Paul D. Thomas

The Gene Ontology resource: enriching a GOld mine

Abstract The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene produ...

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

PANTHER (Protein Analysis Through Evolutionary Relationships, http://pantherdb.org) is a resource for the evolutionary and functional classification of genes from organisms acro...

The Sequence of the Human Genome

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp ...

Assessment of Genome-Wide Protein Function Classification for <i>Drosophila melanogaster</i>

The functional classification of genes on a genome-wide scale is now in its infancy, and we make a first attempt to assess existing methods and identify sources of error. To thi...

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

The data and tools in PANTHER-a comprehensive, curated database of protein families, trees, subfamilies and functions available at http://pantherdb.org-have undergone continual,...

InterPro in 2011: new developments in the family and domain prediction database

InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available t...

Standardized benchmarking in the quest for orthologs

Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is gen...

InterPro in 2022

Abstract The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important...

The Gene Ontology knowledgebase in 2023

Abstract The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding R...

The InterPro protein families and domains database: 20 years on

Abstract The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important...

<scp>PANTHER</scp>: Making genome‐scale phylogenetics accessible to all

Abstract Phylogenetics is a powerful tool for analyzing protein sequences, by inferring their evolutionary relationships to other proteins. However, phylogenetics analyses can b...

Protocol Update for large-scale genome and gene function analysis with the PANTHER classification system (v.14.0)

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

The InterPro database (http://www.ebi.ac.uk/interpro/) classifies protein sequences into families and predicts the presence of functionally important domains and sites. Here, we...

PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API

Abstract PANTHER (Protein Analysis Through Evolutionary Relationships, http://www.pantherdb.org) is a resource for the evolutionary and functional classification of protein-codi...