For a complex trait, the pedigree-based llinkage analysis is effective for localizing disease-related genes to within 1cM. Fine-mapping of the disease mutation within this region is often achieved by linkage disequilibrium analysis using haplotypes. Haplotypes can also be very useful for stratifying patients and directing drugs to appropriate subpopulation. The discovery of human single nucleotides polymorphism (SNP) as genetic marker's greatly increases the density of the genetic map and enhances our ability in developing novel disease diagnostic tools and individualized drug therapies. However, with 1.65 million human SNPs single nucleotides polymorphism (SNP) markers identified, the haplotype determination and analysis present a daunting challenge to scientists. The general goal of this research is to advance our computational capability for both the construction of population haplotypes and the utilization of the whole haplotype information in LD mapping.
The specific aims of the proposed research are (a) to propose more efficient and scalable computational strategies for haplotype determination, (b) to demonstrate that in silico approaches to haplotype determinations are effective and economical alternatives to experimental ones, (c) to establish a computational platform that allows for a direct output of haplotypes from high-throughput genotyping readouts, and (d) to design a Bayesian framework for simultaneous haplotype determination, LD mapping, and patients clustering.
| Hu, Ming; Deng, Ke; Qin, Zhaohui et al. (2013) Understanding spatial organizations of chromosomes via statistical analysis of Hi-C data. Quant Biol 1:156-174 |
| Zhong, Wenxuan; Zhang, Tingting; Zhu, Yu et al. (2012) CORRELATION PURSUIT: FORWARD STEPWISE VARIABLE SELECTION FOR INDEX MODELS. J R Stat Soc Series B Stat Methodol 74:849-870 |
| Balaji, Sentil; Mcclendon, Charles; Chowdhary, Rajesh et al. (2012) IMID: integrated molecular interaction database. Bioinformatics 28:747-9 |
| Zhang, Yu; Jiang, Bo; Zhu, Jun et al. (2011) Bayesian models for detecting epistatic interactions from genetic data. Ann Hum Genet 75:183-93 |
| Bell, Lindsey; Chowdhary, Rajesh; Liu, Jun S et al. (2011) Integrated bio-entity network: a system for biological knowledge discovery. PLoS One 6:e21474 |
| Zhang, Jing; Hou, Tingjun; Wang, Wei et al. (2010) Detecting and understanding combinatorial mutation patterns responsible for HIV drug resistance. Proc Natl Acad Sci U S A 107:1321-6 |
| Chowdhary, Rajesh; Bajic, Vladimir B; Dong, Difeng et al. (2010) Genome-wide analysis of regions similar to promoters of histone genes. BMC Syst Biol 4 Suppl 1:S4 |
| Zhang, Wei; Zhu, Jun; Schadt, Eric E et al. (2010) A Bayesian partition method for detecting pleiotropic and epistatic eQTL modules. PLoS Comput Biol 6:e1000642 |
| Chowdhary, Rajesh; Zhang, Jinfeng; Liu, Jun S (2009) Bayesian inference of protein-protein interactions from biological literature. Bioinformatics 25:1536-42 |
| Hsu, Yi-Hsiang; Niu, Tianhua; Song, Yiqing et al. (2008) Genetic variants in the UCP2-UCP3 gene cluster and risk of diabetes in the Women's Health Initiative Observational Study. Diabetes 57:1101-7 |
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