Paul D. Thomas

According to our database1, Paul D. Thomas authored at least 42 papers between 2002 and 2022.

Collaborative distances:

Timeline

Legend:

Book 
In proceedings 
Article 
PhD thesis 
Other 

Links

Online presence:

On csauthors.net:

Bibliography

2022
The Quest for Orthologs orthology benchmark service in 2022.
Nucleic Acids Res., 2022

Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation.
Nucleic Acids Res., 2022

A roadmap for the functional annotation of protein families: a community perspective.
Database J. Biol. Databases Curation, 2022

2021
Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees.
PLoS Comput. Biol., 2021

PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API.
Nucleic Acids Res., 2021

The Gene Ontology resource: enriching a GOld mine.
, , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ,
Nucleic Acids Res., 2021

The InterPro protein families and domains database: 20 years on.
Nucleic Acids Res., 2021

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST).
Bioinform., 2021

Reactome and the Gene Ontology: digital convergence of data resources.
Bioinform., 2021

Setting the basis of best practices and standards for curation and annotation of logical models in biology - highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.
Briefings Bioinform., 2021

2020
The Quest for Orthologs benchmark service and consensus calls in 2020.
Nucleic Acids Res., 2020

Alliance of Genome Resources Portal: unified model organism research platform.
, , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ,
Nucleic Acids Res., 2020

2019
InterPro in 2019: improving coverage, classification and access to protein sequence annotations.
Nucleic Acids Res., 2019

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools.
Nucleic Acids Res., 2019

Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life.
Nucleic Acids Res., 2019

GO functional similarity clustering depends on similarity measure, clustering method, and annotation completeness.
BMC Bioinform., 2019

TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations.
Bioinform., 2019

CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination.
Bioinform., 2019

2018
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

2017
PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements.
Nucleic Acids Res., 2017

InterPro in 2017 - beyond protein family and domain annotations.
Nucleic Acids Res., 2017

2016
PANTHER version 10: expanded protein families and functions, and analysis tools.
Nucleic Acids Res., 2016

PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation.
Bioinform., 2016

Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes.
Database J. Biol. Databases Curation, 2016

2015
The InterPro protein families database: the classification resource after 15 years.
Nucleic Acids Res., 2015

2014
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools.
Nucleic Acids Res., 2014

Big data and other challenges in the quest for orthologs.
Bioinform., 2014

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

2012
On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report.
PLoS Comput. Biol., 2012

InterPro in 2011: new developments in the family and domain prediction database.
Nucleic Acids Res., 2012

2011
BioPAX support in CellDesigner.
Bioinform., 2011

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.
Briefings Bioinform., 2011

2010
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium.
Nucleic Acids Res., 2010

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age.
BMC Bioinform., 2010

2009
InterPro: the integrative protein signature database.
Nucleic Acids Res., 2009

2007
New developments in the InterPro database.
Nucleic Acids Res., 2007

PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways.
Nucleic Acids Res., 2007

2006
Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools.
Nucleic Acids Res., 2006

2005
The PANTHER database of protein families, subfamilies, functions and pathways.
Nucleic Acids Res., 2005

On the quality of tree-based protein classification.
Bioinform., 2005

2003
PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification.
Nucleic Acids Res., 2003

2002
The Celera Discovery SystemTM.
Nucleic Acids Res., 2002


  Loading...