UCLA Department of Chemistry and Biochemistry : UCLA Portal

Website:

Christopher Lee's Laboratory.

Work Email Address:

leec@chem.ucla.edu

Laboratory Address:

Paul Boyer Hall 609

Work Address:

Paul Boyer Hall 601A
CA

Lab Number:

1 (310) 794-4026

Work Phone Number:

1 (310) 825-7374

Professor
Biochemistry

Member
Biochemistry & Molecular Biology (BMB) Graduate Program, Molecular Biology Institute

A Short Biography:

Professor Lee received a B.A. summa cum laude in Biochemistry and Molecular Biology in 1988 from Harvard College, and a Ph.D. in Structural Biology from Stanford University in 1993. He co-founded Molecular Applications Group with Michael Levitt in 1993, and served as Vice-President for Research until 1998. After completing a postdoctoral fellowship in the Department of Chemistry at Stanford, he joined the UCLA faculty in 1998.

Prof. Lee accepts graduate students through the Biochemistry and Molecular Biology (BMB) Graduate Program and the UCLA ACCESS Ph.D. Program.

Awards and Honors:

Harvard Detur Prize ; MIT Technology Review TR100 Award ; UCLA Apple Workgroup Cluster for Bioinformatics Award ; UCLA Seaborg Award ; Camille and Henry Dreyfus New Faculty Award ; Camille and Henry Dreyfus Teacher-Scholar Award ; Harvard's Thomas Hoopes Prize for Undergraduate Thesis Research ; Phi Beta Kappa Junior Twelve ; Searle Scholar Award ; American Cancer Society Postdoctoral Fellowship ; Howard Hughes Medical Institute Predoctoral Fellowship

Research Interest:

Bioinformatics:

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.

Detailed Biography:

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 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.

Publications:

Kim Namshin, Lee Christopher Bioinformatics detection of alternative splicing. Methods Mol. Biol., 2008; 452(1): 179-97.

Xing Yi, Lee Christopher Reconstruction of full-length isoforms from splice graphs. Methods Mol. Biol., 2008; 452(1): 199-205.

Calarco John A, Xing Yi, CÃ¡ceres Mario, Calarco Joseph P, Xiao Xinshu, Pan Qun, Lee Christopher, Preuss Todd M, Blencowe Benjamin J Global analysis of alternative splicing differences between humans and chimpanzees. Genes Dev., 2007; 21(22): 2963-75.

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.

Kim Namshin, Lee Christopher QPRIMER: a quick web-based application for designing conserved PCR primers from multigenome alignments. Bioinformatics, 2007; 23(17): 2331-3.

Kim Namshin, Lee Christopher Three-Dimensional Phylogeny Explorer: distinguishing paralogs, lateral transfer, and violation of BMC Bioinformatics, 2007; 8(3): 213.

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.

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.

Lee Ji-Ann, Xing Yi, Nguyen David, Xie Jiuyong, Lee Christopher J, Black Douglas L Depolarization and CaM kinase IV modulate NMDA receptor splicing through two essential RNA elements. PLoS Biol., 2007; 5(2): e40.

Xing Yi, Lee Christopher Relating alternative splicing to proteome complexity and genome evolution. Adv. Exp. Med. Biol., 2007; 623(2): 36-49.

Kim Namshin, Alekseyenko Alexander V, Roy Meenakshi, Lee Christopher The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species. Nucleic Acids Res., 2007; 35(Database issue): D93-8.

Pan Calvin, Kim Joseph, Chen Lamei, Wang Qi, Lee Christopher The HIV positive selection mutation database. Nucleic Acids Res., 2007; 35(Database issue): D371-5.

Xing Yi, Lee Christopher Alternative splicing and RNA selection pressure--evolutionary consequences for eukaryotic genomes. Nat. Rev. Genet., 2006; 7(7): 499-509.

Xing Yi, Yu Tianwei, Wu Ying Nian, Roy Meenakshi, Kim Joseph, Lee Christopher An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs. Nucleic Acids Res., 2006; 34(10): 3150-60.