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.
Journal Articles
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
Campbell, Peter J., Getz, Gad, Korbel, Jan O., Stuart, Joshua M., Jennings, Jennifer L., Stein, Lincoln D., Perry, Marc D., Nahal-Bose, Hardeep K., Ouellette, B. F. Francis, Li, Constance H., Rheinbay, Esther, Nielsen, G. Petur, Sgroi, Dennis C., Wu, Chin-Lee, Faquin, William C., Deshpande, Vikram, Boutros, Paul C., Lazar, Alexander J., Hoadley, Katherine A., Louis, David N., Dursi, L. Jonathan, Yung, Christina K., Bailey, Matthew H., Saksena, Gordon, Raine, Keiran M., Buchhalter, Ivo, Kleinheinz, Kortine, Schlesner, Matthias, Zhang, Junjun ... Hamdy, Freddie C. (2020). Pan-cancer analysis of whole genomes. Nature, 578 (7793), 82-93. doi: 10.1038/s41586-020-1969-6
Kalimutho, Murugan, Sinha, Debottam, Jeffery, Jessie, Nones, Katia, Srihari, Sriganesh, Fernando, Winnie C., Duijf, Pascal H. G., 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 and Khanna, Kum Kum (2018). CEP55 is a determinant of cell fate during perturbed mitosis in breast cancer. EMBO Molecular Medicine, 10 (9) e8566, e8566. doi: 10.15252/emmm.201708566
McCart Reed, Amy E., Kutasovic, Jamie R., Nones, Katia, Saunus, Jodi M., Da Silva, Leonard, Newell, Felicity, Kazakoff, Stephen, Melville, Lewis, Jayanthan, Janani, Vargas, Ana Cristina, Reid, Lynne E., Beesley, Jonathan, Chen, Xiao Qing, Patch, Anne Marie, David Clouston, D., Porter, Alan, Evans, Elizabeth, Pearson, John V., Chenevix-Trench, Georgia, Cummings, Margaret C., Waddell, Nic, Lakhani, Sunil R. and Simpson, Peter T. (2018). Mixed ductal-lobular carcinomas: evidence for progression from ductal to lobular morphology. The Journal of Pathology, 244 (4), 460-468. doi: 10.1002/path.5040
Johnson, Julie, Bessette, Darrell C., Saunus, Jodi M., Smart, Chanel E., Song, Sarah, Johnston, Rebecca L., Cocciardi, Sibylle, Rozali, Esdy N., Johnstone, Cameron N., Vargas, Ana Christina, Kazakoff, Stephen H., BioBank, Victorian Cancer, Khanna, Kum Kum, Lakhani, Sunil R., Chenevix-Trench, Georgia, Simpson, Peter T., Nones, Katia, Waddell, Nicola and Al-Ejeh, Fares (2018). Characterization of a novel breast cancer cell line derived from a metastatic bone lesion of a breast cancer patient. Breast Cancer Research and Treatment, 170 (1), 179-188. doi: 10.1007/s10549-018-4719-9
Kawamata, Futoshi, Patch, Ann-Marie, Nones, Katia, Bond, Catherine, McKeone, Diane, Pearson, Sally-Ann, Homma, Shigenori, Liu, Cheng, Fennell, Lochlan, Dumenil, Troy, Hartel, Gunter, Kobayasi, Nozomi, Yokoo, Hideki, Fukai, Moto, Nishihara, Hiroshi, Kamiyama, Toshiya, Burge, Matthew E., Karapetis, Christos S., Taketomi, Akinobu, Leggett, Barbara, Waddell, Nicola and Whitehall, Vicki (2018). Copy number profiles of paired primary and metastatic colorectal cancers. Oncotarget, 9 (3), 3394-3405. doi: 10.18632/oncotarget.23277
Hayward, Nicholas K., Wilmott, James S., Waddell, Nicola, Johansson, Peter A., Field, Matthew A., Nones, Katia, Patch, Ann-Marie, Kakavand, Hojabr, Alexandrov, Ludmil B., Burke, Hazel, Jakrot, Valerie, Kazakoff, Stephen, Holmes, Oliver, Leonard, Conrad, Sabarinathan, Radhakrishnan, Mularoni, Loris, Wood, Scott, Xu, Qinying, Waddell, Nick, Tembe, Varsha, Pupo, Gulietta M., De Paoli-Iseppi, Ricardo, Vilain, Ricardo E., Shang, Ping, Lau, Loretta M. S., Dagg, Rebecca A., Schramm, Sarah-Jane, Pritchard, Antonia, Dutton-Regester, Ken ... Mann, Graham J. (2017). Whole-genome landscapes of major melanoma subtypes. Nature, 545 (7653), 175-180. doi: 10.1038/nature22071
Scarpa, Aldo, Chang, David K., Nones, Katia, Corbo, Vincenzo, Patch, Ann-Marie, Bailey, Peter, Lawlor, Rita T., Johns, Amber L., Miller, David K., Mafficini, Andrea, Rusev, Borislav, Scardoni, Maria, Antonello, Davide, Barbi, Stefano, Sikora, Katarzyna O., Cingarlini, Sara, Vicentini, Caterina, McKay, Skye, Quinn, Michael C.J., Bruxner, Timothy J.C., Christ, Angelika N., Harliwong, Ivon, Idrisoglu, Senel, McLean, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wilson, Peter J., Anderson, Matthew J., Fink, J. Lynn ... Grimmond, Sean M. (2017). Whole-genome landscape of pancreatic neuroendocrine tumours. Nature, 543 (7643), 65-71. doi: 10.1038/nature21063
Vitale, Alejandra M., Matigian, Nicholas A., Cristino, Alexandre S., Nones, Katia, Ravishankar, Sugandha, Bellette, Bernadette, Fan, Yongjun, Wood, Stephen A., Wolvetang, Ernst and Mackay-Sim, Alan (2017). DNA methylation in schizophrenia in different patient-derived cell types. Npj Schizophrenia, 3 (1) 6, 6. doi: 10.1038/s41537-016-0006-0
Humphris, Jeremy L., Patch, Ann-Marie, Nones, Katia, Bailey, Peter J., Johns, Amber L., McKay, Skye, Chang, David K., Miller, David K., Pajic, Marina, Kassahn, Karin S., Quinn, Michael C. J., Bruxner, Timothy J. C., Christ, Angelika N., Harliwong, Ivon, Idrisoglu, Senel, Manning, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Stone, Andrew, Wilson, Peter J., Anderson, Matthew, Fink, J. Lynn, Holmes, Oliver, Kazakoff, Stephen, Leonard, Conrad, Newell, Felicity, Waddell, Nick, Wood, Scott, Mead, Ronald S. ... Biankin, Andrew V. (2017). Hypermutation in pancreatic cancer. Gastroenterology, 152 (1), 68-74.e2. doi: 10.1053/j.gastro.2016.09.060
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 and Barbour, Andrew P. (2016). Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma. Carcinogenesis, 37 (4), 356-365. doi: 10.1093/carcin/bgw018
Secrier, Maria, Li, Xiaodun, De Silva, Nadeera, Eldridge, Matthew D., Contino, Gianmarco, Bornschein, Jan, Macrae, Shona, Grehan, Nicola, O'Donovan, Maria, Miremadi, Ahmad, Yang, Tsun-Po, Bower, Lawrence, Chettouh, Hamza, Crawte, Jason, Galeano-Dalmau, Núria, Grabowska, Anna, Saunders, John, Underwood, Tim, Waddell, Nicola, Barbour, Andrew P., Nutzinger, Barbara, Achilleos, Achilleas, Edwards, Paul A. W., Lynch, Andy G., Tavare, Simon, Fitzgerald, Rebecca C., Noorani, Ayesha, Elliott, Rachael Fels, Weaver, Jamie ... Grimmond, Sean M. (2016). Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance. Nature Genetics, 48 (10), 1131-1141. doi: 10.1038/ng.3659
Li, Jun, Woods, Susan L., Healey, Sue, Beesley, Jonathan, Chen, Xiaoqing, Lee, Jason S., Sivakumaran, Haran, Wayte, Nicci, Nones, Katia, Waterfall, Joshua J., Pearson, John, Patch, Anne-Marie, Senz, Janine, Ferreira, Manuel A., Kaurah, Pardeep, Mackenzie, Robertson, Heravi-Moussavi, Alireza, Hansford, Samantha, Lannagan, Tamsin R. M., Spurdle, Amanda B., Simpson, Peter T., da Silva, Leonard, Lakhani, Sunil R., Clouston, Andrew D., Bettington, Mark, Grimpen, Florian, Busuttil, Rita A., Di Costanzo, Natasha, Boussioutas, Alex ... Chenevix-Trench, Georgia (2016). Point mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant. American Journal of Human Genetics, 98 (5), 830-842. doi: 10.1016/j.ajhg.2016.03.001
Moura, A. S. A. M. T., Ledur, M. C., Boschiero, C., Nones, K., Pinto, L. F. B., Jaenisch, F. R. F., Burt, D. W. and Coutinho, L. L. (2016). Quantitative trait loci with sex-specific effects for internal organs weights and hematocrit value in a broiler-layer cross. Journal of Applied Genetics, 57 (2), 215-224. doi: 10.1007/s13353-015-0325-2
Baile, Peter, Chang, David K., Nones, Katia, Johns, Amber L., Patch, Ann-Marie, Gingras, Marie-Claude, Miller, David K., Christ, Angelika N., Bruxner, Tim J. C., Quinn, Michael C., Nourse, Craig, Murtaugh, L. Charles, Harliwong, Ivon, Idrisoglu, Senel, Manning, Suzanne, Nourbakhsh, Ehsan, Wani, Shivangi, Fink, Lynn, Holmes, Oliver, Chin, Vencssa, Anderson, Matthew J., Kazakoff, Stephen, Leonard, Conrad, Newell, Felicity, Waddell, Nick, Wood, Scott, Xu, Qinying, Wilson, Peter J., Cloonan, Nicole ... Grimmond, Sean M. (2016). Genomic analyses identify molecular subtypes of pancreatic cancer. Nature, 531 (7592), 47-52. doi: 10.1038/nature16965
Patch, Ann-Marie, Christie, Elizabeth L., Etemadmoghadam, Dariush, Garsed, Dale W., George, Joshy, Fereday, Sian, Nones, Katia, Cowin, Prue, Alsop, Kathryn, Bailey, Peter J., Kassahn, Karin S., Newell, Felicity, Quinn, Michael C. J., Kazakoff, Stephen, Quek, Kelly, Wilhelm-Benartzi, Charlotte, Curry, Ed, Leong, Huei San, Australian Ovarian Cancer Study Group, Hamilton, Anne, Mileshkin, Linda, Au-Yeung, George, Kennedy, Catherine, Hung, Jillian, Chiew, Yoke-Eng, Harnett, Paul, Friedlander, Michael, Quinn, Michael, Pyman, Jan ... Bowtell, David D. L. (2015). Corrigendum: Whole-genome characterization of chemoresistant ovarian cancer. Nature, 527 (7578), 398-398. doi: 10.1038/nature15716
Saunus, Jodi M., Quinn, MIchael C. J., Patch, Ann-Marie, Pearson, John V., Bailey, Peter J., Nones, Katia, McCart Reed, Amy E., Miller, David, Peter J. Wilson, Al-Ejeh, Fares, Mariasegaram, Mythily, Lau, Queenie, Withers, Teresa, Jeffree, Rosalind L., Reid, Lynne E., Da Silva, Leonard, Matsika, Admire, Niland, Colleen M., Cummings, Margaret C., Bruxner, Timothy J. C., Christ, Angelika N., Harliwong, Ivon, Idrisoglu, Senel, Manning, Suzanne, Nourse, Craig, Nourbakhsh, Ehsan, Wani, Shivangi, Anderson, Matthew J., Fink, J. Lynn ... Lakhani, Sunil R. (2015). Integrated genomic and transcriptomic analysis of human brain metastases identifies recurrently altered pathways of potential clinical significance. Journal of Pathology, 237 (3), 363-378. doi: 10.1002/path.4583
Patch, Ann-Marie, Christie, Elizabeth L., Etemadmoghadam, Dariush, Garsed, Dale W., George, Joshy, Fereday, Sian, Nones, Katia, Cowin, Prue, Alsop, Kathryn, Bailey, Peter J., Kassahn, Karin S., Newell, Felicity, Quinn, Michael C. J., Kazakoff, Stephen, Quek, Kelly, Wilhelm-Benartzi, Charlotte, Curry, Ed, Leong, Huei San, The Australian Ovarian Cancer Study Group, Hamilton, Anne, Mileshkin, Linda, Au-Yeung, George, Kennedy, Catherine, Hung, Jillian, Chiew, Yoke-Eng, Harnett, Paul, Friedlander, Michael, Quinn, Michael, Pyman, Jan ... Bowtell, David D. L. (2015). Whole-genome characterization of chemoresistant ovarian cancer. Nature, 521 (7553), 489-494. doi: 10.1038/nature14410
Wood, David L. A., Nones, Katia, Steptoe, Anita, Christ, Angelika, Harliwong, Ivon, Newell, Felicity, Bruxner, Timothy J. C., Miller, David, Cloonan, Nicole and Grimmond, Sean M. (2015). Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data. PLoS One, 10 (5) 0126911, e0126911-e0126911. doi: 10.1371/journal.pone.0126911
Nagaraj, Shiv Hiriyur, Waddell, Nicola, Madugundu, Anil K., Wood, Scott, Jones, Alun, Mandyam, Ramya, Nones, Katia, Pearson, John and Grimmond, Sean M. (2015). PGTools: a software suite for proteogenomic data analysis and visualization. Journal of Proteome Research, 14 (5), 2255-2266. doi: 10.1021/acs.jproteome.5b00029
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
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
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
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
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
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
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
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
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), 73-89. 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
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
Conference Papers
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
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