Research Topics
| Desmond SmithSummaryAffiliation: University of California Country: USA Publications
Research Grants
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Detail Information
Publications
Learning pair-wise gene functional similarity by multiplex gene expression mapsLi 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...- Effects of genome-wide copy number variation on expression in mammalian cellsRichard 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)... - Gene networks associated with conditional fear in mice identified using a systems genetics approachChristopher 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... - Analysis of multiplex gene expression maps obtained by voxelationLi 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... 
The allelic structure of common diseaseDesmond 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...- Mitochondrial dysfunction in mouse models of Parkinson's disease revealed by transcriptomics and proteomicsDesmond 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.... - Mitochondrial dysfunction, oxidative stress, and apoptosis revealed by proteomic and transcriptomic analyses of the striata in two mouse models of Parkinson's diseaseMark 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... - High-resolution mapping of gene expression using association in an outbred mouse stockAnatole 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... - Identifying loci for behavioral traits using genome-tagged miceDahai 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... - A genome-wide set of congenic mouse strains derived from DBA/2J on a C57BL/6J backgroundRichard 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... - Fine mapping of regulatory loci for mammalian gene expression using radiation hybridsChristopher 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... - Multiplex three-dimensional brain gene expression mapping in a mouse model of Parkinson's diseaseVanessa 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.... 
Screening reveals conserved and nonconserved transcriptional regulatory elements including an E3/E4 allele-dependent APOE coding region enhancerHsuan 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...- A genome-scale map of expression for a mouse brain section obtained using voxelationMark 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... - An integrative genetics approach to identify candidate genes regulating BMD: combining linkage, gene expression, and associationCharles 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... - Voxelation methods for genome scale imaging of brain gene expressionDaniel M Sforza
Department of Molecular and Medical Pharmacology, UCLA School of Medicine, Los Angeles, California 90095, USA
Methods Enzymol 386:314-23. 2004 - High-resolution voxelation mapping of human and rodent brain gene expressionRam 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... - Dual spatial maps of transcript and protein abundance in the mouse brainChristopher 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... - Finding new candidate genes for learning and memoryTarek 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... - Gene expression tomographyVanessa 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... - Genome scale mapping of brain gene expressionRam 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... - Voxelation and gene expression tomography for the acquisition of 3-D gene expression maps in the brainDahai 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... - Mapping behavioral traits by use of genome-tagged miceDahai 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..CONCLUSIONS: The GTMs should be a valuable resource for mapping and confirmation of loci contributing to complex behavioral traits in the mouse, with ultimate implications for human genomic-based research, as well... - Anatomical methods for voxelation of the mammalian brainDaniel 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... - A genome-wide map of human genetic interactions inferred from radiation hybrid genotypesAndy 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... - Genes regulated by learning in the hippocampusTarek 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... - Differential expression and function of ABCG1 and ABCG4 during development and agingDragana 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... - Directed mammalian gene regulatory networks using expression and comparative genomic hybridization microarray data from radiation hybridsSangtae 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... - Investigation of different transcript quantitation tools for high-throughput mapping of brain gene expression using voxelationRam 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... - High-throughput imaging of brain gene expressionVanessa 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 Grants
- Genome-tagged mice to identify behavior genesDesmond 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. ..
- Voxelation: a new method for 3D gene expression analysisDesmond 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. ..
- Transcriptome and proteome mapping of the mouse brainDesmond 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 ..