Paul D Thomas

Summary

Affiliation: Celera Genomics
Country: USA

Publications

  1. ncbi 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
  2. ncbi 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
  3. ncbi 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
  4. ncbi 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
  5. ncbi 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
  6. ncbi 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
  7. ncbi 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
  8. ncbi 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
  9. ncbi 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
  10. ncbi 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

Collaborators

Detail Information

Publications13

  1. ncbi 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...
  2. ncbi 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...
  3. ncbi 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?..
  4. ncbi 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...
  5. ncbi 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...
  6. ncbi 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...
  7. ncbi 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...
  8. ncbi 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
    ....
  9. ncbi 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...
  10. ncbi 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...
  11. ncbi 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...
  12. ncbi 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...
  13. ncbi 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...