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Shiu, S.-H. and W.H. Li (2004) Origins, lineage-specific expansions, and multiple

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241. Tan, Y., A. D. Yoder, N. Yamashita and W.-H. Li (2005) Evidence from opsin genes
243. Prachumwat, A. and W.-H. Li (2006) Protein function, connectivity, and duplicability in
246. Byrnes, J. K., G. P. Morris and W.-H. Li (2006) Reorganization of adjacent gene

219. Shiu, S.-H. and W.H. Li (2004) Origins, lineage-specific expansions, and multiple

losses of tyrosine kinases in eukaryotes. Mol. Biol. Evol. 21:828-840.

220. Yu, N., M. I. Jensen-Seaman, L. Chemnick, O. Ryder and W.-H. Li (2004) Nucleotide

diversity in gorillas. Genetics 166:1375-1383.
221. Shiu, S.-H., W. M. Karlowski, R. Pan, Y.-H. Tzeng, K. F. X. Mayer, and W.H. Li

(2004) Comparative analysis of the receptor-like kinase family. The Plant Cell 16:

1220-1234.
222. Gu, Z., S. A. Rifkin, K. P. White, and W.H. Li (2004) Duplicate genes increase gene

expression diversity within and between Species. Nat. Genet. 36, 577 – 579. PMID:

15122255

223. Chen, H.-C., H.-C. Lee, T.-Y. Lin, W.H. Li and B.- S. Chen (2004) Quantitative

characterization of the transcriptional regulatory network in the yeast cell cycle.

Bioinformatics 20:1914-1927.

224. Marland, E., A. Prachumwat, N. Maltsev, Z. Gu, and W.H. Li (2004) Higher gene

duplicabilities for metabolic proteins than for non-metabolic proteins in yeast and E.

coli. J. Mol. Evol. 59:806-814.
225. Yang, J. and W.H. Li (2004) Developmental constraint on gene duplicability in fruit

flies and nematodes. Gene 340:237-240.
226. Zhang, P., W. Min and W.H. Li (2004) Different age distribution patterns of human,

nematode and Arabidopsis duplicate genes. Gene 342: 263-268.
227. Tzeng, Y-H, R. Pan and W.H. Li (2004) Comparison of three methods for estimating

rates of synonymous and non-synonymous nucleotide substitutions. Mol. Biol. Evol.

21:2290-2298.
228. Qin, H., W.-B Wu, J. M. Comeron, M. Kreitman and W.-H. Li (2004) Intragenic

Spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes.

Genetics 168: 2245-2260.
229. Wang, D., M. Hsieh and W.H. Li (2005) A General tendency for conservation of

protein length across eukaryotic kingdoms. Mol. Biol. Evol. 22:142-147.

230. Zhang, L., H. H.S. Lu, W.-Y. Chung, J. Yang and W.-H. Li (2005) Patterns of

segmental duplications in the human genome. Mol. Biol. Evol. 22: 135-141.
231. Oakley, T. H., Z. Gu, E. Abouheif, N. H. Patel and W.-H. Li (2005) Comparative

methods for the analysis of gene expression evolution: An example of using yeast

functional genomic data. Mol. Biol. Evol. 22:40-50.
232. Chen, T.-M., C.-C. Lu and W.H. Li (2005) Prediction of splice sites with dependency

graphs and their expanded Bayesian networks. Bioinformatics 21:471-482.

233. 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.
234. 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.

235. 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.

236. Ponger, L. and W.-H. Li (2005) Evolutionary diversification of DNA

methyltransferases in eukaryotic genomes. Mol. Biol. Evol. 22:1119-1128.
237. Yang, J., A. Su and W.H. Li (2005) Gene expression evolves faster in narrowly than

in broadly expressed mammalian genes. Mol. Biol. Evol. 22:2113-2118.

238. Shiu, S.-H., M-C. Shih, and W.H. Li (2005) Transcription factor families have much

higher expansion rates in plants than in animals. Plant Physiology 139:18-26.

239. Tsai, H.K, H. H.-S. Lu and W.-H. Li (2005) Statistical methods for identifying yeast

cell cycle transcription factors. Proc. Natl. Acad. Sci. USA. 102:13532-13537.
240. Zhang, L. and W.-H. Li (2005) Human SNPs reveal no evidence of frequent positive

selection. Mol. Biol. Evol. 22:2504-2507.

241. 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-

14716.

242. Lin, L. H., H. C. Lee, W. H. Li and B. S. Chen (2005) Dynamic modeling and gene

expression prediction for cis regulatory circuits via cross gene-identification. BMC

Bioinformatics 6:258 (17 pages). PMID: 16232312

243. Prachumwat, A. and W.-H. Li (2006) Protein function, connectivity, and duplicability in

yeast. Mol. Biol. Evol. 23:30-39. PMID: 16120800

244. Shiu, S.-H., J. K. Byrnes, R. Pan, P. Zhang and W.-H. Li (2006) Role of positive

selection in the retention of duplicate genes in mammalian genomes. Proc. Natl.

Acad. Sci. USA. 103: 2232-2236.

245. 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.

246. Byrnes, J. K., G. P. Morris and W.-H. Li (2006) Reorganization of adjacent gene

relationships in yeast genomes by whole genome duplication and gene deletion. Mol.

Biol. Evol. 23:1136-1143.

247. Tsai, H.-K., G.T.-W. Huang, M.-Y. Chou, H. H.-S. Lu and W.-H. Li (2006) Method for

identifying transcription factor binding sites in yeast. Bioinformatics 22:1675-1681. PMID: 16644789

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

385:50-56.

249. Zhongming Zhao, Z. Y. Yu, Y.-X. Fu, and W.-H. Li (2006) Nucleotide variation and

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