Statistical Methods and Computational Analysis of Genomic Data

Wang H, Tzeng YH, Li WH. Improved variance estimators for one- and two-parameter models of nucleotide substitution. J Theor Biol. In press

Han L, Su B, Li WH, Zhao Z. (2008) CpG island density and its correlations with genomic features in mammalian genomes. Genome Biol. 9(5):R79.

Sanna CR, Li WH, Zhang L. Overlapping genes in the human and mouse genomes. BMC Genomics. 9:169.

Tzeng J, Lu HH, Li WH. (2008) Multidimensional scaling for large genomic data sets. BMC Bioinformatics. 9:179.

Zhang C, Li WH, Krainer AR, Zhang MQ. (2008) RNA landscape of evolution for optimal exon and intron discrimination. Proc Natl Acad Sci U S A.105(15):5797-802.

Hanada, K., S.-H. Shiu, and W.-H. Li  (2007) Comparison of the nonsynonymous/synonymous substitution rate ratio and the radical/conservative replacement rate ratio in the evolution of mammalian genes. Mol. Biol. Evol., 24(10):2235-41.

Jiang, C., L. Han, B. Su, W.-H. Li, and Z. Zhao (2007) Features and trend of loss of promoter-associated CpG islands in the human and mouse Genomes. Mol. Biol. Evol. 24(9):1991-2000.

Tsai, H.-K., M.-Y. Chou, C.-H. Shih, G. Huang, T.-H. Chang and W.-H. Li (2007) MYBS: A comprehensive web server for mining transcription factor binding sites. Nucleic Acid Res. 35(Web Server Issue): W221-226.

Shih, A. C.-C., T.-C. Hsiao, M.-S. Ho and W.-H. Li (2007) Simultaneous amino acid substitutions at antigenic sites drive influenza A hemagglutinin evolution. Proc. Natl. Acad. Sci. USA. 104, 6283-6288.

Lin, Y.-S., Wei-Lun Hsu, J.-K. Hwang, and W.-H. Li (2007) Proportion of solvent-exposed amino acids in a protein and rate of protein evolution. Mol. Biol. Evol. 24:1005-1011

Tzeng, Y.-H. Li, and T.-J. Chuang (2007) Mathematical properties of some measures of evolutionary distance. J. Theoret. Biol. 245:790-792

Hanada, K., X. Zhang, J. O. Borevitz, W.-H. Li , and S.-H. Shiu  (2007) A large number of novel small open reading frames (sORFs) in the intergenic regions of the A. thaliana genome are transcribed or under purifying selection. Genome Res., 17(5): 632-640.

Chen, B.-S., Wan.-S. Wu, Wei.-S. Wu, and W.-H. Li (2007) On the adaptive design rules of biochemical networks in evolution. Evolutionary Bioinformatics 2: 27-39.

Chen, F.-C., C.-J. Chen, W.-H. Li and T.-J. Chuang (2007) Human-specific insertions and deletions inferred from mammalian genome sequences. Genome Res. 17:16-22.

Saunders, M.A., J. M. Good, E. Lawrence, R. Ferrell, W.-H. Li, and M. W. Nachman (2006) Human adaptive evolution at Myostatin, a regulator of muscle growth. Am. J. Hum. Genet. 79:1089-1097.

Hanada, K., T. Gojobori and W.-H. Li (2006)  Radical amino acid change versus positive  selection in the evolution of viral envelope proteins. Gene 385:83-88.

Zhongming Zhao, Z. Y. Yu, Y.-X. Fu,  and W.-H. Li (2006)  Nucleotide variation and haplotype diversity in a 10-kb noncoding region in three continental human populations. Genetics 174:399-409.

Gu, J. and W.-H. Li (2006)  Are GC-rich isochores vanishing in mammals? Gene 385:50-56.

Chen, F.-C., S.-S. Wang, C.-J. Chen, W.-H. Li and T.-J. Chuang (2006) Alternatively and constitutively spliced exons are subject to different evolutionary forces. Mol. Biol. Evol. 23:675-682.

Tan, Y., A. D. Yoder, N. Yamashita and W.-H. Li (2005) Evidence from opsin genes rejects nocturnality in ancestral primates. Proc. Natl. Acad. Sci. USA. 102: 14712-147.

Zhang, L. and W.-H. Li (2005) Human SNPs reveal no evidence of frequent positive selection. Mol. Biol. Evol. 22:2504-2507.

Ponger, L. and W.-H. Li (2005) Evolutionary diversification of DNA methyltransferases in eukaryotic genomes. Mol. Biol. Evol. 22:1119-1128.

Yi, S. and W.-H. Li (2005) Molecular evolution of recombination hotspots and highly recombining pseudoautosomal regions in hominoids. Mol. Biol. Evol. 22:1223-1230.

Chen, B-S, Y-C Wang, W-S Wu and W.H. Li (2005) A new measure of the robustness of biochemical networks. Bioinformatics 21: 2698-2705.

Huang, S.-W., R. Friedman, N. Yu, A. Yu and W.-H. Li (2005)  How strong is the mutagenicity of recombination in mammals? Mol. Biol. Evol. 22: 426-431.