Abstract

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.

  Funding Agency

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 #
5R37GM030998-20
Application #
6635877
Study Section
Genetics Study Section (GEN)
Program Officer
Eckstrand, Irene A
Project Start
1982-07-01
Project End
2005-03-31
Budget Start
2003-04-01
Budget End
2004-03-31
Support Year
20
Fiscal Year
2003
Total Cost
$161,792
Indirect Cost

  Institution

Name
University of Chicago
Department
Biology
Type
Schools of Medicine
DUNS #
005421136
City
Chicago
State
IL
Country
United States
Zip Code
60637

  Publications

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
Yun, Jieun; Frankenberger, Casey A; Kuo, Wen-Liang et al. (2011) Signalling pathway for RKIP and Let-7 regulates and predicts metastatic breast cancer. EMBO J 30:4500-14
Lin, Zhenguo; Li, Wen-Hsiung (2011) The evolution of aerobic fermentation in Schizosaccharomyces pombe was associated with regulatory reprogramming but not nucleosome reorganization. Mol Biol Evol 28:1407-13
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

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