FACULTY RESEARCH

Faculty List

Desmond Smith, M.D., Ph.D.

Work Email Address: dsmith@mednet.ucla.edu

Lab Number: 310-794-5711

Office Phone Number: 310-206-0086

Smith Lab

Work Address:
CHS
Los Angeles, CA 90095 23-120 CHS
Campus - 173517
CA CHS
Los Angeles, CA 90095

Department / Division Affiliations
Professor, Molecular & Medical Pharmacology
Member, Bioinformatics GPB Home Area, Brain Research Institute, Genetics & Genomics GPB Home Area, Molecular Pharmacology GPB Home Area, Neuroscience GPB Home Area

Research Interests
We are developing experimental and analytical tools to extract biological meaning from the flood of information being produced by the genome projects. One effort is devoted toward creating comprehensive atlases of gene and protein expression in the mammalian brain. Other projects are aimed towards identifying genes for neural phenotypes in the mouse and dissecting gene regulatory networks in normal and cancer cells. My laboratory will continue to refine new technologies to study living matter at a genome-wide level and to develop new, highly specific therapeutic strategies for common diseases.


Publications

A selected list of publications:

Zheutlin AB, Viehman RW, Fortgang R, Borg J, Smith DJ, Suvisaari J, Therman S, Hultman CM, Cannon TD.   Cognitive endophenotypes inform genome-wide expression profiling in schizophrenia, Neuropsychology, 2016; 30: 40-52.
Khan AH, Bloom JS, Faridmoayer E, Smith DJ.   Genetic screening reveals a link between Wnt signaling and antitubulin drugs, Pharmacogenomics J, 2016; 16: 164-172.
Hasin-Brumshtein Y, Khan AH, Hormozdiari F, Pan C, Parks B, Petyuk VA, Piehowski PD, Bruemmer A, Pellegrini M, Xiao X, Eskin E, Smith RD, Lusis AJ, Smith DJ.   Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes, eLife, 2016; 5: e15614.
Lusis AJ, Seldin MM, Allayee H, Bennett B, Civelek M, Davis R, Eskin E, Farber C, Hui S, Mehrabian M, Norheim F, Pan C, Parks B, Rau CD, Smith DJ, Vallim T, Wang Y, Wang J.   The hybrid mouse diversity panel: a resource for systems genetics analysis of metabolic and cardiovascular traits. , J Lipid Res, 2016; 57: 925-942.
Lin A, Smith DJ.   Copy number networks to guide combinatorial therapy of cancer and proliferative disorders, In "Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology - Algorithms and Software Tools" , 2015; 401-419.
Zacharaki EI, Skoura A, An L, Smith DJ, Megalooikonomou V.   Combining gene expression and function in a spatially localized approach, Artificial Intelligence Applications and Innovations, IFIP Advances in Information and Communication Technology, 2012; 382: 566-575.
Khan AH, Lin A, Smith DJ.   Discovery and characterization of human exonic transcriptional regulatory elements, PLoS ONE, 2012; 7: e46098.
An L, Ling H, Obradovic Z, Smith DJ, Megalooikonomou V.   Learning pair-wise gene functional similarity by multiplex gene expression maps, BMC Bioinformatics, 2012; 13(Suppl 3): S1.
Ghazalpour Anatole, Bennett Brian, Petyuk Vladislav A, Orozco Luz, Hagopian Raffi, Mungrue Imran N, Farber Charles R, Sinsheimer Janet, Kang Hyun M, Furlotte Nicholas, Park Christopher C, Wen Ping-Zi, Brewer Heather, Weitz Karl, Camp David G, Pan Calvin, Yordanova Roumyana, Neuhaus Isaac, Tilford Charles, Siemers Nathan, Gargalovic Peter, Eskin Eleazar, Kirchgessner Todd, Smith Desmond J, Smith Richard D, Lusis Aldons J   Comparative analysis of proteome and transcriptome variation in mouse PLoS genetics, 2011; 7(6): e1001393.
Wang Richard T, Ahn Sangtae, Park Christopher C, Khan Arshad H, Lange Kenneth, Smith Desmond J   Effects of genome-wide copy number variation on expression in mammalian cells BMC genomics, 2011; 12(1): 562.
Park Christopher C, Gale Greg D, de Jong Simone, Ghazalpour Anatole, Bennett Brian J, Farber Charles R, Langfelder Peter, Lin Andy, Khan Arshad H, Eskin Eleazar, Horvath Steve, Lusis Aldons J, Ophoff Roel A, Smith Desmond J   Gene networks associated with conditional fear in mice identified using a systems genetics approach BMC systems biology, 2011; 5(6): 43.
Ranola John M O, Ahn Sangtae, Sehl Mary, Smith Desmond J, Lange Kenneth   A Poisson model for random multigraphs Bioinformatics (Oxford, England), 2010; 26(16): 2004-11.
Lin Andy, Wang Richard T, Ahn Sangtae, Park Christopher C, Smith Desmond J   A genome-wide map of human genetic interactions inferred from radiation hybrid genotypes Genome research, 2010; 20(8): 1122-32.
Bojanic Dragana D, Tarr Paul T, Gale Greg D, Smith Desmond J, Bok Dean, Chen Bryan, Nusinowitz Steven, LÃvgren-Sandblom Anita, BjÃrkhem Ingemar, Edwards Peter A   Differential expression and function of ABCG1 and ABCG4 during development and aging Journal of lipid research, 2010; 51(1): 169-81.
Zhang Xu, Monroe Matthew E, Chen Baowei, Chin Mark H, Heibeck Tyler H, Schepmoes Athena A, Yang Feng, Petritis Brianne O, Camp David G, Pounds Joel G, Jacobs Jon M, Smith Desmond J, Bigelow Diana J, Smith Richard D, Qian Wei-Jun   Endogenous 3,4-dihydroxyphenylalanine and dopaquinone modifications on protein tyrosine: links to mitochondrially derived oxidative stress via hydroxyl radical Molecular & cellular proteomics : MCP, 2010; 9(6): 1199-208.
Petyuk Vladislav A, Qian Wei-Jun, Smith Richard D, Smith Desmond J   Mapping protein abundance patterns in the brain using voxelation combined with liquid chromatography and mass spectrometry Methods (San Diego, Calif.), 2010; 50(2): 77-84.
Zhang Xu, Zhou Jian-Ying, Chin Mark H, Schepmoes Athena A, Petyuk Vladislav A, Weitz Karl K, Petritis Brianne O, Monroe Matthew E, Camp David G, Wood Stephen A, Melega William P, Bigelow Diana J, Smith Desmond J, Qian Wei-Jun, Smith Richard D   Region-specific protein abundance changes in the brain of MPTP-induced Parkinson's disease mouse model Journal of proteome research, 2010; 9(3): 1496-509.
Farber Charles R, van Nas Atila, Ghazalpour Anatole, Aten Jason E, Doss Sudheer, Sos Brandon, Schadt Eric E, Ingram-Drake Leslie, Davis Richard C, Horvath Steve, Smith Desmond J, Drake Thomas A, Lusis Aldons J   An integrative genetics approach to identify candidate genes regulating BMD: combining linkage, gene expression, and association Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research, 2009; 24(1): 105-16.
An Li, Xie Hongbo, Chin Mark H, Obradovic Zoran, Smith Desmond J, Megalooikonomou Vasileios   Analysis of multiplex gene expression maps obtained by voxelation BMC bioinformatics, 2009; 10 Suppl 4(6): S10.
Ahn Sangtae, Wang Richard T, Park Christopher C, Lin Andy, Leahy Richard M, Lange Kenneth, Smith Desmond J   Directed mammalian gene regulatory networks using expression and comparative genomic hybridization microarray data from radiation hybrids PLoS computational biology, 2009; 5(6): e1000407.
Park Christopher C, Petyuk Vladislav A, Qian Wei-Jun, Smith Richard D, Smith Desmond J   Dual spatial maps of transcript and protein abundance in the mouse brain Expert review of proteomics, 2009; 6(3): 243-9.
Guedj FayÃal, SÃbrià Catherine, Rivals Isabelle, Ledru Aurelie, Paly Evelyne, Bizot Jean C, Smith Desmond, Rubin Edward, Gillet Brigitte, Arbones Mariona, Delabar Jean M   Green tea polyphenols rescue of brain defects induced by overexpression of DYRK1A PloS one, 2009; 4(2): e4606.
Smith Desmond J   Mitochondrial dysfunction in mouse models of Parkinson's disease revealed by transcriptomics and proteomics Journal of bioenergetics and biomembranes, 2009; 41(6): 487-91.
Park Christopher C, Ahn Sangtae, Bloom Joshua S, Lin Andy, Wang Richard T, Wu Tongtong, Sekar Aswin, Khan Arshad H, Farr Christine J, Lusis Aldons J, Leahy Richard M, Lange Kenneth, Smith Desmond J   Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids Nature genetics, 2008; 40(4): 421-9.
Ghazalpour Anatole, Doss Sudheer, Kang Hyun, Farber Charles, Wen Ping-Zi, Brozell Alec, Castellanos Ruth, Eskin Eleazar, Smith Desmond J, Drake Thomas A, Lusis Aldons J   High-resolution mapping of gene expression using association in an outbred mouse stock PLoS genetics, 2008; 4(8): e1000149.
Sebrià Catherine, Chabert Caroline, Ledru AurÃlie, Guedj FayÃal, Po Chrystelle, Smith Desmond J, Rubin Edward, Rivals Isabelle, Beloeil Jean-Claude, Gillet Brigitte, Delabar Jean-Maurice   Increased dosage of DYRK1A and brain volumetric alterations in a YAC model of partial trisomy 21 Anatomical record (Hoboken, N.J. : 2007), 2008; 291(3): 254-62.
Chin Mark H, Qian Wei-Jun, Wang Haixing, Petyuk Vladislav A, Bloom Joshua S, Sforza Daniel M, Laćan Goran, Liu Dahai, Khan Arshad H, Cantor Rita M, Bigelow Diana J, Melega William P, Camp David G, Smith Richard D, Smith Desmond J   Mitochondrial dysfunction, oxidative stress, and apoptosis revealed by proteomic and transcriptomic analyses of the striata in two mouse models of Parkinson's disease Journal of proteome research, 2008; 7(2): 666-77.
Chen Hsuan Pu, Lin Andy, Bloom Joshua S, Khan Arshad H, Park Christopher C, Smith Desmond J   Screening reveals conserved and nonconserved transcriptional regulatory elements including an E3/E4 allele-dependent APOE coding region enhancer Genomics, 2008; 92(5): 292-300.
Chin MH, Geng AB, Khan AH, Qian WJ, Petyuk VA, Boline J, Levy S, Toga AW, Smith RD, Leahy RM, Smith DJ.   A genome-scale map of expression for a mouse brain section obtained using voxelation, Physiol Genomics, 2007; 30: 313-321.
Rachidi Mohammed, Lopes Carmela, Vayssettes Catherine, Smith Desmond J, Rubin Edward M, Delabar Jean-Maurice   New cerebellar phenotypes in YAC transgenic mouse in vivo library of human Down syndrome critical region-1 Biochemical and biophysical research communications, 2007; 364(3): 488-94.
Petyuk VA, Qian WJ, Chin MH, Wang H, Livesay EA, Monroe ME, Adkins JN, Jaitly N, Anderson DJ, Camp DG 2nd, Smith DJ, Smith RD.   Spatial mapping of protein abundances in the mouse brain by voxelation integrated with high-throughput liquid chromatography-mass spectrometry, Genome Res, 2007; 17: 328-336.
Davis RC, Schadt EE, Smith DJ, Hsieh EW, Cervino AC, van Nas A, Rosales M, Doss S, Meng H, Allayee H, Lusis AJ.   A genome-wide set of congenic mouse strains derived from DBA/2J on a C57BL/6J background, Genomics, 2005; 86: 259-270.
Sforza DM, Annese J, Liu D, Levy S, Toga AW, Smith DJ   Anatomical methods for voxelation of the mammalian brain, Neurochemical Research, 2004; 29(6): 1299-306.
Singh RP, Liu D, Chaudhari A, Cherry SR, Leahy RM, Smith DJ   Investigation of different transcript quantitation tools for high-throughput mapping of brain gene expression using voxelation, Journal of Molecular Histology, 2004; 35(4): 397-402.
Branchi I, Bichler Z, Minghetti L, Delabar JM, Malchiodi-Albedi F, Gonzalez MC, Chettouh Z, Nicolini A, Chabert C, Smith DJ, Rubin EM, Migliore-Samour D, Alleva E   Transgenic mouse in vivo library of human Down syndrome critical region 1: association between DYRK1A overexpression, brain development abnormalities, and cell cycle protein alteration, Journal of Neuropathology and Experimental Neurology, 2004; 63(5): 429-440.
Sforza DM, Smith DJ   Voxelation methods for genome scale imaging of brain gene expression Methods in enzymology. , 2004; 386: 314-23.
Khan AH, Ossadtchi A, Leahy RM, Smith DJ   Error-correcting microarray design Genomics. , 2003; 81(2): 157-65.
Leil TA, Ossadtchi A, Nichols TE, Leahy RM, Smith DJ.   Genes regulated by learning in the hippocampus J Neurosci Res, 2003; 71: 763-768.
Sforza DM, Smith DJ.   Genetic and genomic strategies in learning and memory, Curr Genomics, 2003; 4:: 475-485.
Singh RP, Smith DJ   Genome scale mapping of brain gene expression Biological psychiatry. , 2003; 53(12): 1069-74.
Singh RP, Brown VM, Chaudhari A, Khan AH, Ossadtchi A, Sforza DM, Meadors AK, Cherry SR, Leahy RM, Smith DJ   High-resolution voxelation mapping of human and rodent brain gene expression Journal of Neuroscience Methods, 2003; 125(1-2): 93-101.
Liu D, Singh RP, Khan AH, Bhavsar K, Lusis AJ, Davis RC, Smith DJ   Identifying loci for behavioral traits using genome-tagged mice Journal of neuroscience research. , 2003; 74(4): 562-9.
Liu D, Singh RP, Khan AH, Lusis AJ, Davis RC, Smith DJ   Mapping behavioral traits by use of genome-tagged mice, The American Journal of Geriatric Psychiatry, 2003; 12(2): 158-65.
Smith DJ, Leil TA, Liu X   Neurotrophin-4 is required for tolerance to morphine in the mouse, Neuroscience Letters, 2003; 340(2): 103-6.
Liu D, Smith DJ   Voxelation and gene expression tomography for the acquisition of 3-D gene expression maps in the brain Methods (San Diego, Calif.) , 2003; 31(4): 317-25.
Shai S-Y, Harpf AE, Babbitt CJ, Jordan MC, Fishbein MC, Chen J, Omura M, Leil TA, Becker, KD, Jiang M, Smith DJ, Cherry SR, Loftus JC, Ross RS.   Cardiac-specific Cre-lox excision of the beta 1 integrin gene results in progressive fibrosis, defective mechanotransduction and cardiac failure, Circ Res, 2002; 90: 458-464.
Smith DJ.   Chips for brains, Curr Genomics, 2002; 3: 1-5.
Leil TA, Ossadtchi A, Cortes J, Leahy RM, Smith DJ.   Finding new candidate genes for learning and memory, J Neurosci Res, 2002; 68: 127-137.
Brown VM, Ossadtchi A, Khan AH, Gambhir SS, Cherry SR, Leahy RM, Smith DJ.   Gene expression tomography Physiol Genomics, 2002; 8: 159-167.
Brown VM, Ossadtchi A, Khan AH, Cherry SR, Leahy RM, Smith DJ.   High-throughput imaging of brain gene expression Genome Res, 2002; 12: 244-254.
Brown VM, Ossadtchi A, Khan AH, Yee S, Lacan G, Melega WP, Cherry SR, Leahy RM, Smith DJ,   Multiplex three-dimensional brain gene expression mapping in a mouse model of Parkinson's disease Genome research. , 2002; 12(6): 868-84.
Ossadtchi A, Brown VM, Khan AH, Cherry SR, Nichols TE, Leahy RM, Smith DJ   Statistical analysis of multiplex brain gene expression images Neurochemical research. , 2002; 27(10): 1113-21.
Smith DJ, Lusis AJ.   The allelic structure of common disease Hum Mol Genetics, 2002; 11: 2455-2461.
Smith, DJ   In vivo libraries of large insert transgenic mice for genetic mapping, Methods in Molecular Biology, 2001; 158: 335-349.
Smith, DJ   RAGE and PRAY, The Pharmacogenomics Journal, 2001; 1(2): 90-91.
Sayah DM, Khan AH, Gasperoni TL, Smith DJ   A genetic screen for novel behavioral mutations in mice Molecular psychiatry. , 2000; 5(4): 369-77.
Xie CW, Sayah D, Chen QS, Wei WZ, Smith DJ, Liu, X.   Deficient long-term memory and long-term potentiation in mice with a targeted deletion of neurotrophin-4 gene Proc Natl Acad Sci USA, 2000; 97: 8116-8121.
Hodgson JG, Agopyan N, Gutekunst CA, Leavitt BR, LePiane F, Singaraja R, Smith DJ, Bissada N, McCutcheon K, Nasir J, Jamot L, Li XJ, Stevens ME, Rosemond E, Roder JC, Phillips AG, Rubin EM, Hersch SM, Hayden MR   A YAC mouse model for Huntington's disease with full-length mutant huntingtin, cytoplasmic toxicity, and selective striatal neurodegeneration Neuron. , 1999; 23(1): 181-92.
Sago H, Carlson EJ, Smith DJ, Kilbridge J, Rubin EM, Mobley WC, Epstein CJ, Huang TT   Ts1Cje, a partial trisomy 16 mouse model for Down syndrome, exhibits learning and behavioral abnormalities Proceedings of the National Academy of Sciences of the United States of America. , 1998; 95(11): 6256-61.
Smith DJ, Stevens ME, Sudanagunta SP, Bronson RT, Makhinson M, Watabe AM, O'Dell TJ, Fung J, Weier HU, Cheng JF, Rubin EM   Functional screening of 2 Mb of human chromosome 21q22.2 in transgenic mice implicates minibrain in learning defects associated with Down syndrome Nature genetics. , 1997; 16(1): 28-36.
Rubin EM, Smith DJ   Optimizing the mouse to sift sequence for function Trends in genetics : TIG. , 1997; 13(11): 423-6.
Hamilton BA, Smith DJ, Mueller KL, Kerrebrock AW, Bronson RT, van Berkel V, Daly MJ, Kruglyak L, Reeve MP, Nemhauser JL, Hawkins TL, Rubin EM, Lander ES   The vibrator mutation causes neurodegeneration via reduced expression of PITP alpha: positional complementation cloning and extragenic suppression Neuron. , 1997; 18(5): 711-22.