Paul D Thomas

Summary

Affiliation: SRI International
Country: USA

Publications

  1. ncbi request reprint On the quality of tree-based protein classification
    Betty Lazareva-Ulitsky
    Computational Biology Department, Applied Biosystems, Foster City, CA 94404, USA
    Bioinformatics 21:1876-90. 2005
  2. pmc Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools
    Paul D Thomas
    Evolutionary Systems Biology Group, SRI International 333 Ravenswood Ave, Menlo Park CA 94025, USA
    Nucleic Acids Res 34:W645-50. 2006
  3. pmc PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways
    Huaiyu Mi
    Evolutionary Systems Biology Group, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
    Nucleic Acids Res 35:D247-52. 2007
  4. pmc PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium
    Huaiyu Mi
    Evolutionary Systems Biology Group, SRI International, Lawrence Berkeley National Laboratory, USA
    Nucleic Acids Res 38:D204-10. 2010
  5. pmc Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire
    C André Lévesque
    Agriculture and Agri Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
    Genome Biol 11:R73. 2010
  6. ncbi request reprint Ontology annotation: mapping genomic regions to biological function
    Paul D Thomas
    Evolutionary Systems Biology Group, Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA
    Curr Opin Chem Biol 11:4-11. 2007
  7. doi request reprint A systems biology network model for genetic association studies of nicotine addiction and treatment
    Paul D Thomas
    Evolutionary Systems Biology, Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA
    Pharmacogenet Genomics 19:538-51. 2009
  8. pmc Dopamine genes and nicotine dependence in treatment-seeking and community smokers
    Andrew W Bergen
    Center for Health Sciences, SRI International, Menlo Park, CA 94025, USA
    Neuropsychopharmacology 34:2252-64. 2009
  9. pmc GIGA: a simple, efficient algorithm for gene tree inference in the genomic age
    Paul D Thomas
    Evolutionary Systems Biology Group, SRI International, Menlo Park, CA, USA
    BMC Bioinformatics 11:312. 2010
  10. doi request reprint PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools
    James C Hu
    Department of Biochemistry and Biophysics, Texas A and M University, College Station, TX 77843, USA, Department of Genetics, Stanford University, Stanford, CA 94305, USA, Department of Biology, Texas A and M University, College Station, TX, 77843, USA, Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA and Deptartment of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
    Nucleic Acids Res 42:D677-84. 2014

Collaborators

Detail Information

Publications20

  1. ncbi request reprint On the quality of tree-based protein classification
    Betty Lazareva-Ulitsky
    Computational Biology Department, Applied Biosystems, Foster City, CA 94404, USA
    Bioinformatics 21:1876-90. 2005
    ..How can these trees be compared in their ability to accurately classify protein sequences?..
  2. pmc Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools
    Paul D Thomas
    Evolutionary Systems Biology Group, SRI International 333 Ravenswood Ave, Menlo Park CA 94025, USA
    Nucleic Acids Res 34:W645-50. 2006
    ..All three web services are available at http://www.pantherdb.org/tools...
  3. pmc PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways
    Huaiyu Mi
    Evolutionary Systems Biology Group, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
    Nucleic Acids Res 35:D247-52. 2007
    ..The HMMs can be downloaded by FTP, and tools for analyzing data in the context of pathways and function ontologies are available at http://www.pantherdb.org...
  4. pmc PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium
    Huaiyu Mi
    Evolutionary Systems Biology Group, SRI International, Lawrence Berkeley National Laboratory, USA
    Nucleic Acids Res 38:D204-10. 2010
    ..In addition, PANTHER trees are being annotated with gene function as part of the Gene Ontology Reference Genome project, resulting in an increasing number of curated functional annotations...
  5. pmc Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire
    C André Lévesque
    Agriculture and Agri Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
    Genome Biol 11:R73. 2010
    ..Pythium ultimum is a ubiquitous oomycete plant pathogen responsible for a variety of diseases on a broad range of crop and ornamental species...
  6. ncbi request reprint Ontology annotation: mapping genomic regions to biological function
    Paul D Thomas
    Evolutionary Systems Biology Group, Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA
    Curr Opin Chem Biol 11:4-11. 2007
    ..Annotations are made using a variety of different types of evidence, which can be used to estimate the relative reliability of different annotations...
  7. doi request reprint A systems biology network model for genetic association studies of nicotine addiction and treatment
    Paul D Thomas
    Evolutionary Systems Biology, Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA
    Pharmacogenet Genomics 19:538-51. 2009
    ..We suggest that known or hypothesized disease risk factors, and causal mechanisms, can be represented using an ontology, a computational specification of a set of concepts and the relations between them...
  8. pmc Dopamine genes and nicotine dependence in treatment-seeking and community smokers
    Andrew W Bergen
    Center for Health Sciences, SRI International, Menlo Park, CA 94025, USA
    Neuropsychopharmacology 34:2252-64. 2009
    ..A community cohort of N=175 multiplex ever-smoking pedigrees (N=423 ever smokers) provided nominal evidence for association with the FTND at these top ranked SNPs, uncorrected for multiple comparisons...
  9. pmc GIGA: a simple, efficient algorithm for gene tree inference in the genomic age
    Paul D Thomas
    Evolutionary Systems Biology Group, SRI International, Menlo Park, CA, USA
    BMC Bioinformatics 11:312. 2010
    ..Additional information beyond gene sequence data has been shown to improve the accuracy of reconstructions, though at great computational cost...
  10. doi request reprint PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools
    James C Hu
    Department of Biochemistry and Biophysics, Texas A and M University, College Station, TX 77843, USA, Department of Genetics, Stanford University, Stanford, CA 94305, USA, Department of Biology, Texas A and M University, College Station, TX, 77843, USA, Artificial Intelligence Center, SRI International, Menlo Park, CA 94025, USA and Deptartment of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
    Nucleic Acids Res 42:D677-84. 2014
    ..PortEco search and data analysis tools are extensively linked to the curated gene, metabolic pathway and regulation content at its sister site, EcoCyc. ..
  11. pmc Ontologies and standards in bioscience research: for machine or for human
    Huaiyu Mi
    SRI International, Menlo Park CA, USA
    Front Physiol 2:5. 2011
    ..Thus, it is crucial that these standards be designed not only for machines to read, but also to be scientifically accurate and intuitive to human biologists...
  12. pmc New developments in the InterPro database
    Nicola J Mulder
    EMBL Outstation European Bioinformatics Institute Hinxton, Cambridge, UK
    Nucleic Acids Res 35:D224-8. 2007
    ..ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro). The InterProScan search tool is now also available via a web service at http://www.ebi.ac.uk/Tools/webservices/WSInterProScan.html...
  13. pmc Accurate prediction of the functional significance of single nucleotide polymorphisms and mutations in the ABCA1 gene
    Liam R Brunham
    Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia
    PLoS Genet 1:e83. 2005
    ....
  14. pmc The PANTHER database of protein families, subfamilies, functions and pathways
    Huaiyu Mi
    Computational Biology, Applied Biosystems, 850 Lincoln Center Drive, Foster City, CA 94404, USA
    Nucleic Acids Res 33:D284-8. 2005
    ..Efforts are underway to add PANTHER to the InterPro suite of databases, and to make PANTHER consistent with the PIRSF database. PANTHER is now publicly available without restriction at http://panther.appliedbiosystems.com...
  15. ncbi request reprint Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios
    Andrew G Clark
    Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
    Science 302:1960-3. 2003
    ..In addition to suggesting adaptive physiological differences between chimps and humans, human-accelerated genes are significantly more likely to underlie major known Mendelian disorders...
  16. pmc PANTHER: a library of protein families and subfamilies indexed by function
    Paul D Thomas
    Protein Informatics, Celera Genomics, Foster City, California 94404, USA
    Genome Res 13:2129-41. 2003
    ..Third, we use the family HMMs to rank missense single nucleotide polymorphisms (SNPs), on a database-wide scale, according to their likelihood of affecting protein function...
  17. pmc Assessment of genome-wide protein function classification for Drosophila melanogaster
    Huaiyu Mi
    Protein Informatics, Celera Genomics, Foster City, California 94404, USA
    Genome Res 13:2118-28. 2003
    ..Often, functional associations are made by one method and not the other, indicating that one of the greatest challenges lies in improving the completeness of available ontology associations...
  18. pmc Nicotinic acetylcholine receptor beta2 subunit gene implicated in a systems-based candidate gene study of smoking cessation
    David V Conti
    Department of Preventive Medicine, Keck School of Medicine, Zilkha Neurogenetics Institute, University of Southern California, 1501 San Pablo Street, ZNI 445, Los Angeles, CA 90089, USA
    Hum Mol Genet 17:2834-48. 2008
    ..0002) and an impact on withdrawal symptoms at target quit date (TQD) (P = 0.0009). Overall, while our results indicate strong evidence for CHRNB2 in ability to quit smoking, these results require replication in an independent sample...
  19. pmc Coding single-nucleotide polymorphisms associated with complex vs. Mendelian disease: evolutionary evidence for differences in molecular effects
    Paul D Thomas
    Informatics and Computational Biology, Applied Biosystems, 850 Lincoln Centre Drive, Foster City, CA 94404, USA
    Proc Natl Acad Sci U S A 101:15398-403. 2004
    ..These findings suggest that caution should be exercised when using Mendelian disease as a model for complex disease, at least with respect to molecular effects on protein function...
  20. pmc PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification
    Paul D Thomas
    Protein Informatics, Celera Genomics, 850 Lincoln Center Drive, Foster City, CA 94404, USA
    Nucleic Acids Res 31:334-41. 2003
    ..PANTHER is publicly available on the web at http://panther.celera.com...