Ms Jessica ChungBioinformatician (Research Assistant)
Mr Peter GeorgesonCasual tutor (completing PhD)
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.
Dr Johan GustafssonSenior Research Fellow, Bioinformatics Engagement
Dr Thomas HarropBioinformatician
Ms Grace HallAcademic Specialist, Software Engineer
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.
Mr Steven MorganBioinformatician
Dr Gayle PhilipResearch Fellow / Computational Biologist
- BSc(Hons) National University of Ireland
- PhD National University of Ireland
Marion ShadboltHuman Genomics Data Specialist, Australian BioCommons
After completing her Masters of Bioinformatics at the University of Melbourne, Marion set off for Vancouver, Canada in search of experience and adventure. At the Karsan lab at BC Cancer, Marion developed knowledge and expertise in clinical genomic assay development and analysed various sequencing datasets from blood cancer patient samples.
During this experience, Marion encountered frustrating inconsistencies in publicly accessible datasets and gaps in the understanding of FAIR data practices at the research lab level. This sparked Marion’s passion for the importance of good data management and curation practices in the genomics realm.
In 2019, she joined EMBL-EBI to work on the Human Cell Atlas (HCA) project to build her knowledge and experience in this field. As part of the Data Coordination Platform team, she worked with collaborators and research labs to facilitate harmonisation and ingestion of vast quantities of cellular resolution data and metadata. In addition, Marion engaged with the single cell community to develop and maintain the HCA metadata standard and contributed to the development of the data ingestion platform.
Dr Anna SymeSenior Bioinformatician, Australian BioCommons
Ms Holly WhitfieldAcademic Support
Uwe WinterBioCloud DevOps Engineer, Australian BioCommons
Uwe graduated with an M.Sc Computational Molecular Biology from Saarland University in Germany in 2009. He moved to Melbourne 8 years ago and has worked as a Software Engineer, Business Consultant and most recently as Product Manager at Dassault Systemes. After 12 years of industry he is now applying his skillset to a new role as DevOps Engineer for the BioCloud.