Research Publications

For a running list of publications by Melbourne Bioinformatics researchers, go to Google doc.

The following publications resulted from collaborations with VLSCI (now Melbourne Bioinformatics) experts as reported to the end 2016:

Afgan, E., Lonie, A., Taylor, J., Skala, K. and Goonasekera, N., 2016, May. Architectural models for deploying and running virtual laboratories in the cloud. In Information and Communication Technology, Electronics and Microelectronics (MIPRO), 2016 39th International Convention on (pp. 282-286). IEEE.

Baglietto, L., Ponzi, E., Haycock, P., Hodge, A., Bianca Assumma, M., Jung, C.H., Chung, J., Fasanelli, F., Guida, F., Campanella, G. and Chadeau‐Hyam, M., 2017. DNA methylation changes measured in pre‐diagnostic peripheral blood samples are associated with smoking and lung cancer risk. International Journal of Cancer140(1), pp.50-61.

Baines, S.L., Howden, B.P., Heffernan, H., Stinear, T.P., Carter, G.P., Seemann, T., Kwong, J.C., Ritchie, S.R. and Williamson, D.A., 2016. Rapid emergence and evolution of Staphylococcus aureus clones harboring fusC-containing staphylococcal cassette chromosome elements. Antimicrobial agents and chemotherapy60(4), pp.2359-2365.

Boritsch, E.C., Khanna, V., Pawlik, A., Honoré, N., Navas, V.H., Ma, L., Bouchier, C., Seemann, T., Supply, P., Stinear, T.P. and Brosch, R., 2016. Key experimental evidence of chromosomal DNA transfer among selected tuberculosis-causing mycobacteria. Proceedings of the National Academy of Sciences113(35), pp.9876-9881.

Buultjens, A.H., Lam, M.M., Ballard, S., Monk, I.R., Mahony, A.A., Grabsch, E.A., Grayson, M.L., Pang, S., Coombs, G.W., Robinson, J.O. and Seemann, T., 2016. Evolutionary origins of the emergent ST796 clone of vancomycin resistant Enterococcus faecium (No. e2562v1). PeerJ Preprints.

Carter, G.P., Buultjens, A.H., Ballard, S.A., Baines, S.L., Tomita, T., Strachan, J., Johnson, P.D., Ferguson, J.K., Seemann, T., Stinear, T.P. and Howden, B.P., 2016. Emergence of endemic MLST non-typeable vancomycin-resistant Enterococcus faeciumJournal of Antimicrobial Chemotherapy, p.dkw314.

Caruana, N.J., Cooke, I.R., Faou, P., Finn, J., Hall, N.E., Norman, M., Pineda, S.S. and Strugnell, J.M., 2016. A combined proteomic and transcriptomic analysis of slime secreted by the southern bottletail squid, Sepiadarium austrinum (Cephalopoda). Journal of Proteomics148, pp.170-182.

Doo, N.W., Makalic, E., Schmidt, D., Joo, J.E., Jung, C.H. and Giles, G.G., 2016. Aberrant DNA Methylation Patterns in Peripheral Blood Are Detectable Years before the Diagnosis of Mature B Cell Neoplasms.

Dugué, P.A., Brinkman, M.T., Milne, R.L., Wong, E.M., FitzGerald, L.M., Bassett, J.K., Joo, J.E., Jung, C.H., Makalic, E., Schmidt, D.F. and Park, D.J., 2016. Genome-wide measures of DNA methylation in peripheral blood and the risk of urothelial cell carcinoma: a prospective nested case–control study. British Journal of Cancer.

Dugué, P.A., English, D.R., MacInnis, R.J., Jung, C.H., Bassett, J.K., FitzGerald, L.M., Wong, E.M., Joo, J.E., Hopper, J.L., Southey, M.C. and Giles, G.G., 2016. Reliability of DNA methylation measures from dried blood spots and mononuclear cells using the HumanMethylation450k BeadArray. Scientific Reports6.

Goonasekera, N., Lonie, A., Taylor, J. and Afgan, E., 2016, July. CloudBridge: a Simple Cross-Cloud Python Library. In Proceedings of the XSEDE16 Conference on Diversity, Big Data, and Science at Scale (p. 37). ACM.

Gorrell, R.J., Zwickel, N., Reynolds, J., Bulach, D. and Kwok, T., 2016. Helicobacter pylori CagL hypervariable motif: a global analysis of geographical diversity and association with gastric cancer. Journal of Infectious Diseases, p.jiw060.

Gouillart, E., Nunez-Iglesias, J. and van der Walt, S., 2017. Analyzing microtomography data with Python and the scikit-image library. Advanced Structural and Chemical Imaging2(1), p.18.

Griffin, P.C., Hangartner, S.B., Fournier-Level, A. and Hoffmann, A.A., 2016. Genomic Trajectories to Desiccation Resistance: Convergence and Divergence Among Replicate Selected Drosophila Lines. Genetics, pp.genetics-116.

Hall, N.E., Hanzak, J., Allcock, A.L., Cooke, I.R., Ogura, A. and Strugnell, J.M., 2016. The complete mitochondrial genome of the pygmy squid, Idiosepius (Cephalopoda: Decapodiformes): the first representative from the family Idiosepiidae. Mitochondrial DNA Part A27(1), pp.5-6.

Hasmad, H.N., Lai, K.N., Wen, W.X., Park, D.J., Nguyen-Dumont, T., Kang, P.C.E., Thirthagiri, E., Ma’som, M., Lim, B.K., Southey, M. and Woo, Y.L., 2016. Evaluation of germline BRCA1 and BRCA2 mutations in a multi-ethnic Asian cohort of ovarian cancer patients. Gynecologic oncology141(2), pp.318-322.

Jung, C.H., Kim, K.J., Kim, B.Y., Kim, C.H., Kang, S.K. and Mok, J.O., 2016. Relationship between vitamin D status and vascular complications in patients with type 2 diabetes mellitus. Nutrition Research36(2), pp.117-124.

Kpeli, G., Otchere, I.D., Lamelas, A., Buultjens, A., Bulach, D., Baines, S.L., Seemann, T., Giulieri, S., Nakobu, Z., Aboagye, S.Y. and Owusu-Mireku, E., 2016. Possible healthcare-associated transmission as a cause of secondary infection and population structure of Staphylococcus aureus isolates from two wound treatment centres in Ghana. New microbes and new infections13, pp.92-101.

Kwong, J.C., da Silva, A.G., Dyet, K., Williamson, D.A., Stinear, T.P., Howden, B.P. and Seemann, T., 2016. NGMASTER: in silico multi-antigen sequence typing for Neisseria gonorrhoeaeMicrobial Genomics2(8).

Kwong, J.C., Mercoulia, K., Tomita, T., Easton, M., Li, H.Y., Bulach, D.M., Stinear, T.P., Seemann, T. and Howden, B.P., 2016. Prospective whole-genome sequencing enhances national surveillance of Listeria monocytogenesJournal of clinical microbiology54(2), pp.333-342.

Kwong, J.C., Stafford, R., Strain, E., Stinear, T.P., Seemann, T. and Howden, B.P., 2016. Sharing is caring: international sharing of data enhances genomic surveillance of Listeria monocytogenes. Clinical Infectious Diseases, p.ciw359.

Lawrence, S.L., Gorman, M.A., Feil, S.C., Mulhern, T.D., Kuiper, M.J., Ratner, A.J., Tweten, R.K., Morton, C.J. and Parker, M.W., 2016. Structural Basis for Receptor Recognition by the Human CD59-Responsive Cholesterol-Dependent Cytolysins. Structure24(9), pp.1488-1498.

Lee, J.Y., Monk, I.R., Pidot, S.J., Singh, S., Chua, K.Y., Seemann, T., Stinear, T.P. and Howden, B.P., 2016. Functional analysis of the first complete genome sequence of a multidrug resistant sequence type 2 Staphylococcus epidermidisMicrobial Genomics2(9).

Lonsdale, A., Penington, J.S., Rice, T., Walker, M. and Dashnow, H., 2016. Ten simple rules for a bioinformatics journal club. PLoS computational biology12(1), p.e1004526.

MacInnis, R.J., Schmidt, D.F., Makalic, E., Severi, G., FitzGerald, L.M., Reumann, M., Kapuscinski, M.K., Kowalczyk, A., Zhou, Z., Goudey, B. and Qian, G., 2016. Use of a Novel Nonparametric Version of DEPTH to Identify Genomic Regions Associated with Prostate Cancer Risk. Cancer Epidemiology and Prevention Biomarkers.

Miles, M.A., Shekhar, T.M., Hall, N.E. and Hawkins, C.J., 2016. TRAIL causes deletions at the HPRT and TK1 loci of clonogenically competent cells. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis787, pp.15-31.

Moffatt, C.R.M., Greig, A., Valcanis, M., Gao, W., Seemann, T., Howden, B.P. and Kirk, M.D., 2016. A large outbreak of Campylobacter jejuni infection in a university college caused by chicken liver pâté, Australia, 2013. Epidemiology and infection, pp.1-8.

Mofiz, E., Holt, D.C., Seemann, T., Currie, B.J., Fischer, K. and Papenfuss, A.T., 2016. Genomic resources and draft assemblies of the human and porcine varieties of scabies mites, Sarcoptes scabiei var. hominis and var. suisGigaScience5(1), p.23.

Mofiz, E., Seemann, T., Bahlo, M., Holt, D., Currie, B.J., Fischer, K. and Papenfuss, A.T., 2016. Mitochondrial genome sequence of the scabies mite provides insight into the genetic diversity of individual scabies infections. PLoS Negl Trop Dis10(2), p.e0004384.

Monk, I.R., Seemann, T., Howden, B.P. and Stinear, T.P., 2016. Refutation: Structure and mechanism of the essential two-component signal-transduction system WalKR in Staphylococcus aureus. bioRxiv, p.058842.

Ng, A.C., Poudel, G., Stout, J.C., Churchyard, A., Chua, P., Egan, G.F. and Georgiou-Karistianis, N., 2016. Iron accumulation in the basal ganglia in Huntington’s disease: cross-sectional data from the IMAGE-HD study. Journal of Neurology, Neurosurgery & Psychiatry87(5), pp.545-549.

Nor, B., Young, N.D., Korhonen, P.K., Hall, R.S., Tan, P., Lonie, A. and Gasser, R.B., 2016. Pipeline for the identification and classification of ion channels in parasitic flatworms. Parasites & vectors9(1), p.155.

Page, A.J., Steinbiss, S., Taylor, B., Seemann, T. and Keane, J.A., 2016. {GFF} 3toEMBL: Preparing annotated assemblies for submission to {EMBL}. The Journal of Open Source Software1(6).

Page, A.J., Taylor, B., Delaney, A.J., Soares, J., Seemann, T., Keane, J.A. and Harris, S.R., 2016. SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments. Microbial Genomics2(4).

Park, D.J., Li, R., Lau, E., Georgeson, P., Nguyen-Dumont, T. and Pope, B.J., 2016. UNDR ROVER-a fast and accurate variant caller for targeted DNA sequencing. BMC bioinformatics17(1), p.165.

Pope, B.J., Mahmood, K., Jung, C.H. and Park, D.J., 2016. Fine resolution mapping of double-strand break sites for human ribosomal DNA units. Genomics Data10, pp.19-21.

Pope, B.J., Mahmood, K., Jung, C.H., Georgeson, P. and Park, D.J., 2017. Single nucleotide-level mapping of DNA double-strand breaks in human HEK293T cells. Genomics Data11, pp.43-45.

Quek, C., Bellingham, S.A., Jung, C.H., Scicluna, B., Shambrook, M.C., Sharples, R., Cheng, L. and Hill, A.F., 2016. Defining the purity of exosomes required for diagnostic profiling of small RNA suitable for biomarker discovery. RNA biology, (just-accepted), pp.00-00.

Raina, J.B., Tapiolas, D., Motti, C.A., Foret, S., Seemann, T., Tebben, J., Willis, B.L. and Bourne, D.G., 2016. Isolation of an antimicrobial compound produced by bacteria associated with reef-building corals. PeerJ4, p.e2275.

Richardson, K.M., Schiffer, M., Griffin, P.C., Lee, S.F. and Hoffmann, A.A., 2016. Tropical Drosophila pandora carry Wolbachia infections causing cytoplasmic incompatibility or male killing. Evolution70(8), pp.1791-1802.

Robinson, N.A., Hall, N.E., Ross, E.M., Cooke, I.R., Shiel, B.P., Robinson, A.J. and Strugnell, J.M., 2016. The complete mitochondrial genome of Haliotis laevigata (Gastropoda: Haliotidae) using MiSeq and HiSeq sequencing. Mitochondrial DNA Part A27(1), pp.437-438.

Shafee, T.M., Robinson, A.J., van der Weerden, N. and Anderson, M.A., 2016. Structural homology guided alignment of cysteine rich proteins. SpringerPlus5(1), p.27.

Smibert, O., Aung, A.K., Woolnough, E., Seemann, T., Carter, G., Spelman, D. and Peleg, A., 2016, December. Healthcare Worker Hand-Held Devices as Vectors for Multidrug-Resistant Organisms in Intensive Care Patients. In Open Forum Infectious Diseases (Vol. 3, No. suppl 1, p. 254). Oxford University Press.

Stark, Z., Tan, T.Y., Chong, B., Brett, G.R., Yap, P., Walsh, M., Yeung, A., Peters, H., Mordaunt, D., Cowie, S. and Amor, D.J., 2016. A prospective evaluation of whole-exome sequencing as a first-tier molecular test in infants with suspected monogenic disorders. Genetics in Medicine.

Unterweger, B., Bulach, D.M., Scoble, J., Midgley, D.J., Greenfield, P., Lyras, D., Johanesen, P. and Dumsday, G.J., 2016. CYP101J2, CYP101J3, and CYP101J4, 1, 8-Cineole-Hydroxylating Cytochrome P450 Monooxygenases from Sphingobium yanoikuyae Strain B2. Applied and Environmental Microbiology82(22), pp.6507-6517.

Villacorta-Rath, C., Ilyushkina, I., Strugnell, J.M., Green, B.S., Murphy, N.P., Doyle, S.R., Hall, N.E., Robinson, A.J. and Bell, J.J., 2016. Outlier SNPs enable food traceability of the southern rock lobster, Jasus edwardsiiMarine Biology163(11), p.223.

Wakefield, M.J., 2016. SurvivalVolume: interactive volume threshold survival graphs. Journal of Open Source Software, 1(8).

Wakefield, M.J., 2016. Xenomapper: Mapping reads in a mixed species context. Journal of Open Source Software, 1(1).

Whitelaw, B.L., Strugnell, J.M., Faou, P., da Fonseca, R.R., Hall, N.E., Norman, M., Finn, J. and Cooke, I.R., 2016. Combined transcriptomic and proteomic analysis of the posterior salivary gland from the southern blue-ringed octopus and the southern sand octopus. Journal of proteome research15(9), pp.3284-3297.

Wong, N.C., Pope, B.J., Candiloro, I.L., Korbie, D., Trau, M., Wong, S.Q., Mikeska, T., Zhang, X., Pitman, M., Eggers, S. and Doyle, S.R., 2016. MethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing. BMC bioinformatics17(1), p.98.

The following publications resulting from collaborations with VLSCI (now Melbourne Bioinformatics) experts were reported to the end 2015:

Ablordey, A. S., Vandelannoote, K., Frimpong, I. A., Ahortor, E. K., Amissah, N. A., Eddyani, M., Durnez, L., Portaels, F., de Jong, B. C., Leirs, H., Porter, J. L., Mangas, K. M., Lam, M. M. C., Buultjens, A., Seemann, T., Tobias, N. J. & Stinear, T. P. Whole genome comparisons suggest random distribution of Mycobacterium ulcerans genotypes in a Buruli ulcer endemic region of Ghana. PLoS Negl. Trop. Dis. 9, e0003681 (2015).

Afgan, E., Krampis, K., Goonasekera, N., Skala, K. & Taylor, J. Building and provisioning bioinformatics environments on public and private Clouds. in 2015 38th International Convention on Information and Communication Technology, Electronics and Microelectronics (MIPRO) 223–228 (IEEE).

Afgan, E., Sloggett, C., Goonasekera, N., Makunin, I., Benson, D., Crowe, M., Gladman, S., Kowsar, Y., Pheasant, M., Horst, R. & Lonie, A. Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud. PLoS One 10, e0140829 (2015).

Alioto, T. S., Buchhalter, I., Derdak, S., Hutter, B., Eldridge, M. D., Hovig, E., Heisler, L. E., Beck, T. A., Simpson, J. T., Tonon, L., Sertier, A.-S., Patch, A.-M., Jäger, N., Ginsbach, P., Drews, R., Paramasivam, N., Kabbe, R., Chotewutmontri, S., Diessl, N., Previti, C., Schmidt, S., Brors, B., Feuerbach, L., Heinold, M., Gröbner, S., Korshunov, A., Tarpey, P. S., Butler, A. P., Hinton, J., Jones, D., Menzies, A., Raine, K., Shepherd, R., Stebbings, L., Teague, J. W., Ribeca, P., Giner, F. C., Beltran, S., Raineri, E., Dabad, M., Heath, S. C., Gut, M., Denroche, R. E., Harding, N. J., Yamaguchi, T. N., Fujimoto, A., Nakagawa, H., Quesada, V., Valdés-Mas, R., Nakken, S., Vodák, D., Bower, L., Lynch, A. G., Anderson, C. L., Waddell, N., Pearson, J. V., Grimmond, S. M., Peto, M., Spellman, P., He, M., Kandoth, C., Lee, S., Zhang, J., Létourneau, L., Ma, S., Seth, S., Torrents, D., Xi, L., Wheeler, D. A., López-Otín, C., Campo, E., Campbell, P. J., Boutros, P. C., Puente, X. S., Gerhard, D. S., Pfister, S. M., McPherson, J. D., Hudson, T. J., Schlesner, M., Lichter, P., Eils, R., Jones, D. T. W. & Gut, I. G. A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nat. Commun. 6, 10001 (2015).

Baines, S. L., Holt, K. E., Schultz, M. B., Seemann, T., Howden, B. O., Jensen, S. O., van Hal, S. J., Coombs, G. W., Firth, N., Powell, D. R., Stinear, T. P. & Howden, B. P. Convergent adaptation in the dominant global hospital clone ST239 of methicillin-resistant Staphylococcus aureus. MBio 6, e00080 (2015).

Boekel, J., Chilton, J. M., Cooke, I. R., Horvatovich, P. L., Jagtap, P. D., Käll, L., Lehtiö, J., Lukasse, P., Moerland, P. D. & Griffin, T. J. Multi-omic data analysis using Galaxy. Nat. Biotechnol. 33, 137–139 (2015).

Cooke, I. R., Whitelaw, B., Norman, M., Caruana, N. & Strugnell, J. M. in Evolution of Venomous Animals and Their Toxins 1–15 (Springer Netherlands, 2015).

Damiano, J. A., Afawi, Z., Bahlo, M., Mauermann, M., Misk, A., Arsov, T., Oliver, K. L., Dahl, H.-H. M., Shearer, A. E., Smith, R. J. H., Hall, N. E., Mahmood, K., Leventer, R. J., Scheffer, I. E., Muona, M., Lehesjoki, A.-E., Korczyn, A. D., Herrmann, H., Berkovic, S. F. & Hildebrand, M. S. Mutation of the nuclear lamin gene LMNB2 in progressive myoclonus epilepsy with early ataxia. Hum. Mol. Genet. 24, 4483–4490 (2015).

Dugué, P.-A., English, D. R., MacInnis, R. J., Joo, J. E., Jung, C.-H. & Milne, R. L. The repeatability of DNA methylation measures may also affect the power of epigenome-wide association studies. Int. J. Epidemiol. 44, 1460–1461 (2015).

Eddyani, M., Vandelannoote, K., Meehan, C. J., Bhuju, S., Porter, J. L., Aguiar, J., Seemann, T., Jarek, M., Singh, M., Portaels, F., Stinear, T. P. & de Jong, B. C. A Genomic Approach to Resolving Relapse versus Reinfection among Four Cases of Buruli Ulcer. PLoS Negl. Trop. Dis. 9, e0004158 (2015).

Gao, W., Monk, I. R., Tobias, N. J., Gladman, S. L., Seemann, T., Stinear, T. P. & Howden, B. P. Large tandem chromosome expansions facilitate niche adaptation during persistent infection with drug-resistant Staphylococcus aureus. Microbial Genomics 1, (2015).

Harrison, P. F., Powell, D. R., Clancy, J. L., Preiss, T., Boag, P. R., Traven, A., Seemann, T. & Beilharz, T. H. PAT-seq: a method to study the integration of 3’-UTR dynamics with gene expression in the eukaryotic transcriptome. RNA 21, 1502–1510 (2015).

Hong, M. K. H., Macintyre, G., Wedge, D. C., Van Loo, P., Patel, K., Lunke, S., Alexandrov, L. B., Sloggett, C., Cmero, M., Marass, F., Tsui, D., Mangiola, S., Lonie, A., Naeem, H., Sapre, N., Phal, P. M., Kurganovs, N., Chin, X., Kerger, M., Warren, A. Y., Neal, D., Gnanapragasam, V., Rosenfeld, N., Pedersen, J. S., Ryan, A., Haviv, I., Costello, A. J., Corcoran, N. M. & Hovens, C. M. Tracking the origins and drivers of subclonal metastatic expansion in prostate cancer. Nat. Commun. 6, 6605 (2015).

Hosking, C. G., Driguez, P., McWilliam, H. E. G., Ilag, L. L., Gladman, S., Li, Y., Piedrafita, D., McManus, D. P., Meeusen, E. N. T. & de Veer, M. J. Using the local immune response from the natural buffalo host to generate an antibody fragment library that binds the early larval stages of Schistosoma japonicum. Int. J. Parasitol. 45, 729–740 (2015).

Hovens, C., Hong, M., Macintyre, G., Wedge, D., Van Loo, P., Lunke, S., Alexandrov, L., Slogget, C., Cmero, M., Mangiola, S., Lonie, A., Naeem, H., Sapre, N., Phal, P., Kerger, M., Pedersen, J., Ryan, A., Haviv, I., Costello, A. & Corcoran, N. Tracking clonal diversity in metastatic prostate cancer progression. J. Clin. Oncol. 33, 193 (2015).

Hsu, A. L., Kondrashova, O., Lunke, S., Love, C. J., Meldrum, C., Marquis-Nicholson, R., Corboy, G., Pham, K., Wakefield, M., Waring, P. M. & Taylor, G. R. AmpliVar: mutation detection in high-throughput sequence from amplicon-based libraries. Hum. Mutat. 36, 411–418 (2015).

Jeffries, T. C., Ostrowski, M., Williams, R. B., Xie, C., Jensen, R. M., Grzymski, J. J., Senstius, S. J., Givskov, M., Hoeke, R., Philip, G. K., Neches, R. Y., Drautz-Moses, D. I., Chénard, C., Paulsen, I. T. & Lauro, F. M. Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll. Sci. Rep. 5, 15383 (2015).

Jung, C. H., O’Brien, M., Singh, M. B. & Bhalla, P. L. Epigenetic landscape of germline specific genes in the sporophyte cells of Arabidopsis thaliana. Front. Plant Sci. 6, 328 (2015).

Kanwal, S., Lonie, A., Sinnott, R. O. & Anderson, C. Challenges of Large-Scale Biomedical Workflows on the Cloud — A Case Study on the Need for Reproducibility of Results. in Computer-Based Medical Systems (CBMS), 2015 IEEE 28th International Symposium on 220–225 (2015).

Khong, J. J., Wang, L. Y., Smyth, G. K., McNab, A. A., Hardy, T. G., Selva, D., Llamas, B., Jung, C.-H., Sharma, S., Burdon, K. P., Ebeling, P. R. & Craig, J. E. Differential Gene Expression Profiling of Orbital Adipose Tissue in Thyroid Orbitopathy. Invest. Ophthalmol. Vis. Sci. 56, 6438–6447 (2015).

Kuiper, M. J., Morton, C. J., Abraham, S. E. & Gray-Weale, A. The biological function of an insect antifreeze protein simulated by molecular dynamics. Elife 4, (2015).

Leeming, M. G., Isaac, A. P., Pope, B. J., Cranswick, N., Wright, C. E., Ziogas, J., O’Hair, R. A. J. & Donald, W. A. High-resolution twin-ion metabolite extraction (HiTIME) mass spectrometry: nontargeted detection of unknown drug metabolites by isotope labeling, liquid chromatography mass spectrometry, and automated high-performance computing. Anal. Chem. 87, 4104–4109 (2015).

Li, S., Wong, E. M., Joo, J. E., Jung, C.-H., Chung, J., Apicella, C., Stone, J., Dite, G. S., Giles, G. G., Southey, M. C. & Hopper, J. L. Genetic and Environmental Causes of Variation in the Difference Between Biological Age Based on DNA Methylation and Chronological Age for Middle-Aged Women. Twin Res. Hum. Genet. 18, 720–726 (2015).

Meumann, E. M., Globan, M., Fyfe, J. A. M., Leslie, D., Porter, J. L., Seemann, T., Denholm, J. & Stinear, T. P. Genome sequence comparisons of serial multi-drug-resistant Mycobacterium tuberculosis isolates over 21 years of infection in a single patient. Microbial Genomics 1, (2015).

Kwong, J. C., Mercoulia, K., Tomita, T., Easton, M., Li, H. Y., Bulach, D. M., Stinear, T. P., Seemann, T. & Howden, B. P. Prospective Whole-Genome Sequencing Enhances National Surveillance of Listeria monocytogenes. J. Clin. Microbiol. 54, 333–342 (2016).

Moustafa, A. M., Seemann, T., Gladman, S., Adler, B., Harper, M., Boyce, J. D. & Bennett, M. D. Comparative Genomic Analysis of Asian Haemorrhagic Septicaemia-Associated Strains of Pasteurella multocida Identifies More than 90 Haemorrhagic Septicaemia-Specific Genes. PLoS One 10, e0130296 (2015).

Murugesan, S., Tay, D. B. H., Cooke, I. & Faou, P. Application of dual tree complex wavelet transform in tandem mass spectrometry. Comput. Biol. Med. 63, 36–41 (2015).

Nepal, S., Surya, N., Richard, S., Carsten, F., Catherine, W., Shiping, C., Sehrish, K., Jinhui, Y. & Andrew, L. TruXy: Trusted Storage Cloud for Scientific Workflows. IEEE Transactions on Cloud Computing 1–1 (2015).

Nguyen-Dumont, T., Hammet, F., Mahmoodi, M., Pope, B. J., Giles, G. G., Hopper, J. L., Southey, M. C. & Park, D. J. Abridged adapter primers increase the target scope of Hi-Plex. Biotechniques 58, 33–36 (2015).

Nguyen-Dumont, T., Hammet, F., Mahmoodi, M., Tsimiklis, H., Teo, Z. L., Li, R., Pope, B. J., Terry, M. B., Buys, S. S., Daly, M., Hopper, J. L., Winship, I., Goldgar, D. E., Park, D. J. & Southey, M. C. Mutation screening of PALB2 in clinically ascertained families from the Breast Cancer Family Registry. Breast Cancer Res. Treat. 149, 547–554 (2015).

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