Research Publications

2022 Publications

  • Baptista, R.P., Li, Y., Sateriale, A., Sanders, M.J., Brooks, K.L., Tracey, A., Ansell, B.R.E., Jex, A.R., Cooper, G.W., Smith, E.D., Xiao, R., Dumaine, J.E., Georgeson, P., Pope, B.J., Berriman, M., Striepen, B., Cotton, J.A., Kissinger, J.C., 2022. Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions. Genome Res 32, 203–213. https://doi.org/10.1101/gr.275325.121
  • Burns, D., Anokian, E., Saunders, E.J., Bristow, R.G., Fraser, M., Reimand, J., Schlomm, T., Sauter, G., Brors, B., Korbel, J., Weischenfeldt, J., Waszak, S.M., Corcoran, N.M., Jung, C.-H., Pope, B.J., Hovens, C.M., Cancel-Tassin, G., Cussenot, O., Loda, M., Sander, C., Hayes, V.M., Dalsgaard Sorensen, K., Lu, Y.-J., Hamdy, F.C., Foster, C.S., Gnanapragasam, V., Butler, A., Lynch, A.G., Massie, C.E., CR-UK/Prostate Cancer UK, ICGC, The PPCG, Woodcock, D.J., Cooper, C.S., Wedge, D.C., Brewer, D.S., Kote-Jarai, Z., Eeles, R.A., 2022. Rare Germline Variants Are Associated with Rapid Biochemical Recurrence After Radical Prostate Cancer Treatment: A Pan Prostate Cancer Group Study. Eur Urol 82, 201–211. https://doi.org/10.1016/j.eururo.2022.05.007
  • Chee, L., Ritchie, D., Ludford-Menting, M., Ripley, J., Chung, J., Park, D., Norton, S., Kenealy, M., Koldej, R., 2022. Dysregulation of immune cell and cytokine signalling correlates with clinical outcomes in myelodysplastic syndrome (MDS). Eur J Haematol 108, 342–353. https://doi.org/10.1111/ejh.13742
  • Cribb, D.M., Varrone, L., Wallace, R.L., McLure, A.T., Smith, J.J., Stafford, R.J., Bulach, D.M., Selvey, L.A., Firestone, S.M., French, N.P., Valcanis, M., Fearnley, E.J., Sloan-Gardner, T.S., Graham, T., Glass, K., Kirk, M.D., 2022. Risk factors for campylobacteriosis in Australia: outcomes of a 2018-2019 case-control study. BMC Infect Dis 22, 586. https://doi.org/10.1186/s12879-022-07553-6
  • Georgeson, P., Harrison, T.A., Pope, B.J., Zaidi, S.H., Qu, C., Steinfelder, R.S., Lin, Y., Joo, J.E., Mahmood, K., Clendenning, M., Walker, R., Amitay, E.L., Berndt, S.I., Brenner, H., Campbell, P.T., Cao, Y., Chan, A.T., Chang-Claude, J., Doheny, K.F., Drew, D.A., Figueiredo, J.C., French, A.J., Gallinger, S., Giannakis, M., Giles, G.G., Gsur, A., Gunter, M.J., Hoffmeister, M., Hsu, L., Huang, W.-Y., Limburg, P., Manson, J.E., Moreno, V., Nassir, R., Nowak, J.A., Obón-Santacana, M., Ogino, S., Phipps, A.I., Potter, J.D., Schoen, R.E., Sun, W., Toland, A.E., Trinh, Q.M., Ugai, T., Macrae, F.A., Rosty, C., Hudson, T.J., Jenkins, M.A., Thibodeau, S.N., Winship, I.M., Peters, U., Buchanan, D.D., 2022. Identifying colorectal cancer caused by biallelic MUTYH pathogenic variants using tumor mutational signatures. Nat Commun 13, 3254. https://doi.org/10.1038/s41467-022-30916-1
  • Heighway, J., Sedo, A., Garg, A., Eldershaw, L., Perreau, V., Berecki, G., Reid, C.A., Petrou, S., Maljevic, S., 2022. Sodium channel expression and transcript variation in the developing brain of human, Rhesus monkey, and mouse. Neurobiol Dis 164, 105622. https://doi.org/10.1016/j.nbd.2022.105622
  • Jung, C.-H., Boutros, P.C., Park, D.J., Corcoran, N.M., Pope, B.J., Hovens, C.M., 2022. Perish and publish: Dynamics of biomedical publications by deceased authors. PLOS ONE 17, e0273783. https://doi.org/10.1371/journal.pone.0273783
  • Lima, Y.S. de, Arnau-Collell, C., Muñoz, J., Herrera-Pariente, C., Moreira, L., Ocaña, T., Díaz-Gay, M., Franch-Expósito, S., Cuatrecasas, M., Carballal, S., Lopez-Novo, A., Moreno, L., Fernàndez, G., Bustamante, A.D. de, Peters, S., Sommer, A.K., Spier, I., Paske, I.B.A.W. te, Herwaarden, Y.J. van, Castells, A., Bujanda, L., Capellà, G., Steinke-Lange, V., Mahmood, K., Joo, J.E., Arnold, J., Parry, S., Macrae, F.A., Winship, I.M., Rosty, C., Cubiella, J., Rodríguez-Alcalde, D., Holinski-Feder, E., Voer, R. de, Buchanan, D.D., Aretz, S., Ruiz-Ponte, C., Valle, L., Balaguer, F., Bonjoch, L., Castellvi-Bel, S., 2022. Germline mutations in WNK2 could be associated with serrated polyposis syndrome. Journal of Medical Genetics. https://doi.org/10.1136/jmg-2022-108684
  • Liow, E., Howard, N., Jung, C.-H., Pope, B., Campbell, B.K., Nguyen, A., Kerger, M., Ruddle, J.B., Anton, A., Thomas, B., Chu, K., Dundee, P., Peters, J.S., Costello, A.J., Ryan, A.S., Hovens, C.M., Tran, B., Corcoran, N.M., 2022. Phase 2 Study of Neoadjuvant FGFR Inhibition and Androgen Deprivation Therapy Prior to Prostatectomy. Clin Genitourin Cancer S1558-7673(22)00112–4. https://doi.org/10.1016/j.clgc.2022.05.007
  • Ishaq, M., Bandara, N., Morgan, S., Nowell, C., Mehdi, A.M., Lyu, R., McCarthy, D., Anderson, D., Creek, D.J., Achen, M.G., Shayan, R., Karnezis, T., 2022. Key signaling networks are dysregulated in patients with the adipose tissue disorder, lipedema. Int J Obes (Lond) 46, 502–514. https://doi.org/10.1038/s41366-021-01002-1
  • Ranawaka, I., Goonasekara, N., Afgan, E., Basney, J., Marru, S., Pierce, M., 2022. Custos Secrets: a Service for Managing User-Provided Resource Credential Secrets for Science Gateways, in: Practice and Experience in Advanced Research Computing, PEARC ’22. Association for Computing Machinery, New York, NY, USA, pp. 1–4. https://doi.org/10.1145/3491418.3535177
  • Yang, Q., Chung, J., Robinson, K.L., Schmidt, T.L., Ross, P.A., Liang, J., Hoffmann, A.A., 2022. Sex-specific distribution and classification of Wolbachia infections and mitochondrial DNA haplogroups in Aedes albopictus from the Indo-Pacific. PLoS Negl Trop Dis 16, e0010139. https://doi.org/10.1371/journal.pntd.0010139

2021 Publications

  • Chan, J.M., Clendenning, M., Joseland, S., Georgeson, P., Mahmood, K., Walker, R., Como, J., Joo, J.E., Preston, S., Hutchinson, R.A., Pope, B.J., Metz, A., Beard, C., Purvis, R., Arnold, J., Vijay, V., Konycheva, G., Atkinson, N., Parry, S., Jenkins, M.A., Macrae, F.A., Rosty, C., Winship, I.M., Buchanan, D.D., 2021. Rare germline variants in the AXIN2 gene in families with colonic polyposis and colorectal cancer. Fam Cancer. https://doi.org/10.1007/s10689-021-00283-9
  • Chan, W.Y., Chung, J., Peplow, L.M., Hoffmann, A.A., van Oppen, M.J., 2021. Maternal effects in gene expression of interspecific coral hybrids. Molecular Ecology 30, 517–527. https://doi.org/10.1111/mec.15727
  • Dugué, P.-A., Hodge, A.M., Wong, E.M., Joo, J.E., Jung, C.-H., Hopper, J.L., English, D.R., Giles, G.G., Milne, R.L., Southey, M.C., 2021. Methylation marks of prenatal exposure to maternal smoking and risk of cancer in adulthood. Int J Epidemiol 50, 105–115. https://doi.org/10.1093/ije/dyaa210
  • Dugué, P.-A., Wilson, R., Lehne, B., Jayasekara, H., Wang, X., Jung, C.-H., Joo, J.E., Makalic, E., Schmidt, D.F., Baglietto, L., Severi, G., Gieger, C., Ladwig, K.-H., Peters, A., Kooner, J.S., Southey, M.C., English, D.R., Waldenberger, M., Chambers, J.C., Giles, G.G., Milne, R.L., 2021. Alcohol consumption is associated with widespread changes in blood DNA methylation: Analysis of cross-sectional and longitudinal data. Addiction Biology 26, e12855. https://doi.org/10.1111/adb.12855
  • Dungan, A.M., Bulach, D., Lin, H., van Oppen, M.J., Blackall, L.L., 2021. Development of a free radical scavenging bacterial consortium to mitigate oxidative stress in cnidarians. Microbial biotechnology 14, 2025–2040. https://doi.org/10.1111/1751-7915.13877
  • Dussex, N., van der Valk, T., Morales, H.E., Wheat, C.W., Díez-del-Molino, D., von Seth, J., Foster, Y., Kutschera, V.E., Guschanski, K., Rhie, A., Phillippy, A.M., Korlach, J., Howe, K., Chow, W., Pelan, S., Mendes Damas, J.D., Lewin, H.A., Hastie, A.R., Formenti, G., Fedrigo, O., Guhlin, J., Harrop, T.W.R., Le Lec, M.F., Dearden, P.K., Haggerty, L., Martin, F.J., Kodali, V., Thibaud-Nissen, F., Iorns, D., Knapp, M., Gemmell, N.J., Robertson, F., Moorhouse, R., Digby, A., Eason, D., Vercoe, D., Howard, J., Jarvis, E.D., Robertson, B.C., Dalén, L., 2021. Population genomics of the critically endangered kākāpō. Cell Genomics 1, 100002. https://doi.org/10.1016/j.xgen.2021.100002
  • Edwards, D.J., Duchene, S., Pope, B., Holt, K.E., 2021. SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments. Microb Genom 7, 000694. https://doi.org/10.1099/mgen.0.000694
  • Georgeson, P., Pope, B.J., Rosty, C., Clendenning, M., Mahmood, K., Joo, J.E., Walker, R., Hutchinson, R.A., Preston, S., Como, J., Joseland, S., Win, A.K., Macrae, F.A., Hopper, J.L., Mouradov, D., Gibbs, P., Sieber, O.M., O’Sullivan, D.E., Brenner, D.R., Gallinger, S., Jenkins, M.A., Winship, I.M., Buchanan, D.D., 2021. Evaluating the utility of tumour mutational signatures for identifying hereditary colorectal cancer and polyposis syndrome carriers. Gut 70, 2138–2149. https://doi.org/10.1136/gutjnl-2019-320462
  • Goonasekera, N., Mahmoud, A., Chilton, J., Afgan, E., 2021. GalaxyCloudRunner: enhancing scalable computing for Galaxy. Bioinformatics 37, 1763–1765. https://doi.org/10.1093/bioinformatics/btaa860
  • Hall, C.R., Griffin, P.C., Lonie, A.J., Christiansen, J.H., 2021. Application of a bioinformatics training delivery method for reaching dispersed and distant trainees. PLOS Computational Biology 17, e1008715. https://doi.org/10.1371/journal.pcbi.1008715
  • Holdsworth-Carson, S.J., Churchill, M., Donoghue, J.F., Mortlock, S., Fung, J.N., Sloggett, C., Chung, J., Cann, L., Teh, W.T., Campbell, K.-R., Luwor, R., Healey, M., Montgomery, G., Girling, J.E., Rogers, P.A.W., 2021. Elucidating the role of long intergenic non-coding RNA 339 in human endometrium and endometriosis. Mol Hum Reprod 27, gaab010. https://doi.org/10.1093/molehr/gaab010
  • Joo, J.E., Clendenning, M., Wong, E.M., Rosty, C., Mahmood, K., Georgeson, P., Winship, I.M., Preston, S.G., Win, A.K., Dugué, P.-A., Jayasekara, H., English, D., Macrae, F.A., Hopper, J.L., Jenkins, M.A., Milne, R.L., Giles, G.G., Southey, M.C., Buchanan, D.D., 2021. DNA Methylation Signatures and the Contribution of Age-Associated Methylomic Drift to Carcinogenesis in Early-Onset Colorectal Cancer. Cancers (Basel) 13, 2589. https://doi.org/10.3390/cancers13112589
  • Lau, M.-J., Schmidt, T.L., Yang, Q., Chung, J., Sankey, L., Ross, P.A., Hoffmann, A.A., 2021. Genetic stability of Aedes aegypti populations following invasion by wMel Wolbachia. BMC genomics 22, 1–13. https://doi.org/10.1186/s12864-021-08200-1
  • Maier, W., Bray, S., van den Beek, M., Bouvier, D., Coraor, N., Miladi, M., Singh, B., De Argila, J.R., Baker, D., Roach, N., Gladman, S., Coppens, F., Martin, D.P., Lonie, A., Grüning, B., Kosakovsky Pond, S.L., Nekrutenko, A., 2021. Ready-to-use public infrastructure for global SARS-CoV-2 monitoring. Nat Biotechnol 39, 1178–1179. https://doi.org/10.1038/s41587-021-01069-1
  • McCoy, P., Mangiola, S., Macintyre, G., Hutchinson, R., Tran, B., Pope, B., Georgeson, P., Hong, M.K.H., Kurganovs, N., Lunke, S., Clarkson, M.J., Cmero, M., Kerger, M., Stuchbery, R., Chow, K., Haviv, I., Ryan, A., Costello, A.J., Corcoran, N.M., Hovens, C.M., 2021. MSH2-deficient prostate tumours have a distinct immune response and clinical outcome compared to MSH2-deficient colorectal or endometrial cancer. Prostate Cancer Prostatic Dis 24, 1167–1180. https://doi.org/10.1038/s41391-021-00379-4
  • McCulloch, G.A., Guhlin, J., Dutoit, L., Harrop, T.W.R., Dearden, P.K., Waters, J.M., 2021. Genomic signatures of parallel alpine adaptation in recently evolved flightless insects. Molecular Ecology 30, 6677–6686. https://doi.org/10.1111/mec.16204
  • Nguyen, T.H., Ho, T.T.M., Nguyen-Hoang, T.-P., Qumar, S., Pham, T.T.D., Bui, Q.N., Bulach, D., Nguyen, T.-V., Rahman, M., 2021. The endemic Helicobacter pylori population in Southern Vietnam has both South East Asian and European origins. Gut pathogens 13, 1–14. https://doi.org/10.1186/s13099-021-00452-2
  • Pope, B.J., Clendenning, M., Rosty, C., Mahmood, K., Georgeson, P., Joo, J.E., Walker, R., Hutchinson, R.A., Jayasekara, H., Joseland, S., Como, J., Preston, S., Spurdle, A.B., Macrae, F.A., Win, A.K., Hopper, J.L., Jenkins, M.A., Winship, I.M., Buchanan, D.D., 2021. Germline and tumor sequencing as a diagnostic tool to resolve suspected Lynch syndrome. The Journal of Molecular Diagnostics 23, 358–371. https://doi.org/10.1016/j.jmoldx.2020.12.003
  • Schmidt, T.L., Swan, T., Chung, J., Karl, S., Demok, S., Yang, Q., Field, M.A., Muzari, M.O., Ehlers, G., Brugh, M., 2021. Spatial population genomics of a recent mosquito invasion. Molecular Ecology 30, 1174–1189. https://doi.org/10.1111/mec.15792
  • Smyth, L.M., Crosbie, J.C., Sloggett, C., Rogers, P.A., Donoghue, J.F., 2021. Spatially Fractionated X-Ray Microbeams Elicit a More Sustained Immune and Inflammatory Response in the Brainstem than Homogenous Irradiation. Radiation Research 196, 355–365. https://doi.org/10.1667/RADE-20-00082.1
  • Southey, M.C., Dowty, J.G., Riaz, M., Steen, J.A., Renault, A.-L., Tucker, K., Kirk, J., James, P., Winship, I., Pachter, N., Poplawski, N., Grist, S., Park, D.J., Pope, B.J., Mahmood, K., Hammet, F., Mahmoodi, M., Tsimiklis, H., Theys, D., Rewse, A., Willis, A., Morrow, A., Speechly, C., Harris, R., Sebra, R., Schadt, E., Lacaze, P., McNeil, J.J., Giles, G.G., Milne, R.L., Hopper, J.L., Nguyen-Dumont, T., 2021. Population-based estimates of breast cancer risk for carriers of pathogenic variants identified by gene-panel testing. npj Breast Cancer 7, 1–7. https://doi.org/10.1038/s41523-021-00360-3
  • Syme, A.E., McLay, T.G.B., Udovicic, F., Cantrill, D.J., Murphy, D.J., McLay, T.G.B., Udovicic, F., Cantrill, D.J., Murphy, D.J., 2021. Long-read assemblies reveal structural diversity in genomes of organelles – an example with Acacia pycnantha. Gigabyte 2021, 1–23. https://doi.org/10.46471/gigabyte.36
  • Wallace, R.L., Bulach, D., McLure, A., Varrone, L., Jennison, A.V., Valcanis, M., Smith, J.J., Polkinghorne, B.G., Glass, K., Kirk, M.D., 2021. Antimicrobial resistance of Campylobacter spp. causing human infection in Australia: an international comparison. Microbial Drug Resistance 27, 518–528. https://doi.org/10.1089/mdr.2020.0082
  • Wallace, R.L., Cribb, D.M., Bulach, D.M., Ingle, D.J., Joensen, K.G., Nielsen, E.M., Leekitcharoenphon, P., Stingl, K., Kirk, M.D., 2021. Campylobacter jejuni ST50, a pathogen of global importance: A comparative genomic analysis of isolates from Australia, Europe and North America. Zoonoses and Public Health 68, 638–649. https://doi.org/10.1111/zph.12853
2020 Publications
  • Baker, D., van den Beek, M., Blankenberg, D., Bouvier, D., Chilton, J., Coraor, N., Coppens, F., Eguinoa, I., Gladman, S., Grüning, B., Keener, N., Larivière, D., Lonie, A., Kosakovsky Pond, S., Maier, W., Nekrutenko, A., Taylor, J., Weaver, S., 2020. No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics. PLoS Pathog 16, e1008643. https://doi.org/10.1371/journal.ppat.1008643
  • Blasdell, K.R., Davis, S.S., Voysey, R., Bulach, D.M., Middleton, D., Williams, S., Harmsen, M.B., Weir, R.P., Crameri, S., Walsh, S.J., Peck, G.R., Tesh, R.B., Boyle, D.B., Melville, L.F., Walker, P.J., 2020. Hayes Yard virus: a novel ephemerovirus isolated from a bull with severe clinical signs of bovine ephemeral fever is most closely related to Puchong virus. Vet Res 51, 58. https://doi.org/10.1186/s13567-020-00781-1
  • Dugué, P.-A., Chamberlain, J.A., Bassett, J.K., Hodge, A.M., Brinkman, M.T., Joo, J.E., Jung, C.-H., Wong, E.M., Makalic, E., Schmidt, D.F., Hopper, J.L., Buchanan, D.D., English, D.R., Milne, R.L., Southey, M.C., Giles, G.G., 2020. Overall lack of replication of associations between dietary intake of folate and vitamin B-12 and DNA methylation in peripheral blood. Am J Clin Nutr 111, 228–230. https://doi.org/10.1093/ajcn/nqz253
  • Dugué, P.-A., Jung, C.-H., Joo, J.E., Wang, X., Wong, E.M., Makalic, E., Schmidt, D.F., Baglietto, L., Severi, G., Southey, M.C., English, D.R., Giles, G.G., Milne, R.L., 2020. Smoking and blood DNA methylation: an epigenome-wide association study and assessment of reversibility. Epigenetics 15, 358–368. https://doi.org/10.1080/15592294.2019.1668739
  • Elsayed, F.A., Grolleman, J.E., Ragunathan, A., NTHL1 study group, Buchanan, D.D., van Wezel, T., de Voer, R.M., 2020. Monoallelic NTHL1 Loss-of-Function Variants and Risk of Polyposis and Colorectal Cancer. Gastroenterology 159, 2241-2243.e6. https://doi.org/10.1053/j.gastro.2020.08.042
  • Endersby-Harshman, N.M., Schmidt, T.L., Chung, J., van Rooyen, A., Weeks, A.R., Hoffmann, A.A., 2020. Heterogeneous genetic invasions of three insecticide resistance mutations in Indo-Pacific populations of Aedes aegypti (L.). Mol Ecol 29, 1628–1641. https://doi.org/10.1111/mec.15430
  • Fisicaro, N., Salvaris, E.J., Philip, G.K., Wakefield, M.J., Nottle, M.B., Hawthorne, W.J., Cowan, P.J., 2020. FokI-dCas9 mediates high-fidelity genome editing in pigs. Xenotransplantation 27, e12551. https://doi.org/10.1111/xen.12551
  • Holdsworth-Carson, S.J., Chung, J., Sloggett, C., Mortlock, S., Fung, J.N., Montgomery, G.W., Dior, U.P., Healey, M., Rogers, P.A., Girling, J.E., 2020. Obesity does not alter endometrial gene expression in women with endometriosis. Reprod Biomed Online 41, 113–118. https://doi.org/10.1016/j.rbmo.2020.03.015
  • Lau, E., McCoy, P., Reeves, F., Chow, K., Clarkson, M., Kwan, E.M., Packwood, K., Northen, H., He, M., Kingsbury, Z., Mangiola, S., Kerger, M., Furrer, M.A., Crowe, H., Costello, A.J., McBride, D.J., Ross, M.T., Pope, B., Hovens, C.M., Corcoran, N.M., 2020. Detection of ctDNA in plasma of patients with clinically localised prostate cancer is associated with rapid disease progression. Genome Medicine 12, 72. https://doi.org/10.1186/s13073-020-00770-1
  • Leeming, M.G., Isaac, A.P., Zappia, L., O’Hair, R.A.J., Donald, W.A., Pope, B.J., 2020. HiTIME: An efficient model-selection approach for the detection of unknown drug metabolites in LC-MS data. SoftwareX 12, 100559. https://doi.org/10.1016/j.softx.2020.100559
  • Nguyen-Dumont, Tu, Karpinski, P., Sasiadek, M.M., Akopyan, H., Steen, J.A., Theys, D., Hammet, F., Tsimiklis, H., Park, D.J., Pope, B.J., Slezak, R., Stembalska, A., Pesz, K., Kitsera, N., Siekierzynska, A., Southey, M.C., Myszka, A., 2020. Genetic testing in Poland and Ukraine: should comprehensive germline testing of BRCA1 and BRCA2 be recommended for women with breast and ovarian cancer? Genet Res (Camb) 102, e6. https://doi.org/10.1017/S0016672320000075
  • Nguyen-Dumont, Tú, MacInnis, R.J., Steen, J.A., Theys, D., Tsimiklis, H., Hammet, F., Mahmoodi, M., Pope, B.J., Park, D.J., Mahmood, K., Severi, G., Bolton, D., Milne, R.L., Giles, G.G., Southey, M.C., 2020. Rare germline genetic variants and risk of aggressive prostate cancer. Int J Cancer 147, 2142–2149. https://doi.org/10.1002/ijc.33024
  • Nguyen-Dumont, Tu, Steen, J.A., Winship, I., Park, D.J., Pope, B.J., Hammet, F., Mahmoodi, M., Tsimiklis, H., Theys, D., Clendenning, M., Giles, G.G., Hopper, J.L., Southey, M.C., 2020. Mismatch repair gene pathogenic germline variants in a population-based cohort of breast cancer. Fam Cancer 19, 197–202. https://doi.org/10.1007/s10689-020-00164-7
  • Plummer, E.L., Vodstrcil, L.A., Murray, G.L., Fairley, C.K., Danielewski, J.A., Garland, S.M., Chow, E.P.F., Bulach, D.M., Fethers, K.A., Hocking, J.S., Bradshaw, C.S., 2020. Gardnerella vaginalis Clade Distribution Is Associated With Behavioral Practices and Nugent Score in Women Who Have Sex With Women. J Infect Dis 221, 454–463. https://doi.org/10.1093/infdis/jiz474
  • Sanij, E., Hannan, K.M., Xuan, J., Yan, S., Ahern, J.E., Trigos, A.S., Brajanovski, N., Son, J., Chan, K.T., Kondrashova, O., Lieschke, E., Wakefield, M.J., Frank, D., Ellis, S., Cullinane, C., Kang, J., Poortinga, G., Nag, P., Deans, A.J., Khanna, K.K., Mileshkin, L., McArthur, G.A., Soong, J., Berns, E.M.J.J., Hannan, R.D., Scott, C.L., Sheppard, K.E., Pearson, R.B., 2020. CX-5461 activates the DNA damage response and demonstrates therapeutic efficacy in high-grade serous ovarian cancer. Nat Commun 11, 2641. https://doi.org/10.1038/s41467-020-16393-4/li>
  • Schmidt, T.L., Chung, J., Honnen, A.-C., Weeks, A.R., Hoffmann, A.A., 2020. Population genomics of two invasive mosquitoes (Aedes aegypti and Aedes albopictus) from the Indo-Pacific. PLoS Negl Trop Dis 14, e0008463. https://doi.org/10.1371/journal.pntd.0008463
  • Schmidt, T.L., Chung, J., van Rooyen, A.R., Sly, A., Weeks, A.R., Hoffmann, A.A., 2020. Incursion pathways of the Asian tiger mosquito (Aedes albopictus) into Australia contrast sharply with those of the yellow fever mosquito (Aedes aegypti). Pest Manag Sci 76, 4202–4209. https://doi.org/10.1002/ps.5977
  • Siddiqee, M.H., Henry, R., Deletic, A., Bulach, D.M., Coleman, R.A., McCarthy, D.T., 2020. Salmonella from a Microtidal Estuary Are Capable of Invading Human Intestinal Cell Lines. Microb Ecol 79, 259–270. https://doi.org/10.1007/s00248-019-01419-2
  • Wallace, R.L., Bulach, D.M., Jennison, A.V., Valcanis, M., McLure, A., Smith, J.J., Graham, T., Saputra, T., Firestone, S., Symes, S., Waters, N., Stylianopoulos, A., Kirk, M.D., Glass, K., 2020. Molecular characterization of Campylobacter spp. recovered from beef, chicken, lamb and pork products at retail in Australia. PLoS One 15, e0236889. https://doi.org/10.1371/journal.pone.0236889
  • Wallace, R.L., Bulach, D., Valcanis, M., Polkinghorne, B.G., Pingault, N., Stylianopoulos, A., Givney, R.C., Glass, K., Kirka, M.D., 2020. Identification of the first erm(B)-positive Campylobacter jejuni and Campylobacter coli associated with novel multidrug resistance genomic islands in Australia. J Glob Antimicrob Resist 23, 311–314. https://doi.org/10.1016/j.jgar.2020.09.009
2019 Publications
  • Afgan, E., Lonie, A., Taylor, J., Goonasekera, N., 2019. CloudLaunch: Discover and deploy cloud applications. Future Generation Computer Systems 94, 802–810. https://doi.org/10.1016/j.future.2018.04.037
  • Ansell, B.R.E., Pope, B.J., Georgeson, P., Emery-Corbin, S.J., Jex, A.R., 2019. Annotation of the Giardia proteome through structure-based homology and machine learning. GigaScience 8, giy150. https://doi.org/10.1093/gigascience/giy150
  • Chan, W.H., Komada, M., Fukushima, T., Southard-Smith, E.M., Anderson, C.R., Wakefield, M.J., 2019. RNA-seq of Isolated Chromaffin Cells Highlights the Role of Sex-Linked and Imprinted Genes in Adrenal Medulla Development. Sci Rep 9, 3929. https://doi.org/10.1038/s41598-019-40501-0
  • Georgeson, P., Syme, A., Sloggett, C., Chung, J., Dashnow, H., Milton, M., Lonsdale, A., Powell, D., Seemann, T., Pope, B., 2019. Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software. Gigascience 8, giz109. https://doi.org/10.1093/gigascience/giz109
  • Georgeson, P., Walsh, M.D., Clendenning, M., Daneshvar, S., Pope, B.J., Mahmood, K., Joo, J.E., Jayasekara, H., Jenkins, M.A., Winship, I.M., Buchanan, D.D., 2019. Tumor mutational signatures in sebaceous skin lesions from individuals with Lynch syndrome. Mol Genet Genomic Med 7, e00781. https://doi.org/10.1002/mgg3.781
  • Hammet, F., Mahmood, K., Green, T.R., Nguyen-Dumont, T., Southey, M.C., Buchanan, D.D., Lonie, A., Nathanson, K.L., Couch, F.J., Pope, B.J., Park, D.J., 2019. Hi-Plex2: a simple and robust approach to targeted sequencing-based genetic screening. Biotechniques 67, 118–122. https://doi.org/10.2144/btn-2019-0026
  • Ingle, D.J., Easton, M., Valcanis, M., Seemann, T., Kwong, J.C., Stephens, N., Carter, G.P., Gonçalves da Silva, A., Adamopoulos, J., Baines, S.L., Holt, K.E., Chow, E.P.F., Fairley, C.K., Chen, M.Y., Kirk, M.D., Howden, B.P., Williamson, D.A., 2019. Co-circulation of Multidrug-resistant Shigella Among Men Who Have Sex With Men in Australia. Clin Infect Dis 69, 1535–1544. https://doi.org/10.1093/cid/ciz005
  • Ingle, D.J., Gonçalves da Silva, A., Valcanis, M., Ballard, S.A., Seemann, T., Jennison, A.V., Bastian, I., Wise, R., Kirk, M.D., Howden, B.P., Williamson, D.A., 2019. Emergence and divergence of major lineages of Shiga-toxin-producing Escherichia coli in Australia. Microb Genom 5. https://doi.org/10.1099/mgen.0.000268
  • Minhas, V., Harvey, R.M., McAllister, L.J., Seemann, T., Syme, A.E., Baines, S.L., Paton, J.C., Trappetti, C., 2019. Capacity To Utilize Raffinose Dictates Pneumococcal Disease Phenotype. mBio 10, e02596-18. https://doi.org/10.1128/mBio.02596-18
  • Monk, I.R., Shaikh, N., Begg, S.L., Gajdiss, M., Sharkey, L.K.R., Lee, J.Y.H., Pidot, S.J., Seemann, T., Kuiper, M., Winnen, B., Hvorup, R., Collins, B.M., Bierbaum, G., Udagedara, S.R., Morey, J.R., Pulyani, N., Howden, B.P., Maher, M.J., McDevitt, C.A., King, G.F., Stinear, T.P., 2019. Zinc-binding to the cytoplasmic PAS domain regulates the essential WalK histidine kinase of Staphylococcus aureus. Nat Commun 10, 3067. https://doi.org/10.1038/s41467-019-10932-4
  • Mu, A., Kwong, J.C., Isles, N.S., Gonçalves da Silva, A., Schultz, M.B., Ballard, S.A., Lane, C.R., Carter, G.P., Williamson, D.A., Seemann, T., Stinear, T.P., Howden, B.P., 2019. Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing. mSphere 4, e00529-18. https://doi.org/10.1128/mSphere.00529-18
  • Plummer, E.L., Vodstrcil, L.A., Fairley, C.K., Tabrizi, S.N., Garland, S.M., Law, M.G., Hocking, J.S., Fethers, K.A., Bulach, D.M., Murray, G.L., Bradshaw, C.S., 2019. Sexual practices have a significant impact on the vaginal microbiota of women who have sex with women. Sci Rep 9, 19749. https://doi.org/10.1038/s41598-019-55929-7
  • Schmidt, T.L., van Rooyen, A.R., Chung, J., Endersby-Harshman, N.M., Griffin, P.C., Sly, A., Hoffmann, A.A., Weeks, A.R., 2019. Tracking genetic invasions: Genome-wide single nucleotide polymorphisms reveal the source of pyrethroid-resistant Aedes aegypti (yellow fever mosquito) incursions at international ports. Evol Appl 12, 1136–1146. https://doi.org/10.1111/eva.12787
  • Schneider, M.V., Griffin, P.C., Tyagi, S., Flannery, M., Dayalan, S., Gladman, S., Watson-Haigh, N., Bayer, P.E., Charleston, M., Cooke, I., Cook, R., Edwards, R.J., Edwards, D., Gorse, D., McConville, M., Powell, D., Wilkins, M.R., Lonie, A., 2019. Establishing a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia. Briefings in Bioinformatics 20, 384–389. https://doi.org/10.1093/bib/bbx071
  • Van Roekel, E.H., Dugué, P.-A., Jung, C.-H., Joo, J.E., Makalic, E., Wong, E.E.M., English, D.R., Southey, M.C., Giles, G.G., Lynch, B.M., Milne, R.L., 2019. Physical Activity, Television Viewing Time, and DNA Methylation in Peripheral Blood. Med Sci Sports Exerc 51, 490–498. https://doi.org/10.1249/MSS.0000000000001827
  • Vidor, C.J., Bulach, D., Awad, M., Lyras, D., 2019. Paeniclostridium sordellii and Clostridioides difficile encode similar and clinically relevant tetracycline resistance loci in diverse genomic locations. BMC Microbiol 19, 53. https://doi.org/10.1186/s12866-019-1427-5
  • Williamson, D.A., Chow, E.P.F., Gorrie, C.L., Seemann, T., Ingle, D.J., Higgins, N., Easton, M., Taiaroa, G., Grad, Y.H., Kwong, J.C., Fairley, C.K., Chen, M.Y., Howden, B.P., 2019. Bridging of Neisseria gonorrhoeae lineages across sexual networks in the HIV pre-exposure prophylaxis era. Nat Commun 10, 3988. https://doi.org/10.1038/s41467-019-12053-4
2018 Publications
  • Afgan, E., Lonie, A., Taylor, J., Goonasekera, N., 2018. CloudLaunch: Discover and deploy cloud applications. Future Generation Computer Systems. https://doi.org/10.1016/j.future.2018.04.037
  • Afgan, E., Jalili, V., Goonasekera, N., Taylor, J., Goecks, J., 2018. Federated Galaxy: Biomedical Computing at the Frontier, in: 2018 IEEE 11th International Conference on Cloud Computing (CLOUD). Presented at the 2018 IEEE 11th International Conference on Cloud Computing (CLOUD), pp. 871–874. https://doi.org/10.1109/CLOUD.2018.00124
  • Amy, J., Bulach, D., Knight, D., Riley, T., Johanesen, P., Lyras, D., 2018. Identification of large cryptic plasmids in Clostridioides (Clostridium) difficile. Plasmid 96–97, 25–38. https://doi.org/10.1016/j.plasmid.2018.04.001
  • Batut, B., Hiltemann, S., Bagnacani, A., Baker, D., Bhardwaj, V., Blank, C., Bretaudeau, A., Brillet-Guéguen, L., Čech, M., Chilton, J., Clements, D., Doppelt-Azeroual, O., Erxleben, A., Freeberg, M.A., Gladman, S., Hoogstrate, Y., Hotz, H.-R., Houwaart, T., Jagtap, P., Larivière, D., Le Corguillé, G., Manke, T., Mareuil, F., Ramírez, F., Ryan, D., Sigloch, F.C., Soranzo, N., Wolff, J., Videm, P., Wolfien, M., Wubuli, A., Yusuf, D., Taylor, J., Backofen, R., Nekrutenko, A., Grüning, B., 2018. Community-Driven Data Analysis Training for Biology. Cell Systems 6, 752-758.e1. https://doi.org/10.1016/j.cels.2018.05.012
  • Buchanan, D.D., Stewart, J.R., Clendenning, M., Rosty, C., Mahmood, K., Pope, B.J., Jenkins, M.A., Hopper, J.L., Southey, M.C., Macrae, F.A., Winship, I.M., Win, A.K., 2018. Risk of colorectal cancer for carriers of a germ-line mutation in POLE or POLD1. Genet Med 20, 890–895. https://doi.org/10.1038/gim.2017.185
  • Bulach, D., Adler, B., 2018. Leptospiral Genomics and Pathogenesis. Curr Top Microbiol Immunol 415, 189–214. https://doi.org/10.1007/82_2018_87
  • Buultjens, A.H., Vandelannoote, K., Meehan, C.J., Eddyani, M., de Jong, B.C., Fyfe, J.A.M., Globan, M., Tobias, N.J., Porter, J.L., Tomita, T., Tay, E.L., Seemann, T., Howden, B.P., Johnson, P.D.R., Stinear, T.P., 2018. Comparative Genomics Shows That Mycobacterium ulcerans Migration and Expansion Preceded the Rise of Buruli Ulcer in Southeastern Australia. Appl. Environ. Microbiol. 84, e02612-17. https://doi.org/10.1128/AEM.02612-17
  • Chamberlain, J.A., Bassett, J.K., Brinkman, M.T., Hodge, A.M., English, D.R., Giles, G.G., Hopper, J.L., Dugué, P.-A., Milne, R.L., Southey, M.C., Schmidt, D.F., Makalic, E., Buchanan, D.D., Joo, J.E., Jung, C.-H., 2018. Dietary intake of one-carbon metabolism nutrients and DNA methylation in peripheral blood. The American Journal of Clinical Nutrition 108, 611–621. https://doi.org/10.1093/ajcn/nqy119
  • Clendenning, M., Huang, A., Jayasekara, H., Lorans, M., Preston, S., O’Callaghan, N., Pope, B.J., Macrae, F.A., Winship, I.M., Milne, R.L., Giles, G.G., English, D.R., Hopper, J.L., Win, A.K., Jenkins, M.A., Southey, M.C., Rosty, C., Buchanan, D.D., investigators from the Melbourne Collaborative Cohort Study and the Australasian Colorectal Cancer Family Registry Cohort, 2018. Somatic mutations of the coding microsatellites within the beta-2-microglobulin gene in mismatch repair-deficient colorectal cancers and adenomas. Fam Cancer 17, 91–100. https://doi.org/10.1007/s10689-017-0013-y
  • Deveson Lucas, D., Crane, B., Wright, A., Han, M.-L., Moffatt, J., Bulach, D., Gladman, S.L., Powell, D., Aranda, J., Seemann, T., Machado, D., Pacheco, T., Marques, T., Viveiros, M., Nation, R., Li, J., Harper, M., Boyce, J.D., 2018. Emergence of High-Level Colistin Resistance in an Acinetobacter baumannii Clinical Isolate Mediated by Inactivation of the Global Regulator H-NS. Antimicrob. Agents Chemother. 62, e02442-17. https://doi.org/10.1128/AAC.02442-17
  • Dugué, P.-A., Bassett, J.K., Joo, J.E., Baglietto, L., Jung, C.-H., Wong, E.M., Fiorito, G., Schmidt, D., Makalic, E., Li, S., Moreno-Betancur, M., Buchanan, D.D., Vineis, P., English, D.R., Hopper, J.L., Severi, G., Southey, M.C., Giles, G.G., Milne, R.L., 2018. Association of DNA Methylation-Based Biological Age With Health Risk Factors and Overall and Cause-Specific Mortality. American Journal of Epidemiology 187, 529–538. https://doi.org/10.1093/aje/kwx291
  • Dugué, P.-A., Bassett, J.K., Joo, J.E., Jung, C.-H., Ming Wong, E., Moreno-Betancur, M., Schmidt, D., Makalic, E., Li, S., Severi, G., Hodge, A.M., Buchanan, D.D., English, D.R., Hopper, J.L., Southey, M.C., Giles, G.G., Milne, R.L., 2018. DNA methylation-based biological aging and cancer risk and survival: Pooled analysis of seven prospective studies. International Journal of Cancer 142, 1611–1619. https://doi.org/10.1002/ijc.31189
  • Dugué, P.-A., Wilson, R., Lehne, B., Jayasekara, H., Wang, X., Jung, C.-H., Joo, J.E., Makalic, E., Schmidt, D.F., Baglietto, L., Severi, G., Gieger, C., Ladwig, K.-H., Peters, A., Kooner, Jaspal S., Southey, M., English, D., Waldenberger, M., Chambers, J.C., Giles, G., Milne, R., 2018. Alcohol consumption is associated with widespread changes in blood DNA methylation: analysis of cross-sectional and longitudinal data. bioRxiv 452953. https://doi.org/10.1101/452953
  • Emery-Corbin, S.J., Ansell, B.R.E., Jex, A.R., Georgeson, P., Pope, B.J., 2018. Annotation of the Giardia proteome through structure-based homology and machine learning. GigaScience 8. https://doi.org/10.1093/gigascience/giy150
  • FitzGerald, L.M., Jung, C., Wong, E.M., Joo, J.E., Gould, J.A., Vasic, V., Bassett, J.K., O’Callaghan, N., Nottle, T., Pedersen, J., Giles, G.G., Southey, M.C., 2018. Obtaining high quality transcriptome data from formalin-fixed, paraffin-embedded diagnostic prostate tumor specimens. Laboratory Investigation 98, 537–550. https://doi.org/10.1038/s41374-017-0001-8
  • Ford, L., Carter, G.P., Wang, Q., Seemann, T., Sintchenko, V., Glass, K., Williamson, D.A., Howard, P., Valcanis, M., Castillo, C.F.S., Sait, M., Howden, B.P., Kirk, M.D., 2018. Incorporating Whole-Genome Sequencing into Public Health Surveillance: Lessons from Prospective Sequencing of Salmonella Typhimurium in Australia. Foodborne Pathogens and Disease 15, 161–167. https://doi.org/10.1089/fpd.2017.2352
  • Ford, L., Wang, Q., Stafford, R., Ressler, K.-A., Norton, S., Shadbolt, C., Hope, K., Franklin, N., Krsteski, R., Carswell, A., Carter, G.P., Seemann, T., Howard, P., Valcanis, M., Castillo, C.F.S., Bates, J., Glass, K., Williamson, D.A., Sintchenko, V., Howden, B.P., Kirk, M.D., 2018. Seven Salmonella Typhimurium Outbreaks in Australia Linked by Trace-Back and Whole Genome Sequencing. Foodborne Pathogens and Disease 15, 285–292. https://doi.org/10.1089/fpd.2017.2353
  • Geurts, Y.M., Dugué, P.-A., Joo, J.E., Makalic, E., Jung, C.-H., Guan, W., Nguyen, S., Grove, M.L., Wong, E.M., Hodge, A.M., Bassett, J.K., FitzGerald, L.M., Tsimiklis, H., Baglietto, L., Severi, G., Schmidt, D.F., Buchanan, D.D., MacInnis, R.J., Hopper, J.L., Pankow, J.S., Demerath, E.W., Southey, M.C., Giles, G.G., English, D.R., Milne, R.L., 2018. Novel associations between blood DNA methylation and body mass index in middle-aged and older adults. Int J Obes (Lond) 42, 887–896. https://doi.org/10.1038/ijo.2017.269
  • Gherardin, N.A., Souter, M.N., Koay, H.-F., Mangas, K.M., Seemann, T., Stinear, T.P., Eckle, S.B., Berzins, S.P., d’Udekem, Y., Konstantinov, I.E., Fairlie, D.P., Ritchie, D.S., Neeson, P.J., Pellicci, D.G., Uldrich, A.P., McCluskey, J., Godfrey, D.I., 2018. Human blood MAIT cell subsets defined using MR1 tetramers. Immunology & Cell Biology 96, 507–525. https://doi.org/10.1111/imcb.12021
  • Giulieri, S.G., Baines, S.L., Guerillot, R., Seemann, T., Gonçalves da Silva, A., Schultz, M., Massey, R.C., Holmes, N.E., Stinear, T.P., Howden, B.P., 2018. Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia. Genome Medicine 10, 65. https://doi.org/10.1186/s13073-018-0574-x
  • Gonçalves da Silva, A., Bulach, D.M., Carter, G.P., Strachan, J., Schultz, M.B., Ballard, S., Lee, R.S., Howden, B.P., Kwong, J.C., Baines, S.L., Stinear, T.P., Seemann, T., 2018a. The changing landscape of vancomycin-resistant Enterococcus faecium in Australia: a population-level genomic study. Journal of Antimicrobial Chemotherapy 73, 3268–3278. https://doi.org/10.1093/jac/dky331
  • Griffin, P., Khadake, J., LeMay, K., Lewis, S., Orchard, S., Pask, A., Pope, B., Roessner, U., Russell, K., Seemann, T., Treloar, A., Tyagi, S., Christiansen, J., Dayalan, S., Gladman, S., Hangartner, S., Hayden, H., Ho, W., Keeble-Gagnere, G., Korhonen, P., Neish, P., Prestes, P., Richardson, M., Watson-Haigh, N., Wyres, K., Young, N., Schneider, M., 2018. Best practice data life cycle approaches for the life sciences [version 2; referees: 2 approved]. F1000Research 6. https://doi.org/10.12688/f1000research.12344.2
  • Guérillot, R., Gonçalves da Silva, A., Monk, I., Giulieri, S., Tomita, T., Alison, E., Porter, J., Pidot, S., Gao, W., Peleg, A.Y., Seemann, T., Stinear, T.P., Howden, B.P., 2018. Convergent Evolution Driven by Rifampin Exacerbates the Global Burden of Drug-Resistant Staphylococcus aureus. mSphere 3, e00550-17. https://doi.org/10.1128/mSphere.00550-17
  • Guérillot, R., Li, L., Baines, S., Howden, B., Schultz, M.B., Seemann, T., Monk, I., Pidot, S.J., Gao, W., Giulieri, S., Gonçalves da Silva, A., D’Agata, A., Tomita, T., Peleg, A.Y., Stinear, T.P., Howden, B.P., 2018. Comprehensive antibiotic-linked mutation assessment by resistance mutation sequencing (RM-seq). Genome Medicine 10, 63. https://doi.org/10.1186/s13073-018-0572-z
  • Gulliver, E.L., Wright, A., Lucas, D.D., Mégroz, M., Kleifeld, O., Schittenhelm, R.B., Powell, D.R., Seemann, T., Bulitta, J.B., Harper, M., Boyce, J.D., 2018. Determination of the small RNA GcvB regulon in the Gram-negative bacterial pathogen Pasteurella multocida and identification of the GcvB seed binding region. RNA 24, 704–720. https://doi.org/10.1261/rna.063248.117
  • Herisse, M., Porter, J.L., Guerillot, R., Tomita, T., Goncalves Da Silva, A., Seemann, T., Howden, B.P., Stinear, T.P., Pidot, S.J., 2018. The ΦBT1 large serine recombinase catalyzes DNA integration at pseudo-attB sites in the genus Nocardia. PeerJ 6, e4784. https://doi.org/10.7717/peerj.4784
  • Janic, A., Valente, L.J., Wakefield, M.J., Di Stefano, L., Milla, L., Wilcox, S., Yang, H., Tai, L., Vandenberg, C.J., Kueh, A.J., Mizutani, S., Brennan, M.S., Schenk, R.L., Lindqvist, L.M., Papenfuss, A.T., O’Connor, L., Strasser, A., Herold, M.J., 2018. DNA repair processes are critical mediators of p53-dependent tumor suppression. Nature Medicine 24, 947–953. https://doi.org/10.1038/s41591-018-0043-5
  • Jung, C.-H., Park, J.D., Georgeson, P., Mahmood, K., Milne, L.R., Southey, C.M., Pope, J.B., 2018. sEst: Accurate Sex-Estimation and Abnormality Detection in Methylation Microarray Data. International Journal of Molecular Sciences 19. https://doi.org/10.3390/ijms19103172
  • Karthikaichamy, A., Deore, P., Srivastava, S., Coppel, R., Bulach, D., Beardall, J., Noronha, S., 2018. Temporal acclimation of Microchloropsis gaditana CCMP526 in response to hypersalinity. Bioresource Technology 254, 23–30. https://doi.org/10.1016/j.biortech.2018.01.062
  • Kondrashova, O., Topp, M., Nesic, K., Lieschke, E., Ho, G.-Y., Harrell, M.I., Zapparoli, G.V., Hadley, A., Holian, R., Boehm, E., Heong, V., Sanij, E., Pearson, R.B., Krais, J.J., Johnson, N., McNally, O., Ananda, S., Alsop, K., Hutt, K.J., Kaufmann, S.H., Lin, K.K., Harding, T.C., Traficante, N., Chenevix-Trench, G., Green, A., Webb, P., Gertig, D., Fereday, S., Moore, S., Hung, J., Harrap, K., Sadkowsky, T., Pandeya, N., Malt, M., Mellon, A., Robertson, R., Vanden Bergh, T., Jones, M., Mackenzie, P., Maidens, J., Nattress, K., Chiew, Y.E., Stenlake, A., Sullivan, H., Alexander, B., Ashover, P., Brown, S., Corrish, T., Green, L., Jackman, L., Ferguson, K., Martin, K., Martyn, A., Ranieri, B., White, J., Jayde, V., Mamers, P., Bowes, L., Galletta, L., Giles, D., Hendley, J., Schmidt, T., Shirley, H., Ball, C., Young, C., Viduka, S., Tran, H., Bilic, S., Glavinas, L., Brooks, J., Stuart-Harris, R., Kirsten, F., Rutovitz, J., Clingan, P., Glasgow, A., Proietto, A., Braye, S., Otton, G., Shannon, J., Bonaventura, T., Stewart, J., Begbie, S., Friedlander, M., Bell, D., Baron-Hay, S., Ferrier, A., Gard, G., Nevell, D., Pavlakis, N., Valmadre, S., Young, B., Camaris, C., Crouch, R., Edwards, L., Hacker, N., Marsden, D., Robertson, G., Beale, P., Beith, J., Carter, J., Dalrymple, C., Houghton, R., Russell, P., Links, M., Grygiel, J., Hill, J., Brand, A., Byth, K., Jaworski, R., Harnett, P., Sharma, R., Wain, G., Ward, B., Papadimos, D., Crandon, A., Cummings, M., Horwood, K., Obermair, A., Perrin, L., Wyld, D., Nicklin, J., Davy, M., Oehler, M.K., Hall, C., Dodd, T., Healy, T., Pittman, K., Henderson, D., Miller, J., Pierdes, J., Blomfield, P., Challis, D., McIntosh, R., Parker, A., Brown, B., Rome, R., Allen, D., Grant, P., Hyde, S., Laurie, R., Robbie, M., Healy, D., Jobling, T., Manolitsas, T., McNealage, J., Rogers, P., Susil, B., Sumithran, E., Simpson, I., Phillips, K., Rischin, D., Fox, S., Johnson, D., Lade, S., Loughrey, M., O’Callaghan, N., Murray, W., Waring, P., Billson, V., Pyman, J., Neesham, D., Quinn, M., Underhill, C., Bell, R., Ng, L.F., Blum, R., Ganju, V., Hammond, I., Leung, Y., McCartney, A., Buck, M., Haviv, I., Purdie, D., Whiteman, D., Zeps, N., deFazio, A., McNeish, I.A., Bowtell, D.D., Swisher, E.M., Dobrovic, A., Wakefield, M.J., Scott, C.L., Australian Ovarian Cancer Study (AOCS), 2018. Methylation of all BRCA1 copies predicts response to the PARP inhibitor rucaparib in ovarian carcinoma. Nature Communications 9, 3970. https://doi.org/10.1038/s41467-018-05564-z
  • Kwong, Jason C, Chow, E.P.F., Stevens, K., Stinear, T.P., Seemann, T., Fairley, C.K., Chen, M.Y., Howden, B.P., 2018. Whole-genome sequencing reveals transmission of gonococcal antibiotic resistance among men who have sex with men: an observational study. Sex Transm Infect 94, 151. https://doi.org/10.1136/sextrans-2017-053287
  • Kwong, Jason C., Lane, C.R., Romanes, F., Gonçalves da Silva, A., Easton, M., Cronin, K., Waters, M.J., Tomita, T., Stevens, K., Schultz, M.B., Baines, S.L., Sherry, N.L., Carter, G.P., Mu, A., Sait, M., Ballard, S.A., Seemann, T., Stinear, T.P., Howden, B.P., 2018. Translating genomics into practice for real-time surveillance and response to carbapenemase-producing Enterobacteriaceae: evidence from a complex multi-institutional KPC outbreak. PeerJ 6, e4210. https://doi.org/10.7717/peerj.4210
  • Lacey, J.A., Allnutt, T.R., Vezina, B., Van, T.T.H., Stent, T., Han, X., Rood, J.I., Wade, B., Keyburn, A.L., Seemann, T., Chen, H., Haring, V., Johanesen, P.A., Lyras, D., Moore, R.J., 2018. Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens. BMC Genomics 19, 379. https://doi.org/10.1186/s12864-018-4771-1
  • Lee, J.Y.H., Monk, I.R., Gonçalves da Silva, A., Seemann, T., Chua, K.Y.L., Kearns, A., Hill, R., Woodford, N., Bartels, M.D., Strommenger, B., Laurent, F., Dodémont, M., Deplano, A., Patel, R., Larsen, A.R., Korman, T.M., Stinear, T.P., Howden, B.P., 2018. Global spread of three multidrug-resistant lineages of Staphylococcus epidermidis. Nature Microbiology 3, 1175–1185. https://doi.org/10.1038/s41564-018-0230-7
  • Lee, R.S., Gonçalves da Silva, A., Baines, S.L., Strachan, J., Ballard, S., Carter, G.P., Kwong, J.C., Schultz, M.B., Bulach, D.M., Seemann, T., Stinear, T.P., Howden, B.P., 2018. The changing landscape of vancomycin-resistant Enterococcus faecium in Australia: a population-level genomic study. Journal of Antimicrobial Chemotherapy 73, 3268–3278. https://doi.org/10.1093/jac/dky331
  • Lee, R.S., Seemann, T., Heffernan, H., Kwong, J.C., Gonçalves da Silva, A., Carter, G.P., Woodhouse, R., Dyet, K.H., Bulach, D.M., Stinear, T.P., Howden, B.P., Williamson, D.A., 2018. Genomic epidemiology and antimicrobial resistance of Neisseria gonorrhoeae in New Zealand. Journal of Antimicrobial Chemotherapy 73, 353–364. https://doi.org/10.1093/jac/dkx405
  • Mahony, A.A., Buultjens, A.H., Ballard, S.A., Grabsch, E.A., Xie, S., Seemann, T., Stuart, R.L., Kotsanas, D., Cheng, A., Heffernan, H., Roberts, S.A., Coombs, G.W., Bak, N., Ferguson, J.K., Carter, G.C., Howden, B.P., Stinear, T.P., Johnson, P.D.R., 2018. Vancomycin-resistant Enterococcus faecium sequence type 796 – rapid international dissemination of a new epidemic clone. Antimicrobial Resistance & Infection Control 7, 44. https://doi.org/10.1186/s13756-018-0335-z
  • Myszka, A., Nguyen-Dumont, T., Karpinski, P., Sasiadek, M.M., Akopyan, H., Hammet, F., Tsimiklis, H., Park, D.J., Pope, B.J., Slezak, R., Kitsera, N., Siekierzynska, A., Southey, M.C., 2018. Targeted massively parallel sequencing characterises the mutation spectrum of PALB2 in breast and ovarian cancer cases from Poland and Ukraine. Familial Cancer 17, 345–349. https://doi.org/10.1007/s10689-017-0050-6
  • Nesic, K., Wakefield, M., Kondrashova, O., Scott, C.L., McNeish, I.A., 2018. Targeting DNA repair: the genome as a potential biomarker. The Journal of Pathology 244, 586–597. https://doi.org/10.1002/path.5025
  • Nguyen-Dumont, Tú, Myszka, A., Karpinski, P., Sasiadek, M.M., Akopyan, H., Hammet, F., Tsimiklis, H., Park, D.J., Pope, B.J., Slezak, R., Kitsera, N., Siekierzynska, A., Southey, M.C., 2018. FANCM and RECQL genetic variants and breast cancer susceptibility: relevance to South Poland and West Ukraine. BMC Medical Genetics 19, 12. https://doi.org/10.1186/s12881-018-0524-x
  • Nguyen-Dumont, Tu, Teo, Z.L., Hammet, F., Roberge, A., Mahmoodi, M., Tsimiklis, H., Park, D.J., Pope, B.J., Lonie, A., Kapuscinski, M.K., Mahmood, K., Goldgar, D.E., Giles, G.G., Winship, I., Hopper, J.L., Southey, M.C., 2018. Is RNASEL:p.Glu265* a modifier of early-onset breast cancer risk for carriers of  high-risk mutations? BMC Cancer 18, 165. https://doi.org/10.1186/s12885-018-4028-z
  • Nunez-Iglesias, J., Blanch, A.J., Looker, O., Dixon, M.W., Tilley, L., 2018. A new Python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton. PeerJ Preprints 6, e3521v1. https://doi.org/10.7287/peerj.preprints.3521v1
  • Pidot, S.J., Gao, W., Buultjens, A.H., Monk, I.R., Guerillot, R., Carter, G.P., Lee, J.Y.H., Lam, M.M.C., Grayson, M.L., Ballard, S.A., Mahony, A.A., Grabsch, E.A., Kotsanas, D., Korman, T.M., Coombs, G.W., Robinson, J.O., Gonçalves da Silva, A., Seemann, T., Howden, B.P., Johnson, P.D.R., Stinear, T.P., 2018. Increasing tolerance of hospital Enterococcus faecium to handwash alcohols. Science Translational Medicine 10, eaar6115. https://doi.org/10.1126/scitranslmed.aar6115
  • Plummer, E.L., Bulach, D.M., Murray, G.L., Jacobs, Susan E., Tabrizi, Sepehr N., Garland, Suzanne M., Garland, S. M., Jacobs, S. E., Tobin, J.M., Tabrizi, S. N., Pirotta, M., Donath, S., Opie, G.F., Tang, M.L.K., Morley, C.J., Hickey, L., Tan, K., Lewis, A., Veldman, A., Travadi, J., Wright, I.M.R., Osborn, D.A., Sinn, J., Levison, J., Stack, J.A., DePaoli, A.G., Austin, N.C., Darlow, B.A., Alsweiler, J.M., Buksh, M.J., for the ProPrems Study Group, 2018. Gut microbiota of preterm infants supplemented with probiotics: sub-study of the ProPrems trial. BMC Microbiology 18, 184. https://doi.org/10.1186/s12866-018-1326-1
  • Pope, B.J., Hammet, F., Nguyen-Dumont, T., Park, D.J., 2018. Hi-Plex for Simple, Accurate, and Cost-Effective Amplicon-based Targeted DNA Sequencing, in: Head, S.R., Ordoukhanian, P., Salomon, D.R. (Eds.), Next Generation Sequencing: Methods and Protocols. Springer New York, New York, NY, pp. 53–70. https://doi.org/10.1007/978-1-4939-7514-3_5
  • Russell, S.J., Caly, L., Kostecki, R., McGuinness, L.S., Carter, G., Bulach, D., Seemann, T., Stinear, P.T., Baird, R., Catton, M., Druce, J., 2018. The First Isolation and Whole Genome Sequencing of Murray Valley Encephalitis Virus from Cerebrospinal Fluid of a Patient with Encephalitis. Viruses 10. https://doi.org/10.3390/v10060319
  • Scott, C.M., Wong, E.M., Joo, J.E., Dugué, P.-A., Jung, C.-H., O’Callaghan, N., Dowty, J., Giles, G.G., Hopper, J.L., Southey, M.C., 2018. Genome-wide DNA methylation assessment of ‘BRCA1-like’ early-onset breast cancer: Data from the Australian Breast Cancer Family Registry. Experimental and Molecular Pathology 105, 404–410. https://doi.org/10.1016/j.yexmp.2018.11.006
  • Smibert, O.C., Aung, A.K., Woolnough, E., Carter, G.P., Schultz, M.B., Howden, B.P., Seemann, T., Spelman, D., McGloughlin, S., Peleg, A.Y., 2018. Mobile phones and computer keyboards: unlikely reservoirs of multidrug-resistant organisms in the tertiary intensive care unit. Journal of Hospital Infection 99, 295–298. https://doi.org/10.1016/j.jhin.2018.02.013
  • Srinivasalu, N., McFadden, S.A., Medcalf, C., Fuchs, L., Chung, J., Philip, G., Richardson, A., Riaz, M., Baird, P.N., 2018. Gene Expression and Pathways Underlying Form Deprivation Myopia in the Guinea Pig ScleraPathways Underlying Myopia in Guinea Pig Sclera. Investigative Ophthalmology & Visual Science 59, 1425–1434. https://doi.org/10.1167/iovs.16-21278
  • Varrone, L., Stafford, R.J., Lilly, K., Selvey, L., Glass, K., Ford, L., Bulach, D., Kirk, M.D., 2018. Investigating locally relevant risk factors for Campylobacter infection in Australia: protocol for a case–control study and genomic analysis. BMJ Open 8, e026630. https://doi.org/10.1136/bmjopen-2018-026630
  • Vidor, C.J., Watts, T.D., Adams, V., Bulach, D., Couchman, E., Rood, J.I., Fairweather, N.F., Awad, M., Lyras, D., 2018. Clostridium sordellii Pathogenicity Locus Plasmid pCS1-1 Encodes a Novel Clostridial Conjugation Locus. mBio 9, e01761-17. https://doi.org/10.1128/mBio.01761-17
2017 Publications
  • Alfouzan, W., Bulach, D., Izumiya, H., AlBassam, K., Sheikh, S., Alrubai’aan, N., Albert, M.J., 2017. Carbuncle due to Salmonella Enteritidis: a novel presentation. Gut Pathog 9, 51. https://doi.org/10.1186/s13099-017-0200-2
  • Bassett, J.K., English, D.R., Giles, G.G., Milne, R.L., Dugué, P.-A., Southey, M.C., Baglietto, L., Severi, G., Schmidt, D., Makalic, E., Hopper, J.L., Li, S., Moreno-Betancur, M., Buchanan, D.D., Wong, E.M., Joo, J.E., Jung, C.-H., Fiorito, G., Vineis, P., 2017. Association of DNA Methylation-Based Biological Age With Health Risk Factors and Overall and Cause-Specific Mortality. American Journal of Epidemiology 187, 529–538. https://doi.org/10.1093/aje/kwx291
  • Bulach, D.M., Carter, G.P., Stinear, T.P., Gonçalves da Silva, A., Howden, B.P., Williamson, D.A., Kwong, J.C., Lee, R.S., Seemann, T., Heffernan, H., Dyet, K.H., Woodhouse, R., 2017. Genomic epidemiology and antimicrobial resistance of Neisseria gonorrhoeae in New Zealand. Journal of Antimicrobial Chemotherapy 73, 353–364. https://doi.org/10.1093/jac/dkx405
  • Geurts, Y.M., Dugué, P.-A., Joo, J.E., Makalic, E., Jung, C.-H., Guan, W., Nguyen, S., Grove, M.L., Wong, E.M., Hodge, A.M., Bassett, J.K., FitzGerald, L.M., Tsimiklis, H., Baglietto, L., Severi, G., Schmidt, D.F., Buchanan, D.D., MacInnis, R.J., Hopper, J.L., Pankow, J.S., Demerath, E.W., Southey, M.C., Giles, G.G., English, D.R., Milne, R.L., 2017. Novel associations between blood DNA methylation and body mass index in middle-aged and older adults. International Journal Of Obesity 42, 887.
  • Griffin, P.C., Khadake, J., LeMay, K.S., Lewis, S.E., Orchard, S., Pask, A., Pope, B., Roessner, U., Russell, K., Seemann, T., Treloar, A., Tyagi, S., Christiansen, J.H., Dayalan, S., Gladman, S., Hangartner, S.B., Hayden, H.L., Ho, W.W.H., Keeble-Gagnère, G., Korhonen, P.K., Neish, P., Prestes, P.R., Richardson, M.F., Watson-Haigh, N.S., Wyres, K.L., Young, N.D., Schneider, M.V., 2017. Best practice data life cycle approaches for the life sciences. F1000Res 6, 1618. https://doi.org/10.12688/f1000research.12344.2
  • Hirst, M.J., Griffin, P.C., Sexton, J.P., Hoffmann, A.A., 2017. Testing the niche-breadth-range-size hypothesis: habitat specialization vs. performance in Australian alpine daisies. Ecology 98, 2708–2724. https://doi.org/10.1002/ecy.1964
  • Kanwal, S., Khan, F.Z., Lonie, A., Sinnott, R.O., 2017. Investigating reproducibility and tracking provenance – A genomic workflow case study. BMC Bioinformatics 18, 337. https://doi.org/10.1186/s12859-017-1747-0
  • Kondrashova, O., Nguyen, M., Shield-Artin, K., Tinker, A.V., Teng, N.N.H., Harrell, M.I., Kuiper, M.J., Ho, G.-Y., Barker, H., Jasin, M., Prakash, R., Kass, E.M., Sullivan, M.R., Brunette, G.J., Bernstein, K.A., Coleman, R.L., Floquet, A., Friedlander, M., Kichenadasse, G., O’Malley, D.M., Oza, A., Sun, J., Robillard, L., Maloney, L., Bowtell, D., Giordano, H., Wakefield, M.J., Kaufmann, S.H., Simmons, A.D., Harding, T.C., Raponi, M., McNeish, I.A., Swisher, E.M., Lin, K.K., Scott, C.L., AOCS Study Group, 2017. Secondary Somatic Mutations Restoring RAD51C and RAD51D Associated with Acquired Resistance to the PARP Inhibitor Rucaparib in High-Grade Ovarian Carcinoma. Cancer Discov 7, 984–998. https://doi.org/10.1158/2159-8290.CD-17-0419
  • Mahmood, K., Jung, C.-H., Philip, G., Georgeson, P., Chung, J., Pope, B.J., Park, D.J., 2017. Variant effect prediction tools assessed using independent, functional assay-based datasets: implications for discovery and diagnostics. Hum Genomics 11, 10. https://doi.org/10.1186/s40246-017-0104-8
  • Mamrot, J., Legaie, R., Ellery, S.J., Wilson, T., Seemann, T., Powell, D.R., Gardner, D.K., Walker, D.W., Temple-Smith, P., Papenfuss, A.T., Dickinson, H., 2017. De novo transcriptome assembly for the spiny mouse (Acomys cahirinus). Sci Rep 7, 8996. https://doi.org/10.1038/s41598-017-09334-7
  • Seemann, T., Bulach, D.M., Carter, G., Albert, M.J., 2017. Draft Genome Sequences of Two Strains of a Newly Described Species, Sphingobacterium cellulitidis. Genome Announc 5, e00956-17. https://doi.org/10.1128/genomeA.00956-17
  • Sparham, S.J., Kwong, J.C., Valcanis, M., Easton, M., Trott, D.J., Seemann, T., Stinear, T.P., Howden, B.P., 2017. Emergence of multidrug resistance in locally-acquired human infections with Salmonella Typhimurium in Australia owing to a new clade harbouring blaCTX-M-9. Int J Antimicrob Agents 50, 101–105. https://doi.org/10.1016/j.ijantimicag.2017.02.014