Liqing Zhang Assistant Professor Department of Computer Science Virginia Tech Blacksburg, VA 24061 Email: lqzhang (at vt dot edu) Phone: (540) 231-9413 Fax: (540) 231-6075 Office: 2160K Torgersen Hall

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. We are currently developing a program for detecting gene conversions using machine learning approach. Together with Tao Jiang at UCR, we are also working on developing a high-throughput approach to assign orthologs based on genome rearrangement and on understanding the evolutionary history of duplicated genes (NSF IIS: Collaborative research: Jiang & Zhang). See the project website for details.

Teaching

• CS2204: Unix
• CS3824: Introduction to Computational Biology and Bioinformatics
• CS4114: Introduction to Formal Languages and Automata Theory
• CS4984: Introduction to Computation Biology
• CS5045: Computation for Life Science
• CS6824: Advanced Topics in Computational Biology and Bioinformatics

Education

• B.S. Biochemistry, Lanzhou University China
• Ph.D. Molecular Evolution, University California, Irvine, with Dr. Brandon S. Gaut
• Postdoc, University of Chicago, with Dr. Wen-Hsiung Li
• Assistant Professor, Virginia Tech

Journal Publications

• Lawson, M.J. and L.Q. Zhang. Sexy gene conversions: Locating gene conversions on the X-chromosome. Nucleic Acid Research In press, 2009, 1-10. Link
• Pan, D. and L.Q. Zhang. Burst of young retrogenes and independent retrogene formation in mammals. PLoS ONE 4, 2009, 1-19. Link
• Huang, W. H., P. Wang, Z. Liu, L. Q. Zhang. Identifying disease associations via genome-wide association studies. BMC Bioinformatics 10, 2009, 1-11. Link
• Zhang, L.Q. and L.T. Watson. Analysis of the fitness effect of compensatory mutations. HFSP J 3, 2009, 47-54. Link
• Pan, D. and L.Q. Zhang. Tandemly arrayed genes in vertebrate genomes. Comparative and Functional Genomics 2008, 2008, 1-11. Link
• Yang, K. and L.Q. Zhang. Performance comparison of gene family clustering methods with expert-curated gene family dataset in Arabidopsis thaliana. Planta 228, 2008, 439-447. Link
• Sanna, C., W.H. Li, and L.Q. Zhang. Overlapping genes in the human and mouse genomes. BMC Genomics 9, 2008, 1-10. Link
• Yang, K. and L.Q. Zhang. Performance comparison between k-tuple distance and four model-based distances in phylogenetic tree reconstruction. Nucleic Acids Research 36, 2008, 1-9. Link
• Lawson, M.J. and L.Q. Zhang. Housekeeping and tissue-specific genes differ in simple sequence repeats in the 5’-UTR region. Gene 407, 2008, 54-62. Link
• Zhang, L.Q. Adaptive evolution and frequent gene conversion in the brain expressed X-linked (BEX) gene family in mammals. Biochemical Genetics 46, 2008, 293- 311. Link
• Zhang, L.Q. and L. T. Watson. Note on the computation of critical effective population sizes. Journal of Computational Biology 14, 2007, 950-960. Link
• Pan, D. 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 8, 2007, 1-11. Link
• Shoja, V., T. M. Murali, and L.Q. Zhang. Expression divergence of tandemly arrayed genes in human and mouse. Comparative and Functional Genomics 2007, 2007, 1-8. Link
• Shoja, V. and L.Q. Zhang. A roadmap of tandemly arrayed genes in the three mammalian genomes. Molecular Biology and Evolution 23, 2006, 2134-2141. Link
• Lawson, M.J. and L.Q. Zhang. Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes. Genome Biology 7, 2006, 1-11. Link
• Zhang, L.Q. and W.H. Li. Human SNPs reveal no evidence of frequent positive selection. Molecular Biology and Evolution 22, 2005, 2504-2507. Link
• Zhang, L.Q., H. Lu, W-Y. Chung, J. Yang, and W.H. Li. Patterns of segmental duplications in the human genome. Molecular Biology and Evolution 22, 2005, 135-141. Link
• Zhang, L.Q. andW.H. Li. Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Molecular Biology and Evolution 21, 2004, 236–239. Link
• Zhang, L.Q. and B.S. Gaut. Does recombination shape the distribution and evolution of tandemly arrayed genes (TAGs) in the Arabidopsis thaliana genome? Genome Research 13, 2003, 2533–2540. Link
• Zhang, L.Q., T. Vision and B.S. Gaut. Patterns of nucleotide substitution among simultaneously duplicated gene pairs in Arabidopsis thaliana. Molecular Biology and Evolution 19, 2002, 1464–1473. Link
• Zhang, L.Q., 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 162, 2002, 851–860. Link
• Zhang, L.Q., B.S. Gaut and T. Vision. The evolution of duplicated genes. Science 293, 2001, 1551-1552. Link
• Zhang, L.Q., S.K. Pond and B.S. Gaut. A survey of the molecular evolutionary dynamics of twenty-five multigene families from four grass taxa. Journal of Molecular Evolution 52, 2001, 144–156.
Link

Peer-reviewed Conference Publications

• Shi, G., L.Q. Zhang, and T. Jiang. MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement. Computational Systems Biology (CSB) Conference 2009.
• Huang, W. H., P. Wang, Z. Liu, L. Q. Zhang. Identifying disease associations via genome-wide association studies. Proceedings for the 7th Asia Pacific Bioinformatics Conference, 2009, 729–737.
• Lawson, M. J., L. Heath, N. Ramakrishnam, and L.Q. Zhang. Using cost-sensitive learning to determine gene conversions. LNCS Advanced Intelligent Computing Theories and Applications, 2008, 1030-1038.
• Huang, W. and L.Q. Zhang. A novel framework to understand the mechanism of toxicity. LNCS Advanced Intelligent Computing Theories and Applications, 2008, 996-1003.
• Pang, D. and L.Q.Zhang. A Holistic View of Evolutionary Rates in Paralogous and Orthologous Genes. LNCS Advanced Intelligent Computing Theories and Applications, 2008, 967–974.
• M. Lawson and L.Q. Zhang. The Identification of Antisense Gene Pairs through Available Software. ISBRA 2007. LNBI 4463,372-381.

Students and Postdocs

Current

• Mark Lawson, 5th year PhD student.
• Dan Qiao, 1st year PhD student.
• David Beck, 4th year student.
• Wenhui Huang, 3rd year PhD student.

Former

• Deng Pan, postdoc, now at the University of Chicago.
• Valia Shoja
• Chaitanya Sanna

Summer Students and Interns

• Shuhbi Mishra
• Shilpa Nadimpalli
• Ioana Oriana Bercea

Open Position

A NSF-funded postdoc position is immediately available. Details here.

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