Computational and Evolutionary Genomics
 | URL: http://bioinformatics.cs.vt.edu/~zhanglab Contact: Liqing Zhang We analyze genomes to infer interesting evolutionary events, with a focus on the divergence of duplicated genes in both primary sequences and function. We develop methods to analyze the human SNPs (single nucleotide polymorphisms) to understand the associations between different genetic diseases. We also develop open source software and online databases for analyzing high throughput data. We are currently developing a program for detecting gene conversion (non-reciprocal transfer of genetic information from one sequence to another) using machine learning approach. |
2008
"Housekeeping and tissue-specific genes differ in simple sequence repeats in the 5'-UTR region.",
Gene, vol. 407, no. 1-2, pp. 54-62, 2008.
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"Performance comparison between k-tuple distance and four model-based distances in phylogenetic tree reconstruction.",
Nucleic Acids Res, vol. 36, no. 5, pp. e33, 2008.
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"Performance comparison of gene family clustering methods with expert curated gene family data set in Arabidopsis thaliana.",
Planta, vol. 228, no. 3, pp. 439-47, 2008.
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"Overlapping genes in the human and mouse genomes.",
BMC Genomics, vol. 9, pp. 169, 2008.
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"Adaptive Evolution and Frequent Gene Conversion in the Brain Expressed X-Linked Gene Family in Mammals.",
Biochem Genet, 2008.
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2007
"Expression Divergence of Tandemly Arrayed Genes in Human and Mouse",
Comparative and Functional Genomics, vol. 2007, pp. Article ID 60964, 8 pages, 2007.
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"Expression divergence of tandemly arrayed genes in human and mouse.",
Comp Funct Genomics, pp. 60964, 2007.
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"Note on the computation of critical effective population sizes.",
J Comput Biol, vol. 14, no. 7, pp. 950-60, 2007.
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"Quantifying the major mechanisms of recent gene duplications in the human and mouse genomes: a novel strategy to estimate gene duplication rates.",
Genome Biol, vol. 8, no. 8, pp. R158, 2007.
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2006
"Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes.",
Genome Biol, vol. 7, no. 2, pp. R14, 2006.
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"A roadmap of tandemly arrayed genes in the genomes of human, mouse, and rat.",
Mol Biol Evol, vol. 23, no. 11, pp. 2134-41, 2006.
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2005
"Patterns of segmental duplication in the human genome.",
Mol Biol Evol, vol. 22, no. 1, pp. 135-41, 2005.
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"Human SNPs reveal no evidence of frequent positive selection.",
Mol Biol Evol, vol. 22, no. 12, pp. 2504-7, 2005.
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2004
"Mammalian housekeeping genes evolve more slowly than tissue-specific genes.",
Mol Biol Evol, vol. 21, no. 2, pp. 236-9, 2004.
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2003
"Does recombination shape the distribution and evolution of tandemly arrayed genes (TAGs) in the Arabidopsis thaliana genome?",
Genome Res, vol. 13, no. 12, pp. 2533-40, 2003.
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2002
"Population genetics of duplicated disease-defense genes, hm1 and hm2, in maize (Zea mays ssp. mays L.) and its wild ancestor (Zea mays ssp. parviglumis).",
Genetics, vol. 162, no. 2, pp. 851-60, 2002.
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"Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana.",
Mol Biol Evol, vol. 19, no. 9, pp. 1464-73, 2002.
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2001
"A survey of the molecular evolutionary dynamics of twenty-five multigene families from four grass taxa.",
J Mol Evol, vol. 52, no. 2, pp. 144-56, 2001.
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"Gene duplication and evolution.",
Science, vol. 293, no. 5535, pp. 1551, 2001.
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