Couts, Kasey L., Vergara, Ismael A., Long, Georgina V., Barbour, Andrew P., Nieweg, Omgo E., Shivalingam, Brindha, Robinson, William A., Stretch, Jonathan R., Spillane, Andrew J., Saw, Robyn P.M., Shannon, Kerwin F. ... Hayward, Nicholas K. (2022). Comparative genomics provides etiological and biological insights into melanoma subtypes. Cancer Discovery, 12 (12), OF1-OF24. doi: 10.1158/2159-8290.cd-22-0603
Ramarao-Milne, P, Kondrashova, O, Patch, A-M, Nones, K, Koufariotis, L T, Newell, F, Addala, V, Lakis, V, Holmes, O, Leonard, C, Wood, S, Xu, Q, Mukhopadhyay, P, Naeini, M M, Steinfort, D, Williamson, J P, Bint, M, Pahoff, C, Nguyen, P T, Twaddell, S, Arnold, D, Grainge, C, Basirzadeh, F, Fielding, D, Dalley, A J, Chittoory, H, Simpson, P T, Aoude, L G, Bonazzi, V F ... Waddell, N (2022). Comparison of actionable events detected in cancer genomes by whole-genome sequencing, in silico whole-exome and mutation panels. ESMO Open, 7 (4) 100540, 1-11. doi: 10.1016/j.esmoop.2022.100540
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. and Waddell, Nicola (2022). Comprehensive genomic and tumour immune profiling reveals potential therapeutic targets in malignant pleural mesothelioma. Genome Medicine, 14 (1) 58, 1-18. doi: 10.1186/s13073-022-01060-8
Holmes, Oliver, Nones, Katia, Tang, Yue Hang, Loffler, Kelly A., Lee, Michael, Patch, Ann-Marie, Dagg, Rebecca A., Lau, Loretta M. S., Leonard, Conrad, Wood, Scott, Xu, Qinying, Pickett, Hilda A., Reddel, Roger R., Barbour, Andrew P., Grimmond, Sean M., Waddell, Nicola and Pearson, John V. (2022). qmotif: determination of telomere content from whole-genome sequence data. Bioinformatics Advances, 2 (1) vbac005, 1-3. doi: 10.1093/bioadv/vbac005
Ganesamoorthy, Devika, Robertson, Alan James, Chen, Wenhan, Hall, Michael B., Cao, Minh Duc, Ferguson, Kaltin, Lakhani, Sunil R., Nones, Katia, Simpson, Peter T. and Coin, Lachlan J. M. (2022). Whole genome deep sequencing analysis of cell-free DNA in samples with low tumour content. BMC Cancer, 22 (1) 85, 85. doi: 10.1186/s12885-021-09160-1
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 and Pollock, Pamela M. (2022). Patient-derived xenograft models capture genomic heterogeneity in endometrial cancer. Genome Medicine, 14 (1) 3, 1-19. doi: 10.1186/s13073-021-00990-z
Newell, Felicity, Pires da Silva, Ines, Johansson, Peter A., Menzies, Alexander M., Wilmott, James S., Addala, Venkateswar, Carlino, Matteo S., Rizos, Helen, Nones, Katia, Edwards, Jarem J., Lakis, Vanessa, Kazakoff, Stephen H., Mukhopadhyay, Pamela, Ferguson, Peter M., Leonard, Conrad, Koufariotis, Lambros T., Wood, Scott, Blank, Christian U., Thompson, John F., Spillane, Andrew J., Saw, Robyn P.M., Shannon, Kerwin F., Pearson, John V., Mann, Graham J., Hayward, Nicholas K., Scolyer, Richard A., Waddell, Nicola and Long, Georgina V. (2022). Multiomic profiling of checkpoint inhibitor-treated melanoma: Identifying predictors of response and resistance, and markers of biological discordance. Cancer Cell, 40 (1), 88-102.e7. doi: 10.1016/j.ccell.2021.11.012
Dreyer, Stephan B., Upstill-Goddard, Rosie, Legrini, Assya, Biankin, Andrew V., Allison, Sarah, Beraldi, Dario, Cameron, Euan, Chang, David K., Cooke, Susanna L., Cunningham, Richard, Dreyer, Stephan, Grimwood, Paul, Kelly, Shane, Marshall, John, McDade, Brian, Musgrove, Elizabeth A., Ramsay, Donna, Evers, Lisa, Rebus, Selma, Rahib, Lola, Serrels, Bryan, Jamieson, Nigel B., McKay, Colin J., Westwood, Paul, Williams, Nicola, Duthie, Fraser, Shen, William, Pea, Antonio, Johns, Amber L. ... Bassi, Claudio (2022). Genomic and molecular analyses identify molecular subtypes of pancreatic cancer recurrence. Gastroenterology, 162 (1), 320-324. doi: 10.1053/j.gastro.2021.09.022
Lakis, Vanessa, Lawlor, Rita T., Newell, Felicity, Patch, Ann-Marie, Mafficini, Andrea, Sadanandam, Anguraj, Koufariotis, Lambros T., Johnston, Rebecca L., Leonard, Conrad, Wood, Scott, Rusev, Borislav, Corbo, Vincenzo, Luchini, Claudio, Cingarlini, Sara, Landoni, Luca, Salvia, Roberto, Milella, Michele, Chang, David, Bailey, Peter, Jamieson, Nigel B., Duthie, Fraser, Gingras, Marie-Claude, Muzny, Donna M., Wheeler, David A., Gibbs, Richard A., Milione, Massimo, Chantrill, Lorraine A., Timpson, Paul, Chou, Angela ... Scarpa, Aldo (2021). DNA methylation patterns identify subgroups of pancreatic neuroendocrine tumors with clinical association. Communications Biology, 4 (1) 155, 1-11. doi: 10.1038/s42003-020-01469-0
Liu, Dongli, Sharbeen, George, Phillips, Phoebe, Johns, Amber L., Gill, Anthony J., Chantrill, Lorraine A., Timpson, Paul, Chou, Angela, Pajic, Marina, Dwarte, Tanya, Herrmann, David, Vennin, Claire, Cox, Thomas R., Pereira, Brooke, Ritchie, Shona, Reed, Daniel A., Chambers, Cecilia R., Metcalf, Xanthe, Nobis, Max, Waddell, Nicola, Pearson, John V., Patch, Ann-Marie, Nones, Katia, Newell, Felicity, Mukhopadhyay, Pamela, Addala, Venkateswar, Kazakoff, Stephen, Holmes, Oliver, Leonard, Conrad ... Ford, Caroline E. (2021). ROR1 and ROR2 expression in pancreatic cancer. BMC Cancer, 21 (1) 1199. doi: 10.1186/s12885-021-08952-9
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 I., Kee, Damien, Olesen, Inger, McNally, Orla, Traficante, Nadia, Study, Australian Ovarian Cancer, DeFazio, Anna, Bowtell, David D.L., Swisher, Elizabeth M., Weroha, S. John, Nones, Katia, Waddell, Nicola, Kaufmann, Scott H., Dobrovic, Alexander, Wakefield, Matthew J. and Scott, Clare L. (2021). Acquired RAD51C promoter methylation loss causes parp inhibitor resistance in high-grade serous ovarian carcinoma. Cancer Research, 81 (18), 4709-4722. doi: 10.1158/0008-5472.can-21-0774
McCart Reed, Amy E., Foong, Samuel, Kutasovic, Jamie R., Nones, Katia, Waddell, Nicola, Lakhani, Sunil R. and Simpson, Peter T. (2021). Correction: McCart Reed et al. The Genomic Landscape of Lobular Breast Cancer. Cancers 2021, 13, 1950. Cancers, 13 (16) 4010, 4010. doi: 10.3390/cancers13164010
McCart Reed, Amy E., Foong, Samuel, Kutasovic, Jamie R., Nones, Katia, Waddell, Nicola, Lakhani, Sunil R. and Simpson, Peter T. (2021). The genomic landscape of lobular breast cancer. Cancers, 13 (8) 1950, 1950. doi: 10.3390/cancers13081950
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 and Waddell, Nicola (2021). Verifying explainability of a deep learning tissue classifier trained on RNA-seq data. Scientific Reports, 11 (1) 2641. doi: 10.1038/s41598-021-81773-9
Dreyer, Stephan B., Upstill-Goddard, Rosie, Paulus-Hock, Viola, Paris, Clara, Lampraki, Eirini-Maria, Dray, Eloise, Serrels, Bryan, Caligiuri, Giuseppina, Rebus, Selma, Plenker, Dennis, Galluzzo, Zachary, Brunton, Holly, Cunningham, Richard, Tesson, Mathias, Nourse, Craig, Bailey, Ulla-Maja, Jones, Marc D., Moran-Jones, Kim, Wright, Derek W., Duthie, Fraser, Oien, Karin, Evers, Lisa, McKay, Colin J., McGregor, Grant A., Gulati, Aditi, Brough, Rachel, Bajrami, Ilirjana, Pettitt, Stephan, Dziubinski, Michele L. ... Sansom, Owen J. (2021). Targeting DNA damage response and replication stress in pancreatic cancer. Gastroenterology, 160 (1), 362-377.e13. doi: 10.1053/j.gastro.2020.09.043
Cmero, Marek, Yuan, Ke, Ong, Cheng Soon, Schröder, Jan, Adams, David J., Anur, Pavana, Beroukhim, Rameen, Boutros, Paul C., Bowtell, David D. L., Campbell, Peter J., Cao, Shaolong, Christie, Elizabeth L., Cun, Yupeng, Dawson, Kevin J., Demeulemeester, Jonas, Dentro, Stefan C., Deshwar, Amit G., Donmez, Nilgun, Drews, Ruben M., Eils, Roland, Fan, Yu, Fittall, Matthew W., Garsed, Dale W., Gerstung, Moritz, Getz, Gad, Gonzalez, Santiago, Ha, Gavin, Haase, Kerstin, Imielinski, Marcin ... von Mering, Christian (2020). Inferring structural variant cancer cell fraction. Nature Communications, 11 (1) 730. doi: 10.1038/s41467-020-14351-8
Aoude, Lauren G., Bonazzi, Vanessa F., Brosda, Sandra, Patel, Kalpana, Koufariotis, Lambros T., Oey, Harald, Nones, Katia, Wood, Scott, Pearson, John V., Lonie, James M., Arneil, Melissa, Atkinson, Victoria, Smithers, B. Mark, Waddell, Nicola and Barbour, Andrew P. (2020). Pathogenic germline variants are associated with poor survival in stage III/IV melanoma patients. Scientific Reports, 10 (1) 17687, 17687. doi: 10.1038/s41598-020-74956-3
Newell, Felicity, Wilmott, James S., Johansson, Peter A., Nones, Katia, Addala, Venkateswar, Mukhopadhyay, Pamela, Broit, Natasa, Amato, Carol M., Van Gulick, Robert, Kazakoff, Stephen H., Patch, Ann-Marie, Koufariotis, Lambros T., Lakis, Vanessa, Leonard, Conrad, Wood, Scott, Holmes, Oliver, Xu, Qinying, Lewis, Karl, Medina, Theresa, Gonzalez, Rene, Saw, Robyn P. M., Spillane, Andrew J., Stretch, Jonathan R., Rawson, Robert V., Ferguson, Peter M., Dodds, Tristan J., Thompson, John F., Long, Georgina V., Levesque, Mitchell P. ... Hayward, Nicholas K. (2020). Whole-genome sequencing of acral melanoma reveals genomic complexity and diversity. Nature Communications, 11 (1) 5259, 5259. doi: 10.1038/s41467-020-18988-3
Nones, Katia and Patch, Ann-Marie (2020). The Impact of Next Generation Sequencing in Cancer Research. Cancers, 12 (10) 2928, 2928-4. doi: 10.3390/cancers12102928
de Luca, Xavier M., Newell, Felicity, Kazakoff, Stephen H., Hartel, Gunter, McCart Reed, Amy E., Holmes, Oliver, Xu, Qinying, Wood, Scott, Leonard, Conrad, Pearson, John V., Lakhani, Sunil R., Waddell, Nicola, Nones, Katia and Simpson, Peter T. (2020). Using whole-genome sequencing data to derive the homologous recombination deficiency scores. npj Breast Cancer, 6 (1) 33, 33. doi: 10.1038/s41523-020-0172-0
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 and Schofield, Deborah J. (2020). Estimating the costs of genomic sequencing in cancer control. BMC Health Services Research, 20 (1) 492, 492. doi: 10.1186/s12913-020-05318-y
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Waddell, Nicola, Pajic, Marina, Patch, Anne-Marie, Chang, David K, Kassahn, Karin S, Bailey, Peter, Johns, Amber L, Miller, David, Nones, Katia, Quek, Kelly, Quinn, Michael C. J, Robertson, Alan J, Fadlullah, Muhammad Z.H, Bruxner, Tim J.C, Christ, Angelika N, Harliwong, Ivon, Idrisoglu, Senel, Manning, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wani, Shivangi, Wilson, Peter J, Markham, Emma, Cloonan, Nicole, Anderson, Matthew J, Fink, J. Lynn, Holmes, Oliver, Kazakoff, Stephen H, Leonard, Conrad ... Grimmond, Sean M (2015). Whole genomes redefine the mutational landscape of pancreatic cancer. Nature, 518 (7540), 495-501. doi: 10.1038/nature14169
Ragognetti, B.N.N., Stafuzza, N.B., da Silva, T.B.R., Chud, T.C.S., Grupioni, N.V., Cruz, V.A.R., Peixoto, J.O., Nones, K., Ledur, M.C. and Munari, D.P. (2015). Genetic parameters and mapping quantitative trait loci associated with tibia traits in broilers. Genetics and Molecular Research, 14 (4), 17544-17554. doi: 10.4238/2015.december.21.27
Nones, Katia, Waddell, Nicola, Wayte, Nicci, Patch, Ann-Marie, Bailey, Peter, Newell, Felicity, Holmes, Oliver, Fink, J. Lynn, Quinn, Michael C. J., Tang, Yue Hang, Lampe, Guy, Quek, Kelly, Loffler, Kelly A., Manning, Suzanne, Idrisoglu, Senel, Miller, David, Xu, Qinying, Waddell, Nick, Wilson, Peter J., Bruxner, Timothy J. C., Christ, Angelika N., Harliwong, Ivon, Nourse, Craig, Nourbakhsh, Ehsan, Anderson, Matthew, Kazakoff, Stephen, Leonard, Conrad, Wood, Scott, Simpson, Peter T. ... Barbour, Andrew P. (2014). Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesis. Nature Communications, 5 (1) 6224, 5224.1-5224.9. doi: 10.1038/ncomms6224
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 ... Grimmond, Sean M. (2014). Genome-wide DNA methylation patterns in pancreatic ductal adenocarcinoma reveal epigenetic deregulation of SLIT-ROBO, ITGA2 and MET signaling. International Journal of Cancer, 2014 (5), 1110-1118. doi: 10.1002/ijc.28765
Quek, Kelly, Nones, Katia, Patch, Ann-Marie, Fink, J. Lynn, Newell, Felicity, Cloonan, Nicole, Miller, David, Fadlullah, Muhammad Z. H., Kassahn, Karin, Christ, Angelika N., Bruxner, Timothy J. C., Manning, Suzanne, Harliwong, Ivon, Idrisoglu, Senel, Nourse, Craig, Nourbakhsh, Ehsan, Wani, Shivangi, Steptoe, Anita, Anderson, Matthew, Holmes, Oliver, Leonard, Conrad, Taylor, Darrin, Wood, Scott, Xu, Qinying, Australian Pancreatic Cancer Genome Initiative, Wilson, Peter, Biankin, Andrew V., Pearson, John V., Waddell, Nic and Grimmond, Sean M. (2014). A workflow to increase verification rate of chromosomal structural rearrangements using high-throughput next-generation sequencing. BioTechniques, 57 (1), 31-38. doi: 10.2144/000114189
Martin, Hilary C., Wani, Shivangi, Steptoe, Anita L., Krishnan, Keerthana, Nones, Katia, Nourbakhsh, Ehsan, Vlassov, Alexander, Grimmond, Sean M. and Cloonan, Nicole (2014). Imperfect centered miRNA binding sites are common and can mediate repression of target mRNAs. Genome Biology, 15 (3) R51. doi: 10.1186/gb-2014-15-3-r51
Krishnan, Keerthana, Steptoe, Anita, Martin, Hilary, Pattabiraman, Diwakar R., Nones, Katia, Waddell, Nicola, Mariasegaram, Mythily, Simpson, Peter T., Lakhani, Sunil R., Vlassov, Alexander, Grimmond, Sean M. and Cloonan, Nicole (2013). miR-139-5p is a regulator of metastatic pathways in breast cancer. RNA, 19 (12), 1767-1780. doi: 10.1261/rna.042143.113
Kassahn, Karin S., Holmes, Oliver, Nones, Katia, Patch, Ann-Marie, Miller, David K., Christ, Angelika K., Harliwong, Ivon, Bruxner, Timothy J., Xu, Qinying, Anderson, Matthew, Wood, Scott, Leonard, Conrad, Taylor, Darrin, Newell, Felicity, Song, Sarah, Idrisoglu, Senel, Nourse, Craig, Nourbakhsh, Ehsan, Manning, Suzanne, Wani, Shivangi, Steptoe, Anita, Pajic, Marina, Cowley, Mark J., Pinese, Mark, Chang, David K., Gill, Anthony J., Johns, Amber L., Wu, Jianmin, Wilson, Peter J. ... Pearson, John V. (2013). Somatic point mutation calling in low cellularity tumors. PloS One, 8 (11) e74380, e74380.1-e74380.10. doi: 10.1371/journal.pone.0074380
Barnett, Matthew P. G., Cooney, Janine M., Dommels, Yvonne E. M., Nones, Katia, Brewster, Diane T., Park, Zaneta, Butts, Christine A., McNabb, Warren C., Laing, William A. and Roy, Nicole C. (2013). Modulation of colonic inflammation in Mdr1a-/- mice by green tea polyphenols and their effects on the colon transcriptome and proteome. Journal of Nutritional Biochemistry, 24 (10), 1678-1690. doi: 10.1016/j.jnutbio.2013.02.007
Chou, Angela, Waddell, Nicola, Cowley, Mark J., Gill, Anthony J., Chang, David K., Patch, Ann-Marie, Nones, Katia, Wu, Jianmin, Pinese, Mark, Johns, Amber L., Miller, David K., Kassahn, Karin S., Nagrial, Adnan M., Wasan, Harpreet, Goldstein, David, Toon, Christopher W., Chin, Venessa, Chantrill, Lorraine, Humphris, Jeremy, Mead, R. Scott, Rooman, Ilse, Samra, Jaswinder S., Pajic, Marina, Musgrove, Elizabeth A., Pearson, John V., Morey, Adrienne L., Grimmond, Sean M. and Biankin, Andrew V. (2013). Clinical and molecular characterization of HER2 amplified-pancreatic cancer. Genome Medicine, 5 (8) 78, 78.1-78.10. doi: 10.1186/gm482
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 and Grimmond, Sean M. (2013). MicroRNA-182-5-p targets a network of genes involved in DNA repair. RNA, 19 (2), 230-242. doi: 10.1261/rna.034926.112
Boschiero, Clarissa, Jorge, Erika C., Ninov, Kerli, Nones, Katia, do Rosario, Millor Fernandes, Coutinho, Luiz Lehmann, Ledur, Monica Correa, Burt, David W. and Moura, Ana Silvia A. M. T. (2013). Association of IGF1 and KDM5A polymorphisms with performance, fatness and carcass traits in chickens. Journal of Applied Genetics, 54 (1), 103-112. doi: 10.1007/s13353-012-0129-6
Barry, Guy, Briggs, J. A., Vanichkina, D. P., Poth, E. M., Beveridge, N. J., Vikram Ratnu, Nayler, S. P., Nones, K., Hu, J., Timothy Bredy, Nakagawa, S., Rigo, F., Taft, R. J., Cairns, M. J., Blackshaw, S., Wolvetang, E. J. and Mattick, J. S. (2013). The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing. Molecular Psychiatry, 19 (4), 486-494. doi: 10.1038/mp.2013.45
Biankin, Andrew V., Waddell, Nicola, Kassahn, Karin S., Gingras, Marie-Claude, Muthuswamy, Lakshmi B., Johns, Amber L., Miller, David K., Wilson, Peter J., Patch, Ann-Marie, Wu, Jianmin, Chang, David K., Cowley, Mark J., Gardiner, Brooke B., Song, Sarah, Harliwong, Ivon, Idrisoglu, Senel, Nourse, Craig, Nourbakhsh, Ehsan, Manning, Suzanne, Wani, Shivangi, Gongora, Milena, Pajic, Marina, Scarlett, Christopher J., Gill, Anthony J., Pinho, Andreia V., Rooman, Ilse, Anderson, Matthew, Holmes, Oliver, Leonard, Conrad ... Grimmond, Sean M. (2012). Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes. Nature, 491 (7424), 399-405. doi: 10.1038/nature11547
Nones, K., Ledur, M. C., Zanella, E. L., Klein, C., Pinto, L. F. B., Moura, A. S. A. M. T., Ruy, D. C., Baron, E. E., Ambo, M., Campos, R. L. R., Boschiero, C., Burt, D. W. and Coutinho, L. L. (2012). Quantitative trait loci associated with chemical composition of the chicken carcass. Animal Genetics, 43 (5), 570-576. doi: 10.1111/j.1365-2052.2012.02321.x
Tactacan, Carole M., Chang, David K., Cowley, Mark J., Humphrey, Emily S., Wu, Jianmin, Gill, Anthony J., Chou, Angela, Nones, Katia, Grimmond, Sean M., Sutherland, Robert L., Biankin, Andrew V., Daly, Roger J. and Australian Pancreratic Genome Initiative (2012). RON is not a prognostic marker for resectable pancreatic cancer. BMC Cancer, 12 (Article No.395) 395. doi: 10.1186/1471-2407-12-395
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. and Pearson, John V. (2012). qpure: a tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles. PLoS One, 7 (9) e45835, e45835.1-e45835.7. doi: 10.1371/journal.pone.0045835
Mandimika, Tafadzwa, Paturi, Gunaranjan, De Guzman, Cloe Erika, Butts, Christine A., Nones, Katia, Monro, John A., Butler, Ruth C., Joyce, Nigel I., Mishra, Suman and Ansell, Juliet (2012). Effects of dietary broccoli fibre and corn oil on serum lipids, faecal bile acid excretion and hepatic gene expression in rats. Food Chemistry, 131 (4), 1272-1278. doi: 10.1016/j.foodchem.2011.09.117
Mann, Karen M., Ward, Jerrold M., Yew, Christopher Chin Kuan, Kovochich, Anne, Dawson, David W., Black, Michael A., Brett, Benjamin T., Sheetz, Benjamin T., 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., Australian Pancreatic Cancer Genome Initiative, Miller, David K., Wilson, Peter J., Patch, Ann-Marie, Song, Sarah, Harliwong, Ivon, Idrisoglu, Senel, Nourse, Craig, Nourbakhsh, Ehsan, Manning, Suzanne, Wani, Shivangi ... Pearson, John V. (2012). Sleeping Beauty mutagenesis reveals cooperating mutations and pathways in pancreatic adenocarcinoma. Proceedings of the National Academy of Sciences of the United States of America, 109 (16), 5934-5941. doi: 10.1073/pnas.1202490109
Cloonan, Nicole, Wani, Shivangi, Xu, Qinying, Gu, Jian, Lea, Kristi, Heater, Sheila, Barbacioru, Catalin, Steptoe, Anita L., Martin, Hilary C., Nourbakhsh, Ehsan, Krishnan, Keerthana, Gardiner, Brooke, Wang, Xiaohui, Nones, Katia, Steen, Jason A., Matigan, Nicholas A., Wood, David L., Kassahn, Karin S., Waddell, Nic, Shepherd, Jill, Lee, Clarence, Ichikawa, Jeff, McKernan, Kevin, Bramlett, Kelli, Kuersten, Scott and Grimmond, Sean M. (2011). MicroRNAs and their isomiRs function cooperatively to target common biological pathways. Genome Biology: biology for the post-genomic era, 12 (12) R126, 1-20. doi: 10.1186/gb-2011-12-12-r126
Nunes, Beatriz do Nascimento, Ramos, Salvador Boccaletti, Savegnago, Rodrigo Pelicioni, Ledur, Mônica Corrêa, Nones, Kátia, Klein, Claudete Hara and Munari, Danísio Prado (2011). Genetic parameters for body weight, carcass chemical composition and yield in a broiler-layer cross developed for QTL mapping. Genetics and Molecular Biology, 34 (3), 429-434. doi: 10.1590/s1415-47572011005000019
Baron, E. E., Moura, A. S. A. M. T., Ledur, M. C., Pinto, L. F. B., Boschiero, C., Ruy, D. C., Nones, K., Zanella, E. L., Rosário, M. F., Burt, D. W. and Coutinho, L. L. (2011). QTL for percentage of carcass and carcass parts in a broiler x layer cross. Animal Genetics, 42 (2), 117-124. doi: 10.1111/j.1365-2052.2010.02105.x
Savegnago, R.P., Buzanskas, M.E., Nunes, B.N., Ramos, S.B., Ledur, M.C., Nones, K. and Munari, D.P. (2011). Heritabilities and genetic correlations for reproductive traits in an F2 reciprocal cross chicken population. Genetics and Molecular Research, 10 (3), 1247-1254. doi: 10.4238/vol10-3gmr1053
Mason, E, Tronc, G, Nones, K, Matigian, N, Kim, J, Aronow, BJ, Wolfinger, RD, Wells, C and Gibson, G (2010). Maternal influences on the transmission of leukocyte gene expression profiles in population samples from Brisbane, Australia. PLoS ONE, 5 (12) e14479, e14479 -1-e14479-12. doi: 10.1371/journal.pone.0014479
Knoch, Bianca, Nones, Katia, Barnett, Matthew P. G., McNabb, Warren C. and Roy, Nicole C. (2010). Diversity of cecal bacteria is altered in interleukin-10 gene-deficient mice before and after colitis onset and when fed polyunsaturated fatty acids.. Microbiology, 156 (11), 3306-3316. doi: 10.1099/mic.0.041723-0
Pinto, Luís Fernando Batista, Packer, Irineu Umberto, Ledur, Mônica Corrêa, Moura, Ana Silvia Alves Meira Tavares, Nones, Kátia and Coutinho, Luiz Lehmann (2010). Mapping quantitative trait loci in Gallus gallus using principal components Mapeamento de locos de características quantitativas em Gallus gallus com utilização de componentes principais. Revista Brasileira de Zootecnia, 39 (11), 2434-2441. doi: 10.1590/S1516-35982010001100016
Paturi, Gunaranjan, Butts, Christine, Monro, John, Nones, Katia, Martell, Sheridan, Butler, Ruth and Sutherland, Juliet (2010). Cecal and colonic responses in rats fed 5 or 30% corn oil diets containing either 7.5% broccoli dietary fiber or microcrystalline cellulose. Journal of Agricultural and Food Chemistry, 58 (10), 6510-6515. doi: 10.1021/jf100296m
Barnett, Matthew P. G., McNabb, Warren C., Cookson, Adrian L., Zhu, Shuotun, Davy, Marcus, Knoch, Bianca, Nones, Katia, Hodgkinson, Alison J. and Roy, Nicole C. (2010). Changes in colon gene expression associated with increased colon inflammation in interleukin-10 gene-deficient mice inoculated with Enterococcus species. BMC Immunology, 11. doi: 10.1186/1471-2172-11-39
Campos, R. L. R., Nones, K., Ledur, M. C., Moura ASAMT, Pinto, L. F. B., Ambo, M., Boschiero, C., Ruy, D. C., Baron, E. E., Ninov, K., Altenhofen, C. A. B., Burt, D. W. and Coutinho, L. L. (2009). Quantitative trait loci associated with fatness in a broiler-layer cross. Animal Genetics, 40 (5), 729-736. doi: 10.1111/j.1365-2052.2009.01910.x
Nones, K., Knoch, B., Dommels, Y. E., Paturi, G., Butts, C., McNabb, W. C. and Roy, N. C. (2009). Multidrug resistance gene deficient (mdr1a(-/-)) mice have an altered caecal microbiota that precedes the onset of intestinal inflammation. Journal of Applied Microbiology, 107 (2), 557-566. doi: 10.1111/j.1365-2672.2009.04225.x
Hayashi, A. A., Nones, K., Roy, N. C., McNabb, W. C., Mackenzie, D. S., Pacheco, D. and McCoard, S. (2009). Initiation and elongation steps of mRNA translation are involved in the increase in milk protein yield caused by growth hormone administration during lactation. Journal of Dairy Science, 92 (5), 1889-1899. doi: 10.3168/jds.2008-1334
Ambo, M., Moura, A. S., Ledur, M. C., Pinto, L. F., Baron, E. E., Ruy, D. C., Nones, K., Campos, R. L., Boschiero, C., Burt, D. W. and Coutinho, L. L. (2009). Quantitative trait loci for performance traits in a broiler x layer cross. Animal Genetics, 40 (2), 200-208. doi: 10.1111/j.1365-2052.2008.01824.x
Knoch, Bianca, Barnett, Matthew P. G., Zhu, Shuotun, Park, Zaneta A., Nones, Katia, Dommels, Yvonne E. M., Knowles, Scott O., McNabb, Warren C. and Roy, Nicole C. (2009). Genome-wide analysis of genes involved in dietary eicosapentaenoic acid- and oleic acid-induced modulation in colon inflammation of interleukin 10 gene deficient mice. Journal of Nutrigenetics and Nutrigenomics, 2 (1), 9-28. doi: 10.1159/000134292
Nones, Katia, Dommels, Yvonne E. M., Martell, Sheridan, Butts, Christine, McNabb, Warren C., Park, Zaneta A., Zhu, Shuotun, Hedderley, Duncan, Barnett, Matthew P. G. and Roy, Nicole C. (2009). The effects of dietary curcumin and rutin on colonic inflammation and gene expression in multidrug resistance gene-deficient (mdr1a-/-) mice, a model of inflammatory bowel diseases. British Journal of Nutrition, 101 (2), 169-181. doi: 10.1017/S0007114508009847
Ninov, Kerli, Ledur, Mônica Corrêa, Alves, Helena Javiel, Do Rosário, Millor Fernandes, Nones, Kátia and Coutinho, Luiz Lehmann (2008). Investigation of Leptin gene in broiler and layer chicken lines. Scientia agricola, 65 (2), 214-219. doi: 10.1590/S0103-90162008000200016
Ambo, Marcel, Campos, Raquel De Lello Rocha, Moura, Ana Sílvia Meira Tavares, Boschiero, Clarissa, Do Rosário, Millor Fernandes, Ledur, Mônica Corrêa, Nones, Kátia and Coutinho, Luiz Lehmann (2008). Genetic linkage maps of chicken chromosomes 6, 7, 8, 11 and 13 from a Brazilian resource population. Scientia Agricola, 65 (5), 447-452. doi: 10.1590/s0103-90162008000500001
Ye, Xianghai, Brown, Stewart R., Nones, Kátia, Coutinho, Luiz L ., Dekkers, Jack C. M. and Lamont, Susan J. (2007). Associations of myostatin gene polymorphisms with performance and mortality traits in broiler chickens. Genetics Selection Evolution, 39 (1) 73, 73-89. doi: 10.1051/gse:2006029
Nones, K., Ledur, M. C., Ruy, D. C., Baron, E. E., Melo, C. M. R., Moura, A. S. A. M. T., Zanella, E. L., Burt, D. W. and Coutinho, L. L. (2006). Mapping QTLs on chicken chromosome 1 for performance and carcass traits in a broiler x layer cross. Animal Genetics, 37 (2), 95-100. doi: 10.1111/j.1365-2052.2005.01387.x
Ruy, Deborah Clea, Nones, Kátia, Baron, Erica Elias, Ledur, Mônica Corrêa, de Melo, Cláudio Manoel Rodrigues, Ambo, Marcel, Campos, Raquel de Lello Rocha and Coutinho, Luiz Lehmann (2005). Strategic marker selection to detect quantitative trait loci in chicken Seleção estratégica de marcadores para detecção de locos para características quantitativas em aves. Scientia Agricola, 62 (2), 111-116. doi: 10.1590/S0103-90162005000200003
Nones, Kátia, Ledur, Mônica Corrêa, Ruy, Deborah Clea, Baron, Erica Elias, Moura, Ana Silvia Alves Meira Tavares and Coutinho, Luiz Lehmann (2005). Genetic linkage map of chicken chromosome 1 from a Brazilian resource population. Scientia Agricola, 62 (1), 12-17. doi: 10.1590/S0103-90162005000100003
Nones, Kátia, de Lima, Gustavo J. M. M., Bellaver, Cláudio and Rutz, Fernando (2002). Diet formulation on swine performance, carcass quality, production and composition of swine manure Formulação das dietas, desempenho e qualidade da carcaça, produção e composição de dejetos de suínos. Scientia Agricola, 59 (4), 635-644. doi: 10.1590/S0103-90162002000400003
Conference Papers
Fielding, David, Dalley, Andrew, Singh, Mahendra, Nandakumar, Lakshmy, Lakis, Vanessa, Chittoory, Haarika, Bashirzadeh, Farzad, Bint, Michael, Pahoff, Carl, Son, Jung, Hodgson, Alan, Sharma, Sowmya, Godbolt, David, Coleman, Kylie, Whitfield, Lenore, Waddell, Nicola, Lakhani, Sunil, Nones, Katia, Hartel, Gunter and Simpson, Peter (2023). Diff-Quik smears from EBUS TBNA procedures: Evaluating measures of tumour cellularity and feasibility of whole genome sequencing (WGS). 26th Congress of the Asian Pacific Society of Respirology Above and Beyond, Seoul, Korea, 17-20 November 2022. Richmond, VIC, Australia: John Wiley & Sons. doi: 10.1111/resp.14433
Naeini, Marjan, Newell, Felicity, Aoude, Lauren G., Bonazzi, Vanessa F., Patel, Kalpana, Koufariotis, Lambros T., Johnson, Rebecca, Addala, Venkateswar, Kondrashova, Olga, Holmes, Oliver, Leonard, Conrad, Wood, Scott, Xu, Christina, Nones, Katia, Pearson, John V., Smithers, Mark, Watson, David, Simes, John, Price, Tim, Gebski, Val, Barbour, Andrew P. and Waddell, Nic (2020). Tracking genomic and transcriptomic features of oesophageal adenocarcinoma for improving patients outcome. HOBOKEN: WILEY.
Reed, A. E. McCart, Kalaw, E., Nones, K., Bettington, M., Lim, M., Bennett, J., Johnstone, K., Kutasovic, J. R., Kazakoff, S., Xu, Q. C., Saunus, J. M., Reid, L. E., Black, D., Niland, C., Ferguson, K., Gresshoff, I., Raghavendra, A., Liu, J. C., Kalinowski, L., Reid, A. S., Davidson, M., Pearson, J. V., Yamaguchi, R., Harris, G., Tse, G., Papadimos, D., Pathmanathan, R., Pathmanathan, N., Tan, P. H. ... Lakhani, S. R. (2019). Dissecting the heterogeneity of metaplastic breast cancer: a morphological, immunohistochemical and genomic analysis of a large cohort. San Antonio Breast Cancer Symposium, San Antonio, TX, United States, 4-8 December 2018. Philadelphia, PA, United States: American Association for Cancer Research. doi: 10.1158/1538-7445.SABCS18-P3-08-03
Simpson, P., Nones, K., Johnson, J., Newell, F., Patch, A-M, Thorne, H., Kazakoff, S., De Luca, X., Parsons, M., Ferguson, K., Reid, L., Reed, A. McCart, Srihari, S., Lakis, V., Davidson, A., Mukhopadhyay, P., Holmes, O., Xu, Q., Wood, S., Leonard, C., Beasley, J., Degasperi, A., Nik-Zainal, S., Ragan, M., Spurdle, A., Khanna, K. K., Lakhani, S., Pearson, J., Chenevix-Trench, G. and Waddell, N. (2019). Using whole genome sequencing and somatic mutation signatures to unravel insight into familial breast cancer aetiology. San Antonio Breast Cancer Symposium, San Antonio, TX, United States, 4-8 December 2018. Philadelphia, PA, United States: American Association for Cancer Research. doi: 10.1158/1538-7445.SABCS18-P5-10-01
Reed, A. E. McCart, Kutasovic, J. R., Nones, K., da Silva, L., Melville, L., Jayanthan, J., Vargas, A. C., Reid, L. E., Saunus, J. M., Cummings, M. M., Porter, A., Evans, E., Waddell, N., Lakhani, S. R. and Simpson, P. T. (2017). Mixed ductal-lobular carcinomas of the breast: Abrogated cell adhesion in the clonal evolution from ductal to lobular morphology. San Antonio Breast Cancer Symposium, San Antonio, TX, United States, 6-10 December 2016. Philadelphia, PA, United States: American Association for Cancer Research. doi: 10.1158/1538-7445.SABCS16-P1-07-08
Lal, S., Reed, A. McCart, Nones, K., Wockner, L., Song, S., Lakhani, S. and Simpson, P. (2017). An integrated molecular analysis of invasive lobular carcinoma. 39th Annual San Antonio Breast Cancer Symposium, San Antonio, Texas, 6-10 December 2016. Philadelphia, PA, United States: American Association for Cancer Research. doi: 10.1158/1538-7445.SABCS16-P1-05-16
Fielding, D., Dalley, A., Bashirzadeh, F., Singh, M., Nandakumar, L., Reed, McCart A., Black, D., Waddell, N., Kazakoff, Stephen, Nones, Katia, Pearson, John, Lakhani, S. and Simpson, P. (2017). Diffquik Stained Cytology Smears Provide Improved Malignant Cell Dna Yields From Lymph Nodes At Endobronchial Ultrasound Transbronchial Needle Aspiration (Ebus-Tbna). ANZSRS/TSANZ Annual Scientific Meeting, Canberra, Australia, 24-28 March 2017. Richmond, VIC, Australia: Wiley-Blackwell.
Fielding, D., Bashirzadeh, F., Singh, M., Nandakumar, L., Reed, Mccart A., Black, D., Dalley, A., Pearson, J., Nones, K., Waddell, N., Simpson, P. and Lakhani, S. (2016). Next Generation Sequencing On Endobronchial Ultrasound Transbronchial Needle Aspirate Lymph Node Specimens in Lung Cancer Shows a High Incidence of Mutations and Consistency with Single Gene Testing. Thoracic Society of Australia & New Zealand and the Australian & New Zealand Society of Respiratory Science, Annual Scientific Meeting, Perth, WA, Australia, 1-6 April 2016. Wiley. doi: 10.1111/resp.12754_12
Lal, Samir, McCart Reed, Amy E, Nones, Katia, Wockner Leesa, Song, Sarah, Waddell, Nic, Lakhani, Sunil and Simpson, Peter t (2016). An integrative analysis of invasive lobular breast cancer. Lorne Cancer Conference, Lorne VIC, Australia, February 11-13th 2016.
Saunus, J. M., Quinn, M. C. J., Patch, A. M., Pearson, J. V., Bailey, P. J., Cloonan, N., Nones, K., Miller, D., Mariasegaram, M., Lau, Q., Jeffree, L., Khanna, K. K., Chenevix-Trench, G., Grimmond, S. M., Simpson, P. T., Waddell, N. and Lakhani, S. R. (2015). Genomic and transcriptomic landscapes of human brain metastases. 15th International Biennial Congress of the Metastasis Research Society, Heidelberg, Germany, June 28th–July 1st, 2014. Dordrecht, Netherlands: Springer Netherlands. doi: 10.1007/s10585-015-9708-3
Packer, L., Byron, S., Mahon, C., Loch, D., Wortmann, A., Nones, K., Grimmond, S., Pearson, J., Waddell, N. and Pollock, P. (2014). Elucidating mechanisms of resistance to FGFR inhibitors in endometrial cancer. 26th EORTC-NCI-AACR Symposium on Molecular Targets and Cancer Therapeutics, Barcelona Spain, 18-21 November 2014. Kidlington, Oxford, United Kingdom: Pergamon Press. doi: 10.1016/S0959-8049(14)70220-5
Chin, V. T., Waddell, N., Nones, K., Quek, K., Mawson, A., Johns, A., Grimmond, S. and Biankin, A. (2012). Individualised Measurement of Tumour-Derived Circulating Dna in Patients with Pancreatic Cancer: a Marker of Prognosis and Therapeutic Response. Medical Oncology Group of Australia Incorporated Annual Scientific Meeting, Brisbane, QLD, Australia, 8-10 August 2012. Chichester, West Sussex, United Kingdom: Wiley-Blackwell. doi: 10.1111/j.1743-7563.2012.01578.x