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Comparative
Genomics and Evolution
Instructor: Xun Gu
Lectures: TR 3:40 - 5:00, MBB 1424. Web Page: http://xgu.zool.iastate.edu Grading 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.
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