Lee, Christopher J.

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Structural and Computational Biology
Proteomics and Bioinformatics
Molecular Biology Institute

Contact Information

Boyer Hall 601A
(310) 825-7374
Boyer Hall 609
(310) 794-4026

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 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.

Research Interests


  1. 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.
  2. 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.
  3. 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.


Honors & Awards

  • 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


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