Wen-Hsiung Li

My major interest is in the processes and mechanisms of molecular and genomic evolution. We conduct both experimental and theoretical studies. Current projects include: I. Evolution of gene regulation. Although regulatory evolution has been prosed 40 years to play a major role in morphological evolution and may account for the conspicuous morphological differences between humans and chimps, this topic has not been well studied, mainly because of experimental difficulties. This issue can now be pursued in detail, thanks to advances in molecular biology and genomics. We are now using both microarrays and real time PCR to study the evolution of gene regulation in yeast strains and species. We choose yeast because it is easy to manipulate and because it is well known in genetics, functional genomics, and proteomics. Our major question is whether evolution of gene regulation is mainly due to changes in cis elements or to changes in trans elements. We are also pursuing this issue in other eukaryotes, analyzing available gene expression data (mainly microarray data) and genomic sequence data. II. Evolution of duplicate genes. We study how duplicate genes diverge in expression and function and what factors determine the survival of duplicate genes in evolution. III. Development of statistical methods and statistical analysis of genomic data. The huge amount of genomic data is a tremendous resource for understanding the organization and evolution of genomes. We have been developing tools for comparative genomics and data mining and have been conducting systematic analyses of sequence and functional genomic data.

My major interest is in the processes and mechanisms of molecular and genomic evolution. We conduct both experimental and theoretical studies. Current projects include: I. Evolution of gene regulation. Although regulatory evolution has been prosed 40 years to play a major role in morphological evolution and may account for the conspicuous morphological differences between humans and chimps, this topic has not been well studied, mainly because of experimental difficulties. This issue can now be pursued in detail, thanks to advances in molecular biology and genomics. We are now using both microarrays and real time PCR to study the evolution of gene regulation in yeast strains and species. We choose yeast because it is easy to manipulate and because it is well known in genetics, functional genomics, and proteomics. Our major question is whether evolution of gene regulation is mainly due to changes in cis elements or to changes in trans elements. We are also pursuing this issue in other eukaryotes, analyzing available gene expression data (mainly microarray data) and genomic sequence data. II. Evolution of duplicate genes. We study how duplicate genes diverge in expression and function and what factors determine the survival of duplicate genes in evolution. III. Development of statistical methods and statistical analysis of genomic data....

Li, W.H., J. Yang and X. Gu (2005) Expression divergence between duplicate genes. Trends Genet. 21:620-607.  

Liang, H. and W.-H. Li (2007) Gene essentiality, gene duplicability and protein connectivity in human and mouse. Trends in Genetics 23: 375-378.  

Liang, H. and W.-H. Li (2007) MicroRNA regulation of human protein-protein interaction network. RNA 13:1402-1408. 46: 494-496. 

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  

Prachumwat, A. and W.-H. Li (2006) Protein function, connectivity, and duplicability in yeast. Mol. Biol. Evol. 23:30-39. Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors. Genome Research 17:1161-1169.  

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.  

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 Research 17:1161-1169.  

Li, W.H., J. Yang and X. Gu (2005) Expression divergence between duplicate genes. Trends Genet. 21:620-607.  

Liang, H. and W.-H. Li (2007) Gene essentiality, gene duplicability and protein connectivity in human and mouse. Trends in Genetics 23: 375-378.  

Liang, H. and W.-H. Li (2007) MicroRNA regulation of human protein-protein interaction network. RNA 13:1402-1408. 46: 494-496. 

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  

Prachumwat, A. and W.-H. Li (2006) Protein function, connectivity, and duplicability in yeast. Mol. Biol. Evol. 23:30-39. Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors. Genome Research 17:1161-1169.