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Christopher John Lee - Publications

Affiliations: 
University of California, Los Angeles University of California, Los Angeles, Los Angeles, CA 
Area:
Biochemistry, Molecular Biology
Website:
http://faculty.chemistry.ucla.edu/institution/personnel?personnel_id=45756
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64 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2013 Lee C, Harper M. Phenotype Sequencing: High-Throughput Discovery of the Genetic Causes of a Phenotype: Mutagenesis combined with DNA sequencing provides a rapid, relatively inexpensive approach for determining the genetic causes of specific phenotypes Microbe Magazine. 8: 321-327. DOI: 10.1128/Microbe.8.321.1  0.345
2012 Harper M, Lee CJ. Genome-wide analysis of mutagenesis bias and context sensitivity of N-methyl-N'-nitro-N-nitrosoguanidine (NTG). Mutation Research. 731: 64-7. PMID 22080106 DOI: 10.1016/J.Mrfmmm.2011.10.011  0.323
2012 Xu Q, Lee C. An analysis of cancer-related alternative splicing through a genomics-based approach. Discovery Medicine. 3: 50-1. PMID 20704866  0.342
2011 Harper MA, Chen Z, Toy T, Machado IM, Nelson SF, Liao JC, Lee CJ. Phenotype sequencing: identifying the genes that cause a phenotype directly from pooled sequencing of independent mutants. Plos One. 6: e16517. PMID 21364744 DOI: 10.1371/Journal.Pone.0016517  0.421
2010 Lee C, Kim N, Roy M, Graveley BR. Massive expansions of Dscam splicing diversity via staggered homologous recombination during arthropod evolution. Rna (New York, N.Y.). 16: 91-105. PMID 19934230 DOI: 10.1261/Rna.1812710  0.349
2009 Lu H, Lin L, Sato S, Xing Y, Lee CJ. Predicting functional alternative splicing by measuring RNA selection pressure from multigenome alignments. Plos Computational Biology. 5: e1000608. PMID 20019791 DOI: 10.1371/Journal.Pcbi.1000608  0.578
2009 Guffanti A, Iacono M, Pelucchi P, Kim N, Soldà G, Croft LJ, Taft RJ, Rizzi E, Askarian-Amiri M, Bonnal RJ, Callari M, Mignone F, Pesole G, Bertalot G, Bernardi LR, ... ... Lee C, et al. A transcriptional sketch of a primary human breast cancer by 454 deep sequencing. Bmc Genomics. 10: 163. PMID 19379481 DOI: 10.1186/1471-2164-10-163  0.389
2008 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 (New York, N.Y.). 14: 2478-88. PMID 18974280 DOI: 10.1261/Rna.1252608  0.338
2008 Alekseyenko AV, Lee CJ, Suchard MA. Wagner and Dollo: a stochastic duet by composing two parsimonious solos. Systematic Biology. 57: 772-84. PMID 18853363 DOI: 10.1080/10635150802434394  0.309
2008 Roy M, Kim N, Xing Y, Lee C. The effect of intron length on exon creation ratios during the evolution of mammalian genomes. Rna (New York, N.Y.). 14: 2261-73. PMID 18796579 DOI: 10.1261/Rna.1024908  0.588
2008 Parker DS, Hsiao RL, Xing Y, Resch AM, Lee CJ. Solving the problem of Trans-Genomic Query with alignment tables. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 5: 432-47. PMID 18670046 DOI: 10.1109/Tcbb.2007.1073  0.776
2008 Xing Y, Lee C. Reconstruction of full-length isoforms from splice graphs. Methods in Molecular Biology (Clifton, N.J.). 452: 199-205. PMID 18566766 DOI: 10.1007/978-1-60327-159-2_10  0.561
2008 Kim N, Lee C. Bioinformatics Detection of Alternative Splicing Methods of Molecular Biology. 452: 179-197. PMID 18566765 DOI: 10.1007/978-1-60327-159-2_9  0.483
2007 Xing Y, Lee C. Relating alternative splicing to proteome complexity and genome evolution. Advances in Experimental Medicine and Biology. 623: 36-49. PMID 18380339 DOI: 10.1007/978-0-387-77374-2_3  0.586
2007 Calarco JA, Xing Y, Cáceres M, Calarco JP, Xiao X, Pan Q, Lee C, Preuss TM, Blencowe BJ. Global analysis of alternative splicing differences between humans and chimpanzees. Genes & Development. 21: 2963-75. PMID 17978102 DOI: 10.1101/Gad.1606907  0.544
2007 Wang Q, Lee C. Distinguishing functional amino acid covariation from background linkage disequilibrium in HIV protease and reverse transcriptase. Plos One. 2: e814. PMID 17726544 DOI: 10.1371/Journal.Pone.0000814  0.31
2007 Kim N, Lee C. QPRIMER: a quick web-based application for designing conserved PCR primers from multigenome alignments. Bioinformatics (Oxford, England). 23: 2331-3. PMID 17599926 DOI: 10.1093/Bioinformatics/Btm343  0.394
2007 Alekseyenko AV, Kim N, Lee CJ. Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes. Rna (New York, N.Y.). 13: 661-70. PMID 17369312 DOI: 10.1261/Rna.325107  0.468
2007 Lee JA, Xing Y, Nguyen D, Xie J, Lee CJ, Black DL. Depolarization and CaM kinase IV modulate NMDA receptor splicing through two essential RNA elements. Plos Biology. 5: e40. PMID 17298178 DOI: 10.1371/Journal.Pbio.0050040  0.494
2007 Alekseyenko AV, Lee CJ. Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases. Bioinformatics (Oxford, England). 23: 1386-93. PMID 17234640 DOI: 10.1093/Bioinformatics/Btl647  0.363
2007 Pan C, Kim J, Chen L, Wang Q, Lee C. The HIV positive selection mutation database. Nucleic Acids Research. 35: D371-5. PMID 17108357 DOI: 10.1093/Nar/Gkl855  0.696
2007 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 Research. 35: D93-8. PMID 17108355 DOI: 10.1093/Nar/Gkl884  0.434
2006 Xing Y, Lee C. Alternative splicing and RNA selection pressure - Evolutionary consequences for eukaryotic genomes Nature Reviews Genetics. 7: 499-509. PMID 16770337 DOI: 10.1038/Nrg1896  0.573
2006 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 Research. 34: 3150-60. PMID 16757580 DOI: 10.1093/Nar/Gkl396  0.491
2006 Chen L, Lee C. Distinguishing HIV-1 drug resistance, accessory, and viral fitness mutations using conditional selection pressure analysis of treated versus untreated patient samples. Biology Direct. 1: 14. PMID 16737543 DOI: 10.1186/1745-6150-1-14  0.691
2006 Xing Y, Wang Q, Lee C. Evolutionary divergence of exon flanks: a dissection of mutability and selection. Genetics. 173: 1787-91. PMID 16702427 DOI: 10.1534/Genetics.106.057919  0.543
2006 Xing Y, Lee C. Can RNA selection pressure distort the measurement of Ka / Ks? Gene. 370: 1-5. PMID 16488091 DOI: 10.1016/J.Gene.2005.12.015  0.457
2005 Xing Y, Lee CJ. Protein modularity of alternatively spliced exons is associated with tissue-specific regulation of alternative splicing. Plos Genetics. 1: e34. PMID 16170410 DOI: 10.1371/Journal.Pgen.0010034  0.548
2005 Xing Y, Lee C. Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences. Proceedings of the National Academy of Sciences of the United States of America. 102: 13526-13531. PMID 16157889 DOI: 10.1073/Pnas.0501213102  0.545
2005 Roy M, Xu Q, Lee C. Evidence that public database records for many cancer-associated genes reflect a splice form found in tumors and lack normal splice forms. Nucleic Acids Research. 33: 5026-33. PMID 16147986 DOI: 10.1093/Nar/Gki792  0.348
2005 Xing Y, Lee C. Assessing the application of Ka/Ks ratio test to alternatively spliced exons. Bioinformatics (Oxford, England). 21: 3701-3. PMID 16091412 DOI: 10.1093/Bioinformatics/Bti613  0.569
2005 Atanelov L, Xu Q, Rad R, Lee C. Targeting alternatively spliced sequence features for cancer diagnosis and therapeutics. Journal of Gastroenterology. 14-20. PMID 15902958 DOI: 10.1007/Bf02990573  0.357
2005 Lee C, Wang Q. Bioinformatics analysis of alternative splicing. Briefings in Bioinformatics. 6: 23-33. PMID 15826354 DOI: 10.1093/Bib/6.1.23  0.506
2005 Chen J, Call GB, Beyer E, Bui C, Cespedes A, Chan A, Chan J, Chan S, Chhabra A, Dang P, Deravanesian A, Hermogeno B, Jen J, Kim E, Lee E, ... ... Lee C, et al. Discovery-based science education: functional genomic dissection in Drosophila by undergraduate researchers. Plos Biology. 3: e59. PMID 15719063 DOI: 10.1371/Journal.Pbio.0030059  0.3
2005 Xing Y, Lee C. Evidence of functional selection pressure for alternative splicingevents that accelerate evolution of protein subsequences Genome Biology. 6: 8. DOI: 10.1186/Gb-2005-6-5-P8  0.552
2004 Le K, Mitsouras K, Roy M, Wang Q, Xu Q, Nelson SF, Lee C. Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data Nucleic Acids Research. 32. PMID 15598820 DOI: 10.1093/Nar/Gnh173  0.403
2004 Xing Y, Lee CJ. Negative selection pressure against premature protein truncation is reduced by alternative splicing and diploidy. Trends in Genetics : Tig. 20: 472-5. PMID 15363899 DOI: 10.1016/J.Tig.2004.07.009  0.576
2004 Chen L, Perlina A, Lee CJ. Positive selection detection in 40,000 human immunodeficiency virus (HIV) type 1 sequences automatically identifies drug resistance and positive fitness mutations in HIV protease and reverse transcriptase. Journal of Virology. 78: 3722-32. PMID 15016892 DOI: 10.1128/Jvi.78.7.3722-3732.2004  0.691
2004 Resch A, Xing Y, Modrek B, Gorlick M, Riley R, Lee C. Assessing the impact of alternative splicing on domain interactions in the human proteome. Journal of Proteome Research. 3: 76-83. PMID 14998166 DOI: 10.1021/Pr034064V  0.764
2004 Grasso C, Modrek B, Xing Y, Lee C. Genome-wide detection of alternative splicing in expressed sequences using partial order multiple sequence alignment graphs. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 29-41. PMID 14992490  0.792
2004 Resch A, Xing Y, Alekseyenko A, Modrek B, Lee C. Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation. Nucleic Acids Research. 32: 1261-9. PMID 14982953 DOI: 10.1093/Nar/Gkh284  0.785
2004 Xing Y, Resch A, Lee C. The multiassembly problems: Reconstructing multiple transcript isoforms from EST fragment mixtures Genome Research. 14: 426-441. PMID 14962984 DOI: 10.1101/Gr.1304504  0.795
2004 Grasso C, Lee C. Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems. Bioinformatics (Oxford, England). 20: 1546-56. PMID 14962922 DOI: 10.1093/Bioinformatics/Bth126  0.339
2004 Xing Y, Xu Q, Lee C. Widespread production of novel soluble protein isoforms by alternative splicing removal of transmembrane anchoring domains. Febs Letters. 555: 572-8. PMID 14675776 DOI: 10.1016/s0014-5793(03)01354-1  0.479
2004 Xing Y, Lee C. Negative selection pressure against premature protein truncation is reduced by both alternative splicing and diploidy Genome Biology. 5: 12. DOI: 10.1186/Gb-2004-5-6-P12  0.579
2003 Lee CJ, Irizarry K. Alternative splicing in the nervous system: an emerging source of diversity and regulation. Biological Psychiatry. 54: 771-6. PMID 14550676 DOI: 10.1016/S0006-3223(03)00375-5  0.443
2003 Xu Q, Lee C. Discovery of novel splice forms and functional analysis of cancer‐specific alternative splicing in human expressed sequences Nucleic Acids Research. 31: 5635-5643. PMID 14500827 DOI: 10.1093/Nar/Gkg786  0.404
2003 Grasso C, Quist M, Ke K, Lee C. POAVIZ: a Partial order multiple sequence alignment visualizer. Bioinformatics (Oxford, England). 19: 1446-8. PMID 12874062 DOI: 10.1093/Bioinformatics/Btg175  0.359
2003 Lee C. Generating consensus sequences from partial order multiple sequence alignment graphs. Bioinformatics (Oxford, England). 19: 999-1008. PMID 12761063 DOI: 10.1093/Bioinformatics/Btg109  0.377
2003 Modrek B, Lee CJ. Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nature Genetics. 34: 177-80. PMID 12730695 DOI: 10.1038/Ng1159  0.795
2003 Lee C, Atanelov L, Modrek B, Xing Y. ASAP: the Alternative Splicing Annotation Project. Nucleic Acids Research. 31: 101-5. PMID 12519958 DOI: 10.1093/Nar/Gkg029  0.815
2003 Xing Y, Xu Q, Lee C. Widespread production of novel soluble protein isoforms by alternative splicing removal of transmembrane anchoring domains Febs Letters. 555: 572-578. DOI: 10.1016/S0014-5793(03)01354-1  0.544
2002 Xu Q, Modrek B, Lee C. Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. Nucleic Acids Research. 30: 3754-66. PMID 12202761 DOI: 10.1093/Nar/Gkf492  0.774
2002 Hu G, Modrek B, Riise Stensland HM, Saarela J, Pajukanta P, Kustanovich V, Peltonen L, Nelson SF, Lee C. Efficient discovery of single-nucleotide polymorphisms in coding regions of human genes. The Pharmacogenomics Journal. 2: 236-42. PMID 12196912 DOI: 10.1038/Sj.Tpj.6500109  0.769
2002 Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics (Oxford, England). 18: 452-64. PMID 11934745 DOI: 10.1093/Bioinformatics/18.3.452  0.342
2002 Modrek B, Lee C. A genomic view of alternative splicing. Nature Genetics. 30: 13-9. PMID 11753382 DOI: 10.1038/Ng0102-13  0.791
2001 Modrek B, Resch A, Grasso C, Lee C. Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Research. 29: 2850-9. PMID 11433032 DOI: 10.1093/Nar/29.13.2850  0.79
2001 Lee C. The incredible shrinking human genome. Trends in Genetics. 17: 187-188. PMID 11357825 DOI: 10.1016/S0168-9525(01)02266-1  0.352
2001 Lee C, Irizarry K. The GeneMine system for genome/proteome annotation and collaborative data mining Ibm Systems Journal. 40: 592-603. DOI: 10.1147/Sj.402.0592  0.385
2000 Irizarry K, Kustanovich V, Li C, Brown N, Nelson S, Wong W, Lee CJ. Genome-wide analysis of single-nucleotide polymorphisms in human expressed sequences. Nature Genetics. 26: 233-6. PMID 11017085 DOI: 10.1038/79981  0.378
1998 Lee C, Liang MN, Tate KM, Rabinowitz JD, Beeson C, Jones PP, McConnell HM. Evidence that the autoimmune antigen myelin basic protein (MBP) Ac1-9 binds towards one end of the major histocompatibility complex (MHC) cleft. The Journal of Experimental Medicine. 187: 1505-16. PMID 9565642 DOI: 10.1084/Jem.187.9.1505  0.685
1996 Liang MN, Lee C, Xia Y, McConnell HM. Molecular modeling and design of invariant chain peptides with altered dissociation kinetics from class II MHC. Biochemistry. 35: 14734-42. PMID 8942634 DOI: 10.1021/Bi961725B  0.477
1996 Beeson C, Andersen TG, Lee C, McConnell HM. Isomeric complexes of peptides with class II proteins of the major histocompatibility complex Journal of the American Chemical Society. 118: 977-980. DOI: 10.1021/Ja951502T  0.63
1991 Lee C, Levitt M. Accurate prediction of the stability and activity effects of site-directed mutagenesis on a protein core. Nature. 352: 448-51. PMID 1861725 DOI: 10.1038/352448A0  0.461
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