Paul D. Thomas

发表

The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database

Neil D. Rawlings, Alan J. Barrett, Robert D. Finn, 2017, Nucleic Acids Res..

GO functional similarity clustering depends on similarity measure, clustering method, and annotation completeness

Meng Liu, Paul D. Thomas, P. Thomas, 2019, BMC Bioinformatics.

BioPAX support in CellDesigner

Yukiko Matsuoka, Hiroaki Kitano, Anushya Muruganujan, 2011, Bioinform..

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age

Paul D. Thomas, P. Thomas, 2010, BMC Bioinformatics.

PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways

Nan Guo, Huaiyu Mi, Paul D. Thomas, 2006, Nucleic Acids Res..

InterPro in 2017—beyond protein family and domain annotations

Silvio C. E. Tosatto, Neil D. Rawlings, Huaiyu Mi, 2016, Nucleic Acids Res..

Industrial Application of Fuzzy Systems; Part I; Fuzzy Feature Extraction and Defect Classification

Ahmad Lotfi, Paul D. Thomas, Michael S. Mitchell, 1997 .

Big data and other challenges in the quest for orthologs

Maria Jesus Martin, Toni Gabaldón, Erik L. L. Sonnhammer, 2014, Bioinform..

The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species

Li Ni, Kimberly Van Auken, Kara Dolinski, 2009, PLoS Comput. Biol..

Large-scale gene function analysis with the PANTHER classification system

Anushya Muruganujan, Huaiyu Mi, Paul D. Thomas, 2013, Nature Protocols.

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

Anushya Muruganujan, Huaiyu Mi, Paul D. Thomas, 2003, Nucleic Acids Res..

InterPro: the integrative protein signature database

Robert D. Finn, Cathy H. Wu, Alex Bateman, 2008, Nucleic Acids Res..

CausalTab: PSI-MITAB 2.8 updated format for signaling data representation and dissemination

Henning Hermjakob, Martin Kuiper, Marcio Luis Acencio, 2018, bioRxiv.

New developments in the InterPro database

Robert D. Finn, Robert Petryszak, Cathy H. Wu, 2007, Nucleic Acids Res..

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

Anushya Muruganujan, Huaiyu Mi, Paul D. Thomas, 2018, Nucleic Acids Res..

On the quality of tree-based protein classification

Paul D. Thomas, Karen Diemer, Betty Lazareva-Ulitsky, 2005, Bioinform..

The PANTHER database of protein families, subfamilies, functions and pathways

Hiroaki Kitano, Anushya Muruganujan, Huaiyu Mi, 2004, Nucleic Acids Res..

The InterPro protein families database: the classification resource after 15 years

Huaiyu Mi, Robert D. Finn, Matthew Fraser, 2014, Nucleic Acids Res..

On the automatic annotation of gene functions using observational data and phylogenetic trees

Huaiyu Mi, Paul Marjoram, Paul D. Thomas, 2020, bioRxiv.

Ontologies and Standards in Bioscience Research: For Machine or for Human

Huaiyu Mi, Paul D. Thomas, P. Thomas, 2010, Front. Physio..

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

Robert D. Finn, Paul D. Thomas, Haiming Tang, 2018, Bioinform..

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

Anushya Muruganujan, Huaiyu Mi, Paul D. Thomas, 2012, Nucleic Acids Res..

Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life

Anushya Muruganujan, Paul D. Thomas, Xiaosong Huang, 2018, Nucleic Acids Res..

PANTHER version 10: expanded protein families and functions, and analysis tools

Anushya Muruganujan, Huaiyu Mi, Paul D. Thomas, 2015, Nucleic Acids Res..

PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation

Paul D. Thomas, Haiming Tang, P. Thomas, 2016, Bioinform..

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

Suzanna Lewis, Paul D. Thomas, Pascale Gaudet, 2011, Briefings Bioinform..

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report

Judith A. Blake, Chris Mungall, Suzanna Lewis, 2012, PLoS Comput. Biol..

Applications for protein sequence–function evolution data: mRNA/protein expression analysis and coding SNP scoring tools

Anushya Muruganujan, Huaiyu Mi, Paul D. Thomas, 2006, Nucleic Acids Res..

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

Silvio C. E. Tosatto, Neil D. Rawlings, Robert D. Finn, 2018, Nucleic Acids Res..

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

Anushya Muruganujan, Suzanna Lewis, Qing Dong, 2009, Nucleic Acids Res..

PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools

Anushya Muruganujan, Peter D. Karp, Deborah A. Siegele, 2013, Nucleic Acids Res..

Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes

Suzanna Lewis, Huaiyu Mi, Paul D. Thomas, 2016, Database J. Biol. Databases Curation.

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements

Anushya Muruganujan, Huaiyu Mi, Paul D. Thomas, 2016, Nucleic Acids Res..

CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination

Henning Hermjakob, Marcio L. Acencio, Livia Perfetto, 2019, Bioinform..

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

Robert D. Finn, Matthew Fraser, Cathy H. Wu, 2011, Nucleic acids research.

Reactome and the Gene Ontology: digital convergence of data resources

Kimberly Van Auken, Judith A. Blake, Benjamin M. Good, 2021, Bioinform..

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

Aurélien Naldi, Denis Thieffry, Claudine Chaouiya, 2020, Briefings Bioinform..

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

Anushya Muruganujan, Huaiyu Mi, Paul D. Thomas, 2020, Nucleic Acids Res..

Alliance of Genome Resources Portal: unified model organism research platform

Anushya Muruganujan, Kimberly Van Auken, Juancarlos Chan, 2019, Nucleic Acids Res..

PANTHER: Protein families and subfamilies modeled on the divergence of function

Paul D. Thomas, P. Thomas, 2006 .