Paul D Thomas
Affiliation: SRI International
- On the quality of tree-based protein classificationBetty 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?..
- Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring toolsPaul 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...
- PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathwaysHuaiyu 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...
- PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology ConsortiumHuaiyu 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...
- Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoireC 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...
- Ontology annotation: mapping genomic regions to biological functionPaul 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...
- A systems biology network model for genetic association studies of nicotine addiction and treatmentPaul 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...
- Dopamine genes and nicotine dependence in treatment-seeking and community smokersAndrew 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...
- GIGA: a simple, efficient algorithm for gene tree inference in the genomic agePaul 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...
- PortEco: a resource for exploring bacterial biology through high-throughput data and analysis toolsJames 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. ..
- Ontologies and standards in bioscience research: for machine or for humanHuaiyu 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...
- New developments in the InterPro databaseNicola 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...
- Accurate prediction of the functional significance of single nucleotide polymorphisms and mutations in the ABCA1 geneLiam 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....
- The PANTHER database of protein families, subfamilies, functions and pathwaysHuaiyu 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...
- Inferring nonneutral evolution from human-chimp-mouse orthologous gene triosAndrew 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...
- PANTHER: a library of protein families and subfamilies indexed by functionPaul 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...
- Assessment of genome-wide protein function classification for Drosophila melanogasterHuaiyu 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...
- Nicotinic acetylcholine receptor beta2 subunit gene implicated in a systems-based candidate gene study of smoking cessationDavid 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...
- Coding single-nucleotide polymorphisms associated with complex vs. Mendelian disease: evolutionary evidence for differences in molecular effectsPaul 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...
- PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classificationPaul 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...