James H Thomas

Summary

Affiliation: University of Washington
Country: USA

Publications

  1. pmc Analysis of homologous gene clusters in Caenorhabditis elegans reveals striking regional cluster domains
    James H Thomas
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Genetics 172:127-43. 2006
  2. pmc Adaptive evolution in two large families of ubiquitin-ligase adapters in nematodes and plants
    James H Thomas
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Genome Res 16:1017-30. 2006
  3. pmc Adaptive evolution in the SRZ chemoreceptor families of Caenorhabditis elegans and Caenorhabditis briggsae
    James H Thomas
    Department of Genome Sciences, University of Washington, Seattle, WA 91895, USA
    Proc Natl Acad Sci U S A 102:4476-81. 2005
  4. pmc The Caenorhabditis chemoreceptor gene families
    James H Thomas
    Department of Genome Sciences, University of Washington, Seattle, WA, USA
    BMC Biol 6:42. 2008
  5. pmc Evolution of C2H2-zinc finger genes revisited
    James H Thomas
    Department of Genome Sciences, University of Washington, Seattle, 91895, USA
    BMC Evol Biol 9:51. 2009
  6. pmc Extraordinary molecular evolution in the PRDM9 fertility gene
    James H Thomas
    Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
    PLoS ONE 4:e8505. 2009
  7. pmc Coevolution of retroelements and tandem zinc finger genes
    James H Thomas
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Genome Res 21:1800-12. 2011
  8. doi request reprint Genome evolution in Caenorhabditis
    James H Thomas
    Department of Genome Sciences, University of Washington, Seattle, WA, USA
    Brief Funct Genomic Proteomic 7:211-6. 2008
  9. pmc Rapid birth-death evolution specific to xenobiotic cytochrome P450 genes in vertebrates
    James H Thomas
    Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
    PLoS Genet 3:e67. 2007
  10. pmc Concerted evolution of two novel protein families in Caenorhabditis species
    James H Thomas
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Genetics 172:2269-81. 2006

Research Grants

  1. NEURAL CONTROL OF A MOTOR PROGRAM
    James Thomas; Fiscal Year: 2002
  2. GENETIC ANALYSIS OF CHEMOSENSATION IN C ELEGANS
    James Thomas; Fiscal Year: 2003
  3. Proteogenomic Analysis of C. elegans
    James Thomas; Fiscal Year: 2007

Collaborators

Detail Information

Publications40

  1. pmc Analysis of homologous gene clusters in Caenorhabditis elegans reveals striking regional cluster domains
    James H Thomas
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Genetics 172:127-43. 2006
    ..Although specific gene clusters have been documented in C. elegans, their abundance, genomic distribution, and unusual molecular identities were previously unrecognized...
  2. pmc Adaptive evolution in two large families of ubiquitin-ligase adapters in nematodes and plants
    James H Thomas
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Genome Res 16:1017-30. 2006
    ..I speculate that this system functions to combat viral pathogens or bacterial protein toxins...
  3. pmc Adaptive evolution in the SRZ chemoreceptor families of Caenorhabditis elegans and Caenorhabditis briggsae
    James H Thomas
    Department of Genome Sciences, University of Washington, Seattle, WA 91895, USA
    Proc Natl Acad Sci U S A 102:4476-81. 2005
    ..We interpret these results as indicating that the srz family is under positive selection, probably driven by ligand binding...
  4. pmc The Caenorhabditis chemoreceptor gene families
    James H Thomas
    Department of Genome Sciences, University of Washington, Seattle, WA, USA
    BMC Biol 6:42. 2008
    ..Animal genomes contain families of genes encoding chemoreceptors that mediate taste, olfaction, and pheromone responses. The size and diversity of these families reflect the biology of chemoperception in specific species...
  5. pmc Evolution of C2H2-zinc finger genes revisited
    James H Thomas
    Department of Genome Sciences, University of Washington, Seattle, 91895, USA
    BMC Evol Biol 9:51. 2009
    ..The authors also present evidence concerning the ancestral order in which the ZF-associated KRAB and SCAN domains were recruited to ZF proteins...
  6. pmc Extraordinary molecular evolution in the PRDM9 fertility gene
    James H Thomas
    Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
    PLoS ONE 4:e8505. 2009
    ..We suggest instead that PRDM9 is involved in some aspect of centromere segregation conflict and that rapidly evolving centromeric DNA drives changes in PRDM9 DNA-binding domains...
  7. pmc Coevolution of retroelements and tandem zinc finger genes
    James H Thomas
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Genome Res 21:1800-12. 2011
    ..Our results support a host-pathogen model for tandem ZF gene evolution, in which new LTR retroelement challenges drive duplication and divergence of host tandem ZF genes...
  8. doi request reprint Genome evolution in Caenorhabditis
    James H Thomas
    Department of Genome Sciences, University of Washington, Seattle, WA, USA
    Brief Funct Genomic Proteomic 7:211-6. 2008
    ....
  9. pmc Rapid birth-death evolution specific to xenobiotic cytochrome P450 genes in vertebrates
    James H Thomas
    Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
    PLoS Genet 3:e67. 2007
    ..Unstable gene islands in vertebrates share some functional properties with bacterial genomic islands, though they arise by local gene duplication rather than horizontal gene transfer...
  10. pmc Concerted evolution of two novel protein families in Caenorhabditis species
    James H Thomas
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Genetics 172:2269-81. 2006
    ..I speculate that these genes encode rapidly evolving antimicrobial peptides...
  11. pmc Identification of a novel gene family involved in osmotic stress response in Caenorhabditis elegans
    Jeanna M Wheeler
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Genetics 174:1327-36. 2006
    ..The phenotypes of osm-7 are not suppressed by mutations in MAP kinase or PKC pathways, suggesting that C. elegans uses signaling pathways different from yeast to mount a response to osmotic stress...
  12. pmc High genetic diversity in the chemoreceptor superfamily of Caenorhabditis elegans
    Mary K Stewart
    Department of Genome Sciences, University of Washington, Seattle, 98195, USA
    Genetics 169:1985-96. 2005
    ..This suggests that our sampling of wild diversity in C. elegans is narrow and that identification of additional strains from similarly isolated regions will greatly expand the diversity available for study...
  13. pmc Quantitative evidence for conserved longevity pathways between divergent eukaryotic species
    Erica D Smith
    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
    Genome Res 18:564-70. 2008
    ..Together, these findings indicate that the genetic component of life span determination is significantly conserved between divergent eukaryotic species, and suggest pathways that are likely to play a similar role in mammalian aging...
  14. ncbi request reprint NCR-1 and NCR-2, the C. elegans homologs of the human Niemann-Pick type C1 disease protein, function upstream of DAF-9 in the dauer formation pathways
    Jie Li
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
    Development 131:5741-52. 2004
    ..Our results support the hypothesis that ncr-1 and ncr-2 are involved in intracellular cholesterol processing in C. elegans, and that a sterol-signaling defect is responsible for the Daf-c phenotype of the ncr-2; ncr-1 mutant...
  15. pmc Adaptive evolution in zinc finger transcription factors
    Ryan O Emerson
    Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
    PLoS Genet 5:e1000325. 2009
    ..These results suggest that the poly-ZF genes are a major source of new transcriptional repression activity in humans and other primates...
  16. pmc Gypsy and the birth of the SCAN domain
    Ryan O Emerson
    Department of Genome Sciences, University of Washington, Seattle, Washington, USA
    J Virol 85:12043-52. 2011
    ..We speculate that the SCAN domain originally functioned to target host ZF proteins to retroelement capsids...
  17. pmc Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection
    Renee D George
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Genome Res 21:1686-94. 2011
    ..These results demonstrate the power of second-generation sequencing in comparative genomics and greatly expand the repertoire of available primate coding sequences...
  18. ncbi request reprint Behavioral genetics of caenorhabditis elegans unc-103-encoded erg-like K(+) channel
    David J Reiner
    Department of Genome Sciences, University of Washington, Seattle, WA, USA
    J Neurogenet 20:41-66. 2006
    ..In the egg-laying circuit, unc-103 is expressed in vulval muscles and the HSN neurons from different promoters. Supplying the proper UNC-103 isoform to the vulval muscles is sufficient to restore regulation to egg-laying behavior...
  19. pmc Fluoxetine-resistance genes in Caenorhabditis elegans function in the intestine and may act in drug transport
    Robert K M Choy
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    Genetics 172:885-92. 2006
    ..One model that explains these findings is that NRF-5 binds fluoxetine and influences its presentation or availability to in vivo targets...
  20. ncbi request reprint Lifespan extension in Caenorhabditis elegans by complete removal of food
    Tammi L Kaeberlein
    Department of Microbiology, University of Washington, Seattle, WA, USA
    Aging Cell 5:487-94. 2006
    ..Removal of bacterial food also increases lifespan when initiated in postreproductive adults, suggesting that dietary restriction started during middle age can result in a substantial longevity benefit that is independent of reproduction...
  21. pmc Comparative genomics and adaptive selection of the ATP-binding-cassette gene family in caenorhabditis species
    Zhongying Zhao
    British Columbia Cancer Research Center, Vancouver, British Columbia V5Z 1L6, Canada
    Genetics 175:1407-18. 2007
    ..Sites undergoing positive selection within subfamily D, which are implicated in very-long-chain fatty acid transport, were identified. The evolution of these sites might be driven by the changes in food source with time...
  22. pmc Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations
    Gennifer E Merrihew
    University of Washington, Department of Genome Sciences, Seattle, Washington 98195, USA
    Genome Res 18:1660-9. 2008
    ..In addition, the collection of identified peptides should facilitate future proteomics experiments targeted at specific proteins of interest...
  23. ncbi request reprint Molecular pathways that influence human tau-induced pathology in Caenorhabditis elegans
    Brian C Kraemer
    Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA 98108 1597, USA
    Hum Mol Genet 15:1483-96. 2006
    ..This work uncovers novel candidate genes that prevent tau toxicity, as well as genes previously implicated in tau-mediated neurodegeneration...
  24. ncbi request reprint Transcriptional outputs of the Caenorhabditis elegans forkhead protein DAF-16
    Joshua McElwee
    Molecular and Cellular Biology Program of the University of Washington and Fred Hutchinson Cancer Research Center, Seattle, WA 98195, USA
    Aging Cell 2:111-21. 2003
    ..Finally, we examined the in vivo role of 35 of these target genes by RNA-mediated interference and identified one gene encoding a putative protease that is necessary for the daf-2 Age phenotype...
  25. pmc The protein chaperone HSP90 can facilitate the divergence of gene duplicates
    Jennifer Lachowiec
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
    Genetics 193:1269-77. 2013
    ..Our data provide evidence that HSP90 influences selection on genes encoding its clients and facilitates divergence between gene duplicates...
  26. pmc Isolation and characterization of high-temperature-induced Dauer formation mutants in Caenorhabditis elegans
    Michael Ailion
    Molecular and Cellular Biology Program of the University of Washington and Fred Hutchinson Cancer Research Center, University of Washington, Seattle, Washington 98195, USA
    Genetics 165:127-44. 2003
    ..We also molecularly identify hid-1 and show that it encodes a novel highly conserved putative transmembrane protein expressed in neurons...
  27. pmc Neurodegeneration and defective neurotransmission in a Caenorhabditis elegans model of tauopathy
    Brian C Kraemer
    Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA 98108 1597, USA
    Proc Natl Acad Sci U S A 100:9980-5. 2003
    ..Postsynaptic transmission is intact. This transgenic model will enable mechanistic dissection of tau-induced neurodegeneration and identification of genes and compounds that inhibit pathological tau formation...
  28. ncbi request reprint Analysis of xbx genes in C. elegans
    Evgeni Efimenko
    Karolinska Institute, Department of Biosciences and Södertörn University College, Section of Natural Sciences, S 14189 Huddinge, Sweden
    Development 132:1923-34. 2005
    ..elegans, which includes genes for cilium structure, transport machinery, receptors and other factors...
  29. pmc In vivo identification of genes that modify ether-a-go-go-related gene activity in Caenorhabditis elegans may also affect human cardiac arrhythmia
    Christina I Petersen
    Department of Anesthesiology and Division of Clinical Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
    Proc Natl Acad Sci U S A 101:11773-8. 2004
    ..Our studies demonstrate the feasibility of using C. elegans to assay and potentially identify aLQTS candidate genes...
  30. pmc C. elegans anaplastic lymphoma kinase ortholog SCD-2 controls dauer formation by modulating TGF-beta signaling
    David J Reiner
    Howard Hughes Medical Institute and Department of Cell Biology, University of California, Berkeley, CA 94720, USA
    Curr Biol 18:1101-9. 2008
    ....
  31. ncbi request reprint Shared transcriptional signature in Caenorhabditis elegans Dauer larvae and long-lived daf-2 mutants implicates detoxification system in longevity assurance
    Joshua J McElwee
    Department of Biology, University College London, WC1E 6BT, United Kingdom
    J Biol Chem 279:44533-43. 2004
    ..By contrast, the daf-16-associated element was enriched in genes down-regulated in dauers and daf-2 mutants. Thus, particular promoter elements appear longevity-associated or aging associated...
  32. pmc Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization
    Jason S Maydan
    Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
    Genome Res 17:337-47. 2007
    ..elegans we used the whole-genome array to detect the extensive natural gene content variation (almost 2%) between the N2 Bristol strain and the strain CB4856, a strain isolated in Hawaii and JU258, a strain isolated in Madeira...
  33. pmc Genetic analysis of dauer formation in Caenorhabditis briggsae
    Takao Inoue
    HHMI and Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
    Genetics 177:809-18. 2007
    ..elegans is strongly induced to form dauers at temperatures above 26 degrees, near the upper limit for growth of C. elegans. In contrast, C. briggsae, which is capable of growth at higher temperatures than C. elegans, lacks this response...
  34. ncbi request reprint Dopaminergic neuronal loss and motor deficits in Caenorhabditis elegans overexpressing human alpha-synuclein
    Merja Lakso
    Department of Neurobiology, A I Virtanen Institute, Kuopio University, Finland
    J Neurochem 86:165-72. 2003
    ..This transgenic model in C. elegans, an invertebrate organism with excellent experimental resources for further genetic manipulation, may help facilitate dissection of pathophysiologic mechanisms of various synucleopathies...
  35. pmc Evolutionary conservation of regulated longevity assurance mechanisms
    Joshua J McElwee
    Department of Biology, University College London, London WC1E 6BT, UK
    Genome Biol 8:R132. 2007
    ..To address this, we have applied a novel, multi-level cross-species comparative analysis to compare gene expression changes accompanying increased longevity in mutant nematodes, fruitflies and mice with reduced IIS...
  36. pmc Intestinal signaling to GABAergic neurons regulates a rhythmic behavior in Caenorhabditis elegans
    Timothy R Mahoney
    Department of Anatomy and Neurobiology, Washington University School of Medicine, St Louis, MO 63110, USA
    Proc Natl Acad Sci U S A 105:16350-5. 2008
    ..We propose a model whereby the intestinal genes aex-4 and aex-5 control the DMP by regulating the secretion of a signal, which activates the neuronal receptor aex-2...
  37. pmc Mutator phenotype of Caenorhabditis elegans DNA damage checkpoint mutants
    Jasper Harris
    Department of Biology, University of North Carolina, NC 27599 3280, USA
    Genetics 174:601-16. 2006
    ..Although DNA damage response defects that predispose humans to cancer are known to result in large-scale chromosome aberrations, our results suggest that small- to medium-sized deletions may also play roles in the development of cancer...
  38. pmc An olfactory neuron responds stochastically to temperature and modulates Caenorhabditis elegans thermotactic behavior
    David Biron
    Department of Biology and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02454, USA
    Proc Natl Acad Sci U S A 105:11002-7. 2008
    ..Our observations suggest that the AFD and AWC neurons encode thermal stimuli via distinct strategies to regulate C. elegans thermotactic behavior...
  39. ncbi request reprint From eye of newt to chemical structure
    Piali Sengupta
    Nat Chem Biol 3:368-9. 2007
  40. pmc XBX-1 encodes a dynein light intermediate chain required for retrograde intraflagellar transport and cilia assembly in Caenorhabditis elegans
    Jenny C Schafer
    Department of Cell Biology, University of Alabama at Birmingham Medical Center, 35294, USA
    Mol Biol Cell 14:2057-70. 2003
    ..Our results suggest that the DLIC protein XBX-1 functions together with the CHE-3 dynein in retrograde IFT, downstream of the complex A proteins...

Research Grants3

  1. NEURAL CONTROL OF A MOTOR PROGRAM
    James Thomas; Fiscal Year: 2002
    ..We will also continue genetic screens to identify additional potential targets. ..
  2. GENETIC ANALYSIS OF CHEMOSENSATION IN C ELEGANS
    James Thomas; Fiscal Year: 2003
    ..All of the pathways under study here correspond to important regulatory pathways in humans, and many of the genes are affected in various inherited disorders. ..
  3. Proteogenomic Analysis of C. elegans
    James Thomas; Fiscal Year: 2007
    ..elegans proteome and a high-throughput pipeline that will allow similar analysis of any complex animal or plant proteome whose genome sequence is available. [unreadable] [unreadable] [unreadable]..