Research Publications

2023 Publications

• 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
• Georgeson, P., Steinfelder, R.S., Harrison, T.A., Pope, B.J., Zaidi, S.H., Qu, C., Lin, Y., Joo, J.E., Mahmood, K., Clendenning, M., Walker, R., Aglago, E.K., Berndt, S.I., Brenner, H., Campbell, P.T., Cao, Y., Chan, A.T., Chang-Claude, J., Dimou, N., Doheny, K.F., Drew, D.A., Figueiredo, J.C., French, A.J., Gallinger, S., Giannakis, M., Giles, G.G., Goode, E.L., Gruber, S.B., Gsur, A., Gunter, M.J., Harlid, S., Hoffmeister, M., Hsu, L., Huang, W.-Y., Huyghe, J.R., Manson, J.E., Moreno, V., Murphy, N., Nassir, R., Newton, C.C., Nowak, J.A., Obón-Santacana, M., Ogino, S., Pai, R.K., Papadimitrou, N., Potter, J.D., Schoen, R.E., Song, M., Sun, W., Toland, A.E., Trinh, Q.M., Tsilidis, K., Ugai, T., Um, C.Y., Macrae, F.A., Rosty, C., Hudson, T.J., Winship, I.M., Phipps, A.I., Jenkins, M.A., Peters, U., Buchanan, D.D., 2023. Genotoxic colibactin mutational signature in colorectal cancer is associated with clinicopathological features, specific genomic alterations and better survival. https://doi.org/10.1101/2023.03.10.23287127
• 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
• 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., 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
• 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/li>

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
• 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
• 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
• Murphy, N., Newton, C.C., Song, M., Papadimitriou, N., Hoffmeister, M., Phipps, A.I., Harrison, T.A., Newcomb, P.A., Aglago, E.K., Berndt, S.I., Brenner, H., Buchanan, D.D., Cao, Y., Chan, A.T., Chen, X., Cheng, I., Chang-Claude, J., Dimou, N., Drew, D., Farris, A.B., French, A.J., Gallinger, S., Georgeson, P., Giannakis, M., Giles, G.G., Gruber, S.B., Harlid, S., Hsu, L., Huang, W.-Y., Jenkins, M.A., Laskar, R.S., Le Marchand, L., Limburg, P., Lin, Y., Mandic, M., Nowak, J.A., Obón-Santacana, M., Ogino, S., Qu, C., Sakoda, L.C., Schoen, R.E., Southey, M.C., Stadler, Z.K., Steinfelder, R.S., Sun, W., Thibodeau, S.N., Toland, A.E., Trinh, Q.M., Tsilidis, K.K., Ugai, T., Van Guelpen, B., Wang, X., Woods, M.O., Zaidi, S.H., Gunter, M.J., Peters, U., Campbell, P.T., 2022. Body Mass Index and Molecular Subtypes of Colorectal Cancer. JNCI: Journal of the National Cancer Institute djac215. https://doi.org/10.1093/jnci/djac215<
• 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
• 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

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