Gane Ka-Shu Wong Research Group

Contact

Departments of Medicine and Biological Sciences
University of Alberta

4-126 Katz Group Centre for Pharmacy and Health Research
University of Alberta
Edmonton AB, T6G 2E1
Phone: (780) 492-8663
Fax: (780) 492-2475
gane@ualberta.ca

Professor Department of Biological Sciences and the Department of Medicine, AITF/iCORE Strategic Chair
University of Alberta, Edmonton, AB

Dr. Wong got his Ph.D. in experimental low temperature physics from Cornell University in 1990. After a few years at the California Institute of Technology he was recruited to the Human Genome Project (HGP) by Maynard Olson at the University of Washington. As the project reached its crescendo in the late 1990’s, he accepted an invitation from Jian Wang, Huanming Yang, and Jun Yu to help launch what eventually became BGI-Shenzhen. In 2007 he returned home to Canada, and specifically to the University of Alberta, where he is now a Professor in Biological Sciences, a Professor in Medicine, and the iCORE Chair in Biosystems Informatics. From this position he has launched two new programs: one to sequence the transcriptomes of 1000 plants, and another to develop methodologies to detect novel infectious agents in chronic human diseases.


Relevant Publications

C. Sayou, M. Monniaux, M.H. Nanao, E. Moyroud, S.F. Brockington, E. Thévenon, H. Chahtane, N. Warthmann, M. Melkonian, Y. Zhang, et al. IN PRESS. A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity. Science.

S. Sveinsson, J. McDill, G.K. Wong, J. Li, X. Li, M.K. Deyholos, Q. Cronk. IN PRESS. Phylogenetic pinpointing of a paleopolyploidy event within the flax genus (Linum) using transcriptomics. Ann. Bot.

Z. Lin, A. Farooqui, G. Li, G.K. Wong, A.L. Mason, D. Banner, A.A. Kelvin, D.J. Kelvin, A.J. León. IN PRESS. Next-generation sequencing and bioinformatic approaches to detect and analyze influenza virus in ferrets. J. Infect. Dev. Ctries.

C.J. Rothfels, A. Larsson, F.W. Li, E.M. Sigel, L. Huiet, D.O. Burge, M. Ruhsam, S.W. Graham, D.W. Stevenson, G.K. Wong, et al. Oct 2013. Transcriptome-mining for single-copy nuclear markers in ferns. PLoS One 8: e76957. PMID: 24116189

J. Koehbach, A.F. Attah, A. Berger, R. Hellinger, T.M. Kutchan, E.J. Carpenter, M. Rolf, M.A. Sonibare, J.O. Moody, G.K. Wong, et al. Sep 2013. Cyclotide discovery in Gentianales revisited – identification and characterization of cyclic cystine-knot peptides and their phylogenetic distribution in Rubiaceae plants. Biopolymers 100: 438-452. PMID: 23897543

X. Qi, A.S. Chanderbali, G.K. Wong, D.E. Soltis, P.S. Soltis. Jul 2013. Phylogeny and evolutionary history of glycogen synthase kinase 3/SHAGGY-like kinase genes in land plants. BMC Evol. Biol. 13: 143. PMID: 23834366

J. Law, J. Jovel, J. Patterson, G. Ford, S. O’Keefe, W. Wang, B. Meng, D. Song, Y. Zhang, Z. Tian, … A.L. Mason, G.K. Wong. Apr 2013. Identification of hepatotropic viruses from plasma using deep sequencing: a next generation diagnostic tool. PLoS One 8: e60595. PMID: 23613733

M.T. Johnson, E.J. Carpenter, Z. Tian, R. Bruskiewich, J.N. Burris, C.T. Carrigan, M.W. Chase, N.D. Clarke, S. Covshoff, C.W. dePamphilis, … G.K. Wong. Nov 2012. Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. PLoS One 7: e50226. PMID: 23185583

J.A. Tuszynski, T.J. Craddock, J.Y. Mane, K. Barakat, C.Y. Tseng, M. Gajewski, P. Winter, L. Alisaraie, J. Patterson, E. Carpenter, … G.K. Wong. Nov 2012. Modeling the yew tree tubulin and a comparison of its interaction with paclitaxel to human tubulin. Pharm. Res. 29: 3007-3021. PMID: 22833053

Z. Wang, N. Hobson, L. Galindo, S. Zhu, D. Shi, J. McDill, L. Yang, S. Hawkins, G. Neutelings, R. Datla, … G.K. Wong, J. Wang, M.K. Deyholos. Nov 2012. The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads. The Plant J. 72: 461-473. PMID: 22757964

Y. Jiao, J. Leebens-Mack, S. Ayyampalayam, J.E. Bowers, M.R. McKain, J. McNeal, M. Rolf, D.R. Ruzicka, E. Wafula, N.J. Wickett, et al. Jan 2012. A genome triplication associated with early diversification of the core eudicots. Genome Biol. 13: R3. PMID: 22280555

J. Wang, J. Zhang, R. Li, H. Zheng, J. Li, Y. Zhang, H. Li, P. Ni, S. Li, S. Li, … J. Yu, G.K. Wong. Dec 2010. Evolutionary transients in the rice transcriptome. Genomics Proteomics Bioinformatics 8: 211-228. PMID: 21382590

R. Li, W. Fan, G. Tian, H. Zhu, L. He, J. Cai, Q. Huang, Q. Cai, B. Li, Y .Bai, et al. Jan 2010. The sequence and de novo assembly of the giant panda genome. Nature 463: 311-317. [Cover Story] [F1000 Score 3] PMID: 20010809

J. Li, Z. Zhang, S. Vang, J. Yu, G.K. Wong, J. Wang. Apr 2009. Correlation between Ka/Ks and Ks is related to substitution model and evolutionary lineage. J. Mol. Evol. 68: 414-423. PMID: 19308632

M.A. Groenen, P. Wahlberg, M. Foglio, H.H. Cheng, H.J. Megens, R.P. Crooijmans, F. Besnier, M. Lathrop, W.M. Muir, G.K. Wong, et al. Mar 2009. A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate. Genome Res. 19: 510-519. PMID: 19088305

W.M. Muir, G.K. Wong, Y. Zhang, J. Wang, M.A. Groenen, R.P. Crooijmans, H.J. Megens, H. Zhang, R. Okimoto, A. Vereijken, et al. Nov 2008. Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds. Proc. Natl. Acad. Sci. USA 105: 17312-17317. PMID: 18981413

J. Wang, W. Wang, R. Li, Y. Li, G. Tian, L. Goodman, W. Fan, J. Zhang, J. Li, J. Zhang, et al. Nov 2008. The diploid genome sequence of an Asian individual. Nature 456: 60-65. [Cover Story] [F1000 Score 1] PMID: 18987735

A.L. Mason, K. Doucette, G.K. Wong. Aug 2008. Metagenomics and the case of the deadly hamster. Hepatology 48: 679-683. PMID: 18666226

W.M. Muir, G.K. Wong, Y. Zhang, J. Wang, M.A. Groenen, R.P. Crooijmans, H.J. Megens, H.M. Zhang, J.C. McKay, S. McLeod, et al. Jun 2008. Review of the initial validation and characterization of a 3K chicken SNP array. World’s Poultry Science Journal 64: 219-226. PMID: unavailable

H.S. Hayden, W. Gillett, C. Saenphimmachak, R. Lim, Y. Zhou, M.A. Jacobs, J. Chang, L. Rohmer, D.A. D’Argenio, A. Palmieri, et al. Jun 2008. Large-insert genome analysis technology detects structural variation in Pseudomonas aeruginosa clinical strains from cystic fibrosis patients. Genomics 91: 530–537. PMID: 18445516

S. Xu, T. Clark, H. Zheng, S. Vang, R. Li, G.K. Wong, J. Wang, X. Zheng. Feb 2008. Gene conversion in the rice genome. BMC Genomics 9: 93. PMID: 18298833

A.G. Clark, M.B. Eisen, D.R. Smith, C.M. Bergman, B. Oliver, T.A. Markow, T.C. Kaufman, M. Kellis, W. Gelbart, V.N. Iyer, et al. Nov 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218. [Cover Story] PMID: 17994087

H. Li, L. Guan, T. Liu, Y. Guo, W.M. Zheng, G.K. Wong, J. Wang. Sep 2007. A cross-species alignment tool (CAT). BMC Bioinformatics 8: 349. PMID: 17880681

H.M. Zhang, L.D. Bacon, M. Heidari, W.M. Muir, M.A. Groenen, Y. Zhang, G.K. Wong, J.E. Fulton, N.P. O’Sullivan, G.A. Albers, et al. Aug 2007. Genetic variation at the tumour virus B locus in commercial and laboratory chicken populations assessed by a medium-throughput or a high-throughput assay. Avian Pathol. 36: 283-291. PMID: 17620174

J. Yu, G.K. Wong, S. Liu, J. Wang, H. Yang. Jun 2007. A comprehensive crop genome research project: the Superhybrid Rice Genome Project in China. Philos. Trans. R. Soc. Lond. B Biol. Sci. 362: 1023-1034. PMID: 17331896

G. Zhang, H. Wang, J. Shi, X. Wang, H. Zheng, G.K. Wong, T. Clark, W. Wang, J. Wang, L. Kang. Apr 2007. Identification and characterization of insect-specific proteins by genome data analysis. BMC Genomics 8: 93. PMID: 17407609

Z. Zhang, J. Li, X.Q. Zhao, J. Wang, G.K. Wong, J. Yu. Nov 2006. KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics Proteomics Bioinformatics 4: 259-263. PMID: 17531802

W. Wang, H. Zheng, C. Fan, J. Li, J. Shi, Z. Cai, G. Zhang, D. Liu, J. Zhang, S. Vang, et al. Aug 2006. High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell 18: 1791-1802. [F1000 Score 4] PMID: 16829590

J. Yu, P. Ni, G.K. Wong. Aug 2006. Comparing the whole-genome-shotgun and map-based sequences of the rice genome. Trends Plant Sci. 11: 387-391. PMID: 16843033

D.M. Muzny, S.E. Scherer, R. Kaul, J. Wang, J. Yu, R. Sudbrak, C.J. Buhay, R. Chen, A. Cree, Y. Ding, et al. Apr 2006. The DNA sequence, annotation and analysis of human chromosome 3. Nature 440: 1194-1198. PMID: 16641997

H. Li, A. Coghlan, J. Ruan, L.J. Coin, J.K. Heriche, L. Osmotherly, R. Li, T. Liu, Z. Zhang, L. Bolund, et al. Jan 2006. TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res. 34: D572-D580. PMID: 16381935

R. Li, J. Ye, S. Li, J. Wang, Y. Han, C. Ye, J. Wang, H. Yang, J. Yu, G.K. Wong, J. Wang. Sep 2005. ReAS: recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun. PLoS Comput. Biol. 1: e43. [F1000 Score 1] PMID: 16184192

L. Ma, C. Chen, X. Liu, Y. Jiao, N. Su, L. Li, X. Wang, M. Cao, N. Sun, X. Zhang, et al. Sep 2005. A microarray analysis of the rice transcriptome and its comparison to Arabidopsis. Genome Res. 15: 1274-1283. [F1000 Score 1] PMID: 16140994

W. Wang, H. Zheng, S. Yang, H. Yu, J. Li, H. Jiang, J. Su, L. Yang, J. Zhang, J. McDermott, … G.K. Wong, J. Wang. Sep 2005. Origin and evolution of new exons in rodents. Genome Res. 15: 1258-1264. [F1000 Score 1] PMID: 16109974

R. Wernersson, M.H. Schierup, F.G. Jorgensen, J. Gorodkin, F. Panitz, H.H. Staerfeldt, O.F. Christensen, T. Mailund, H. Hornshoj, A. Klein, et al. May 2005. Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. BMC Genomics 6: 70. PMID: 15885146

J. Yu and G.K. Wong. Feb 2005. Genome biology: the second modern synthesis. Genomics Proteomics Bioinformatics 3: 3-4. PMID: 16144517

J. Yu, J. Wang, W. Lin, S. Li, H. Li, J. Zhou, P. Ni, W. Dong, S. Hu, C. Zeng, … G.K. Wong, H. Yang. Feb 2005. The genomes of Oryza sativa: a history of duplications. PLoS Biol. 3: e38. [Cover Story] [F1000 Score 6] PMID: 15685292

J. Wang, Q. Xia, X. He, M. Dai, J. Ruan, J. Chen, G. Yu, H. Yuan, Y. Hu, R. Li, et al. Jan 2005. SilkDB: a knowledgebase for silkworm biology and genomics. Nucleic Acids Res. 33: D399-D402. PMID: 15608225

J. Wang, X. He, J. Ruan, M. Dai, J. Chen, Y. Zhang, Y. Hu, C. Ye, S. Li, L. Cong, et al. Jan 2005. ChickVD: a sequence variation database for the chicken genome. Nucleic Acids Res. 33: D438-D441. PMID: 15608233

Contact

Departments of Medicine and Biological Sciences
University of Alberta

4-126 Katz Group Centre for Pharmacy and Health Research
University of Alberta
Edmonton AB, T6G 2E1
Phone: (780) 492-8663
Fax: (780) 492-2475
gane@ualberta.ca

Team Members

Eric John Carpenter
Glenn Ford
Jordan Dacey Lee Patterson
Sandra Lynn O'Keefe
Tracy Nicole Jordan
Troy Anthony Mitchell
Weiwei Wang, PhD