Keck School Faculty

Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation Nucleic Acids Res. 2022 May 30. . View in PubMed

The Quest for Orthologs orthology benchmark service in 2022 Nucleic Acids Res. 2022 May 12. . View in PubMed

PANTHER: Making genome-scale phylogenetics accessible to all Protein Sci. 2022 01; 31(1):8-22. . View in PubMed

Gene Ontology representation for transcription factor functions Biochim Biophys Acta Gene Regul Mech. 2021 Nov-Dec; 1864(11-12):194752. . View in PubMed

Reactome and the Gene Ontology: Digital convergence of data resources Bioinformatics. 2021 May 08. . View in PubMed

Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees PLoS Comput Biol. 2021 02; 17(2):e1007948. . View in PubMed

Ten Years of Collaborative Progress in the Quest for Orthologs Mol Biol Evol. 2021 07 29; 38(8):3033-3045. . View in PubMed

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST) Bioinformatics. 2021 04 05; 36(24):5712-5718. . View in PubMed

The InterPro protein families and domains database: 20 years on Nucleic Acids Res. 2021 01 08; 49(D1):D344-D354. . View in PubMed

PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API Nucleic Acids Res. 2021 01 08; 49(D1):D394-D403. . View in PubMed

PhyloGenes: An online phylogenetics and functional genomics resource for plant gene function inference Plant Direct. 2020 Dec; 4(12):e00293. . View in PubMed

The Quest for Orthologs benchmark service and consensus calls in 2020 Nucleic Acids Res. 2020 07 02; 48(W1):W538-W545. . View in PubMed

PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence PLoS One. 2020; 15(12):e0243791. . View in PubMed

GO functional similarity clustering depends on similarity measure, clustering method, and annotation completeness BMC Bioinformatics. 2019 Mar 27; 20(1):155. . View in PubMed

Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems Nat Genet. 2019 10; 51(10):1429-1433. . View in PubMed

Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v14. 0). Nat Protoc. 2019 03; 14(3):703-721. . View in PubMed

Advances and Applications in the Quest for Orthologs Mol Biol Evol. 2019 10 01; 36(10):2157-2164. . View in PubMed

SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the SynapseNeuron. 2019 07 17; 103(2):217-234. e4. . View in PubMed

TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations Bioinformatics. 2019 02 01; 35(3):518-520. . View in PubMed

InterPro in 2019: improving coverage, classification and access to protein sequence annotations Nucleic Acids Res. 2019 01 08; 47(D1):D351-D360. . View in PubMed

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools Nucleic Acids Res. 2019 01 08; 47(D1):D419-D426. . View in PubMed

Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life Nucleic Acids Res. 2019 01 08; 47(D1):D271-D279. . View in PubMed

The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database Nucleic Acids Res. 2018 01 04; 46(D1):D624-D632. . View in PubMed

The Gene Ontology and the Meaning of Biological Function Methods Mol Biol. 2017; 1446:15-24. . View in PubMed

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements Nucleic Acids Res. 2017 01 04; 45(D1):D183-D189. . View in PubMed

InterPro in 2017-beyond protein family and domain annotations Nucleic Acids Res. 2017 01 04; 45(D1):D190-D199. . View in PubMed

Kat3 coactivators in somatic stem cells and cancer stem cells: biological roles, evolution, and pharmacologic manipulation Cell Biol Toxicol. 2016 Feb; 32(1):61-81. . View in PubMed

PANTHER version 10: expanded protein families and functions, and analysis tools Nucleic Acids Res. 2016 Jan 04; 44(D1):D336-42. . View in PubMed

Tools for Predicting the Functional Impact of Nonsynonymous Genetic Variation Genetics. 2016 06; 203(2):635-47. . View in PubMed

Standardized benchmarking in the quest for orthologs Nat Methods. 2016 05; 13(5):425-30. . View in PubMed

Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes Database (Oxford). 2016; 2016. . View in PubMed

PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation Bioinformatics. 2016 07 15; 32(14):2230-2. . View in PubMed

The InterPro protein families database: the classification resource after 15 years Nucleic Acids Res. 2015 Jan; 43(Database issue):D213-21. . View in PubMed

Big data and other challenges in the quest for orthologs Bioinformatics. 2014 Nov 01; 30(21):2993-8. . View in PubMed

PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools Nucleic Acids Res. 2014 Jan; 42(Database issue):D677-84. . View in PubMed

CAFA and the open world of protein function predictions Trends Genet. 2013 Nov; 29(11):609-10. . View in PubMed

Large-scale gene function analysis with the PANTHER classification system Nat Protoc. 2013 Aug; 8(8):1551-66. . View in PubMed

Gene Ontology annotations and resources Nucleic Acids Res. 2013 Jan; 41(Database issue):D530-5. . View in PubMed

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees Nucleic Acids Res. 2013 Jan; 41(Database issue):D377-86. . View in PubMed

InterPro in 2011: new developments in the family and domain prediction database Nucleic Acids Res. 2012 Jan; 40(Database issue):D306-12. . View in PubMed

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report PLoS Comput Biol. 2012; 8(2):e1002386. . View in PubMed

BioPAX support in CellDesigner Bioinformatics. 2011 Dec 15; 27(24):3437-8. . View in PubMed

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium Brief Bioinform. 2011 Sep; 12(5):449-62. . View in PubMed

PharmGKB summary: dopamine receptor D2 Pharmacogenet Genomics. 2011 Jun; 21(6):350-6. . View in PubMed

Ontologies and standards in bioscience research: for machine or for human Front Physiol. 2011; 2:5. . View in PubMed

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age BMC Bioinformatics. 2010 Jun 09; 11:312. . View in PubMed

The use of orthologous sequences to predict the impact of amino acid substitutions on protein function PLoS Genet. 2010 May 27; 6(5):e1000968. . View in PubMed

Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire Genome Biol. 2010; 11(7):R73. . View in PubMed

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium Nucleic Acids Res. 2010 Jan; 38(Database issue):D204-10. . View in PubMed

Dopamine genes and nicotine dependence in treatment-seeking and community smokers Neuropsychopharmacology. 2009 Sep; 34(10):2252-64. . View in PubMed

A systems biology network model for genetic association studies of nicotine addiction and treatment Pharmacogenet Genomics. 2009 Jul; 19(7):538-51. . View in PubMed

InterPro: the integrative protein signature database Nucleic Acids Res. 2009 Jan; 37(Database issue):D211-5. . View in PubMed

Nicotinic acetylcholine receptor beta2 subunit gene implicated in a systems-based candidate gene study of smoking cessation Hum Mol Genet. 2008 Sep 15; 17(18):2834-48. . View in PubMed

Ontology annotation: mapping genomic regions to biological function Curr Opin Chem Biol. 2007 Feb; 11(1):4-11. . View in PubMed

New developments in the InterPro database Nucleic Acids Res. 2007 Jan; 35(Database issue):D224-8. . View in PubMed

PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways Nucleic Acids Res. 2007 Jan; 35(Database issue):D247-52. . View in PubMed

Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools Nucleic Acids Res. 2006 Jul 01; 34(Web Server issue):W645-50. . View in PubMed

Accurate prediction of the functional significance of single nucleotide polymorphisms and mutations in the ABCA1 gene PLoS Genet. 2005 Dec; 1(6):e83. . View in PubMed

On the quality of tree-based protein classification Bioinformatics. 2005 May 01; 21(9):1876-90. . View in PubMed

The PANTHER database of protein families, subfamilies, functions and pathways Nucleic Acids Res. 2005 Jan 01; 33(Database issue):D284-8. . View in PubMed

Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios Science. 2003 Dec 12; 302(5652):1960-3. . View in PubMed

Assessment of genome-wide protein function classification for Drosophila melanogaster Genome Res. 2003 Sep; 13(9):2118-28. . View in PubMed

PANTHER: a library of protein families and subfamilies indexed by function Genome Res. 2003 Sep; 13(9):2129-41. . View in PubMed

PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification Nucleic Acids Res. 2003 Jan 01; 31(1):334-41. . View in PubMed

The sequence of the human genome Science. 2001 02 16; 291(5507):1304-51. . View in PubMed