Gene Expression and Regulation

Chang YW, Robert Liu FG, Yu N, Sung HM, Yang P, Wang D, Huang CJ, Shih MC, Li WH. (2008) Roles of cis- and trans-changes in the regulatory evolution of genes in the gluconeogenic pathway in yeast. Mol Biol Evol. In press

Liang H, Lin YS, Li WH. Fast evolution of core promoters in primate genomes. (2008) Mol Biol Evol. 25(6):1239-44.

Chen CY, Tsai HK, Hsu CM, May Chen MJ, Hung HG, Huang GT, Li WH. (2008) Discovering gapped binding sites of yeast transcription factors. Proc Natl Acad Sci U S A. 2008 105(7):2527-32.

Lin LH, Lee HC, Li WH, Chen BS. A systematic approach to detecting transcription factors in response to environmental stresses.(2007) BMC Bioinformatics 8(1):473

Lin, YC, Hsieh, LC, Kuo, MW, Yu J, Kuo HH, Lo WL, Lin RJ, Yu AL, Li WH. (2007) Human TRIM71 and its nematode homologue are targets of let-7 microRNA and its zebrafish orthologue is essential for development. Mol Biol Evol. 24(11):2525-34.

Liang, H. and W.-H. Li (2007) MicroRNA regulation of human protein-protein interaction network. RNA 14(9): 1402-1408

Wu, W-S, W.-H. Li, and B.-S. Chen (2007) Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data. BMC Bioinformatics 8: 188.

Wu, W-S, W.-H. Li, and B.-S. Chen (2007) Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics 7: 421.

Wang, D., H.-M. Sung, T.-Y. Wang, C.-J. Huang, P. Yang, T. Chang, Y.-C. Wang, D.-L. Tseng, J.-P Wu, T.-S. Lee, M.-C. Shih  and W.-H. Li (2007) Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors. Genome Res.17(8): 1161-1169.

Saunders, M.A*., H. Liang*, and W.-H. Li (2007) Human polymorphism at microRNAs and microRNA target sites. Proc. Natl. Acad. Sci. USA. 104: 3300-3305. [*equally contributed]

Ha, M., W.-H. Li and Z. J. Chen (2007) External factors accelerate expression divergence between duplicate genes. Trends Genet. 23:162-166.

Kim, J., S.-H. Shiu, S. Thoma, W.-H. Li and S. Patterson (2006) Patterns of expansion and expression divergence in the plant polygalacturonase gene family. Genome Biology, 7:R87.

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.

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.

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.

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.

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.

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.

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.

Zhang, L. and W.-H. Li (2004) Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Mol. Biol. Evol. 21:236-239.

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