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.
2012
Huang, Y., M. Liu, and L. Zhang, "Gene Selection for Cancer Classification by Multiple PCA with Sparsity", Fourth International Conference on Bioinformatics and Computational Biology (BICoB-2012), Las Vegas, 2012.
2011
Heath, L. S., and N. Ramakrishnan, The Problem Solving Handbook for Computational Biology and Bioinformatics, , Berlin, Springer, pp. 347, 2011.
Zhang, L., L. T. Watson, and L. S. Heath, "A Network of SCOP Hidden Markov Models and Its Analysis", BMC Bioinformatics, vol. 12, pp. 11 pages, 2011.
Lawson, M. J., L. S. Heath, H. Zhao, and L. Zhang, "Optimizing a Cost Matrix to Solve Rare-Class Biological Problems", 2011 International Conference on Bioinformatics and Computational Biology (BIOCOMP'11), Las Vegas, Nevada, 2011.
Zhang, L., L. T. Watson, and L. S. Heath, "A Network of Hidden Markov Models and Its Analysis", 2011 International Conference on Bioinformatics and Computational Biology (BIOCOMP'11), Las Vegas, Nevada, 2011.
Liu, M., Y. Huang, L. Zhang, and D. R. Bevan, "A new functional association-based protein complex prediction", BIBM Workshop, Atlanta, 2011.
Adelman, Zach; Anderson, M.;, M. Liu, L. Zhang, and K. Myles, "Sindbis virus induces the production of a novel class of endogenous siRNAs in Aedes aegypti mosquitoes.", Insect Molecular Biology, 2011.
Egon Urgard, Tnu Vooder, U. V. K. V. M. L., R. R. T. A. J. L. C. F. M. Cheng Luo, Fabian Hoti, L. Zhang, and A. Metspalu, "Metagenes Associated with Survival in Non- Small Cell Lung Cancer", Cancer Informatics, vol. 10, 2011.
Lewis SN, N. E., Q. D. Weeks C, and L. Zhang, "Prediction of Disease and Phenotype Associations from Genome-Wide Association Studies", PLoS ONE, vol. 6, 2011.
2010
Zhang, L., and L. T. Watson, "The expected fitness cost of a mutation fixation under the one-dimensional Fisher model", Internat. J. Pure Appl. Math., vol. 62, pp. 129--150, 2010.
Warren, A., R. Anandakrishnan, and L. Zhang, "Functional bias in molecular evolution rate of Arabidopsis thaliana", BMC Evolutionary Biology, vol. 10, no. 1, pp. 125, 2010. Abstract
Dalloul RA, and L. Zhang, "Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis", PLOS Biology, vol. e1000475, 2010.
Chen, Y. L., Q. Z. Li, and L. Q. Zhang, "Using increment of diversity to predict mitochondrial proteins of malaria parasite: integrating pseudo-amino acid composition and structural alphabet.", Amino Acids, 2010.
2009
Pan, D., and L. Zhang, "An Atlas of the Speed of Copy Number Changes in Animal Gene Families and Its Implications", PLoS ONE, vol. 4, no. 10: Public Library of Science, pp. 13, 2009.
Pan, D., and L. Zhang, "Burst of Young Retrogenes and Independent Retrogene Formation in Mammals", PLOS ONE, 2009.
2008
Lawson, M. J., and L. Zhang, "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. Abstract
Yang, K., and L. Zhang, "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. Abstract
Yang, K., and L. Zhang, "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. Abstract
Sanna, C. R., W. H. Li, and L. Zhang, "Overlapping genes in the human and mouse genomes.", BMC Genomics, vol. 9, pp. 169, 2008. Abstract
Zhang, L., "Adaptive Evolution and Frequent Gene Conversion in the Brain Expressed X-Linked Gene Family in Mammals.", Biochem Genet, 2008. Abstract
2007
Shoja, V., T. M. Murali, and L. Zhang, "Expression Divergence of Tandemly Arrayed Genes in Human and Mouse", Comparative and Functional Genomics, vol. 2007, pp. Article ID 60964, 8 pages, 2007.
Shoja, V., T. M. Murali, and L. Zhang, "Expression divergence of tandemly arrayed genes in human and mouse.", Comp Funct Genomics, pp. 60964, 2007. Abstract
Zhang, L., and L. T. Watson, "Note on the computation of critical effective population sizes.", J Comput Biol, vol. 14, no. 7, pp. 950-60, 2007. Abstract
Pan, D., and L. Zhang, "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. Abstract
2006
Lawson, M. J., and L. Zhang, "Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes.", Genome Biol, vol. 7, no. 2, pp. R14, 2006. Abstract
Shoja, V., and L. Zhang, "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. Abstract
2005
Zhang, L., H. H. Lu, W. Y. Chung, J. Yang, and W. H. Li, "Patterns of segmental duplication in the human genome.", Mol Biol Evol, vol. 22, no. 1, pp. 135-41, 2005. Abstract
Zhang, L., and W. H. Li, "Human SNPs reveal no evidence of frequent positive selection.", Mol Biol Evol, vol. 22, no. 12, pp. 2504-7, 2005. Abstract
2004
Zhang, L., and W. H. Li, "Mammalian housekeeping genes evolve more slowly than tissue-specific genes.", Mol Biol Evol, vol. 21, no. 2, pp. 236-9, 2004. Abstract
2003
Zhang, L., and B. S. Gaut, "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. Abstract
2002
Zhang, L., A. S. Peek, D. Dunams, and B. S. Gaut, "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. Abstract
Zhang, L., T. J. Vision, and B. S. Gaut, "Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana.", Mol Biol Evol, vol. 19, no. 9, pp. 1464-73, 2002. Abstract
2001
Zhang, L., S. K. Pond, and B. S. Gaut, "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. Abstract
Zhang, L., B. S. Gaut, and T. J. Vision, "Gene duplication and evolution.", Science, vol. 293, no. 5535, pp. 1551, 2001.