Publications

2026

Melbourne Bioinformatics authors in bold.

Bye, C.R., Qian, E., Lim, K., Daniszewski, M., Garton, F.C., Trần-Lê, B.C., Liang, H.H., Lin, T., Lock, J.G., Crombie, D.E., Morgan, S., Hu, Y., Barton, S.K., Palmer, L.M., Djouma, E., Kodikara, S., Lê Cao, K.-A., Dharmadasa, T., Henders, A.K., Ziser, L.A., Kiernan, M.C., Talbot, K., Needham, M., Fletcher, S., Talman, P., Mathers, S., Wray, N.R., Hewitt, A.W., Pebay, A., Turner, B.J., 2026. Large-scale drug screening in iPSC-derived motor neurons from sporadic ALS patients identifies a potential combinatorial therapy. Nat Neurosci 29, 40–52. https://doi.org/10.1038/s41593-025-02118-7
Huang, M., Pianta, T., Barit, D., Mahmood, K., Colville, D., Mack, H., Savige, J., 2026. Monogenic kidney disease and monogenic diabetes are present in renal clinic patients with non-genetic diagnoses. Sci Rep. https://doi.org/10.1038/s41598-026-52836-6
Le, S., Dooley, N., Murphy, D., Liu, S., Gandolfo, L.C., Ge, Z., May, R., Cozijnsen, A., Burn, T.N., Jennison, C., Bachem, A., Xu, C., Koay, H.-F., Schröder, J., Oyong, D., Nalubega, M., Kenangalem, E., Gras, S., Cockburn, I.A., Bedoui, S., Mackay, L.K., McFadden, G.I., Fernandez-Ruiz, D., Boyle, M., Heath, W.R., Beattie, L., 2026. γδ T cell-derived IL-4 initiates CD8+ T cell immunity. Nat Immunol 27, 295–307. https://doi.org/10.1038/s41590-025-02397-z
Li, Y., Zhang, J., Yin, Z.J., Zhou, Z., Huang, B., Mahmood, K., Colville, D., Barit, D., Auwardt, R., Fassett, R., Paizis, K., Ierino, F., Pianta, T., Langsford, D., Huang, M., Savige, J., 2026. Coexisting genetic kidney disease explains many cases of ‘familial’ IgA nephropathy where the proband has biopsy-confirmed mesangial IgA deposits. Front. Med. 12. https://doi.org/10.3389/fmed.2025.1647695
Waymouth, V., Miller, R.E., Kasel, S., Philip, G., Ede, F., Aponte, C., 2026. Soil origin shapes root-associated fungal communities and plant growth in myrtaceous species used in riparian revegetation. Applied Soil Ecology 222, 106988. https://doi.org/10.1016/j.apsoil.2026.106988

2025

Melbourne Bioinformatics authors in bold.

Buchanan, D.D., Georgeson, P., Walker, R., Joo, J.E., Clendenning, M., Como, J., O’Keeffe, R., Prisc, A., Chu, Y.L., Jenkins, M.A., Rosty, C., Winship, I.M., Macrae, F.A., Ip, E., Harris, R., Goodwin, A., Mahmood, K., 2025. The germline POLD1 c.1420 C > A (p.Leu474Ile) variant segregates with endometrial cancer, colorectal cancer and colonic polyps demonstrating hypermutation and defective POLD1 mutational signatures. Familial Cancer 24, 82. https://doi.org/10.1007/s10689-025-00506-3
Bye, C.R., Qian, E., Lim, K., Daniszewski, M., Garton, F.C., Trần-Lê, B.C., Liang, H.H., Lin, T., Lock, J.G., Crombie, D.E., Morgan, S., Hu, Y., Barton, S.K., Palmer, L.M., Djouma, E., Kodikara, S., Lê Cao, K.-A., Dharmadasa, T., Henders, A.K., Ziser, L.A., Kiernan, M.C., Talbot, K., Needham, M., Fletcher, S., Talman, P., Mathers, S., Wray, N.R., Hewitt, A.W., Pebay, A., Turner, B.J., 2025. Large-scale drug screening in iPSC-derived motor neurons from sporadic ALS patients identifies a potential combinatorial therapy. Nat Neurosci 1–13. https://doi.org/10.1038/s41593-025-02118-7
Chu, Y.L., Georgeson, P., Clendenning, M., Mahmood, K., Walker, R., Como, J., Joseland, S., Preston, S.G., Rice, T., Lynch, B.M., Milne, R.L., Southey, M.C., Giles, G.G., Phipps, A.I., Hopper, J.L., Win, A.K., Rosty, C., Macrae, F.A., Winship, I., Jenkins, M.A., Buchanan, D.D., Joo, J.E., 2025. Intratumoural pks+ Escherichia coli is associated with risk of metachronous colorectal cancer and adenoma development in people with Lynch syndrome. eBioMedicine 114, 105661. https://doi.org/10.1016/j.ebiom.2025.105661
Chung, J., Rogers, P.A., 2025. Improving Replication in Endometrial Omics: Understanding the Influence of the Menstrual Cycle. International Journal of Molecular Sciences 26, 857. https://doi.org/10.3390/ijms26020857
Gheybi, K., Soh, P.X.Y., Jiang, J., Mbeki, T.M.N., Louw, M., Burns, D., Mundra, P., Kiriy, D., Hasan, M.M., Jaratlerdsiri, W., Lebelo, M.T., Campbell, R.A., Radzuma, M.B., Nenzhelele, M., Obida, Muvhulawa, Obida, Martin, Ombuki, W.M., Oyaro, M.O., Patrick, S.M., Loda, M., Wedge, D.C., Bristow, R.G., Brewer, D.S., Cooper, C.S., Reimand, J., Cancel-Tassin, G., Cussenot, O., Hovens, C.M., Cocoran, N.M., Stricker, P.D., Schlomm, T., Prins, G.S., Sørensen, K.D., Pan Prostate Cancer Group, HEROIC PCaPH Africa1K, Weischenfeldt, J., Mutambirwa, S.B.A., Ngugi, P.M., Thomas, D.M., Kote-Jarai, Z., Eeles, R.A., Bornman, M.S.R., Hayes, V.M., 2025. Pathogenic variants reveal candidate genes for prostate cancer germline testing for men of African ancestry. Nat Commun 16, 8799. https://doi.org/10.1038/s41467-025-63865-6
Gotze, C.R., Dungan, A.M., van de Meene, A.M.L., Damjanovic, K., Philip, G.K., Maire, J., Høj, L., Blackall, L.L., van Oppen, M.J.H., 2025. Differential aggregation patterns of Endozoicomonas within tissues of the coral Acropora loripes. The ISME Journal. https://doi.org/10.1093/ismejo/wraf059
Gotze, C.R., Tandon, K., Philip, G.K., Dungan, A.M., Maire, J., Høj, L., Blackall, L.L., Oppen, M.J.H. van, 2025. Genomic prediction of symbiotic interactions between two Endozoicomonas clades and their coral host, Acropora loripes. anim microbiome 7, 94. https://doi.org/10.1186/s42523-025-00455-3
Joo, J.E., Mahmood, K., Clendenning, M., Walker, R., Georgeson, P., Como, J., Jenkins, M.A., Walsh, M.D., Winship, I.M., Buchanan, D.D., 2025. Causes of DNA mismatch repair deficiency in sebaceous skin lesions demonstrating loss of MLH1 protein expression: constitutional over somatic MLH1 promoter methylation. Familial Cancer 24, 36. https://doi.org/10.1007/s10689-025-00456-w
Merid, M.W., Xu, L., Zhou, Y., van der Mei, I., Park, D., Simpson-Yap, S., 2025. A systematic review and meta-analysis on gene-environment interaction effects on the associations of vitamin D and sun exposure with multiple sclerosis risk. Multiple Sclerosis and Related Disorders 106634. https://doi.org/10.1016/j.msard.2025.106634
Meyers, A.L., Dowty, J.G., Mahmood, K., Macrae, F.A., Rosty, C., Buchanan, D.D., Jenkins, M.A., 2025. Age-specific trends in colorectal, appendiceal, and anal tumour incidence by histological subtype in Australia from 1990 to 2020: a population-based time-series analysis. The Lancet Regional Health – Western Pacific 64. https://doi.org/10.1016/j.lanwpc.2025.101728
Park, D.J., 2025. A unifying model for multiple sclerosis. Clin Exp Med 25, 133. https://doi.org/10.1007/s10238-025-01666-3
Simpson-Yap, S., Morwitch, E., Tanner, S.A., Thomson, S.M., Eisner, A., Lea, R.A., Kilpatrick, T.J., Lechner-Scott, J., Scott, R.J., Xavier, A., Maltby, V.E., Lucas, R.M., Taylor, B.V., Lidbury, B.A., Broadley, S.A., van der Mei, I., Merid, M.W., Novakovic, B., Saffery, R., Hedström, A.K., Stridh, P., Olsson, T., Jagodic, M., Alfredsson, L., Ponsonby, A.-L., Ausimmune Investigator Group, 2025. Epstein-Barr Virus, Lower Vitamin D, Low Sun Exposure, and HLA-DRB1*1501 Risk Variant Share Common Epigenetic Pathways Leading to Multiple Sclerosis Onset. Ann Neurol. https://doi.org/10.1002/ana.78043
Walker, R., Joo, J.E., Mahmood, K., Georgeson, P., Winship, I.M., Buchanan, D.D., 2025. DNA mismatch repair (MMR) gene mosaicism is rare in people with MMR-deficient cancers. Gastroenterology. https://doi.org/10.1053/j.gastro.2024.12.027
Walker, R., Joo, J.E., Mahmood, K., Clendenning, M., Como, J., Preston, S.G., Joseland, S., Pope, B.J., Medeiros, A.B.D., Murillo, B.V., Pachter, N., Sweet, K., Spigelman, A.D., Groves, A., Gleeson, M., Bernatowicz, K., Poplawski, N., Andrews, L., Healey, E., Gallinger, S., Grant, R.C., Win, A.K., Hopper, J.L., Jenkins, M.A., Torrezan, G.T., Rosty, C., Macrae, F.A., Winship, I.M., Buchanan, D.D., Georgeson, P., 2025. Adenomas from individuals with pathogenic biallelic variants in the MUTYH and NTHL1 genes demonstrate base excision repair tumour mutational signature profiles similar to colorectal cancers, expanding potential diagnostic and variant classification applications. Translational Oncology 52, 102266. https://doi.org/10.1016/j.tranon.2024.102266
Yamaguchi, T.N., Houlahan, K.E., Zhu, H., Kurganovs, N., Livingstone, J., Fox, N.S., Yuan, J., Sietsma Penington, J., Jung, C.-H., Schwarz, T., Jaratlerdsiri, W., van Riet, J., Georgeson, P., Mangiola, S., Taraszka, K., Lesurf, R., Jiang, J., Chow, K., Heisler, L.E., Shiah, Y.-J., Ramanand, S.G., Clarkson, M.J., Nguyen, A., Espiritu, S.M.G., Stuchbery, R., Jovelin, R., Huang, V., Bell, C., O’Connor, E., McCoy, P.J., Lalansingh, C.M., Cmero, M., Salcedo, A., Chan, E.K.F., Liu, L.Y., Stricker, P.D., Bhandari, V., Bornman, R.M.S., Sendorek, D.HS., Lonie, A., Prokopec, S.D., Fraser, M., Peters, J.S., Foucal, A., Mutambirwa, S.B.A., Mcintosh, L., Orain, M., Wakefield, M., Picard, V., Park, D.J., Hovington, H., Kerger, M., Bergeron, A., Sabelnykova, V., Seo, J.-H., Pomerantz, M.M., Zaitlen, N., Waszak, S.M., Gusev, A., Lacombe, L., Fradet, Y., Ryan, A., Kishan, A.U., Lolkema, M.P., Weischenfeldt, J., Têtu, B., Costello, A.J., Hayes, V.M., Hung, R.J., He, H.H., McPherson, J.D., Pasaniuc, B., van der Kwast, T., Papenfuss, A.T., Freedman, M.L., Pope, B.J., Bristow, R.G., Mani, R.S., Corcoran, N.M., Reimand, J., Hovens, C.M., Boutros, P.C., 2025. The Germline and Somatic Origins of Prostate Cancer Heterogeneity. Cancer Discovery. https://doi.org/10.1158/2159-8290.CD-23-0882

2024

Melbourne Bioinformatics authors in bold.

Bruinsma, F., Harraka, P., Jordan, S., Park, D.J., Pope, B., Steen, J., Milne, R.L., Giles, G.G., Winship, I., Tucker, K.M., Southey, M.C., Nguyen-Dumont, T., 2024. Prevalence of Germline Pathogenic Variants in Renal Cancer Predisposition Genes in a Population-Based Study of Renal Cell Carcinoma. Cancers 16, 2985. https://doi.org/10.3390/cancers16172985
Chan, J.M., Clendenning, M., Joseland, S., Georgeson, P., Mahmood, K., Joo, J.E., Walker, R., Como, J., Preston, S., Chai, S.M., Chu, Y.L., Meyers, A.L., Pope, B.J., Duggan, D., Fink, J.L., Macrae, F.A., Rosty, C., Winship, I.M., Jenkins, M.A., Buchanan, D.D., 2024. Inherited BRCA1 and RNF43 pathogenic variants in a familial colorectal cancer type X family. Familial Cancer 23, 9–21. https://doi.org/10.1007/s10689-023-00351-2
FitzGerald, L.M., Jung, C.-H., Wong, E.M, Joo, J.E., Bassett, J.K., Dowty, J.G., Wang, X., Dai, J.Y., Stanford, J.L., O'Callaghan, N., Nottle, T., Pedersen, J., Giles, G.C., Southey, M.C., 2024. Detection of Differentially Methylated CpGs between Tumour and Adjacent Benign Cells in Diagnostic Prostate Cancer Samples. Scientific Reports 14, 17877. https://doi.org/10.1038/s41598-024-66488-x.
Holdsworth-Carson, S.J., Chung, J., Machalek, D.A., Li, R., Jun, B.K., Griffiths, M.J., Churchill, M., McCaughey, T., Nisbet, D., Dior, U., Donoghue, J.F., Montgomery, G.W., Reddington, C., Girling, J.E., Healey, M., Rogers, P.A.W., 2024. Predicting disease recurrence in patients with endometriosis: an observational study. BMC Medicine 22, 320. https://doi.org/10.1186/s12916-024-03508-7
Inwood, S.N., Harrop, T.W.R., Shields, M.W., Goldson, S.L., Dearden, P.K., 2024. Immune system modulation & virus transmission during parasitism identified by multi-species transcriptomics of a declining insect biocontrol system. BMC Genomics 25, 1–21. https://doi.org/10.1186/s12864-024-10215-3
Joo, J.E., Chu, Y.L., Georgeson, P., Walker, R., Mahmood, K., Clendenning, M., Meyers, A.L., Como, J., Joseland, S., Preston, S.G., Diepenhorst, N., Toner, J., Ingle, D.J., Sherry, N.L., Metz, A., Lynch, B.M., Milne, R.L., Southey, M.C., Hopper, J.L., Win, A.K., Macrae, F.A., Winship, I.M., Rosty, C., Jenkins, M.A., Buchanan, D.D., 2024. Intratumoral presence of the genotoxic gut bacteria pks+ E. coli, Enterotoxigenic Bacteroides fragilis, and Fusobacterium nucleatum and their association with clinicopathological and molecular features of colorectal cancer. Br J Cancer 1–13. https://doi.org/10.1038/s41416-023-02554-x
Morgan, S., Reid, I., Bendon, C., Ishaq, M., Shayan, R., Pope, B., Park, D., Karnezis, T., 2024. A Family-Based Study of Inherited Genetic Risk in Lipedema. Lymphatic Research and Biology. https://doi.org/10.1089/lrb.2023.0065
Pope, B., Park, G., Lau, E., Belic, J., Lach, R., George, A., McCoy, P., Nguyen, A., Grima, C., Campbell, B., Jung, C.-H., Ditter, E.-J., Zhao, H., Pan Prostate Cancer Group (PPCG), Wedge, D.C., Brewer, D.S., Lynch, A.G., Dev, H., Gnanpragasam, V.J., Rosenfeld, N., Hovens, C.M., Corcoran, N.M., Massie, C.E., 2024. Ultrasensitive Detection of Circulating Tumour DNA enriches for Patients with a Greater Risk of Recurrence of Clinically Localised Prostate Cancer. Eur Urol 85, 407–410. https://doi.org/10.1016/j.eururo.2024.01.002
Spier, I., Yin, X., Richardson, M., Pineda, M., Laner, A., Ritter, D., Boyle, J., Mur, P., Hansen, T. v O., Shi, X., Mahmood, K., Plazzer, J.-P., Ognedal, E., Nordling, M., Farrington, S.M., Yamamoto, G., Baert-Desurmont, S., Martins, A., Borras, E., Tops, C., Webb, E., Beshay, V., Genuardi, M., Pesaran, T., Capellá, G., Tavtigian, S.V., Latchford, A., Frayling, I.M., Plon, S.E., Greenblatt, M., Macrae, F.A., Aretz, S., 2024. Gene-specific ACMG/AMP classification criteria for germline APC variants: Recommendations from the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel. Genetics in Medicine 26. https://doi.org/10.1016/j.gim.2023.100992
Stoeckel, S., Becheler, R., Portillo-Lemus, L., Harang, M., Besnard, A.-L., Lassalle, G., Causse-Védrines, R., Michon-Coudouel, S., Park, D.J., Pope, B.J., Petit, E.J., Barloy, D., 2024. Reproductive modes in populations of late-acting self-incompatible and self-compatible polyploid Ludwigia grandiflora subsp. hexapetala in western Europe. Peer Community Journal 4. https://doi.org/10.24072/pcjournal.458
Woodcock, D.J., Sahli, A., Teslo, R., Bhandari, V., Gruber, A.J., Ziubroniewicz, A., Gundem, G., Xu, Y., Butler, A., Anokian, E., Pope, B.J., Jung, C.-H., Tarabichi, M., Dentro, S.C., Farmery, J.H.R., Van Loo, P., Warren, A.Y., Gnanapragasam, V., Hamdy, F.C., Bova, G.S., Foster, C.S., Neal, D.E., Lu, Y.-J., Kote-Jarai, Z., Fraser, M., Bristow, R.G., Boutros, P.C., Costello, A.J., Corcoran, N.M., Hovens, C.M., Massie, C.E., Lynch, A.G., Brewer, D.S., Eeles, R.A., Cooper, C.S., Wedge, D.C., 2024. Genomic evolution shapes prostate cancer disease type. Cell Genomics 100511. https://doi.org/10.1016/j.xgen.2024.100511
Yin, X., Richardson, M., Laner, A., Shi, X., Ognedal, E., Vasta, V., Hansen, T. v O., Pineda, M., Ritter, D., Dunnen, J. de, Hassanin, E., Lin, W.L., Borras, E., Krahn, K., Nordling, M., Martins, A., Mahmood, K., Nadeau, E., Beshay, V., Tops, C., Genuardi, M., Pesaran, T., Frayling, I.M., Capellá, G., Latchford, A., Tavtigian, S.V., Maj, C., Plon, S.E., Greenblatt, M.S., Macrae, F.A., Spier, I., Aretz, S., 2024. Large-scale application of ClinGen-InSiGHT APC-specific ACMG/AMP variant classification criteria leads to substantial reduction in VUS. The American Journal of Human Genetics 0. https://doi.org/10.1016/j.ajhg.2024.09.002

2023

Melbourne Bioinformatics authors in bold.

Cain, S.A., Pope, B., Mangiola, S., Mantamadiotis, T., Drummond, K.J., 2023. Somatic mutation landscape in a cohort of meningiomas that have undergone grade progression. BMC Cancer 23, 216. https://doi.org/10.1186/s12885-023-10624-9
Gooley, K., Williams, P., Mack, H., Zhu, V., Langsford, D., Pianta, T., Barit, D., Mahmood, K., Savige, J., 2023. A comparison of the ocular features in Pierson and Alport syndrome: a case report and literature review. Ophthalmic Genetics 1–6. https://doi.org/10.1080/13816810.2023.2240881
Hiltemann, S., Rasche, H., Gladman, S., Hotz, H.-R., Larivière, D., Blankenberg, D., Jagtap, P.D., Wollmann, T., Bretaudeau, A., Goué, N., Griffin, T.J., Royaux, C., Bras, Y.L., Mehta, S., Syme, A., Coppens, F., Droesbeke, B., Soranzo, N., Bacon, W., Psomopoulos, F., Gallardo-Alba, C., Davis, J., Föll, M.C., Fahrner, M., Doyle, M.A., Serrano-Solano, B., Fouilloux, A.C., Heusden, P. van, Maier, W., Clements, D., Heyl, F., Galaxy Training Network, Grüning, B., Batut, B., 2023. Galaxy Training: A powerful framework for teaching! PLOS Computational Biology 19, e1010752. https://doi.org/10.1371/journal.pcbi.1010752
Houlahan, K.E., Livingstone, J., Fox, N.S., Kurganovs, N., Zhu, H., Sietsma Penington, J., Jung, C.-H., Yamaguchi, T.N., Heisler, L.E., Jovelin, R., Costello, A.J., Pope, B.J., Kishan, A.U., Corcoran, N.M., Bristow, R.G., Waszak, S.M., Weischenfeldt, J., He, H.H., Hung, R.J., Hovens, C.M., Boutros, P.C., 2023. A polygenic two-hit hypothesis for prostate cancer. JNCI: Journal of the National Cancer Institute. https://doi.org/10.1093/jnci/djad001
Inwood, S.N., Harrop, T.W.R., Dearden, P.K., 2023. The venom composition and parthenogenesis mechanism of the parasitoid wasp Microctonus hyperodae, a declining biocontrol agent. Insect Biochemistry and Molecular Biology 153, 103897. https://doi.org/10.1016/j.ibmb.2022.103897
Inwood, S.N., Skelly, J., Guhlin, J.G., Harrop, T.W.R., Goldson, S.L., Dearden, P.K., 2023. Chromosome-level genome assemblies of two parasitoid biocontrol wasps reveal the parthenogenesis mechanism and an associated novel virus. BMC Genomics 24, 440. https://doi.org/10.1186/s12864-023-09538-4
Joo, J.E., Mahmood, K., Walker, R., Georgeson, P., Candiloro, I., Clendenning, M., Como, J., Joseland, S., Preston, S., Graversen, L., Wilding, M., Field, M., Lemon, M., Wakeling, J., Marfan, H., Susman, R., Isbister, J., Edwards, E., Bowman, M., Kirk, J., Ip, E., McKay, L., Antill, Y., Hopper, J.L., Boussioutas, A., Macrae, F.A., Dobrovic, A., Jenkins, M.A., Rosty, C., Winship, I.M., Buchanan, D.D., 2023. Identifying primary and secondary MLH1 epimutation carriers displaying low-level constitutional MLH1 methylation using droplet digital PCR and genome-wide DNA methylation profiling of colorectal cancers. Clinical Epigenetics 15, 95. https://doi.org/10.1186/s13148-023-01511-y
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., 2023. Germline mutations in WNK2 could be associated with serrated polyposis syndrome. Journal of Medical Genetics 60, 557–567. https://doi.org/10.1136/jmg-2022-108684
Mahmood, K., Thomas, M., Qu, C., Wang, X., Huyghe, J.R., Joo, J.E., Georgeson, P., Arndt, V., Berndt, S.I., Bézieau, S., Bien, S.A., Bishop, D.T., Brenner, H., Brezina, S., Burnett-Hartman, A., Campbell, P.T., Casey, G., Castellví-Bel, S., Chan, A.T., Chang-Claude, J., Chen, X., Conti, D.V., Cremolini, C., Diergaarde, B., Figueiredo, J.C., FitzGerald, L.M., Gago-Dominguez, M., Gallinger, S., Giles, G.G., Gsur, A., Gunter, M.J., Hampe, J., Hampel, H., Harrison, T.A., Hoffmeister, M., Keku, T.O., Kundaje, A., Le Marchand, L., Lenz, H.-J., Li, C.I., Li, L., Lin, Y., Lindblom, A., Moreno, V., Murphy, N., Newcomb, P.A., Newton, C.C., Obón-Santacana, M., Ogino, S., Pai, R.K., Palmer, J.R., Pearlman, R., Pharoah, P.D.P., Phipps, A.I., Platz, E.A., Potter, J.D., Rennert, G., Sakoda, L.C., Schafmayer, C., Schmit, S.L., Schoen, R.E., Slattery, M.L., Stadler, Z.K., Steinfelder, R.S., Thibodeau, S.N., Ulrich, C.M., Um, C.Y., van Duijnhoven, F.JB., Van Guelpen, B., Visvanathan, K., Vodicka, P., Vodickova, L., Vymetalkova, V., Weinstein, S.J., White, E., Winship, I.M., Wolk, A., Gruber, S.B., Jenkins, M.A., Hsu, L., Buchanan, D.D., Peters, U., 2023. Elucidating the risk of colorectal cancer for variants in hereditary colorectal cancer genes. Gastroenterology. https://doi.org/10.1053/j.gastro.2023.06.032
Maire, J., Philip, G.K., Livingston, J., Judd, L.M., Blackall, L.L., van Oppen, M.J.H., 2023. Functional potential and evolutionary response to long-term heat selection of bacterial associates of coral photosymbionts. mSystems 0, e00860-23. https://doi.org/10.1128/msystems.00860-23
Maire, J., Tandon, K., Collingro, A., van de Meene, A., Damjanovic, K., Gotze, C.R., Stephenson, S., Philip, G.K., Horn, M., Cantin, N.E., Blackall, L.L., van Oppen, M.J.H., 2023. Colocalization and potential interactions of Endozoicomonas and chlamydiae in microbial aggregates of the coral Pocillopora acuta. Science Advances 9, eadg0773. https://doi.org/10.1126/sciadv.adg0773
Mu, A., Klare, W.P., Baines, S.L., Ignatius Pang, C.N., Guérillot, R., Harbison-Price, N., Keller, N., Wilksch, J., Nhu, N.T.K., Phan, M.-D., Keller, B., Nijagal, B., Tull, D., Dayalan, S., Chua, H.H.C., Skoneczny, D., Koval, J., Hachani, A., Shah, A.D., Neha, N., Jadhav, S., Partridge, S.R., Cork, A.J., Peters, K., Bertolla, O., Brouwer, S., Hancock, S.J., Álvarez-Fraga, L., De Oliveira, D.M.P., Forde, B., Dale, A., Mujchariyakul, W., Walsh, C.J., Monk, I., Fitzgerald, A., Lum, M., Correa-Ospina, C., Roy Chowdhury, P., Parton, R.G., De Voss, J., Beckett, J., Monty, F., McKinnon, J., Song, X., Stephen, J.R., Everest, M., Bellgard, M.I., Tinning, M., Leeming, M., Hocking, D., Jebeli, L., Wang, N., Ben Zakour, N., Yasar, S.A., Vecchiarelli, S., Russell, T., Zaw, T., Chen, T., Teng, D., Kassir, Z., Lithgow, T., Jenney, A., Cole, J.N., Nizet, V., Sorrell, T.C., Peleg, A.Y., Paterson, D.L., Beatson, S.A., Wu, J., Molloy, M.P., Syme, A.E., Goode, R.J.A., Hunter, A.A., Bowland, G., West, N.P., Wilkins, M.R., Djordjevic, S.P., Davies, M.R., Seemann, T., Howden, B.P., Pascovici, D., Tyagi, S., Schittenhelm, R.B., De Souza, D.P., McConville, M.J., Iredell, J.R., Cordwell, S.J., Strugnell, R.A., Stinear, T.P., Schembri, M.A., Walker, M.J., 2023. Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria. Nat Commun 14, 1530. https://doi.org/10.1038/s41467-023-37200-w
Teh, W.T., Chung, J., Holdsworth-Carson, S.J., Donoghue, J.F., Healey, M., Rees, H.C., Bittinger, S., Obers, V., Sloggett, C., Kendarsari, R., Fung, J.N., Mortlock, S., Montgomery, G.W., Girling, J.E., Rogers, P. a. W., 2023. A molecular staging model for accurately dating the endometrial biopsy. Nat Commun 14, 6222. https://doi.org/10.1038/s41467-023-41979-z
Walker, R., Georgeson, P., Mahmood, K., Joo, J.E., Makalic, E., Clendenning, M., Como, J., Preston, S., Joseland, S., Pope, B.J., Hutchinson, R.A., Kasem, K., Walsh, M.D., Macrae, F.A., Win, A.K., Hopper, J.L., Mouradov, D., Gibbs, P., Sieber, O.M., O’Sullivan, D.E., Brenner, D.R., Gallinger, S., Jenkins, M.A., Rosty, C., Winship, I.M., Buchanan, D.D., 2023. Evaluating Multiple Next-Generation Sequencing–Derived Tumor Features to Accurately Predict DNA Mismatch Repair Status. The Journal of Molecular Diagnostics 25, 94–109. https://doi.org/10.1016/j.jmoldx.2022.10.003
Walker, R., Mahmood, K., Joo, J.E., Clendenning, M., Georgeson, P., Como, J., Joseland, S., Preston, S.G., Antill, Y., Austin, R., Boussioutas, A., Bowman, M., Burke, J., Campbell, A., Daneshvar, S., Edwards, E., Gleeson, M., Goodwin, A., Harris, M.T., Henderson, A., Higgins, M., Hopper, J.L., Hutchinson, R.A., Ip, E., Isbister, J., Kasem, K., Marfan, H., Milnes, D., Ng, A., Nichols, C., O’Connell, S., Pachter, N., Pope, B.J., Poplawski, N., Ragunathan, A., Smyth, C., Spigelman, A., Storey, K., Susman, R., Taylor, J.A., Warwick, L., Wilding, M., Williams, R., Win, A.K., Walsh, M.D., Macrae, F.A., Jenkins, M.A., Rosty, C., Winship, I.M., Buchanan, D.D., Family Cancer Clinics of Australia, 2023. A tumor focused approach to resolving the etiology of DNA mismatch repair deficient tumors classified as suspected Lynch syndrome. J Transl Med 21, 282. https://doi.org/10.1186/s12967-023-04143-1

2022

Melbourne Bioinformatics authors in bold.

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
The Galaxy Community, 2022. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Research 50, W345–W351. https://doi.org/10.1093/nar/gkac247
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
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
Raspin, K., Marthick, J.R., Donovan, S., Blizzard, L., Malley, R.C., Jung, C.-H., Banks, A., Redwig, F., Skala, M., Dickinson, J.L., FitzGerald, L.M., 2022. Identification of a novel recurrent EEF2 gene amplification in familial prostate tumours. Genes, Chromosomes and Cancer. https://doi.org/10.1002/gcc.23117
Tichkule, S., Myung, Y., Naung, M.T., Ansell, B.R.E., Guy, A.J., Srivastava, N., Mehra, S., Cacciò, S.M., Mueller, I., Barry, A.E., van Oosterhout, C., Pope, B., Ascher, D.B., Jex, A.R., 2022. VIVID: A Web Application for Variant Interpretation and Visualization in Multi-dimensional Analyses. Molecular Biology and Evolution 39. https://doi.org/10.1093/molbev/msac196
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

Melbourne Bioinformatics authors in bold.

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., 2022. Rare germline variants in the AXIN2 gene in families with colonic polyposis and colorectal cancer. Familial Cancer 21, 399–413. 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
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
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
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

Melbourne Bioinformatics authors in bold.

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
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
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
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
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

Melbourne Bioinformatics authors in bold.

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

Melbourne Bioinformatics/VLSCI authors in bold.

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
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
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
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
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
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
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., 2018. Best practice data life cycle approaches for the life sciences. 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
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
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., deFazio, A., McNeish, I.A., Bowtell, D.D., Swisher, E.M., Dobrovic, A., Wakefield, M.J., Scott, C.L., 2018. Methylation of all BRCA1 copies predicts response to the PARP inhibitor rucaparib in ovarian carcinoma. Nat Commun 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 6, e4312. https://doi.org/10.7717/peerj.4312
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
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
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

2017

Melbourne Bioinformatics authors in bold.

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
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