Our goals are to develop methods for statistical analyses of DNA sequence data and to understand the mechanisms of DNA evolution.
The specific aims are: l. To examine current methods and develop new methods for estimating evolutionary dates, which is now a central issue in molecular evolution. We shall use the new methods to study divergence dates in mammals, which have recently become very controversial. 2. To develop methods for estimating selection intensities in different regions of a gene and to carry out statistical analyses of DNA sequence data from mammals. 3. To develop fast algorithms for finding optimal trees for the following methods: maximum likelihood, maximum parsimony, and minimum evolution. Such algorithms are much needed because these methods require a tremendous amount of computer time-and are not feasible for large trees. 4. An expert system for choosing the best tree reconstruction method for a data set according to the attributes of the data. 5. To introduce the neural network approach into phylogenetic study; this approach has proved extremely powerful in many branches of science and engineering.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Method to Extend Research in Time (MERIT) Award (R37)
Project #
5R37GM030998-18
Application #
6385455
Study Section
Genetics Study Section (GEN)
Program Officer
Eckstrand, Irene A
Project Start
1982-07-01
Project End
2005-03-31
Budget Start
2001-04-01
Budget End
2002-03-31
Support Year
18
Fiscal Year
2001
Total Cost
$161,792
Indirect Cost
Name
University of Chicago
Department
Biology
Type
Schools of Medicine
DUNS #
225410919
City
Chicago
State
IL
Country
United States
Zip Code
60637
Ha, Misook; Hong, Soondo; Li, Wen-Hsiung (2013) Predicting the probability of H3K4me3 occupation at a base pair from the genome sequence context. Bioinformatics 29:1199-205
Tseng, Yan Yuan; Li, Wen-Hsiung (2012) Classification of protein functional surfaces using structural characteristics. Proc Natl Acad Sci U S A 109:1170-5
Rest, Joshua S; Bullaughey, Kevin; Morris, Geoffrey P et al. (2012) Contribution of transcription factor binding site motif variants to condition-specific gene expression patterns in budding yeast. PLoS One 7:e32274
Woo, Yong H; Li, Wen-Hsiung (2012) Evolutionary conservation of histone modifications in mammals. Mol Biol Evol 29:1757-67
Lin, Zhenguo; Li, Wen-Hsiung (2012) Evolution of 5' untranslated region length and gene expression reprogramming in yeasts. Mol Biol Evol 29:81-9
Lin, Zhenguo; Li, Wen-Hsiung (2011) Expansion of hexose transporter genes was associated with the evolution of aerobic fermentation in yeasts. Mol Biol Evol 28:131-42
Chen, Sean Chun-Chang; Chuang, Trees-Juen; Li, Wen-Hsiung (2011) The relationships among microRNA regulation, intrinsically disordered regions, and other indicators of protein evolutionary rate. Mol Biol Evol 28:2513-20
Tseng, Yan Yuan; Li, Wen-Hsiung (2011) Evolutionary approach to predicting the binding site residues of a protein from its primary sequence. Proc Natl Acad Sci U S A 108:5313-8
Woo, Yong H; Li, Wen-Hsiung (2011) Gene clustering pattern, promoter architecture, and gene expression stability in eukaryotic genomes. Proc Natl Acad Sci U S A 108:3306-11
Ha, Misook; Ng, Danny W-K; Li, Wen-Hsiung et al. (2011) Coordinated histone modifications are associated with gene expression variation within and between species. Genome Res 21:590-8

Showing the most recent 10 out of 120 publications