Biotech One, Rm 1-114A
Department of Psychiatry (VIPBG)
Virginia Commonwealth University
800 E. Leigh St.
Richmond VA 23219
SNP analysis, DNA polymorphism in human population, Bioinformatics in psychiatric genetics
BBSI project: Sequence context analysis of SNPs in mammalian genomes
Single nucleotide polymorphisms (SNPs) are major genetic variations in genomes and have been widely used in the studies of diseases, molecular evolution and population genetics. Approximately 20 million SNPs are available in the public dbSNP database. The abundant data provide us a great opportunity to investigate the evolutionary patterns of SNPs in mammalian genomes. In this project, we will first examine and compare the sequence context of SNPs in mammalian genomes and in their specific genomic regions such as exonic, promoter and noncoding regions. The second part of the project is to infer the muational spectrum (i.e., muational direction) in the mammalian genome. This project would provide experience in data collection from public databases, large-scale data analyses by programming, and interpretation of the results.
Zhang, F., & Zhao, Z. (2004) The influence of neighboring-nucleotide composition on single nucleotide polymorphisms (SNPs) in the mouse genome and its comparison with human SNPs. Genomics 84:785-795 abstract.
Zhang F., & Zhao, Z. (2005) SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs). Bioinformatics 21:2517-2519
Other research interests
DNA polymorphisms in the worldwide human populations
The distribution and common/unique patterns of DNA polymorphism, genotype and haplotype within and between subpopulations; Neutrality tests of mutation; evolutionary history of human population.
Bioinformatics in psychiatric genetics
Data management of various types of data (microarray, genotype, and phenotype data); Algorithm development for selecting candidate genes or genetic markers; interface implementation; literature/text mining.