Dr. Simon Wong

Dr. Simon Wong
PhD
Computational Scientist
E-mail:
Tel: +353 1 5241608 (ext 25)

Simon holds an undergraduate degree in Human Genetics from Trinity College Dublin, where he also completed his PhD in Prof. Ken Wolfe's lab at the Genetics Department. His PhD work covered a range of topics including whole genome duplication, evolution of yeast mating types and selection for a specific gene cluster in anaerobic yeast species. He then held a postdoctoral position in Prof. Mark Ragan's lab at The University of Queensland in Brisbane, Australia, where he developed a method to classify protein subsequence families and was involved with projects dealing with large-scale protein-protein interaction & subcellular localisation datasets.

He joined ICHEC as a computational scientist in 2008 and is primarily involved in supporting the bioinformatics/life sciences community. As many in the community are relatively new to HPC, he has been active in introducing researchers to ICHEC facilities and software packages. He works closely with a number of groups on active research projects (see Consortium Support), and is especially interested in tackling computational challenges posed by next-generation sequencing projects. Simon is also involved in the Irish BioPortal project, which aims to provide a resource to highlight Irish bioinformatics software, as well as a more general platform for bioinformatics researchers to run compute-intensive applications on HPC resources.

Publications

Shin C.J., Wong S., Davis M.J. and Ragan M.A. (2009) Protein-protein interaction as a predictor of subcellular location. BMC Systems Biology 3:28.

Wong S. and Ragan M.A. (2008) MACHOS: Markov clusters of homologous subsequences. Bioinformatics 24:i77-85.

Scannell D.R., Byrne K.P., Gordon J.L., Wong S. and Wolfe K.H. (2006) Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature 440:341-345.

Wong S. and Wolfe, K.H. (2006). Duplication of genes and genomes in yeasts. In Comparative genomics (Sunnerhagen P. and Piskur J., eds.), Vol. 15, pp. 78-99. Springer-Verlag, Heidelberg.

Wong S. and Wolfe K.H. (2005) Birth of a metabolic gene cluster in yeast by adaptive gene relocation. Nature Genetics 37:777-782.

Logue M.E., Wong S., Wolfe K.H. and Butler G. (2005) A genome sequence survey shows that the pathogenic yeast Candida parapsilosis has a defective MTLa1 allele at its mating type locus. Eukaryotic Cell 4:1009-1017.

Wong S., Fares M.A., Zimmermann W., Butler G. and Wolfe K.H. (2003) Evidence from comparative genomics for a complete sexual cycle in the 'asexual' pathogenic yeast Candida glabrata. Genome Biology 4:R10.

Wong S., Butler G. and Wolfe K.H. (2002) Gene order evolution and paleopolyploidy in hemiascomycete yeasts. Proceedings of the National Academy of Sciences, USA 99:9272-9277.