Research Publications

The following publications resulting from collaborations with VLSCI (now Melbourne Bioinformatics) experts were reported to the end 2015 (2016 data is currently being collected):

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).

Patch, A.-M., Christie, E. L., Etemadmoghadam, D., Garsed, D. W., George, J., Fereday, S., Nones, K., Cowin, P., Alsop, K., Bailey, P. J., Kassahn, K. S., Newell, F., Quinn, M. C. J., Kazakoff, S., Quek, K., Wilhelm-Benartzi, C., Curry, E., Leong, H. S., The Australian Ovarian Cancer Study Group, Hamilton, A., Mileshkin, L., Au-Yeung, G., Kennedy, C., Hung, J., Chiew, Y.-E., Harnett, P., Friedlander, M., Quinn, M., Pyman, J., Cordner, S., O’Brien, P., Leditschke, J., Young, G., Strachan, K., Waring, P., Azar, W., Mitchell, C., Traficante, N., Hendley, J., Thorne, H., Shackleton, M., Miller, D. K., Arnau, G. M., Tothill, R. W., Holloway, T. P., Semple, T., Harliwong, I., Nourse, C., Nourbakhsh, E., Manning, S., Idrisoglu, S., Bruxner, T. J. C., Christ, A. N., Poudel, B., Holmes, O., Anderson, M., Leonard, C., Lonie, A., Hall, N., Wood, S., Taylor, D. F., Xu, Q., Lynn Fink, J., Waddell, N., Drapkin, R., Stronach, E., Gabra, H., Brown, R., Jewell, A., Nagaraj, S. H., Markham, E., Wilson, P. J., Ellul, J., McNally, O., Doyle, M. A., Vedururu, R., Stewart, C., Lengyel, E., Pearson, J. V., Waddell, N., deFazio, A., Grimmond, S. M. & Bowtell, D. D. L. Whole–genome characterization of chemoresistant ovarian cancer. Nature 521, 489–494 (2015).

Quek, C., Jung, C.-H., Bellingham, S. A., Lonie, A. & Hill, A. F. iSRAP – a one-touch research tool for rapid profiling of small RNA-seq data. Journal of Extracellular Vesicles 4, (2015).

Sadedin, S. P., Dashnow, H., James, P. A., Bahlo, M., Bauer, D. C., Lonie, A., Lunke, S., Macciocca, I., Ross, J. P., Siemering, K. R., Stark, Z., White, S. M., Melbourne Genomics Health Alliance, Taylor, G., Gaff, C., Oshlack, A. & Thorne, N. P. Cpipe: a shared variant detection pipeline designed for diagnostic settings. Genome Med. 7, 68 (2015).

Shiller, J., Van de Wouw, A. P., Taranto, A. P., Bowen, J. K., Dubois, D., Robinson, A., Deng, C. H. & Plummer, K. M. A Large Family of AvrLm6-like Genes in the Apple and Pear Scab Pathogens, Venturia inaequalis and Venturia pirina. Front. Plant Sci. 6, 980 (2015).

Takemura, S.-Y., Xu, C. S., Lu, Z., Rivlin, P. K., Parag, T., Olbris, D. J., Plaza, S., Zhao, T., Katz, W. T., Umayam, L., Weaver, C., Hess, H. F., Horne, J. A., Nunez-Iglesias, J., Aniceto, R., Chang, L.-A., Lauchie, S., Nasca, A., Ogundeyi, O., Sigmund, C., Takemura, S., Tran, J., Langille, C., Le Lacheur, K., McLin, S., Shinomiya, A., Chklovskii, D. B., Meinertzhagen, I. A. & Scheffer, L. K. Synaptic circuits and their variations within different columns in the visual system of Drosophila. Proc. Natl. Acad. Sci. U. S. A. 112, 13711–13716 (2015).

Wade, K. R., Hotze, E. M., Kuiper, M. J., Morton, C. J., Parker, M. W. & Tweten, R. K. An intermolecular electrostatic interaction controls the prepore-to-pore transition in a cholesterol-dependent cytolysin. Proc. Natl. Acad. Sci. U. S. A. 112, 2204–2209 (2015).

Wong Doo, N., Makalic, E., Joo, J. E., Vajdic, C. M., Schmidt, D. F., Wong, E. M., Jung, C.-H., Severi, G., Park, D. J., Chung, J., Baglietto, L., Prince, H. M., Seymour, J. F., Tam, C., Hopper, J. L., English, D. R., Milne, R. L., Harrison, S. J., Southey, M. C. & Giles, G. G. Global measures of peripheral blood-derived DNA methylation as a risk factor in the development of mature B-cell neoplasms. Epigenomics 8, 55–66 (2016).

Wong, N. C., Pope, B. J., Candiloro, I., Korbie, D., Trau, M., Wong, S. Q., Mikeska, T., van Denderen, B. J. W., Thompson, E. W., Eggers, S., Doyle, S. R. & Dobrovic, A. Exemplary multiplex bisulfite amplicon data used to demonstrate the utility of Methpat. Gigascience 4, 55 (2015).

Yeoh, L. M., Goodman, C. D., Hall, N. E., van Dooren, G. G., McFadden, G. I. & Ralph, S. A. A serine–arginine-rich (SR) splicing factor modulates alternative splicing of over a thousand genes in Toxoplasma gondii. Nucleic Acids Res. 43, 4661–4675 (2015).

Zhu, W., Ausin, I., Seleznev, A., Méndez-Vigo, B., Picó, F. X., Sureshkumar, S., Sundaramoorthi, V., Bulach, D., Powell, D., Seemann, T., Alonso-Blanco, C. & Balasubramanian, S. Natural Variation Identifies ICARUS1, a Universal Gene Required for Cell Proliferation and Growth at High Temperatures in Arabidopsis thaliana. PLoS Genet. 11, e1005085 (2015).