Christopher Lee

Summary

Affiliation: University of California
Country: USA

Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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

Collaborators

  • Yi Xing
  • Qiang Xu
  • Qi Wang
  • David J Ross
  • Alexander V Alekseyenko
  • Tianwei Yu
  • David Eisenberg
  • Chiara Sabatti
  • Namshin Kim
  • Meenakshi Roy
  • Alissa Resch
  • Catherine Grasso
  • Barmak Modrek
  • Fereidoun G Abtin
  • Robert Riley
  • Sanggu Kim
  • Sachin Rastogi
  • Calvin Pan
  • Levan Atanelov
  • Keith Le
  • Mark R Davies
  • Antonio J Gutierrez
  • Robert D Suh
  • Michael C Fishbein
  • Jilbert Eradat
  • Noriko Salamon
  • Samson A Chow
  • Beihua Dong
  • Eric A Klein
  • Serena A Lee
  • Jaydip Das Gupta
  • Christina Gaughan
  • Robert H Silverman
  • David Boren
  • Joseph Kim
  • Lamei Chen
  • Ramin Rad
  • Michael Gorlick
  • Stanley F Nelson
  • Katherine Mitsouras
  • Xuguang Zhang
  • Daniel E Afar
  • Michael Quist
  • Kevin Ke
  • Yu Po Lee
  • Jay R Lieberman

Detail Information

Publications37

  1. 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...
  2. 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...
  3. 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...
  4. 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
    ....
  5. 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...
  6. 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...
  7. 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...
  8. 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...
  9. 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...
  10. 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
    ....
  11. 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...
  12. 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...
  13. 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...
  14. 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...
  15. 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...
  16. 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...
  17. 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...
  18. 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...
  19. 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...
  20. 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...
  21. 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...
  22. 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?..
  23. 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...
  24. 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
    ....
  25. 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
    ....
  26. 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/...
  27. 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...
  28. 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...
  29. pmc Radiofrequency ablation of lung tumors: imaging features of the postablation zone
    Fereidoun G Abtin
    Division of Thoracic Imaging and Intervention, Department of Radiological Sciences, UCLA Medical Center, 757 Westwood Plaza, Suite 1621, Los Angeles, CA 90095, USA
    Radiographics 32:947-69. 2012
    ....
  30. 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
    ....
  31. 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
    ....
  32. 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...
  33. 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...
  34. 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...
  35. 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...
  36. 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...
  37. 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...