Contact Information
Office Boyer Hall 601A
(310) 825-7374
Lab Boyer Hall 609
(310) 794-4026
Short bio

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.

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Honors & Rewards

  • 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

Selected Publications


Lu H, Lin L, Sato S, Xing Y, Lee CJ
Predicting functional alternative splicing by measuring RNA selection pressure from multigenome alignments.

PLoS Comput. Biol.. Dec 2009. 5(12):e1000608. 2009 PMID: 20019791
| PMC2784930 | 10.1371/journal.pcbi.1000608


Wang Q, Barr I, Guo F, Lee C
Evidence of a novel RNA secondary structure in the coding region of HIV-1 pol gene.

RNA. Dec 2008. 14(12):2478-88. 2008 PMID: 18974280
| PMC2590956 | 10.1261/rna.1252608

Roy M, Kim N, Xing Y, Lee C
The effect of intron length on exon creation ratios during the evolution of mammalian genomes.

RNA. Nov 2008. 14(11):2261-73. 2008 PMID: 18796579
| PMC2578852 | 10.1261/rna.1024908

Kim N, Lee C
Bioinformatics detection of alternative splicing.

Methods Mol. Biol.. 2008. 452:179-97. 2008 PMID: 18566765
| PMC2578852 | 10.1007/978-1-60327-159-2_9

Xing Y, Lee C
Reconstruction of full-length isoforms from splice graphs.

Methods Mol. Biol.. 2008. 452:199-205. 2008 PMID: 18566766
| PMC2578852 | 10.1007/978-1-60327-159-2_10

Parker DS, Hsiao RL, Xing Y, Resch AM, Lee CJ
Solving the problem of Trans-Genomic Query with alignment tables.

IEEE/ACM Trans Comput Biol Bioinform. . 5(3):432-47. 2008 PMID: 18670046
| PMC2578852 | 10.1109/TCBB.2007.1073


Kim N, Lee C
QPRIMER: a quick web-based application for designing conserved PCR primers from multigenome alignments.

Bioinformatics. Sep 2007. 23(17):2331-3. 2007 PMID: 17599926
| PMC2578852 | 10.1093/bioinformatics/btm343

Kim N, Lee C
QPRIMER: a quick web-based application for designing conserved PCR primers from multigenome alignments.

Bioinformatics. Sep 2007. 23(17):2331-3. 2007 PMID: 17599926
| PMC2578852 | 10.1093/bioinformatics/btm343

Alekseyenko AV, Lee CJ
Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases.

Bioinformatics. Jun 2007. 23(11):1386-93. 2007 PMID: 17234640
| PMC2578852 | 10.1093/bioinformatics/btl647

Alekseyenko AV, Kim N, Lee CJ
Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes.

RNA. May 2007. 13(5):661-70. 2007 PMID: 17369312
| PMC1852814 | 10.1261/rna.325107

Kim N, Alekseyenko AV, Roy M, Lee C
The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.

Nucleic Acids Res.. Jan 2007. 35(Database issue):D93-8. 2007 PMID: 17108355
| PMC1669709 | 10.1093/nar/gkl884

Pan C, Kim J, Chen L, Wang Q, Lee C
The HIV positive selection mutation database.

Nucleic Acids Res.. Jan 2007. 35(Database issue):D371-5. 2007 PMID: 17108357
| PMC1669717 | 10.1093/nar/gkl855

Wang Q, Lee C
Distinguishing functional amino acid covariation from background linkage disequilibrium in HIV protease and reverse transcriptase.

PLoS ONE. 2007. 2(8):e814. 2007 PMID: 17726544
| PMC1950573 | 10.1371/journal.pone.0000814

Xing Y, Lee C
Relating alternative splicing to proteome complexity and genome evolution.

Adv. Exp. Med. Biol.. 2007. 623:36-49. 2007 PMID: 18380339
| PMC1950573


Xing Y, Lee C
Alternative splicing and RNA selection pressure–evolutionary consequences for eukaryotic genomes.

Nat. Rev. Genet.. Jul 2006. 7(7):499-509. 2006 PMID: 16770337
| PMC1906840 | 10.1038/nrg1896

Xing Y, Yu T, Wu YN, Roy M, Kim J, Lee C
An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs.

Nucleic Acids Res.. 2006. 34(10):3150-60. 2006 PMID: 16757580
| PMC1475746 | 10.1093/nar/gkl396