Desmond Smith

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc Learning pair-wise gene functional similarity by multiplex gene expression maps
    Li An
    Data Engineering Laboratory, Department of Computer and Information Sciences, Temple University, PA, USA
    BMC Bioinformatics 13:S1. 2012
  2. pmc Effects of genome-wide copy number variation on expression in mammalian cells
    Richard T Wang
    Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
    BMC Genomics 12:562. 2011
  3. pmc Gene networks associated with conditional fear in mice identified using a systems genetics approach
    Christopher C Park
    Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
    BMC Syst Biol 5:43. 2011
  4. pmc Analysis of multiplex gene expression maps obtained by voxelation
    Li An
    Data Engineering Laboratory, Department of Computer and Information Sciences, Temple University, PA, USA
    BMC Bioinformatics 10:S10. 2009
  5. ncbi request reprint The allelic structure of common disease
    Desmond J Smith
    Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095 1735, USA
    Hum Mol Genet 11:2455-61. 2002
  6. pmc Mitochondrial dysfunction in mouse models of Parkinson's disease revealed by transcriptomics and proteomics
    Desmond J Smith
    Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, CHS 23 120, Box 951735, Los Angeles, CA 90095 1735, USA
    J Bioenerg Biomembr 41:487-91. 2009
  7. pmc Mitochondrial dysfunction, oxidative stress, and apoptosis revealed by proteomic and transcriptomic analyses of the striata in two mouse models of Parkinson's disease
    Mark H Chin
    Department of Molecular and Medical Pharmacology, Human Genetics, Laboratory of Neuroimaging, Department of Neurology, and Surgery, David Geffen School of Medicine at University of California Los Angeles UCLA, Los Angeles, California 90095, USA
    J Proteome Res 7:666-77. 2008
  8. pmc High-resolution mapping of gene expression using association in an outbred mouse stock
    Anatole Ghazalpour
    Department of Human Genetics, University of California Los Angeles, Los Angeles, California, United States of America
    PLoS Genet 4:e1000149. 2008
  9. ncbi request reprint Identifying loci for behavioral traits using genome-tagged mice
    Dahai Liu
    Department of Molecular and Medical Pharmacology, UCLA School of Medicine, Los Angeles, California 90095 1735, USA
    J Neurosci Res 74:562-9. 2003
  10. ncbi request reprint A genome-wide set of congenic mouse strains derived from DBA/2J on a C57BL/6J background
    Richard C Davis
    Department of Microbiology, Immunology and Molecular Genetics, Department of Medicine, and Department of Human Genetics, University of California, Los Angeles, CA 90095 1679, USA
    Genomics 86:259-70. 2005

Research Grants

Collaborators

Detail Information

Publications30

  1. pmc Learning pair-wise gene functional similarity by multiplex gene expression maps
    Li An
    Data Engineering Laboratory, Department of Computer and Information Sciences, Temple University, PA, USA
    BMC Bioinformatics 13:S1. 2012
    ..On the other hand, although unsupervised learning methods have been commonly used in functional genomics, supervised learning cannot be directly applied to a set of normal genes without having a target (class) attribute...
  2. pmc Effects of genome-wide copy number variation on expression in mammalian cells
    Richard T Wang
    Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
    BMC Genomics 12:562. 2011
    ..We fine mapped cis and trans regulatory loci due to copy number change for essentially all genes using a human-hamster radiation hybrid (RH) panel. These loci are called copy number expression quantitative trait loci (ceQTLs)...
  3. pmc Gene networks associated with conditional fear in mice identified using a systems genetics approach
    Christopher C Park
    Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
    BMC Syst Biol 5:43. 2011
    ..To explore the genetic networks governing the biology of conditional fear, we used a systems genetics approach to analyze a hybrid mouse diversity panel (HMDP) with high mapping resolution...
  4. pmc Analysis of multiplex gene expression maps obtained by voxelation
    Li An
    Data Engineering Laboratory, Department of Computer and Information Sciences, Temple University, PA, USA
    BMC Bioinformatics 10:S10. 2009
    ..In this paper, we present an approach for identifying the relation between gene expression maps obtained by voxelation and gene functions...
  5. ncbi request reprint The allelic structure of common disease
    Desmond J Smith
    Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095 1735, USA
    Hum Mol Genet 11:2455-61. 2002
    ..It appears that neither position has been proved or disproved, but the available evidence indicates that common diseases are due at least in part to genes with a small number of disease-associated alleles...
  6. pmc Mitochondrial dysfunction in mouse models of Parkinson's disease revealed by transcriptomics and proteomics
    Desmond J Smith
    Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, CHS 23 120, Box 951735, Los Angeles, CA 90095 1735, USA
    J Bioenerg Biomembr 41:487-91. 2009
    ....
  7. pmc Mitochondrial dysfunction, oxidative stress, and apoptosis revealed by proteomic and transcriptomic analyses of the striata in two mouse models of Parkinson's disease
    Mark H Chin
    Department of Molecular and Medical Pharmacology, Human Genetics, Laboratory of Neuroimaging, Department of Neurology, and Surgery, David Geffen School of Medicine at University of California Los Angeles UCLA, Los Angeles, California 90095, USA
    J Proteome Res 7:666-77. 2008
    ..These results constitute one of the largest descriptive data sets integrating protein and transcript changes for these neurotoxin models with many similar end point phenotypes but distinct mechanisms...
  8. pmc High-resolution mapping of gene expression using association in an outbred mouse stock
    Anatole Ghazalpour
    Department of Human Genetics, University of California Los Angeles, Los Angeles, California, United States of America
    PLoS Genet 4:e1000149. 2008
    ..Our results also highlight the importance of correcting for population structure in whole-genome association studies in the outbred stock...
  9. ncbi request reprint Identifying loci for behavioral traits using genome-tagged mice
    Dahai Liu
    Department of Molecular and Medical Pharmacology, UCLA School of Medicine, Los Angeles, California 90095 1735, USA
    J Neurosci Res 74:562-9. 2003
    ..These results suggest that the GTMs should be a valuable resource for mapping and confirmation of loci contributing to complex behavioral traits in the mouse...
  10. ncbi request reprint A genome-wide set of congenic mouse strains derived from DBA/2J on a C57BL/6J background
    Richard C Davis
    Department of Microbiology, Immunology and Molecular Genetics, Department of Medicine, and Department of Human Genetics, University of California, Los Angeles, CA 90095 1679, USA
    Genomics 86:259-70. 2005
    ..These 65 strains cover more than 95% of the autosomal genome and should facilitate the analysis of the many genetic trait differences that have been reported between these parental strains...
  11. pmc Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids
    Christopher C Park
    Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
    Nat Genet 40:421-9. 2008
    ..Further, this work identifies 2,761 trans ceQTLs harboring no known genes, and provides evidence for a mode of gene expression autoregulation specific to the X chromosome...
  12. pmc Multiplex three-dimensional brain gene expression mapping in a mouse model of Parkinson's disease
    Vanessa M Brown
    Department of Molecular and Medical Pharmacology, School of Medicine, University of California, Los Angeles, CA 90095, USA
    Genome Res 12:868-84. 2002
    ....
  13. doi request reprint Screening reveals conserved and nonconserved transcriptional regulatory elements including an E3/E4 allele-dependent APOE coding region enhancer
    Hsuan Pu Chen
    Department of Biomedical Engineering, University of California, Los Angeles, CA 90095, USA
    Genomics 92:292-300. 2008
    ..Our results suggest a wider variety of mammalian transcriptional regulatory sequences than is currently recognized and that these may include coding region SNPs...
  14. pmc A genome-scale map of expression for a mouse brain section obtained using voxelation
    Mark H Chin
    Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
    Physiol Genomics 30:313-21. 2007
    ..The genome-scale maps of gene expression obtained using voxelation will be a valuable tool for the neuroscience community...
  15. pmc An integrative genetics approach to identify candidate genes regulating BMD: combining linkage, gene expression, and association
    Charles R Farber
    Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, California, USA
    J Bone Miner Res 24:105-16. 2009
    ..Integration of multiple genetic and genomic data sets can substantially improve the efficiency of QTL fine-mapping and candidate gene identification...
  16. ncbi request reprint Voxelation methods for genome scale imaging of brain gene expression
    Daniel M Sforza
    Department of Molecular and Medical Pharmacology, UCLA School of Medicine, Los Angeles, California 90095, USA
    Methods Enzymol 386:314-23. 2004
  17. ncbi request reprint High-resolution voxelation mapping of human and rodent brain gene expression
    Ram P Singh
    Department of Molecular and Medical Pharmacology, UCLA School of Medicine, 23 120 CHS, 90095 1735, Los Angeles, CA, USA
    J Neurosci Methods 125:93-101. 2003
    ..The voxelation instruments and their future iterations represent a valuable approach to the genome scale acquisition of gene expression patterns in the human and rodent brain...
  18. pmc Dual spatial maps of transcript and protein abundance in the mouse brain
    Christopher C Park
    Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
    Expert Rev Proteomics 6:243-9. 2009
    ..Genes are also identified that have strong correlations between mRNA and protein abundance. In addition, transcriptomic and proteomic analysis of mouse models of Parkinson's disease are discussed...
  19. ncbi request reprint Finding new candidate genes for learning and memory
    Tarek A Leil
    Department of Molecular and Medical Pharmacology, UCLA School of Medicine, Los Angeles, CA 90095, USA
    J Neurosci Res 68:127-37. 2002
    ..Using multiple strains to narrow down the number of candidate genes should be a useful general approach to genome-wide studies of behavioral and other complex traits...
  20. ncbi request reprint Gene expression tomography
    Vanessa M Brown
    Department of Molecular and Medical Pharmacology, University of California, Los Angeles 90095, USA
    Physiol Genomics 8:159-67. 2002
    ..A Monte-Carlo analysis confirmed the good quality of the GET image reconstruction. By speeding acquisition of gene expression patterns, GET may help improve our understanding of the genomics of the brain in both health and disease...
  21. ncbi request reprint Genome scale mapping of brain gene expression
    Ram P Singh
    Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, UCLA School of Medicine, Los Angeles, California 90095, USA
    Biol Psychiatry 53:1069-74. 2003
    ..These methods have been used to investigate neurologic diseases and their models in both humans and mice. The results of these studies are discussed, as is the future of high-throughput gene expression mapping in the brain...
  22. ncbi request reprint Voxelation and gene expression tomography for the acquisition of 3-D gene expression maps in the brain
    Dahai Liu
    Department of Molecular and Medical Pharmacology, UCLA School of Medicine, University of California, 23 120 CHS, Box 951735, Los Angeles, CA 90095 1735, USA
    Methods 31:317-25. 2003
    ..Here, we describe the methodologies underlying voxelation and GET and briefly outline the insights that can be obtained from these approaches...
  23. ncbi request reprint Mapping behavioral traits by use of genome-tagged mice
    Dahai Liu
    Department of Molecular and Medical Pharmacology and Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095 1735, USA
    Am J Geriatr Psychiatry 12:158-65. 2004
    ..Genome-tagged mice (GTMs) are sets of congenic mouse strains that span the entire mouse genome and are a promising reagent for localization of genes contributing to behavior...
  24. ncbi request reprint Anatomical methods for voxelation of the mammalian brain
    Daniel M Sforza
    Department of Molecular and Medical Pharmacology, School of Medicine, University of California, Los Angeles, California 90095 1735, USA
    Neurochem Res 29:1299-306. 2004
    ..It appears that the best protocol to provide the necessary resolution of neuroanatomical information in voxelation entails a controlled dose of fixation and thorough cryoprotection, complemented by histological staining...
  25. pmc A genome-wide map of human genetic interactions inferred from radiation hybrid genotypes
    Andy Lin
    Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
    Genome Res 20:1122-32. 2010
    ..The radiation hybrid (RH) network constitutes a platform for understanding the systems biology of the mammalian cell...
  26. ncbi request reprint Genes regulated by learning in the hippocampus
    Tarek A Leil
    Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, UCLA School of Medicine, Los Angeles, California, USA
    J Neurosci Res 71:763-8. 2003
    ..These genes may provide useful insights into the molecular mechanisms of hippocampal learning...
  27. pmc Differential expression and function of ABCG1 and ABCG4 during development and aging
    Dragana D Bojanic
    Department of Biological Chemistry at UCLA Los Angeles, CA 90095, USA
    J Lipid Res 51:169-81. 2010
    ..Finally, behavioral tests show that Abcg4(-/-) mice have a general deficit in associative fear memory. Together, these data indicate that loss of ABCG1 and/or ABCG4 from the CNS results in changes in metabolic pathways and in behavior...
  28. pmc Directed mammalian gene regulatory networks using expression and comparative genomic hybridization microarray data from radiation hybrids
    Sangtae Ahn
    Signal and Image Processing Institute, University of Southern California, Los Angeles, California, USA
    PLoS Comput Biol 5:e1000407. 2009
    ..Directed RH genetic networks thus showed concordance with pre-existing networks while also yielding information inaccessible to current undirected approaches...
  29. ncbi request reprint Investigation of different transcript quantitation tools for high-throughput mapping of brain gene expression using voxelation
    Ram P Singh
    Department of Molecular and Medical Pharmacology, UCLA School of Medicine, Los Angeles, CA 90095, USA
    J Mol Histol 35:397-402. 2004
    ..These data indicate the suitability of a number of transcript profiling tools for various levels of spatial resolution in voxelation...
  30. ncbi request reprint High-throughput imaging of brain gene expression
    Vanessa M Brown
    Department of Molecular and Medical Pharmacology, School of Medicine, University of California, Los Angeles, California 90095, USA
    Genome Res 12:244-54. 2002
    ..The results suggest that voxelation will be a useful approach for understanding how the genome constructs the brain...

Research Grants16

  1. Genome-tagged mice to identify behavior genes
    Desmond Smith; Fiscal Year: 2009
    ..v) Transgenic studies will confirm the identity of the responsible mutation. (2) The second aim is to analyze the entire set of GTMs using the battery of behavioral tests and localize additional loci of interest genome-wide. ..
  2. Voxelation: a new method for 3D gene expression analysis
    Desmond Smith; Fiscal Year: 2006
    ..This research promises important new insights into the nexus of genome and brain, in health and disease, and may also provide novel avenues to therapy. ..
  3. Transcriptome and proteome mapping of the mouse brain
    Desmond Smith; Fiscal Year: 2009
    ..1) At UCLA, Desmond Smith will map gene expression patterns at a genome-wide scale in the mouse brain at volumetric resolutions of 11 ul ..