James W Thomas

Summary

Affiliation: Emory University
Country: USA

Publications

  1. pmc Uprobe 2008: an online resource for universal overgo hybridization-based probe retrieval and design
    Robert T Sullivan
    Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
    Nucleic Acids Res 36:W149-53. 2008
  2. pmc Evolution of a bitter taste receptor gene cluster in a New World sparrow
    Jamie K Davis
    Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
    Genome Biol Evol 2:358-70. 2010
  3. pmc The chromosomal polymorphism linked to variation in social behavior in the white-throated sparrow (Zonotrichia albicollis) is a complex rearrangement and suppressor of recombination
    James W Thomas
    Department of Human Genetics, Emory University, Atlanta, Georgia 30322, USA
    Genetics 179:1455-68. 2008
  4. ncbi request reprint Comparative sequence analysis of a single-gene conserved segment in mouse and human
    James W Thomas
    Department of Human Genetics, Emory University School of Medicine, 615 Michael St, Suite 301 Atlanta, Georgia 30322, USA
    Mamm Genome 14:673-8. 2003
  5. pmc Haplotype-based genomic sequencing of a chromosomal polymorphism in the white-throated sparrow (Zonotrichia albicollis)
    Jamie K Davis
    Department of Human Genetics, Emory University School of Medicine, 615 Michael St, Suite 301, Atlanta, GA 30322, USA
    J Hered 102:380-90. 2011
  6. pmc Behavioral characterization of a white-throated sparrow homozygous for the ZAL2(m) chromosomal rearrangement
    Brent M Horton
    Department of Psychology, Emory University, Atlanta, GA 30322, USA
    Behav Genet 43:60-70. 2013
  7. pmc Development of genomic resources for the prairie vole (Microtus ochrogaster): construction of a BAC library and vole-mouse comparative cytogenetic map
    Lisa A McGraw
    Center for Behavioral Neuroscience, Emory University, Atlanta, GA, USA
    BMC Genomics 11:70. 2010
  8. pmc Variable molecular clocks in hominoids
    Navin Elango
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
    Proc Natl Acad Sci U S A 103:1370-5. 2006
  9. pmc BAC-based sequencing of behaviorally-relevant genes in the prairie vole
    Lisa A McGraw
    Center for Translational Social Neuroscience and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
    PLoS ONE 7:e29345. 2012
  10. pmc Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes
    Brent M Horton
    Department of Psychology, Emory University, Atlanta, GA 30322
    Proc Natl Acad Sci U S A 111:1443-8. 2014

Collaborators

  • Mario Cáceres
  • Lisa A McGraw
  • Brent M Horton
  • Lynn Y Huynh
  • D L Maney
  • David J Cutler
  • Ignacio T Moore
  • Todd M Preuss
  • Soojin V Yi
  • Pei Hsun Cheng
  • Judith L Fridovich-Keil
  • E D Green
  • Larry Young
  • WEBB COLBY MILLER
  • Mauricio Rojas
  • Arcadi Navarro
  • Alaine C Keebaugh
  • Jamie K Davis
  • Robert T Sullivan
  • Pamela J Thomas
  • Carlos A Acevedo-Suárez
  • Emily J Woodward
  • Josh J Lowman
  • Christa L Martin
  • Amanda E Carney
  • Shang Hsun Yang
  • Navin Elango
  • Wendy A Kellner
  • Jelena S Bezbradica
  • Tomas Marques-Bonet
  • Andres Rojas
  • Udaya DeSilva
  • Gaylen L Edwards
  • David Weinshenker
  • Kimberly G Freeman
  • Heather A Mitchell
  • Louis B Mittel
  • Meriem Gaval-Cruz
  • Pieter J de Jong
  • Maxim Koriabine
  • Boudewijn F H ten Hallers
  • Kerry R Garza
  • Lora J H Bean
  • Rebecca D Sanders
  • Lee Anne McGaha
  • Natalie L Kurtkaya
  • Bradford W Coffee
  • Anthony W S Chan
  • Caroline B Morehouse
  • Dawn M Kilkenny
  • Martha B Reich
  • Luc Van Kaer
  • Sebastian Joyce
  • Jeffrey A Bluestone
  • Naoto Matsuki
  • Helene Bour-Jordan
  • Aleksandar K Stanic
  • Brian H Carlson
  • Chrys Hulbert
  • Derya Unutmaz
  • Jaume Bertranpetit
  • Fingping Xu
  • Jennifer C McDowell
  • Laura Elnitski
  • Stephen M Beckstrom-Sternberg
  • Robert W Blakesley
  • Jeffrey W Touchman
  • Nicole L Dietrich
  • Jacquelyn R Idol
  • Weiniu Gan
  • Scott Schwartz
  • Gerard G Bouffard
  • Johannah L Doyle

Detail Information

Publications34

  1. pmc Uprobe 2008: an online resource for universal overgo hybridization-based probe retrieval and design
    Robert T Sullivan
    Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
    Nucleic Acids Res 36:W149-53. 2008
    ..In addition, Uprobe has the capability to design custom probes from multiple-species sequence alignments provided by the user, thus providing a general tool for targeted comparative physical mapping...
  2. pmc Evolution of a bitter taste receptor gene cluster in a New World sparrow
    Jamie K Davis
    Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
    Genome Biol Evol 2:358-70. 2010
    ..These results suggest that interspecies and intraspecies genetic variability does exist in avian TAS2Rs and that these differences could contribute to variation in bitter taste perception in birds...
  3. pmc The chromosomal polymorphism linked to variation in social behavior in the white-throated sparrow (Zonotrichia albicollis) is a complex rearrangement and suppressor of recombination
    James W Thomas
    Department of Human Genetics, Emory University, Atlanta, Georgia 30322, USA
    Genetics 179:1455-68. 2008
    ....
  4. ncbi request reprint Comparative sequence analysis of a single-gene conserved segment in mouse and human
    James W Thomas
    Department of Human Genetics, Emory University School of Medicine, 615 Michael St, Suite 301 Atlanta, Georgia 30322, USA
    Mamm Genome 14:673-8. 2003
    ..These finding illustrate that small genomic regions outside the large mouse-human conserved segments can contain a single gene as well as sequences that are apparently unique to one genome...
  5. pmc Haplotype-based genomic sequencing of a chromosomal polymorphism in the white-throated sparrow (Zonotrichia albicollis)
    Jamie K Davis
    Department of Human Genetics, Emory University School of Medicine, 615 Michael St, Suite 301, Atlanta, GA 30322, USA
    J Hered 102:380-90. 2011
    ..Overall, these results provide important insights into the genomic attributes of an inversion polymorphism linked to mate choice and variation in social behavior...
  6. pmc Behavioral characterization of a white-throated sparrow homozygous for the ZAL2(m) chromosomal rearrangement
    Brent M Horton
    Department of Psychology, Emory University, Atlanta, GA 30322, USA
    Behav Genet 43:60-70. 2013
    ....
  7. pmc Development of genomic resources for the prairie vole (Microtus ochrogaster): construction of a BAC library and vole-mouse comparative cytogenetic map
    Lisa A McGraw
    Center for Behavioral Neuroscience, Emory University, Atlanta, GA, USA
    BMC Genomics 11:70. 2010
    ....
  8. pmc Variable molecular clocks in hominoids
    Navin Elango
    School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
    Proc Natl Acad Sci U S A 103:1370-5. 2006
    ..Notably, chimpanzees also exhibit a slower rate of molecular evolution compared to gorillas and orangutans in the regions analyzed...
  9. pmc BAC-based sequencing of behaviorally-relevant genes in the prairie vole
    Lisa A McGraw
    Center for Translational Social Neuroscience and Yerkes National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
    PLoS ONE 7:e29345. 2012
    ..In summary, the results of our study provide the genomic resources necessary for the molecular and genetic characterization of a high-priority set of candidate genes for regulating social behavior in the prairie vole...
  10. pmc Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes
    Brent M Horton
    Department of Psychology, Emory University, Atlanta, GA 30322
    Proc Natl Acad Sci U S A 111:1443-8. 2014
    ..Our results suggest that in this species, differentiation of ESR1 has played a causal role in the evolution of phenotypes with alternative life-history strategies. ..
  11. ncbi request reprint Gene duplication and inactivation in the HPRT gene family
    Alaine C Keebaugh
    Department of Human Genetics, School of Medicine, Atlanta, GA 30322, USA
    Genomics 89:134-42. 2007
    ..Finally, we report our finding that PRTFDC1 was recently inactivated in the mouse lineage and propose the loss of function of this gene as a candidate genetic basis for the phenotypic disparity between HPRT-deficient humans and mice...
  12. pmc A genetic linkage map and comparative mapping of the prairie vole (Microtus ochrogaster) genome
    Lisa A McGraw
    Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
    BMC Genet 12:60. 2011
    ..Though a karyotype for the prairie vole has been reported and low-resolution comparative cytogenetic analyses have been done in this species, other basic genetic resources for this species, such as a genetic linkage map, are lacking...
  13. pmc A W-linked palindrome and gene conversion in New World sparrows and blackbirds
    Jamie K Davis
    Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
    Chromosome Res 18:543-53. 2010
    ..Near-identical palindromes are therefore present on the avian W chromosome and may persist due to the same forces proposed for the enrichment of these elements on the human sex chromosomes...
  14. ncbi request reprint The gene of retroviral origin Syncytin 1 is specific to hominoids and is inactive in Old World monkeys
    Mario Cáceres
    Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Suite 301, Atlanta, GA 30322, USA
    J Hered 97:100-6. 2006
    ..Our results indicate that Syncytin 1 is indeed a hominoid-specific gene and illustrate the complex and dynamic process associated with the origin of new genes...
  15. pmc PRTFDC1 is a genetic modifier of HPRT-deficiency in the mouse
    Alaine C Keebaugh
    Yerkes National Primate Research Center, Atlanta, Georgia, United States of America
    PLoS ONE 6:e22381. 2011
    ..These results demonstrate that PRTFDC1 is a genetic modifier of HPRT-deficiency in the mouse and could therefore have important implications for unraveling the molecular etiology of LND...
  16. pmc Contrasting population genetic patterns within the white-throated sparrow genome (Zonotrichia albicollis)
    Lynn Y Huynh
    Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
    BMC Genet 11:96. 2010
    ..It has thus been predicted that nucleotide diversity is negatively correlated with chromosome size in aves. However, there is limited empirical evidence to support this prediction...
  17. pmc Uprobe: a genome-wide universal probe resource for comparative physical mapping in vertebrates
    Wendy A Kellner
    Emory University School of Medicine, Department of Human Genetics, Atlanta, Georgia 30322, USA
    Genome Res 15:166-73. 2005
    ..Future implementation of the universal probe design strategy will be used to create an expanded number of whole-genome probe sets that will encompass all vertebrate genomes...
  18. pmc The evolutionary fate of the genes encoding the purine catabolic enzymes in hominoids, birds, and reptiles
    Alaine C Keebaugh
    Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
    Mol Biol Evol 27:1359-69. 2010
    ..Thus, adaptive single-gene losses have the potential to influence the long-term evolutionary fate of functionally interrelated genes...
  19. doi request reprint Comparative physical mapping: Universal overgo hybridization probe design and BAC library hybridization
    James W Thomas
    Department of Human Genetics, Emory University School of Medicine, Atlanta, GA
    Methods Mol Biol 422:119-32. 2008
    ..Once 'universal' overgo hybridization probes are designed, simple and uniform labeling and hybridization conditions can be carried out to exploit the utility of these probes for targeted comparative physical mapping...
  20. ncbi request reprint Increased cortical expression of two synaptogenic thrombospondins in human brain evolution
    Mario Cáceres
    Division of Neuroscience and Center for Behavioral Neuroscience, Yerkes National Primate Research Center, Emory University, 954 Gatewood Road, Atlanta, GA 30329, USA
    Cereb Cortex 17:2312-21. 2007
    ....
  21. doi request reprint Lentiviral integration preferences in transgenic mice
    Shang Hsun Yang
    Division of Neuroscience, Yerkes National Primate Research Center, Emory University, 954 Gatewood Road N E, Atlanta, GA 30329, USA
    Genesis 46:711-8. 2008
    ..Our findings suggested that lentiviruses were biased to integrate into the intragenic regions of early embryonic genome of mouse...
  22. pmc Origins, distribution and expression of the Duarte-2 (D2) allele of galactose-1-phosphate uridylyltransferase
    Amanda E Carney
    Emory University, Atlanta, USA
    Hum Mol Genet 18:1624-32. 2009
    ....
  23. pmc The genomes of the South American opossum (Monodelphis domestica) and platypus (Ornithorhynchus anatinus) encode a more complete purine catabolic pathway than placental mammals
    Alaine C Keebaugh
    Graduate Program in Population Biology, Ecology and Evolution, Emory University, Atlanta, GA 30322, USA
    Comp Biochem Physiol Part D Genomics Proteomics 4:174-8. 2009
    ..Our results therefore provide a revised history for gene loss in the purine catabolic pathway and suggest that marsupials and monotremes represent a third class of mammals with respect to their end products of purine catabolism...
  24. pmc Pericentromeric duplications in the laboratory mouse
    James W Thomas
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 13:55-63. 2003
    ..Together, these findings demonstrate that pericentromeric duplications are not restricted to primates and may be a common mechanism for genome evolution in mammals...
  25. pmc A recurrent inversion on the eutherian X chromosome
    Mario Cáceres
    Genes and Disease Program, Center for Genomic Regulation, 08003 Barcelona, Spain
    Proc Natl Acad Sci U S A 104:18571-6. 2007
    ..These results provide an extreme example in support of the evolutionary breakpoint reusage hypothesis and point out that some near-identical human segmental duplications may, in fact, have originated >100 million years ago...
  26. ncbi request reprint Multiple germline kappa light chains generate anti-insulin B cells in nonobese diabetic mice
    Emily J Woodward
    Department of Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    J Immunol 175:1073-9. 2005
    ..These findings show that a diverse repertoire of anti-insulin B cells is part of the autoimmune process in NOD mice and structural or regulatory elements within the kappa locus may be shared with a systemic autoimmune disease...
  27. ncbi request reprint The natural autoantibody repertoire of nonobese diabetic mice is highly active
    James W Thomas
    Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    J Immunol 169:6617-24. 2002
    ..In NOD, the large pool of self-reactive B cells may fuel autoimmune beta cell destruction by facilitating T-B cell interactions, as evidenced by the identification of one mAb that has undergone Ag-driven somatic hypermutation...
  28. pmc Parallel construction of orthologous sequence-ready clone contig maps in multiple species
    James W Thomas
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 12:1277-85. 2002
    ..The described approach can be used to facilitate the multispecies comparative sequencing of targeted genomic regions and can be adapted for constructing BAC contig maps in other vertebrates...
  29. ncbi request reprint Uncoupling of anergy from developmental arrest in anti-insulin B cells supports the development of autoimmune diabetes
    Carlos A Acevedo-Suárez
    Department of Medicine, Vanderbilt University, Nashville, TN 37232, USA
    J Immunol 174:827-33. 2005
    ..These findings suggest that the degree of functional impairment, rather than an overt breach of tolerance, is a critical feature that governs B cell contribution to T cell-mediated autoimmune disease...
  30. ncbi request reprint Impaired intracellular calcium mobilization and NFATc1 availability in tolerant anti-insulin B cells
    Carlos A Acevedo-Suárez
    Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    J Immunol 177:2234-41. 2006
    ..Rather, BCRs that are occupied by autologous insulin deliver signals that induce changes in intracellular calcium mobilization and maintain tolerance by preventing activation of key transcription factors such as NFAT...
  31. ncbi request reprint Distinct roles of dendritic cells and B cells in Va14Ja18 natural T cell activation in vivo
    Jelena S Bezbradica
    Department of Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
    J Immunol 174:4696-705. 2005
    ..Thus, the differential immune outcome based on the type of APC that displays glycolipid Ags in vivo has implications for the design of therapies that harness the immunoregulatory functions of iNKT cells...
  32. ncbi request reprint Structure and function of CD72 in the non-obese diabetic (NOD) mouse
    Andres Rojas
    Department of Medicine, Vanderbilt University Medical Center, 21st and Garland Avenues, Medical Center North T 3219 Nashville, TN 37232 2681, USA
    Autoimmunity 36:233-9. 2003
    ..NOD and lupus prone strains share the CD72c allele and its functions may contribute to overlapping features of organ specific and systemic autoimmune disorders...
  33. ncbi request reprint Chromosomal rearrangements and the genomic distribution of gene-expression divergence in humans and chimpanzees
    Tomas Marques-Bonet
    Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Doctor Aiguader, 80 08003 Barcelona, Catalonia, Spain
    Trends Genet 20:524-9. 2004
    ..In addition, our results are consistent with a role for some rearrangements in the original speciation events that separated the human and chimpanzee lineages...
  34. pmc Generation and comparative analysis of approximately 3.3 Mb of mouse genomic sequence orthologous to the region of human chromosome 7q11.23 implicated in Williams syndrome
    Udaya DeSilva
    Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
    Genome Res 12:3-15. 2002
    ....

Research Grants5

  1. Comparative Physical Mapping with Universal Probes
    James Thomas; Fiscal Year: 2004
    ..The resulting information and technology will be applicable to the simultaneous construction and comparison of clone-based physical maps in multiple species at any genomic locus. ..
  2. Uprobe: A Genome-Wide Resource for Isolating Nonhuman Primate Genomic Clones
    James Thomas; Fiscal Year: 2007
    ....
  3. Comparative genetics of Lesch-Nyhan disease
    James Thomas; Fiscal Year: 2007
    ....