Thomas Drake

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint Genetic loci determining bone density in mice with diet-induced atherosclerosis
    T A Drake
    Departments of Pathology and Laboratory Medicine, University of California, Los Angeles, California 90095, USA
    Physiol Genomics 5:205-15. 2001
  2. pmc Integrating genetic and gene expression data: application to cardiovascular and metabolic traits in mice
    Thomas A Drake
    Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA 90095 1732, USA
    Mamm Genome 17:466-79. 2006
  3. pmc Tissue-specific expression and regulation of sexually dimorphic genes in mice
    Xia Yang
    Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
    Genome Res 16:995-1004. 2006
  4. pmc Allele-specific expression and eQTL analysis in mouse adipose tissue
    Yehudit Hasin-Brumshtein
    Department of Medicine Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
    BMC Genomics 15:471. 2014
  5. pmc Genomic analysis of metabolic pathway gene expression in mice
    Anatole Ghazalpour
    Department of Human Genetics, Molecular Biology Institute, University of California, Los Angeles, CA 90095 1679, USA
    Genome Biol 6:R59. 2005
  6. ncbi request reprint Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Proteomics approaches to the systems biology of cardiovascular diseases
    Thomas A Drake
    Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, USA
    J Lipid Res 48:1-8. 2007
  7. ncbi request reprint Integrating genetic and gene expression data to study the metabolic syndrome and diabetes in mice
    Thomas A Drake
    Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA 90095 1732, USA
    Am J Ther 12:503-11. 2005
  8. ncbi request reprint Genetic loci influencing natural variations in femoral bone morphometry in mice
    T A Drake
    Department of Pathology, University of California at Los Angeles, 90095 1732, USA
    J Orthop Res 19:511-7. 2001
  9. pmc Integrating genetic and network analysis to characterize genes related to mouse weight
    Anatole Ghazalpour
    Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California, USA
    PLoS Genet 2:e130. 2006
  10. ncbi request reprint Identification of pathways for atherosclerosis in mice: integration of quantitative trait locus analysis and global gene expression data
    Susanna S Wang
    Department of Human Genetics, University of California at Los Angeles, Los Angeles, CA 90095 1679, USA
    Circ Res 101:e11-30. 2007

Research Grants

Collaborators

Detail Information

Publications37

  1. ncbi request reprint Genetic loci determining bone density in mice with diet-induced atherosclerosis
    T A Drake
    Departments of Pathology and Laboratory Medicine, University of California, Los Angeles, California 90095, USA
    Physiol Genomics 5:205-15. 2001
    ..This study shows that bone mass in older female mice with atherosclerosis has multiple genetic determinants and provides phenotypic and genetic evidence linking the regulation of bone density with adipose tissue and plasma lipids...
  2. pmc Integrating genetic and gene expression data: application to cardiovascular and metabolic traits in mice
    Thomas A Drake
    Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA 90095 1732, USA
    Mamm Genome 17:466-79. 2006
    ..In this review we discuss the basic concepts and applications of this integrative genomic approach to cardiovascular and metabolic diseases...
  3. pmc Tissue-specific expression and regulation of sexually dimorphic genes in mice
    Xia Yang
    Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
    Genome Res 16:995-1004. 2006
    ..Moreover, many tissue-specific transcription factor binding sites were found to be enriched in the sexually dimorphic genes...
  4. pmc Allele-specific expression and eQTL analysis in mouse adipose tissue
    Yehudit Hasin-Brumshtein
    Department of Medicine Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
    BMC Genomics 15:471. 2014
    ..Yet, due to technical limitations of expression microarrays, the vast majority of eQTL studies performed in the last decade used a genomic distance based definition as a surrogate for cis, therefore exploring local rather than cis-eQTLs...
  5. pmc Genomic analysis of metabolic pathway gene expression in mice
    Anatole Ghazalpour
    Department of Human Genetics, Molecular Biology Institute, University of California, Los Angeles, CA 90095 1679, USA
    Genome Biol 6:R59. 2005
    ..Quantitative trait locus analyses were applied to the subcutaneous fat-mass trait and all gene-expression data. These data were then used to identify gene sets that are differentially perturbed in lean and obese mice...
  6. ncbi request reprint Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Proteomics approaches to the systems biology of cardiovascular diseases
    Thomas A Drake
    Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, CA, USA
    J Lipid Res 48:1-8. 2007
    ..We survey the key tools and methodologies used, present examples of how these are currently being used in the systems biology context, and discuss future directions...
  7. ncbi request reprint Integrating genetic and gene expression data to study the metabolic syndrome and diabetes in mice
    Thomas A Drake
    Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA 90095 1732, USA
    Am J Ther 12:503-11. 2005
    ..Recent advances in genetics and gene expression technology have greatly increased the knowledge to be derived from this approach when applied to traditional genetic studies...
  8. ncbi request reprint Genetic loci influencing natural variations in femoral bone morphometry in mice
    T A Drake
    Department of Pathology, University of California at Los Angeles, 90095 1732, USA
    J Orthop Res 19:511-7. 2001
    ..These findings show that genetic regulation of femoral bone morphology is complex, and are consistent with the distinct biologic processes that control longitudinal and lateral growth of the femur...
  9. pmc Integrating genetic and network analysis to characterize genes related to mouse weight
    Anatole Ghazalpour
    Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, California, USA
    PLoS Genet 2:e130. 2006
    ..Our approach results in the identification of genetic targets that influence gene modules (pathways) that are related to the clinical phenotypes of interest...
  10. ncbi request reprint Identification of pathways for atherosclerosis in mice: integration of quantitative trait locus analysis and global gene expression data
    Susanna S Wang
    Department of Human Genetics, University of California at Los Angeles, Los Angeles, CA 90095 1679, USA
    Circ Res 101:e11-30. 2007
    ..Thus, global gene expression in peripheral tissues can reflect the systemic perturbations that contribute to atherosclerosis...
  11. pmc Expression quantitative trait loci: replication, tissue- and sex-specificity in mice
    Atila Van Nas
    Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
    Genetics 185:1059-68. 2010
    ..We conclude that most local eQTL are highly replicable between mouse crosses, tissues, and sex as compared to distal eQTL, which exhibited modest replicability...
  12. pmc Cis-acting expression quantitative trait loci in mice
    Sudheer Doss
    Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
    Genome Res 15:681-91. 2005
    ....
  13. pmc Weighted gene coexpression network analysis strategies applied to mouse weight
    Tova F Fuller
    Department of Human Genetics, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California, USA
    Mamm Genome 18:463-72. 2007
    ..These examples provide evidence that integration of network properties may well help chart the path across the gene-trait chasm...
  14. ncbi request reprint Integrating genotypic and expression data in a segregating mouse population to identify 5-lipoxygenase as a susceptibility gene for obesity and bone traits
    Margarete Mehrabian
    Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 90095 1679, USA
    Nat Genet 37:1224-33. 2005
    ....
  15. pmc Genetic and genomic analysis of a fat mass trait with complex inheritance reveals marked sex specificity
    Susanna Wang
    Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
    PLoS Genet 2:e15. 2006
    ..These data have implications on the potential effects of sex on the genetic regulation of other complex traits...
  16. 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...
  17. pmc Identification of Abcc6 as the major causal gene for dystrophic cardiac calcification in mice through integrative genomics
    Haijin Meng
    Department of Medicine, Cardiology Division, University of California Los Angeles, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 104:4530-5. 2007
    ..Our results demonstrate the power of the integrative genomics in discovering causal genes and pathways underlying complex traits...
  18. ncbi request reprint Genetic characterization of the Dyscalc locus
    Veronica V Colinayo
    Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, 90095, USA
    Mamm Genome 13:283-8. 2002
    ..The congenic strains exhibit little or no myocardial or vascular calcification, unlike the background HcB C3H strain, and the calcification segregated as a Mendelian factor, allowing finer mapping of Dyscalc...
  19. pmc Validation of candidate causal genes for obesity that affect shared metabolic pathways and networks
    Xia Yang
    Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
    Nat Genet 41:415-23. 2009
    ..Integration of gene expression in the design and analysis of traditional F(2) intercross studies allows high-confidence prediction of causal genes and identification of pathways and networks involved...
  20. ncbi request reprint Differential effects of two types of formative assessment in predicting performance of first-year medical students
    Sally Krasne
    Department of Physiology, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095 1751, USA
    Adv Health Sci Educ Theory Pract 11:155-71. 2006
    ..Open-book, un-timed assessments of higher order processes appeared to be better predictors of overall summative performance than closed-book, timed assessments of factual recall and image recognition...
  21. pmc Disruption of the aortic elastic lamina and medial calcification share genetic determinants in mice
    Susanna S Wang
    Department of Human Genetics, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
    Circ Cardiovasc Genet 2:573-82. 2009
    ..Disruption of the elastic lamina, as an early indicator of aneurysm formation, and vascular calcification frequently occur together in atherosclerotic lesions of humans...
  22. ncbi request reprint ENU large-scale mutagenesis and quantitative trait linkage (QTL) analysis in mice: novel technologies for searching polygenetic determinants of craniofacial abnormalities
    Ichiro Nishimura
    The Jane and Jerry Weintraub Center for Reconstructive Biotechnology, Division of Advanced Prosthodontics, Biomaterials and Hospital Dentistry, UCLA School of Dentistry, Box 951668, CHS B3 087, Los Angeles, CA 90095, USA
    Crit Rev Oral Biol Med 14:320-30. 2003
    ..These approaches will produce a wealth of new data on critical genes that influence the size and shape of the human face...
  23. 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...
  24. pmc Elucidating the role of gonadal hormones in sexually dimorphic gene coexpression networks
    Atila Van Nas
    Department of Human Genetics, University of California, Los Angeles, California 90095 1679, USA
    Endocrinology 150:1235-49. 2009
    ..This study indicates that gonadal hormones play a strong role in sex differences in gene expression. In addition, it results in the identification of sex-specific gene coexpression networks related to genetic and metabolic traits...
  25. ncbi request reprint Mapping, genetic isolation, and characterization of genetic loci that determine resistance to atherosclerosis in C3H mice
    Susanna S Wang
    UCLA School of Medicine, Dept of Human Genetics, Box 95167, University of California at Los Angeles, Los Angeles, CA 90095 1679, USA
    Arterioscler Thromb Vasc Biol 27:2671-6. 2007
    ..To identify the genetic factors involved in lesion initiation, we studied a cross between C3H and the susceptible strain C57BL/6J (B6) on a hyperlipidemic (apolipoprotein E-null) background...
  26. ncbi request reprint Thematic review series: The pathogenesis of atherosclerosis. Toward a biological network for atherosclerosis
    Anatole Ghazalpour
    Department of Human Genetics, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095 1679, USA
    J Lipid Res 45:1793-805. 2004
    ..In this review, we discuss how the integration of genetics and technologies such as transcriptomics and proteomics, combined with mathematical modeling, may lead to an understanding of such networks...
  27. pmc A high-resolution association mapping panel for the dissection of complex traits in mice
    Brian J Bennett
    Department of Medicine Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
    Genome Res 20:281-90. 2010
    ..This resource, termed the Hybrid Mouse Diversity Panel, makes possible the integration of multiple data sets and should prove useful for systems-based approaches to complex traits and studies of gene-by-environment interactions...
  28. ncbi request reprint Genetic loci contributing to age-related hippocampal lesions in mice
    Kelly L Krass
    Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095, USA
    Neurobiol Dis 13:102-8. 2003
    ..The genomic data indicate that the genetic basis is complex, but with one locus playing a major role in lesion formation. These lesions may represent a useful model for investigating dysregulation of tau protein in the hippocampus...
  29. pmc Upstream transcription factor 1 influences plasma lipid and metabolic traits in mice
    Sulin Wu
    Department of Human Genetics, David Geffen School of Medicine at University of California, Los Angeles, CA 90095, USA
    Hum Mol Genet 19:597-608. 2010
    ..In all three mouse model settings, notable sex specificity was observed, consistent with human studies showing differences in association with USF1 gene polymorphisms between sexes...
  30. ncbi request reprint Genetic loci for diet-induced atherosclerotic lesions and plasma lipids in mice
    Veronica V Colinayo
    Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California 90095, USA
    Mamm Genome 14:464-71. 2003
    ..In this intercross, the genes primarily influencing atherosclerosis are distinct from those controlling plasma lipid levels...
  31. pmc A systems-based framework for understanding complex metabolic and cardiovascular disorders
    Sulin Wu
    Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095 1679, USA
    J Lipid Res 50:S358-63. 2009
    ..By applying statistical methods, relationships between DNA variation, gene expression patterns, and diseases can be modeled...
  32. ncbi request reprint Genetics of gene expression surveyed in maize, mouse and man
    Eric E Schadt
    Rosetta Inpharmatics, LLC, 12040 115th Avenue N E, Kirkland, Washington 98034, USA
    Nature 422:297-302. 2003
    ..We identify a gene expression pattern strongly associated with obesity in a murine cross, and observe two distinct obesity subtypes. Furthermore, we find that these obesity subtypes are under the control of different loci...
  33. pmc Mapping the genetic architecture of gene expression in human liver
    Eric E Schadt
    Rosetta Inpharmatics, Seattle, Washington, United States of America
    PLoS Biol 6:e107. 2008
    ..We also identify SORT1 and CELSR2 as candidate susceptibility genes for a locus recently associated with coronary artery disease and plasma low-density lipoprotein cholesterol levels in the process...
  34. ncbi request reprint Genetic backgrounds but not sizes of atherosclerotic lesions determine medial destruction in the aortic root of apolipoprotein E-deficient mice
    Weibin Shi
    Department of Radiology, University of Virginia, Charlottesville 22908, USA
    Arterioscler Thromb Vasc Biol 23:1901-6. 2003
    ..We sought to assess the integrity of atherosclerotic aortic walls in 2 apoE-/- strains, C57BL/6 (B6) and C3H/HeJ (C3H) that differ markedly in atherosclerosis susceptibility...
  35. pmc An integrative genomics approach to infer causal associations between gene expression and disease
    Eric E Schadt
    Rosetta Inpharmatics, Seattle, Washington 98109, USA
    Nat Genet 37:710-7. 2005
    ..We also demonstrate the utility of this approach by identifying and experimentally validating the involvement of three new genes in susceptibility to obesity...
  36. pmc Variations in DNA elucidate molecular networks that cause disease
    Yanqing Chen
    Rosetta Inpharmatics, LLC, Merck and Co, Inc, 401 Terry Avenue North, Seattle, Washington 98109, USA
    Nature 452:429-35. 2008
    ..Our analysis provides direct experimental support that complex traits such as obesity are emergent properties of molecular networks that are modulated by complex genetic loci and environmental factors...

Research Grants1