Christopher Lee

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Bioinformatics analysis of alternative splicing
    Christopher Lee
    Molecular Biology Institute, Center for Genomics and Proteomics, Dept of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095 1570, USA
    Brief Bioinform 6:23-33. 2005
  2. pmc Evidence that public database records for many cancer-associated genes reflect a splice form found in tumors and lack normal splice forms
    Meenakshi Roy
    Molecular Biology Institute, Center for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095 1570, USA
    Nucleic Acids Res 33:5026-33. 2005
  3. pmc The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species
    Namshin Kim
    Department of Chemistry and Biochemistry, Center for Computational Biology Institute for Genomics and Proteomics, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095 1570, USA
    Nucleic Acids Res 35:D93-8. 2007
  4. pmc Analysis of alternative splicing with microarrays: successes and challenges
    Christopher Lee
    Molecular Biology Institute, Center for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 1570, USA
    Genome Biol 5:231. 2004
  5. ncbi request reprint Generating consensus sequences from partial order multiple sequence alignment graphs
    Christopher Lee
    UCLA DOE Center for Genomics and Proteomics, Molecular Biology Institute Department of Chemistry, University of California, Los Angeles, Los Angeles, CA 90095 1570, USA
    Bioinformatics 19:999-1008. 2003
  6. pmc ASAP: the Alternative Splicing Annotation Project
    Christopher Lee
    Molecular Biology Institute, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 1570, USA
    Nucleic Acids Res 31:101-5. 2003
  7. ncbi request reprint Multiple sequence alignment using partial order graphs
    Christopher Lee
    Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095 1570, USA
    Bioinformatics 18:452-64. 2002
  8. ncbi request reprint Irresistible force meets immovable object: SNP mapping of complex diseases
    Christopher Lee
    Dept of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 1570, USA
    Trends Genet 18:67-9. 2002
  9. pmc The effect of intron length on exon creation ratios during the evolution of mammalian genomes
    Meenakshi Roy
    Molecular Biology Institute, University of California, Los Angeles, California 90024, USA
    RNA 14:2261-73. 2008
  10. pmc The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixtures
    Yi Xing
    UCLA DOE Center for Genomics and Proteomics, Molecular Biology Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095 1570, USA
    Genome Res 14:426-41. 2004

Collaborators

Detail Information

Publications51

  1. ncbi request reprint Bioinformatics analysis of alternative splicing
    Christopher Lee
    Molecular Biology Institute, Center for Genomics and Proteomics, Dept of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095 1570, USA
    Brief Bioinform 6:23-33. 2005
    ..Common to many bioinformatics studies is a new emphasis on graph representations of alternative splicing structures, which have many advantages for analysis...
  2. pmc Evidence that public database records for many cancer-associated genes reflect a splice form found in tumors and lack normal splice forms
    Meenakshi Roy
    Molecular Biology Institute, Center for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095 1570, USA
    Nucleic Acids Res 33:5026-33. 2005
    ..Our database contains 1308 novel normal splice forms, including many known cancer genes...
  3. pmc The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species
    Namshin Kim
    Department of Chemistry and Biochemistry, Center for Computational Biology Institute for Genomics and Proteomics, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095 1570, USA
    Nucleic Acids Res 35:D93-8. 2007
    ..ASAP II is available at http://www.bioinformatics.ucla.edu/ASAP2...
  4. pmc Analysis of alternative splicing with microarrays: successes and challenges
    Christopher Lee
    Molecular Biology Institute, Center for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 1570, USA
    Genome Biol 5:231. 2004
    ..Recently, DNA microarrays have emerged as potentially powerful tools for analyzing alternative splicing. We briefly review the latest results in this field and highlight the current challenges that they have revealed...
  5. ncbi request reprint Generating consensus sequences from partial order multiple sequence alignment graphs
    Christopher Lee
    UCLA DOE Center for Genomics and Proteomics, Molecular Biology Institute Department of Chemistry, University of California, Los Angeles, Los Angeles, CA 90095 1570, USA
    Bioinformatics 19:999-1008. 2003
    ..However, how can a consensus be constructed when its inherent assumption-that the aligned sequences form a single linear consensus-is not true?..
  6. pmc ASAP: the Alternative Splicing Annotation Project
    Christopher Lee
    Molecular Biology Institute, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 1570, USA
    Nucleic Acids Res 31:101-5. 2003
    ..ASAP is intended to be a community resource for collaborative annotation of alternative splice forms, their regulation, and biological functions. The URL for ASAP is http://www.bioinformatics.ucla.edu/ASAP...
  7. ncbi request reprint Multiple sequence alignment using partial order graphs
    Christopher Lee
    Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095 1570, USA
    Bioinformatics 18:452-64. 2002
    ..Progressive Multiple Sequence Alignment (MSA) methods depend on reducing an MSA to a linear profile for each alignment step. However, this leads to loss of information needed for accurate alignment, and gap scoring artifacts...
  8. ncbi request reprint Irresistible force meets immovable object: SNP mapping of complex diseases
    Christopher Lee
    Dept of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 1570, USA
    Trends Genet 18:67-9. 2002
    ..The Fourth Annual Meeting on 'Single Nucleotide Polymorphisms and Complex Genome Analysis' was held in Stockholm, Sweden from 10 to 13 October 2001...
  9. pmc The effect of intron length on exon creation ratios during the evolution of mammalian genomes
    Meenakshi Roy
    Molecular Biology Institute, University of California, Los Angeles, California 90024, USA
    RNA 14:2261-73. 2008
    ..This suggests that the observed correlation of longer intron lengths with alternatively spliced exons may be at least partly due to biases in the probability of exon creation, which is higher in long introns...
  10. pmc The multiassembly problem: reconstructing multiple transcript isoforms from EST fragment mixtures
    Yi Xing
    UCLA DOE Center for Genomics and Proteomics, Molecular Biology Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095 1570, USA
    Genome Res 14:426-41. 2004
    ..0 protein isoforms per gene...
  11. ncbi request reprint Assessing the impact of alternative splicing on domain interactions in the human proteome
    Alissa Resch
    Molecular Biology Institute, University of California Los Angeles, Los Angeles, California 90095 1570, USA
    J Proteome Res 3:76-83. 2004
    ..ASP will enhance the existing pool of protein sequences that are searched by mass spectroscopy software during the identification of peptide fragments...
  12. pmc Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation
    Alissa Resch
    Molecular Biology Institute, Institute for Genomics and Proteomics, and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095 1570, USA
    Nucleic Acids Res 32:1261-9. 2004
    ..These data indicate that a subpopulation of modern alternative splicing events was present in the common ancestors of these genomes, and was under functional selection pressure to preserve the protein reading frame...
  13. pmc Genome-wide detection of tissue-specific alternative splicing in the human transcriptome
    Qiang Xu
    Molecular Biology Institute and Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095 1570, USA
    Nucleic Acids Res 30:3754-66. 2002
    ..Our database greatly expands knowledge of tissue-specific alternative splicing and provides a comprehensive dataset for investigating its functional roles and regulation in different human tissues...
  14. pmc Three-Dimensional Phylogeny Explorer: distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption with 3D visualization
    Namshin Kim
    Center for Computational Biology, Molecular Biology Institute, Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 1570, USA
    BMC Bioinformatics 8:213. 2007
    ..Increases in sequence data and complexity are creating a need for more powerful and insightful tree visualization tools...
  15. doi request reprint Bioinformatics detection of alternative splicing
    Namshin Kim
    Molecular Biology Institute, Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
    Methods Mol Biol 452:179-97. 2008
    ..Such databases can also help automate design of probes for RT-PCR and microarrays, enabling high throughput experimental measurement of alternative splicing...
  16. ncbi request reprint Widespread production of novel soluble protein isoforms by alternative splicing removal of transmembrane anchoring domains
    Yi Xing
    Molecular Biology Institute, UCLA Institute for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, CA 90095 1570, USA
    FEBS Lett 555:572-8. 2003
    ..While many of the soluble isoforms produced by alternative splicing have already been validated, most are novel, and in 57 genes showed a statistically significant association (P-value<0.01) with a specific tissue...
  17. pmc Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data
    Keith Le
    Department of Chemistry and Biochemistry, Center for Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, CA 90095 1570, USA
    Nucleic Acids Res 32:e180. 2004
    ..Our data and analysis source code are available from http://www.bioinformatics.ucla.edu/ASAP...
  18. pmc Massive expansions of Dscam splicing diversity via staggered homologous recombination during arthropod evolution
    Christopher Lee
    Department of Chemistry and Biochemistry, Center for Computational Biology, Institute for Genomics and Proteomics, Molecular BiologyInstitute, University of California at Los Angeles, Los Angeles, California 90095 1570, USA
    RNA 16:91-105. 2010
    ..These data provide a remarkably detailed picture of how complex gene structure evolves and reveal the molecular mechanism behind this process...
  19. ncbi request reprint POAVIZ: a Partial order multiple sequence alignment visualizer
    Catherine Grasso
    Molecular Biology Institute, Center for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 1570, USA
    Bioinformatics 19:1446-8. 2003
    ....
  20. pmc Evolutionary divergence of exon flanks: a dissection of mutability and selection
    Yi Xing
    Molecular Biology Institute, Center for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095 1570, USA
    Genetics 173:1787-91. 2006
    ..Our data provide concrete evidence for increased purifying selection at exon flanks associated with regulation of alternative splicing...
  21. pmc Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences
    Yi Xing
    Molecular Biology Institute, Center for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 102:13526-31. 2005
    ..Thus alternative splicing apparently can create evolutionary "hotspots" within a protein sequence, and these events have evidently been selected for during mammalian evolution...
  22. ncbi request reprint A genomic view of alternative splicing
    Barmak Modrek
    Department of Chemistry, University of California Los Angeles, Los Angeles, California 90095 1570, USA
    Nat Genet 30:13-9. 2002
    ..We recommend a community-based effort to discover and characterize alternative splice forms comprehensively throughout the human genome...
  23. ncbi request reprint Assessing the application of Ka/Ks ratio test to alternatively spliced exons
    Yi Xing
    Department of Chemistry and Biochemistry, Molecular Biology Institute, Center for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095 1570, USA
    Bioinformatics 21:3701-3. 2005
    ..Our analysis suggests a future direction to incorporate comparative genomics-based alternative splicing predictions with the Ka/Ks ratio test in higher eukaryotes with extensive RNA alternative splicing...
  24. ncbi request reprint QPRIMER: a quick web-based application for designing conserved PCR primers from multigenome alignments
    Namshin Kim
    Center for Computational Biology, Molecular Biology Institute, University of California, Los Angeles, 90095 1570, USA
    Bioinformatics 23:2331-3. 2007
    ..QPRIMER supports human, mouse, rat, chicken, dog, zebrafish and fruit fly. Availability: http://www.bioinformatics.ucla.edu/QPRIMER/...
  25. pmc An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs
    Yi Xing
    Molecular Biology Institute, Center for Computational Biology, Department of Chemistry and Biochemistry, University of California Los Angeles, USA
    Nucleic Acids Res 34:3150-60. 2006
    ..Our work establishes a general probabilistic framework for splice graph-based reconstructions of full-length isoforms...
  26. pmc Inferring protein domain interactions from databases of interacting proteins
    Robert Riley
    Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, CA 90095, USA
    Genome Biol 6:R89. 2005
    ..DPEA may prove useful in guiding experiment-based discovery of previously unrecognized domain interactions...
  27. pmc The HIV positive selection mutation database
    Calvin Pan
    Center for Computational Biology, University of California Los Angeles, CA, USA
    Nucleic Acids Res 35:D371-5. 2007
    ..Betts, J. Ravela and R. W. Shafer (2003) Nucleic Acids Res., 31, 298-303]. Comparison between these datasets in the database enables cross-validation with independent datasets and also specific evaluation of the effect of drug treatment...
  28. ncbi request reprint Targeting alternatively spliced sequence features for cancer diagnosis and therapeutics
    Levan Atanelov
    Institute for Genomics and Proteomics, Molecular Biology Institute, and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095 1570, USA
    J Gastroenterol 40:14-20. 2005
    ....
  29. pmc Integration site preference of xenotropic murine leukemia virus-related virus, a new human retrovirus associated with prostate cancer
    Sanggu Kim
    Biomedical Engineering Interdepartmental Program, UCLA School of Medicine, Los Angeles, CA 90095, USA
    J Virol 82:9964-77. 2008
    ..These results are consistent with a model in which XMRV may contribute to tumorigenicity via a paracrine mechanism...
  30. ncbi request reprint Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
    Catherine Grasso
    Department of Chemistry and Biochemistry, Molecular Biology Institute, Center for Genomics and Proteomics, University of California, Los Angeles, CA 90095 1570, USA
    Bioinformatics 20:1546-56. 2004
    ....
  31. ncbi request reprint Can RNA selection pressure distort the measurement of Ka/Ks?
    Yi Xing
    Molecular Biology Institute, Center for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
    Gene 370:1-5. 2006
    ....
  32. pmc Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences
    Qiang Xu
    Institute for Genomics and Proteomics, Molecular Biology Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095 1570, USA
    Nucleic Acids Res 31:5635-43. 2003
    ....
  33. pmc Distinguishing functional amino acid covariation from background linkage disequilibrium in HIV protease and reverse transcriptase
    Qi Wang
    Center for Computational Biology, Molecular Biology Institute, Institute for Genomics and Proteomics, University of California at Los Angeles, Los Angeles, United States of America
    PLoS ONE 2:e814. 2007
    ..Moreover, the specific set of (A,A) interaction pairs was reproducible in different drug treatment studies, and vanished in untreated HIV samples. The (S,S) covariation curves measured a low but detectable level of background LD in HIV...
  34. ncbi request reprint Alternative splicing and RNA selection pressure--evolutionary consequences for eukaryotic genomes
    Yi Xing
    Molecular Biology Institute, Center for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
    Nat Rev Genet 7:499-509. 2006
    ..Here, we consider how alternative splicing has contributed to the evolution of modern genomes, and discuss constraints on evolution associated with alternative splicing that might have important medical implications...
  35. doi request reprint Neuroimaging in pediatric epilepsy: a multimodality approach
    Sachin Rastogi
    Department of Radiological Sciences, David Geffen School of Medicine at UCLA, 10833 Le Conte Ave, Room BL 428 CHS, Los Angeles, CA 90095 1721, USA
    Radiographics 28:1079-95. 2008
    ....
  36. doi request reprint Recurrent pulmonary capillary hemangiomatosis after bilateral lung transplantation
    Christopher Lee
    Department of Radiological Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
    J Thorac Imaging 25:W89-92. 2010
    ..To date, there have been no reported cases of recurrent PCH after lung transplantation. We present a case that describes important radiologic and clinical features of PCH and raises questions about its pathogenesis...
  37. ncbi request reprint Seroepidemiology of hepatitis A in patients with chronic liver disease
    S Saab
    Division of Digestive Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
    J Viral Hepat 12:101-5. 2005
    ..We demonstrated that age-stratified seroprevalence of HAV in patients with CLD of various aetiologies is significantly higher than that of the general population, and identified several independent predictors of HAV prior exposure...
  38. pmc Evidence of a novel RNA secondary structure in the coding region of HIV-1 pol gene
    Qi Wang
    Molecular Biology Institute, University of California at Los Angeles, Los Angeles, California 90095, USA
    RNA 14:2478-88. 2008
    ..Finally, this structure was validated experimentally using selective 2'-hydroxyl acylation and primer extension (SHAPE). Discovery of this novel secondary structure suggests many directions for further functional investigation...
  39. doi request reprint Developmentally regulated inhibition of cell cycle progression by glucocorticoids through repression of cyclin A transcription in primary osteoblast cultures
    Yankel Gabet
    Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California 90033, USA
    J Cell Physiol 226:991-8. 2011
    ..Our data suggest that GCs attenuate cell cycle progression in osteoblasts in a developmental stage-specific manner by repressing Atf4-dependent cyclin A gene expression...
  40. pmc Distinguishing HIV-1 drug resistance, accessory, and viral fitness mutations using conditional selection pressure analysis of treated versus untreated patient samples
    Lamei Chen
    Institute for Genomics and Proteomics, Molecular Biology Institute, Dept of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095 1570, USA
    Biol Direct 1:14. 2006
    ..We have adapted a well-known measure of evolutionary selection pressure (Ka/Ks) and developed a conditional Ka/Ks approach to detect important interactions...
  41. pmc Lef1 haploinsufficient mice display a low turnover and low bone mass phenotype in a gender- and age-specific manner
    Tommy Noh
    Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
    PLoS ONE 4:e5438. 2009
    ..The resistance to Lef1 haploinsufficiency in males with active AR and in old females could be due to the reduced bone turnover in these mice...
  42. ncbi request reprint Use of a SCID mouse model to select for a more aggressive strain of prostate cancer
    Mark R Davies
    Department of Orthopaedic Surgery, UCLA School of Medicine, Los Angeles, CA, USA
    Anticancer Res 23:2245-52. 2003
    ..To better mimic the biology of metastatic prostate cancer, we have developed a model that utilizes both human prostate cancer and human bone in the SCID mouse...
  43. pmc Global analysis of alternative splicing differences between humans and chimpanzees
    John A Calarco
    Banting and Best Department of Medical Research, University of Toronto, Terrence Donnelly Center for Cellular and Biomolecular Research, Toronto, Ontario M5S 3E1, Canada
    Genes Dev 21:2963-75. 2007
    ..The results of this study thus support an important role for alternative splicing in establishing differences between humans and chimpanzees...
  44. doi request reprint Reconstruction of full-length isoforms from splice graphs
    Yi Xing
    Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
    Methods Mol Biol 452:199-205. 2008
    ..This chapter describes a general graph-based approach for computational inference of full-length isoforms...
  45. pmc Implementing the LIM code: the structural basis for cell type-specific assembly of LIM-homeodomain complexes
    Mugdha Bhati
    School of Molecular and Microbial Biosciences, The University of Sydney, New South Wales, Australia
    EMBO J 27:2018-29. 2008
    ..The resulting alternate protein complexes can target different genes to regulate key biological events...
  46. ncbi request reprint Haptic rendering of device and patient impedances in catheter-based simulation
    Christopher Lee
    Medical Simulation Corporation
    Stud Health Technol Inform 125:280-2. 2007
    ..This paper describes the control strategy for the SimSuite haptic platform and some of its mechanical characteristics...
  47. ncbi request reprint Relating alternative splicing to proteome complexity and genome evolution
    Yi Xing
    Department of Internal Medicine, Roy J and Lucille A Carver College of Medicine, University of Iowa, Iowa City, USA
    Adv Exp Med Biol 623:36-49. 2007
    ..In this chapter, we review recent research on alternative splicing's impact on proteomic complexity and its role in genome evolution...
  48. ncbi request reprint Molecular mechanism of AHSP-mediated stabilization of alpha-hemoglobin
    Liang Feng
    Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ 08544, USA
    Cell 119:629-40. 2004
    ..These observations reveal the molecular mechanisms by which AHSP stabilizes free alphaHb...
  49. ncbi request reprint Assembly of the oncogenic DNA-binding complex LMO2-Ldb1-TAL1-E12
    Daniel P Ryan
    School of Molecular and Microbial Biosciences, University of Sydney, Sydney, New South Wales 2006, Australia
    Proteins 70:1461-74. 2008
    ..Our data provide biophysical evidence for a mechanism, by which LMO2 and TAL1 both regulate transcription in normal blood cell development, and synergistically disrupt E2A function in T-cells to promote the onset of leukaemia...
  50. ncbi request reprint 1H, 15N and 13C assignments of an intramolecular Lhx3:ldb1 complex
    Christopher Lee
    J Biomol NMR 33:198. 2005
  51. ncbi request reprint National trends in emergency department antibiotic prescribing for children with acute otitis media, 1996 2005
    Thomas Fischer
    Department of Emergency Medicine, Stony Brook University Medical Center, Stony Brook, NY, USA
    Acad Emerg Med 14:1172-5. 2007
    ..The authors hypothesized that the rates of prescribing antibiotics would decline over time...