King Fung Wong

Thomas Wong
R N Robertson Building
 +61 2 6125 3078 (Office)

Profile

Biography

After I received PhD in Bioinformatics from the Department of Computer Science at the University of Hong Kong, I worked as a post-doctoral fellow in the same university for more than one year and was involved in development of SOAP3 that uses Graphical Processing Unit technology for paralleling the task of aligning short reads of DNA to genomes. Then I came to Canberra and worked as a post-doctoral fellow at CSIRO for three years. I was focusing on modelling the non-stationary evolutionary processes across lineages and across sites for a phylogenetic tree. I am glad to join ANU in 2016 and continue the research on phylogenomic area.

Research

Research interests

My research interest is mainly on the methodologies in phylogenomic area. Due to my Computer Science background, I am interested in developing methodologies and software. My favourite programming language is C++.

Projects
1. Modelling non-stationary evolutionary processes across lineages and across sites
2. Evolutionary analysis on short reads

Publications

S. Kalyaanamoorthy*, B. Q. Minh*, T. K. F. Wong*, A. von Haeseler, L. S. Jermiin, “ModelFinder: fast model selection for accurate phylogenetic estimates”, Nature Methods, 14: 587-589, 2017.

W. T. Tay, T. K. Walsh, S. Downes, C. Anderson, L. S. Jermiin, T. K. F. Wong, M. C. Piper, E. S. Chang, I. B. Macedo, C. Czepak, G. T. Behere, P. Silvie, M,. F. Soria, M. Frayssinet, K. H. J. Gordon, “Mitochondrial DNA and trade data support multiple origins of Helicoverpa armigera (Lepidoptera, Noctuidae) in Brazil”, Scientific Reports, 7: 45302, 2017.

B. Misof, S. Liu, K. Meusemann, R. S. Peters, A. Donath, C. Mayer, P. B. Frandsen, J. Ware, T. Flouri, R. G. Beutel, O. Niehuis, M. Petersen, F. Izquierdo-Carrasco, T. Wappler, J. Rust, A. J. Aberer, U. Aspock, H. Aspock, D. Bartel, A. Blanke, S. Berger, A. Bohm, T. R. Buckley, B. Calcott, J. Chen, F. Friedrich, M. Fukui, M. Fujita, C. Greve, P. Grobe, S. Gu, Y. Huang, L. S. Jermiin, A. Y. Kawahara, L. Krogmann, M. Kubiak, R. Lanfear, H. Letsch, Y. Li, Z. Li, J. Li, H. Lu, R. Machida, Y. Mashimo, P. Kapli, D. D. McKenna, G. Meng, Y. Nakagaki, J. L. Navarrete-Heredia, M. Ott, Y. Ou, G. Pass, L. Podsiadlowski, H. Pohl, B. M. von Reumont, K. Schutte, K. Sekiya, S. Shimizu, A. Slipinski, A. Stamatakis, W. Song, X. Su, N. U. Szucsich, M. Tan, X. Tan, M. Tang, J. Tang, G. Timelthaler, S. Tomizuka, M. Trautwein, X. Tong, T. Uchifune, M. G. Walzl, B. M. Wiegmann, J. Wilbrandt, B. Wipfler, T. K. F. Wong, Q. Wu, G. Wu, Y. Xie, S. Yang, Q. Yang, D. K. Yeates, K. Yoshizawa, Q. Zhang, R. Zhang, W. Zhang, Y. Zhang, J. Zhao, C. Zhou, L. Zhou, T. Ziesmann, S. Zou, Y. Li, X. Xu, Y. Zhang, H. Yang, J. Wang, J. Wang, K. M. Kjer, and X. Zhou, “Phylogenomics resolves the timing and pattern of insect evolution”, Science, 346: 763-767, 2014.

V. Jayaswal, T. K. F. Wong, J. Robinson, L. Poladian, and L. S. Jermiin, “Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages”, Systematic Biology, 63: 726-742, 2014.

X. Hu, T. K. F. Wong, Z. J. Lu, T. F. Chan, T. C. K. Lau, S. M. Yiu, and K. Y. Yip, “Computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data”, Bioinformatics, 30: 1049-1055, 2014.

R. Luo*, T. Wong*, J. Zhu*, C. M. Liu*, X. Zhu, E. Wu, L. K. Lee, H. Lin, W. Zhu, and D. W. Cheung, “SOAP3-dp: fast, accurate and sensitive GPU-based short read aligner”, PloS one, 8: e65632, 2013.

T. K. F. Wong, and S. M. Yiu, “Structural alignment of RNA with triple helix structure”, Journal of Computational Biology, 19: 365-378, 2012.

T. K. F. Wong, Y. Chiu, T. W. Lam, and S. M. Yiu, “Memory efficient algorithms for structural alignment of RNAs with pseudoknots”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9: 161-168, 2012.

C. Ma, T. K. F. Wong, T. W. Lam, W. K. Hon, K. Sadakane, and S. M. Yiu, “An Efficient Alignment Algorithm for Searching Simple Pseudoknots over Long Genomic Sequence”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9: 1629-1638, 2012.

C. M. Liu*, T. Wong*, E. Wu, R. Luo, S. M. Yiu, Y. Li, B. Wang, C. Yu, X. Chu, K. Zhao, R. Li, T. W. Lam, “SOAP3: Ultra-fast GPU-based parallel alignment tool for short reads”, Bioinformatics, 28: 878-879, 2012.

T. K. F. Wong, B. W. Y. Cheung, T. W. Lam, and S. M. Yiu, “Local structural alignment of RNA with affine gap model”, BMC proceedings, 5: S2, 2011.

T. K. F. Wong, K. L. Wan, B. Y. Hsu, B. W. Cheung, W. K. Hon, T. W. Lam, and S. M. Yiu, “RNASAlign: RNA structural alignment system”, Bioinformatics, 27: 2151-2152, 2011.

T. K. F. Wong, T. W. Lam, W. K. Sung, B. W. Cheung, and S. M. Yiu, “Structural alignment of RNA with complex pseudoknot structure”, Journal of Computational Biology, 18: 97-108, 2011.

T. K. F. Wong, and S.M. Yiu, "Structural Alignment of RNAs with Pseudoknots”, Handbook of Research on Computational and Systems Biology: Interdisciplinary Applications, L. Limin Angela, W. Dongqing, L. Yixue and L. Huimin, eds., pp. 550-571, Hershey, PA, USA: IGI Global, 2011.

T. K. F. Wong, T. W. Lam, S. M. Yiu, and S. C. Wong, “Improving the accuracy of signal transduction pathway construction using level-2 neighbours”, International journal of bioinformatics research and applications, 6: 542-555, 2010.

T. K. F. Wong, T. W. Lam, W. K. Sung, and S. M. Yiu, “Adjacent nucleotide dependence in ncRNA and order-1 SCFG for ncRNA identification”, PloS one, 5: e12848, 2010.

Y. Jia*, T. K. F. Wong*, Y. Q. Song, S. M. Yiu, and D. K. Smith, “Refining orthologue groups at the transcript level”, BMC genomics, 11: S11, 2010.

T. K. F. Wong, T. W. Lam, P. Chan, and S. M. Yiu, “Correcting short reads with high error rates for improved sequencing result”, International journal of bioinformatics research and applications, 5: 224-237, 2009.

W. Yang, P. Ng, M. Zhao, T. K. F. Wong, S. M. Yiu, and Y. L. Lau, “Promoter-sharing by different genes in human genome–CPNE1 and RBM12 gene pair as an example”, BMC genomics, 9: 456, 2008.

T. K. F. Wong, T. W. Lam, W. Yang, and S. M. Yiu, “Finding alternative splicing patterns with strong support from expressed sequences on individual exons/introns”, Journal of bioinformatics and computational biology, 6: 1021-1033, 2008.

* Joint first authors

Updated:  24 April 2019/Responsible Officer:  Director RSB/Page Contact:  Webmaster RSB