Liqing Zhang

Assistant Professor

Research Interests

• Evolutionary and Comparative Genomics: Compare genomes to infer evolutionary events and forces shaping the genomes, with a special interest on the evolution of duplicated genes in both primary sequences and function.
• Population Genomics: Develop poplation genetic models that incorporate the non-indepedence of mutations with different fitness effect to understand the evolution of genomes.
• Computational Biology: Develop open source software and online databases for analyzing high throughput data.

Teaching

• CS2204: Unix
• CS3824: Introduction to Computational Biology and Bioinformatics
• CS4984: Introduction to Computation Biology
• CS5045: Computation for Life Science
• CS6824: Genome Bioinformatics

Education

• 1997 B.S. Biochemistry, Lanzhou University China
• 2002 Ph.D. Molecular Evolution, University California, Irvine
• 2004 Postdoc, University of Chicago
• 2004 Assistant Professor, Virginia Tech

Publication

• M. Lawson, L. Heath, N. Ramakrishnam, and L.Q.Zhang. Using boosting to increase the power of predicting gene conversion. submitted.
• Deng Pan and Liqing Zhang. Burst of young retrogenes and independent retrogene formation in mammals. submitted.
• Deng Pan and Liqing Zhang. Tandemly Arrayed Genes in Vertebrate Genomes. submitted.
• Zhang, L.Q. and L.T. Watson. Analysis of the Fitness Effect of Compensatory Mutations. submitted.
• Kuan Yang and Liqing Zhang. Performance comparison of gene family clustering methods with expert-curated gene family dataset in Arabidopsis thaliana. Planta. DOI: 10.1007/s00425-008-0748-7
• C.Sanna, W.H.Li and L.Q.Zhang. Overlapping genes in the Human and Mouse Genomes. BMC Genomics. 2008. 9:169
• Kuan Yang and Liqing Zhang. Performance Comparison between k-tuple Distance and Four Model-based Distances in Phylogenetic Tree Reconstruction. Nucleic acids research.
• Liqing Zhang. Adaptive Evolution and Frequent Gene Conversion in the Brain Expressed X-linked (BEX) Gene Family in Mammals. Biochemical Genetics.
• M. Lawson and L.Q. Zhang. Housekeeping and tissue-specific genes differ in simple sequence repeats in the 5′-UTR region. Gene. 2008. 407: 54-62
• Valia Shoja, T. M. Murali, and Liqing Zhang. Expression Divergence of Tandemly Arrayed Genes in Human and Mouse. Comparative and Functional Genomics.
• Zhang, L.Q. and L.T. Watson. Note on the Computation of Critical Effective Population Sizes. Journal of Computational Biology. 2007. 14: 950-960
• D. Pan and L.Q. Zhang. Quantifying the major mechanisms of recent gene duplications in the human and mouse genomes: a novel strategy to estimate gene duplication rates. Genome Biology 2007, 8:R158
• M. Lawson and L.Q. Zhang. The Identification of Antisense Gene Pairs through Available Software. ISBRA 2007. LNBI 4463,372-381.
• V. Shoja and L.Q. Zhang. A roadmap of tandemly arrayed genes in the three mammalian genomes. Molecular Biology and Evolution 23, 2006, pp. 2134- 2141.
• M. Lawson and L.Q. Zhang. Distinct patterns of SSR distribution in the Arabidopsis thaliana and Rice genomes. Genome Biology, 2006, pp. R14.
• Zhang, L.Q. and W.H. Li. 2005. Human SNPs Reveal No Evidence of Frequent Positive Selection. Molecular Biology and Evolution 22:2504-2507.
• Zhang, L.Q., H. Lu, W-Y, Chung, J. Yang and W.H.Li. 2005. Patterns of segmental duplications in the human genome. 22:135-141
• Zhang, L. Q. and W.H. Li. 2004. Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Molecular Biology and Evolution 21:236-239.
• Zhang, L. Q. and B. S. Gaut. 2003. Recombination rates shape the distribution and evolution of tandemly arrayed genes in Arabidopsis thaliana. Genome Research 13: 2533-2540.
• Zhang, L. Q., T. Vision and B. S. Gaut. 2002. Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana. Molecular Biology and Evolution 19:1464-1473.
• Zhang, L. Q., A. S. Peek, D. Dunams and B. S. Gaut. 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 162:851-860.
• Zhang, L. Q., B. S. Gaut and T. Vision. 2001. The evolution of duplicated genes. Science 293: 1551.
• Zhang, L. Q., S. K. Pond and B. S. Gaut. 2001. A survey of the molecular evolutionary dynamics of twenty-five multigene families from four grass taxa. Journal of Molecular Evolution. 52: 144-156.

OPEN POSITIONS

I am looking for students with strong mathematical background who are interested in Bioinformatics.