Developing realistic models for DNA and protein evolution. Specifically I study to model site-specific substitution heterogeneity with empirical amino acid frequency profile mixture models (such as class frequency model cF4 and posterior mean site frequencies PMSF). Previously I also studied the covarion and other heterotachy models of molecular rate evolution across the phylogeny.
Building software tools for phylogenetic
inference. I have developed PROCOV for covarion modeling and QmmRAxML
for frequency profile mixture model.
Detecting functional shift and divergence of protein families, and protein adaptation in the light of covarion evolution.
Investigating nucleotide compositional bias, patterns of codon usage and amino acid usage as well as the adaptation of the genomes to the environment.
By doing comparative analyses of whole genome sequences, gene expression data, genome features and life styles of different organisms, I hope to address fundamental biological questions such as genome expansion and reduction, host-parasite interaction, the adaptation to different ecological niches, and ultimately improve our understanding of genome evolution and biodiversity.
1. Wang HC, Susko E., Minh BQ. & Roger AJ. (2018) Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation. Systematic Biology 67:216-235
2. Wang HC, Susko E. & Roger AJ. (2016). Split-specific bootstrap measures for quantifying phylogenetic stability and the influence of taxon selection. Molecular Phylogenetics and Evolution 105:114-125
3. Wang HC, Wu J. & Tang P-H. (1989) Superfamily expands. Nature (London) 337: 514
4. Wang HC, Susko E. & Roger AJ. (2014) An amino acid substitution-selection model adjusts residue fitness to improve phylogenetic estimation. Molecular Biology and Evolution 31: 779-792
5. Wang HC, Susko E. & Roger AJ. (2013) The site-likelihood score is a good predictor of genes under positive selection. Journal of Molecular Evolution 76: 280-294
6. Wang HC, Susko E. & Roger AJ. (2011) Fast statistical tests for detecting heterotachy in protein evolution. Molecular Biology and Evolution 28: 2305-2315
7. Wang HC, Susko E. & Roger AJ. (2009) PROCOV: maximum likelihood estimation of phylogeny under covarion models and site-specific covarion pattern analysis. BMC Evolutionary Biology 9: 225
8. Wang HC, Li K., Susko E. & Roger AJ. (2008) A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny. BMC Evolutionary Biology 8: 331 (featured in BMC Evol. Biol. and )
9. Wang HC, Susko E, Spencer M & Roger AJ. (2008) Topological Estimation Biases with Covarion Evolution. Journal of Molecular Evolution 66: 50-60
10. Wang HC, Spencer M, Susko E & Roger AJ. (2007) Testing for Covarion-like Evolution in Protein Sequences. Molecular Biology and Evolution 24: 294-305
11. Wang HC & Hickey DA. (2007) Rapid Divergence of Codon Usage Patterns within the Rice Genome. BMC Evolutionary Biology 7 (Suppl. 1):S6, 1-10
12. Wang HC, Susko E & Roger AJ. (2006) On the Correlation between Genomic G+C Content and Optimal Growth Temperature in Prokaryotes: Data Quality and Confounding Factors. Biochemical and Biophysical Research Communications 342: 681-684
13. Wang HC, Xia X & Hickey DA. (2006) Thermal Adaptation of the Small Subunit Ribosomal RNA Gene: a Comparative Study. Journal of Molecular Evolution 63: 120-126
14. Xia X, Wang HC, Carullo M, Huang H, Xie Z & Hickey D. (2006) Cytosine Usage Modulates the Correlation between CDS Length and CG Content in Prokaryotic Genomes. Molecular Biology and Evolution 23: 1450-1454
15. Wang HC, Singer GAC & Hickey DA. (2004) Mutational Bias Affects Protein Evolution in Flowering Plants. Molecular Biology and Evolution 21: 90-96 (evaluated at Faculty of 1000 Biology for new hypothesis and findings)
16. Wang HC & Hickey DA (2002) Evidence for Strong Selective Constraint Acting on the Nucleotide Composition of 16S Ribosomal RNA Genes. Nucleic Acids Research 30: 2501-2507
17. Wang HC, Badger J, Kearney P& Li M. (2001) Analysis of Codon Usage Patterns of Bacterial Genomes Using the Self-organizing Map. Molecular Biology and Evolution 18: 792-800
18. Wang HC, Dopazo J, Fraga LG, Zhu Y-P & Carazo JM. (1998) Self-organizing Tree Growing Network for the Classification of Protein Sequences. Protein Science 7: 2613-2622
19. Wang HC, Dopazo J & Carazo JM. (1998) Self-organizing Tree Growing Network for Classifying Amino Acids. Bioinformatics 14: 376-377
20. Trelles O, Ceron C, Wang HC, Dopazo J & Carazo JM. (1998) New Phylogenetic Venues Opened by a Novel Implementation of the DNAml Algorithm. Bioinformatics 14: 544-545
21. Dopazo J, Wang HC & Carazo JM. (1997) A New Type of Unsupervised Growing Neural Network for Biological Sequence Classification that Adopts the Topology of a Phylogenetic Tree. Lecture Notes in Computer Science 1240: 932-941
22. Wang HC. (1996) Re-analysis of DNA Sequence Data from a Dinosaur Egg Fossil Found in Xixia of Henan Province. Journal of Genetics and Genomics 23: 183-189
23. Yin Z, Chen H, Wang Z, Zhang Z, Zou Y, Fang X & Wang HC. (1996) Sequence analysis of cytochrome b gene fragment in a dinosaur egg. J. Genetics and Genomics 23:190-195
24. Wang HC. (1996) Internet Tools for Retrieval, Display and Modeling of Protein Tertiary Structures. Bulletin of Chinese Academy of Medical Sciences 20 (3): 64-67
25. Wang HC, Xia Y & He Y. (1996) Rapid Identification of Protein through its Amino Acid Composition. Acta Biochimica et Biophysica Sinica 28: 293-299
26. Wang HC. (1995) Electronic Communication and Sequence Analysis. Progress in Biochemistry and Biophysics 22: 317-322
27. Wang HC (1994) Is the Rice Antifungal Protein a Trypsin Inhabitor? China High Technology Letters 4 (8): 44-46
28. Wang HC & He Y. (1994) PPS: a Computer Program for Searching Protein Motifs Based on the PROSITE Database. China High Technology Letters 4: 30-33
29. Zhu Y-X, Lai C, Wang J, Ji Y, Wang HC & Bai Y. (1993) Human Myeloperoxidase Gene cDNA Cloning and Expression in Acute Leukaemia. Chinese J. Biotechnology 9: 27-32
30. Wang HC, Wu J-J, Zhu Y-X & Wang J-X. (1992) A Pair of Computer Programs for Polymerase Chain Reaction (PCR) Primer Design. Chinese Biochemical Journal 8: 342-346
31. Wang HC. (1992) An Immunoglobulin Switch-like Sequence Found in Epstein-Barr Virus Genome. Bulletin of Chinese Academy of Medical Sciences 16: 32-36
32. Wang HC, Wu J-J & Tang P-H. (1991) Pattern Match Analysis for Searching Ig-like Domains. Chinese Biochemical Journal 7: 249-256
33. Wang HC, Wu J-J, Bai Y. & Tang P-H. (1991) BARF-1 and EC-LF4 Encoded by the Epstein-Barr Virus Genome are Structurally Homologous with Immunoglobulin. Chinese Biochemical Journal 7: 371-380
34. Wang HC. (1991) Structure, Function and Evolution of Immunoglobulin Gene Superfamily. Progress in Physiological Sciences 22: 225-230
35. Wu J-J & Wang HC. (1990) Searching Protein Sequence Database with Domain Patterns. Bulletin of Chinese Academy of Medical Sciences 14: 297-301
Books and book chapters (not peer-reviewed)
36. Xia Y, Lei E & Wang HC. (eds.), Internet: Practical Techniques and Biomedical Applications. AMMS Press, Beijing, 1997
37. Wang HC. Essentials of Sequence Analysis. Renmin Junyi Medical Press, Beijing, 1994.
38. Wang HC. The Development of a software package for polymerase chain reaction primer design and analysis. pp. 261-279. In Li J-T & Lin W-M (eds): Current Status and Future of Clinical Medical Molecular Microbiology. Chinese Science & Technology Press, Beijing, 1993.
39. Wang HC. Computer assisted PCR primer design. pp. 562-567. in Zhu P. (ed): Laboratory Manual for PCR Gene Amplifications. Chinese Science & Technology Press, Beijing, 1992.
Selected conference presentations, invited talks and seminars
1. Fleming S, Cooke C, Liu Y, Wang HC. (2018). Opioid misuse analytics in Nova Scotia. A poster presentation at CADTH Symposium Halifax, April 2018; full paper to be submitted for publication
2. Wang HC. Quantifying the stability of phylogenetic trees. Mathematics Colloquium, Dept. of Mathematics and Statistics, Dalhousie University, Oct. 27 2014
3. Wang HC, Susko E. & Roger AJ. An amino acid substitution-selection model adjusts residue fitness to improve phylogenetic estimation. Models and Algorithms for Genome Evolution. Bromont, Quebec, Canada, Aug. 23-26 2013 (poster)
4. Wang HC. Modeling Heterogeneous Processes of Protein Evolution for Inferring Phylogenies. Joint Math/Statistics Colloquium, Dept. of Mathematics and Statistics, Dalhousie University, Feb 6, 2012
5. Wang HC, Susko E & Roger AJ. A Model-based Approach for Detecting Covarion Positions in a Protein Family. SMBE annual meeting, Iowa city, June 3-7 2009 (oral presentation). Recipient of a competitive travel grant ($1000) from the Society of Molecular Biology and Evolution for postdoctoral fellow attending the meeting.
6. Wang HC, Susko E & Roger AJ. QmmRAxML: a New Phylogenetic Program Implementing Site-specific Amino Acid Frequencies Model for Phylogenetic Inference. Protist 2008 conference, Halifax, July 21-26, 2008 (oral presentation)
7. Wang HC, Susko E & Roger AJ. Does covarion evolution cause problems for phylogeny estimation? SMBE Annual meeting, Halifax, June 24-28 2007 (oral presentation)
8. Wang HC. Nucleotide Compositional Bias and Thermal Adaptation in Prokaryotes. Invited talk at Institute of Bioengineering, Academy of Medical Sciences, Beijing, August 9 2006
9. Wang HC, Susko E & Roger AJ. On the Correlation between Genomic G+C Content and Optimal Growth Temperature in Prokaryotes: Data Quality and Confounding Factors. Canadian Phylogenomics Conference, Sainte-Adele, Quebec, 2006 (poster)
10. Wang HC, Spencer M, Susko E & Roger AJ. Testing Covarion-like Evolution in Protein Sequences. CIAR Evolutionary Biology Program Annual Meeting, Vancouver Island, 2005.
11. Wang HC. Genome Base Composition, Growth Temperature and Life Style in Prokaryotes. Genomics Symposium, Dalhousie University. April 18, 2005 (oral presentation)
12. Wang HC. Is Genomic G+C Content Correlated with Growth Temperature? TIGR International Conference on Microbial Genomes, Halifax, Canada, April 14-16, 2005 (poster)
13. Wang HC. The Effects of DNA Compositional Bias on Genome Evolution. Statistics Colloquium, Dept. of Mathematics and Statistics, Dalhousie University, Feb. 10 2005
14. Wang HC, & Hickey DA. Nucleotide Composition of Ribosomal RNA Genes and Thermal Adaptation. 12th International Conference on Intelligent Systems for Molecular Biology, Glasgow, UK, July 31- Aug. 4., 2004 (poster)
15. Wang HC. Graphical Methods for Codon Usage Pattern Analysis. Proceedings of the MITACS Quebec Interchange, Montreal, Nov. 13-14 2003
16. Wang HC, Singer G & Hickey DA. Nucleotide Bias Affects Amino Acid Composition in Angiosperms. 10th International Conference on Intelligent Systems for Molecular Biology, Edmonton, Canada, Aug. 3-7., 2002 (poster)
17. Wang HC & Hickey DA. Evidence for Strong Selective Constraint Acting on the Nucleotide Composition of 16S Ribosomal RNA Genes. BioNorth 2001, Ottawa, Nov. 5-7, 2001 (poster)
18. Wang HC. Analysis of Codon Usage Patterns of Bacterial Genomes. 1st China National Bioinformatics Conference, Beijing, April 20-22, 2001 (oral presentation)
19. Wang HC. Protein Sequence Analysis with Neural Network Methods. Invited talk at University of Waterloo Bioinformatics Day. Waterloo, Nov. 2 1998