Comparative Genomics and Evolution
BCB/GEN 556 Spring 2005

Instructor: Xun Gu
Office: 322 Science II Hall
Office hour: by appointment

Lectures: TR 3:40 - 5:00, MBB 1424.
Textbook: Molecular Evolution and Phylogenetics (ISBN:0195135857)

Web Page: .

Homework assignments and Discussion (25%)
Term-paper (literature-review) (40%)
Presentation (35%)

Time Schedule

Presentation Schedule:

Apr. 14 No Class.

Apr. 21 Raja Kumar Sankula, Aimin Yan, Scott Emrich.

Apr. 26 Balkz Mertz, Lei Zhu, M. Willkerson.

Apr. 28 Lixia Jin, Yong Huang, M. Serenius, Feihong Wu.

Reading Papers:

[1] A. Nekrutenko, K. Makova, and W. Li(2001) The Ka/Ks Ratio Test for Assessing the Protein-Coding Potential of Genomic Regions: An Empriical and Simulation Study.

[2] J. Zhang, H. Rosenberg, and M. Nei(1998) Positive Darwinian selection after gene duplication in primate ribonuclease genes.

[3] J. Thornton, E. Need, and D. Crews(2003) Resurrecting the Ancestral Steroid Receptor: Ancient Origin of Estrogen Signaling.

[4] G. Golding, and A. Dean(1998) The structural Basis of Molecular Adaptation.

Feb 22,2005

[1] Gu, X (2003) Functional divergence in protein (family) sequence evolution. Genetica 118:133-141.

[2] Gu, X (2001) A site-specific measure for rate-difference after gene duplication or speciation. Mol Biol Evol 18:2327-2330.

[3] Wang Y, Gu X (2001) Predicting functional divergence of caspase gene family. Genetics. 158:1311-1320.

[4] Gu X (1999) Statistical methods for testing functional divergence after gene duplication. Molecular Biology and Evolution 16:1664-1674.

Feb 24,2005

[1] Gu, J, Gu, X (2003) Natural history and functional divergence of protein tyrosine kinases. Gene 317:49-57.

[2] Gaucher EA, Gu X, Miyamoto, M, Benner, S. (2002) Predicting functional divergence in protein evolution by site-specific rate shifts. Trend in Biochemical Sciences (TiBS) 27:315-321.

[3] Gu, J, Wang Y, Gu X (2002) Pattern of Functional divergence in JAK tyrosine protein kinase family. Journal of Molecular Evolution. 54:725-733.

[4] Gu, X, Vander Velden K (2002) DIVERGE: Phylogeny-based Analysis for Functional-Structural Divergence of a Protein Family. Bioinformatics 18:500-501.

Mar 1 & Mar 3,2005

[1] Gu, X*, Zhang, Z., Huang, W. (2005) Rapid Evolution of Expression and Regulatory Divergences after Yeast Gene Duplications. PNAS. 102:707-712.

[2] Gu, X* (2004) Statistical framework for phylogenetic analysis of expression profiles. Genetics 167:531-542.

[3] Gu, Z, Nicolae D, Lu H and Li WH(2002) Rapid divergence in expression between duplicate genes inferred from microarray data.

Mar 10,2005

[1] Gu, J, Gu, X* (2003) Induced gene expression in human brain after the split from chimpanzee. Trend in Genetics 19:63-65.