个人简介

Prof. Lee has been a Faculty member in the Department of Chemistry and Biochemistry since 1998. His training provided an unusual combination of experimental cell biology, biophysics, and algorithm development, which he has applied at UCLA to bioinformatics analysis of genome evolution. He has led efforts to establish a bioinformatics Ph.D. program at UCLA. He has served on the Board of Scientific Counselors, NIH National Center for Biotechnology Information, and serves on the editorial board of Biology Direct . His current research focuses on alternative splicing and its role in genome evolution.

研究领域

Biochemistry/Biophysics/Structural and Computational Biology/Proteomics and Bioinformatics/Theory

alternative splicing and genome evolution: genome-wide analysis of the types and functions of alternative splicing, and its apparent role in evolution of mammalian genomes. Alternative splicing appears to have greatly accelerated major evolutionary events such as exon creation, and now is an exciting new area of research in genome evolution. protein evolutionary pathways. Using a massive dataset of clinical HIV sequences, we have developed new methods to decode the evolutionary pathways by which HIV evolves drug resistance. We have just shown that our methods can measure the detailed "fitness landscape" describing how HIV proteins can evolve, as a kinetic network showing the actual rate of evolution along every possible evolutionary pathway. graph databases for bioinformatics and genomics. We have developed a general framework for working with genomic data as an abstract graph database, for fundamental problems such as multiple genome alignment query and protein interaction network analysis.

近期论文

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Lu Hongchao, Lin Lan, Sato Seiko, Xing Yi, Lee Christopher J Predicting functional alternative splicing by measuring RNA selection pressure from multigenome alignments. PLoS computational biology, 2009; 5(12): e1000608. Kim Namshin, Lee Christopher Bioinformatics detection of alternative splicing. Methods Mol. Biol., 2008; 452(1): 179-97. Wang Qi, Barr Ian, Guo Feng, Lee Christopher Evidence of a novel RNA secondary structure in the coding region of HIV-1 pol gene. RNA (New York, N.Y.), 2008; 14(12): 2478-88. Parker Douglass Stott, Hsiao Ruey-Lung, Xing Yi, Resch Alissa M, Lee Christopher J Solving the problem of Trans-Genomic Query with alignment tables. IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, 2008; 5(3): 432-47. Roy Meenakshi, Kim Namshin, Xing Yi, Lee Christopher The effect of intron length on exon creation ratios during the evolution of mammalian genomes. RNA (New York, N.Y.), 2008; 14(11): 2261-73. Wang Qi, Lee Christopher Distinguishing functional amino acid covariation from background linkage disequilibrium in HIV protease and reverse transcriptase. PLoS ONE, 2007; 2(8): e814. Alekseyenko Alexander V, Kim Namshin, Lee Christopher J Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes. RNA, 2007; 13(5): 661-70. Alekseyenko Alexander V, Lee Christopher J Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases. Bioinformatics, 2007; 23(11): 1386-93. Kim Namshin, Lee Christopher QPRIMER: a quick web-based application for designing conserved PCR primers from multigenome alignments. Bioinformatics, 2007; 23(17): 2331-3. Xing Yi, Lee Christopher Relating alternative splicing to proteome complexity and genome evolution. Adv. Exp. Med. Biol., 2007; 623(2): 36-49