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2015 Journal Article Corrigendum: Whole-genome characterization of chemoresistant ovarian cancerPatch, 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 |
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2015 Journal Article Integrated genomic and transcriptomic analysis of human brain metastases identifies recurrently altered pathways of potential clinical significanceSaunus, 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 |
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2015 Journal Article Whole-genome characterization of chemoresistant ovarian cancerPatch, 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 |
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2015 Journal Article Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq DataWood, 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 |
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2015 Journal Article PGTools: a software suite for proteogenomic data analysis and visualizationNagaraj, 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 |
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2015 Journal Article Whole genomes redefine the mutational landscape of pancreatic cancerWaddell, 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 |
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2015 Conference Publication Genomic and transcriptomic landscapes of human brain metastasesSaunus, 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 |
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2015 Journal Article Genetic parameters and mapping quantitative trait loci associated with tibia traits in broilersRagognetti, 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 |
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2014 Journal Article Genomic catastrophes frequently arise in esophageal adenocarcinoma and drive tumorigenesisNones, 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 |
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2014 Journal Article Genome-wide DNA methylation patterns in pancreatic ductal adenocarcinoma reveal epigenetic deregulation of SLIT-ROBO, ITGA2 and MET signalingNones, 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 |
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2014 Journal Article A workflow to increase verification rate of chromosomal structural rearrangements using high-throughput next-generation sequencingQuek, 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 |
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2014 Journal Article Imperfect centered miRNA binding sites are common and can mediate repression of target mRNAsMartin, 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 |
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2014 Conference Publication Elucidating mechanisms of resistance to FGFR inhibitors in endometrial cancerPacker, 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 |
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2013 Journal Article miR-139-5p is a regulator of metastatic pathways in breast cancerKrishnan, 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 |
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2013 Journal Article Somatic point mutation calling in low cellularity tumorsKassahn, 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 |
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2013 Journal Article Modulation of colonic inflammation in Mdr1a-/- mice by green tea polyphenols and their effects on the colon transcriptome and proteomeBarnett, 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 |
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2013 Journal Article Clinical and molecular characterization of HER2 amplified-pancreatic cancerChou, 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 |
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2013 Journal Article MicroRNA-182-5-p targets a network of genes involved in DNA repairKrishnan, 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 |
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2013 Journal Article Association of IGF1 and KDM5A polymorphisms with performance, fatness and carcass traits in chickensBoschiero, 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 |
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2013 Journal Article The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicingBarry, 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 |
