Assoc Prof Daniel ParkLead, Melbourne Bioinformatics Platform
Dr Vicky PerreauSenior Research Fellow - Bioinformatics Training (Academic Specialist)
Dr Gayle PhilipResearch Fellow / Computational Biologist
- BSc(Hons) National University of Ireland
- PhD National University of Ireland
Dr Chol-Hee JungResearch Scientist
- BSc, University of Korea, South Korea
- MSc, University of Korea, South Korea
- PhD, University of Queensland, QLD, Australia
Joo J.E., E.M. Wong, L. Baglietto, C.H. Jung, H. Tsimiklis, et al. 2013. The use of DNA from archival dried blood spots with the Infinium HumanMethylation450 array. BMC Biotechnol 13: 23.
Jung C.H., C.E. Wong, M.B. Singh, P.L. Bhalla. 2012. Comparative genomic analysis of soybean flowering genes. PLoS One 7: e38250.
Jung, C.H., M.A. Hansen, I.V. Makunin, D.J. Korbie, and J.S. Mattick. 2010. Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data. BMC Genomics 11: 77.
Jung, C.H., I.V. Makunin and J.S. Mattick. 2010. Identification of conserved Drosophila-specific euchromatin-restricted noncoding sequence motifs. Genomic 96: 154-166.
Lee, B.M., Y.J. Park, D.S. Park, H.W. Kang, J.G. Kim, E.S. Song, I.C. Park, U.H. Yoon, J.H. Hahn, B.S. Koo, G.B. Lee, H. Kim, H.S. Park, K.O. Yoon, J.H. Kim, C.H. Jung, N.H. Koh, J.S. Seo, and S.J. Go. 2005. The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice. Nucleic Acids Res 33: 577-586
Seo, J.S., H. Chong, H.S. Park, K.O. Yoon, C. Jung, J.J. Kim, J.H. Hong, H. Kim, J.H. Kim, J.I. Kil, C.J. Park, H.M. Oh, J.S. Lee, S.J. Jin, H.W. Um, H.J. Lee, S.J. Oh, J.Y. Kim, H.L. Kang, S.Y. Lee, K.J. Lee, and H.S. Kang. 2005. The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4. Nat Biotechnol 23: 63-68.
Dr Khalid MahmoodResearch Scientist
- BSc(Hons), KFUPM
- MSc, Monash University
- PhD, Monash University
- Reboul CF, Mahmood K, Whisstock JC, Dunstone MA. (2012) Predicting giant transmembrane β-barrel architecture. Bioinformatics, 15;28(10):1299-302. Epub 2012 Mar 30. [Epub ahead of print]
- Mahmood K, Webb GI, Song J, Whisstock JC, Konagurthu AS. (2011) Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs. Nucleic Acids Res, 40(6): e44.
- Song J, Tan H, Boyd SE, Shen H, Mahmood K, Webb GI, Akutsu T, Whisstock JC, Pike RN. (2011) Bioinformatic approaches for predicting substrates of proteases. J Bioinform Comput Biol. 9(1):149-78. Review.
- Mahmood, K., Konagurthu, A.S., Song, J., Buckle, A.M., Webb, G.I. and Whisstock, J.C. (2010) EGM: encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomes, Bioinformatics, 26(17), 2076-2084.
- Tools: EGM
- Song J, Tan H, Shen H, Mahmood K, Boyd SE, Webb GI, Akutsu T, Whisstock JC (2010) Cascleave: towards more accurate prediction of caspase substrate cleavage sites. Bioinformatics, 26(6):752-760.
- Song J, Tan H, Mahmood K, Law RH, Buckle AM, Webb GI, Akutsu T, Whisstock J.C. (2009) Prodepth: predict residue depth by support vector regression approach from protein sequences only. PLoS One, 4(9):e7072.
- Ashley M. Buckle, David Abramson, Abdullah A. Amin, Mark Bate, Anthony Beitz, Colin Enticott, Noel Faux, Khalid Mahmood, Matthew Swift, Andrew Treloar and Whisstock., J.C. (2007) eResearch Solutions for High Throughput Structural Biology. 3rd IEEE International Conference on e-Science and Grid Computing. IEEE Computer Society, Bangalore, India.
- Faux, N.G., Huttley, G.A., Mahmood, K., Webb, G.I., Garcia de la Banda, M. and Whisstock, J.C. (2007) RCPdb: An evolutionary classification and codon usage database for repeat-containing proteins, Genome Research, 17, 1118-1127.
- Fenalti, G., Law, R.H., Buckle, A.M., Langendorf, C., Tuck, K., Rosado, C.J., Faux, N.G., Mahmood, K., Hampe, C.S., Banga, J.P., Wilce, M., Schmidberger, J., Rossjohn, J., El-Kabbani, O., Pike, R.N., Smith, A.I., Mackay, I.R., Rowley, M.J. and Whisstock, J.C. (2007) GABA production by glutamic acid decarboxylase is regulated by a dynamic catalytic loop, Nat Struct Mol Biol, 14, 280-286.
- Fulton, K.F., Bate, M.A., Faux, N.G., Mahmood, K., Betts, C. and Buckle, A.M. (2007) Protein Folding Database (PFD 2.0): an online environment for the International Foldeomics Consortium, Nucleic Acids Res, 35, D304-307.
Dr Clare SloggettResearch Scientist
BSc(Hons) University of NSW
PhD University of NSW
MSc Science (Bioinformatics)
Clare began life in computational physics before moving into genomics. She is now a researcher at Melbourne Bioinformatics at the University of Melbourne, with a particular interest in algorithms and in the application of machine learning to genomics. Clare has a senior role here at Melbourne Bioinformatics as Lead, Training Program and she also coordinates and teaches in Algorithms in functional genomics (Bioinformatics) as part of the Masters of Science (Bioinformatics) offered through the Faculty of Science. When not involved in training, Clare is involved in several key subscription projects through Melbourne Bioinformatics, including one with Austin Health on Machine Learning for Prediction of Risk in Renal Transplantation (2017-2019).
Mr Patrick GarnautSoftware Developer (Bioinformatics)
Mr James USoftware Developer
Mr Michael FranklinResearch Software Engineer, Portable Pipelines Project
Ms Catherine BromheadSupport Software Developer
Ms Jessica ChungBioinformatician (Research Assistant)
Dr Nuwan GoonasekeraSoftware Engineer
Nuwan is a software engineer at Melbourne Bioinformatics. His research interests include software fault isolation, software design and cloud computing. He is currently working primarily on expanding the cloudman cluster computer platform’s capabilities on Nectar and EC2 clouds. In the past, he worked as a senior software engineer at Industrial & Financial systems, developing enterprise applications. Nuwan’s role is to offer technical support for all aspects of the Genomics Virtual Laboratory.