个人简介

Ph.D. (Doctor of Philosophy)

研究领域

Genomics Proteomics and Bioinformatics

Substantial analytical and computational challenges impede effective exploitation of the massive genomic data sets being generated by next-generation DNA sequencing technologies. To help overcome these impediments, my laboratory is developing novel bioinformatics approaches for the scalable, high-throughput, simulataneous analysis of many genomes using model-based statistical inference. We are particularly interested in bringing modelling advances in molecular evolution and comparative genomics to bear on interpreting personal genomic variation in humans. Areas of current research include: 1. Enabling Next Generation Computational Genomics. Novel computational techniques for large-scale genomic inference and analysis. Development of more realistic models of sequence evolution under complex functional constraints. GPU-accelerated algorithms. 2. Personal, Medical, and Population Genomics of Humans. Predicting the functional consequences and clinical significance of mutations in individual human genomes. Objective experimental design for exome/genome sequencing studies. The ancient genetic changes that "made us human". 3. Genomics of Extraordinary Phenotypes in Non-Human Species. Genetic origins of extraordinary phenotypes in non-human species, with emphasis on those having biomedical significance to humans. Genomics of adaptive evolution. Inference of selection histories in functional regions.

近期论文

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de Koning APJ, Gu W, Castoe TA, and DD Pollock (2012). Phylogenetics, Likelihood, Evolution, and Complexity. Bioinformatics 28(22): 2989-2990. de Koning APJ, Gu W, Castoe TA, Batzer MA, and DD Pollock (2011). Repetitive elements may comprise over two-thirds of the human genome. PLoS Genetics 7(12): e1002384. Pollock DD, de Koning APJ, Kim H, Castoe TA, Churchill M, and K Kechris (2011). Bayesian analysis of high-throughput quantitative measurement of protein-DNA interactions. PLoS ONE6(11): e26105. Castoe TA, de Koning APJ, Hall KT, Yokoyama KD, Gu W, Smith EN, Feschotte C, Uetz P, Ray DA, Dobry J, Bogden R, Mackessy SP, Bronikowski AM, Warren WC, Secor S, and DD Pollock (2011). Sequencing the genome of the Burmese python (Python molurus bivittatus) - a model for studying extreme adaptations in snakes. Genome Biology 12: 406. de Koning APJ, Gu W, and DD Pollock (2010). Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories. Molecular Biology and Evolution 27(2): 249-65. Castoe TA* / de Koning APJ*, Kim H-K, Gu W, Noonan BP, Jiang ZJ, Naylor G, Parkinson CL, and DD Pollock (2009). Evidence for an ancient adaptive episode of convergent molecular evolution. Proc. Natl. Acad. Sci. USA 106: 8986-8991. [* Authors contributed equally.]