The Celera Discovery SystemTM. - Anthony R. Kerlavage; Vivien Bonazzi; Matteo di Tommaso; Charles Lawrence; Peter Li; Frank Mayberry; Richard J. Mural; Marc Nodell; Mark Yandell; Jinghui Zhang; Paul D. Thomas (Nucleic Acids Res., 2002)

PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. - Paul D. Thomas; Anish Kejariwal; Michael J. Campbell; Huaiyu Mi; Karen Diemer; Nan Guo; Istvan Ladunga; Betty Lazareva-Ulitsky; Anushya Muruganujan; Steven Rabkin; Jody A. Vandergriff; Olivier Doremieux (Nucleic Acids Res., 2003)

On the quality of tree-based protein classification. - Betty Lazareva-Ulitsky; Karen Diemer; Paul D. Thomas (Bioinform., 2005)

The PANTHER database of protein families, subfamilies, functions and pathways. - Huaiyu Mi; Betty Lazareva-Ulitsky; Rozina Loo; Anish Kejariwal; Jody A. Vandergriff; Steven Rabkin; Nan Guo; Anushya Muruganujan; Olivier Doremieux; Michael J. Campbell; Hiroaki Kitano; Paul D. Thomas (Nucleic Acids Res., 2005)

Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. - Paul D. Thomas; Anish Kejariwal; Nan Guo; Huaiyu Mi; Michael J. Campbell; Anushya Muruganujan; Betty Lazareva-Ulitsky (Nucleic Acids Res., 2006)

PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. - Huaiyu Mi; Nan Guo; Anish Kejariwal; Paul D. Thomas (Nucleic Acids Res., 2007)

New developments in the InterPro database. - Nicola J. Mulder; Rolf Apweiler; Teresa K. Attwood; Amos Bairoch; Alex Bateman; David Binns; Peer Bork; Virginie Buillard; Lorenzo Cerutti; Richard R. Copley; Emmanuel Courcelle; Ujjwal Das; et al. (Nucleic Acids Res., 2007)

InterPro: the integrative protein signature database. - Sarah Hunter; Rolf Apweiler; Teresa K. Attwood; Amos Bairoch; Alex Bateman; David Binns; Peer Bork; Ujjwal Das; Louise C. Daugherty; Lauranne Duquenne; Robert D. Finn; Julian Gough; et al. (Nucleic Acids Res., 2009)

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age. - Paul D. Thomas (BMC Bioinform., 2010)

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. - Huaiyu Mi; Qing Dong; Anushya Muruganujan; Pascale Gaudet; Suzanna Lewis; Paul D. Thomas (Nucleic Acids Res., 2010)

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. - Pascale Gaudet; Michael S. Livstone; Suzanna E. Lewis; Paul D. Thomas (Briefings Bioinform., 2011)

BioPAX support in CellDesigner. - Huaiyu Mi; Anushya Muruganujan; Emek Demir; Yukiko Matsuoka; Akira Funahashi; Hiroaki Kitano; Paul D. Thomas (Bioinform., 2011)

InterPro in 2011: new developments in the family and domain prediction database. - Sarah Hunter; Philip Jones; Alex L. Mitchell; Rolf Apweiler; Teresa K. Attwood; Alex Bateman; Thomas Bernard; David Binns; Peer Bork; Sarah W. Burge; Edouard De Castro; Penny C. Coggill; et al. (Nucleic Acids Res., 2012)

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. - Paul D. Thomas; Valerie Wood; Christopher J. Mungall; Suzanna E. Lewis; Judith A. Blake (PLoS Comput. Biol., 2012)

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. - Huaiyu Mi; Anushya Muruganujan; Paul D. Thomas (Nucleic Acids Res., 2013)

Big data and other challenges in the quest for orthologs. - Erik L. L. Sonnhammer; Toni Gabaldón; Alan W. Sousa da Silva; Maria Jesus Martin; Marc Robinson-Rechavi; Brigitte Boeckmann; Paul D. Thomas; Christophe Dessimoz; Quest for Orthologs Consortium (Bioinform., 2014)

PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools. - James C. Hu; Gavin Sherlock; Deborah A. Siegele; Suzanne A. Aleksander; Catherine A. Ball; Janos Demeter; Sushanth Gouni; Timothy A. Holland; Peter D. Karp; John E. Lewis; Nathan M. Liles; Brenley K. McIntosh; et al. (Nucleic Acids Res., 2014)

The InterPro protein families database: the classification resource after 15 years. - Alex L. Mitchell; Hsin-Yu Chang; Louise C. Daugherty; Matthew Fraser; Sarah Hunter; Rodrigo Lopez; Craig McAnulla; Conor McMenamin; Gift Nuka; Sebastien Pesseat; Amaia Sangrador-Vegas; Maxim Scheremetjew; et al. (Nucleic Acids Res., 2015)

Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes. - Marc Feuermann; Pascale Gaudet; Huaiyu Mi; Suzanna E. Lewis; Paul D. Thomas (Database J. Biol. Databases Curation, 2016)

PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation. - Haiming Tang; Paul D. Thomas (Bioinform., 2016)

PANTHER version 10: expanded protein families and functions, and analysis tools. - Huaiyu Mi; Sagar Poudel; Anushya Muruganujan; John T. Casagrande; Paul D. Thomas (Nucleic Acids Res., 2016)

InterPro in 2017 - beyond protein family and domain annotations. - Robert D. Finn; Teresa K. Attwood; Patricia C. Babbitt; Alex Bateman; Peer Bork; Alan J. Bridge; Hsin-Yu Chang; Zsuzsanna Dosztányi; Sara El-Gebali; Matthew Fraser; Julian Gough; David Haft; et al. (Nucleic Acids Res., 2017)

PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements. - Huaiyu Mi; Xiaosong Huang; Anushya Muruganujan; Haiming Tang; Caitlin Mills 002; Diane Kang; Paul D. Thomas (Nucleic Acids Res., 2017)

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; Paul D. Thomas; Xiaosong Huang; Alex Bateman; Robert D. Finn (Nucleic Acids Res., 2018)

CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. - Livia Perfetto; Marcio Luis Acencio; Glyn Bradley; Gianni Cesareni; Noemi del-Toro; Dávid Fazekas; Henning Hermjakob; Tamás Korcsmáros; Martin Kuiper; Astrid Lægreid; Prisca Lo Surdo; Ruth C. Lovering; et al. (Bioinform., 2019)

TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations. - Haiming Tang; Robert D. Finn; Paul D. Thomas (Bioinform., 2019)

GO functional similarity clustering depends on similarity measure, clustering method, and annotation completeness. - Meng Liu; Paul D. Thomas (BMC Bioinform., 2019)

Ancestral Genomes: a resource for reconstructed ancestral genes and genomes across the tree of life. - Xiaosong Huang; Laurent-Philippe Albou; Tremayne Mushayahama; Anushya Muruganujan; Haiming Tang; Paul D. Thomas (Nucleic Acids Res., 2019)

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. - Huaiyu Mi; Anushya Muruganujan; Dustin Ebert; Xiaosong Huang; Paul D. Thomas (Nucleic Acids Res., 2019)

InterPro in 2019: improving coverage, classification and access to protein sequence annotations. - Alex L. Mitchell; Teresa K. Attwood; Patricia C. Babbitt; Matthias Blum; Peer Bork; Alan J. Bridge; Shoshana D. Brown; Hsin-Yu Chang; Sara El-Gebali; Matthew Fraser; Julian Gough; David Haft; et al. (Nucleic Acids Res., 2019)

Alliance of Genome Resources Portal: unified model organism research platform. - Julie Agapite; Laurent-Philippe Albou; Suzi A. Aleksander; Joanna Argasinska; Valerio Arnaboldi; Helen Attrill; Susan M. Bello; Judith A. Blake; Olin Blodgett; Yvonne M. Bradford; Carol J. Bult; Scott Cain; et al. (Nucleic Acids Res., 2020)

The Quest for Orthologs benchmark service and consensus calls in 2020. - Adrian M. Altenhoff; Javier Garrayo-Ventas; Salvatore Cosentino; David Emms; Natasha M. Glover; Ana Hernández-Plaza; Yannis Nevers; Vicky Sundesha; Damian Szklarczyk; José María Fernández 001; Laia Codó; Quest for Orthologs Consortium; et al. (Nucleic Acids Res., 2020)

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. - Anna Niarakis; Martin Kuiper; Marek Ostaszewski; Rahuman S. Malik-Sheriff; Cristina Casals-Casas; Denis Thieffry; Tom C. Freeman; Paul D. Thomas; Vasundra Touré; Vincent Noël; Gautier Stoll; Julio Saez-Rodriguez; et al. (Briefings Bioinform., 2021)

Reactome and the Gene Ontology: digital convergence of data resources. - Benjamin M. Good; Kimberly Van Auken; David P. Hill; Huaiyu Mi; Seth Carbon; James P. Balhoff; Laurent-Philippe Albou; Paul D. Thomas; Christopher J. Mungall; Judith A. Blake; Peter D'Eustachio (Bioinform., 2021)

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). - Vasundra Touré; Steven Vercruysse; Marcio Luis Acencio; Ruth C. Lovering; Sandra E. Orchard; Glyn Bradley; Cristina Casals-Casas; Claudine Chaouiya; Noemi del-Toro; Åsmund Flobak; Pascale Gaudet; Henning Hermjakob; et al. (Bioinform., 2021)

The InterPro protein families and domains database: 20 years on. - Matthias Blum; Hsin-Yu Chang; Sara Chuguransky; Tiago Grego; Swaathi Kandasamy; Alex L. Mitchell; Gift Nuka; Typhaine Paysan-Lafosse; Matloob Qureshi; Shriya Raj; Lorna J. Richardson; Gustavo A. Salazar; et al. (Nucleic Acids Res., 2021)

The Gene Ontology resource: enriching a GOld mine. - Seth Carbon; Eric Douglass; Benjamin M. Good; Deepak R. Unni; Nomi L. Harris; Christopher J. Mungall; Siddartha Basu; Rex L. Chisholm; Robert J. Dodson; Eric Hartline; Petra Fey; Paul D. Thomas; et al. (Nucleic Acids Res., 2021)

PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API. - Huaiyu Mi; Dustin Ebert; Anushya Muruganujan; Caitlin Mills 002; Laurent-Philippe Albou; Tremayne Mushayahama; Paul D. Thomas (Nucleic Acids Res., 2021)

Bayesian parameter estimation for automatic annotation of gene functions using observational data and phylogenetic trees. - George G. Vega Yon; Duncan C. Thomas; John Morrison; Huaiyu Mi; Paul D. Thomas; Paul Marjoram (PLoS Comput. Biol., 2021)

A roadmap for the functional annotation of protein families: a community perspective. - Valérie de Crécy-Lagard; Rocio Amorin de Hegedus; Cecilia N. Arighi; Jill Babor; Alex Bateman; Ian Blaby; Crysten Blaby-Haas; Alan J. Bridge; Stephen K. Burley; Stacey Cleveland; Lucy J. Colwell; Ana Conesa; et al. (Database J. Biol. Databases Curation, 2022)

Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation. - Zhu Liu; Tremayne Mushayahama; Bryan Queme; Dustin Ebert; Anushya Muruganujan; Caitlin Mills 002; Paul D. Thomas; Huaiyu Mi (Nucleic Acids Res., 2022)

The Quest for Orthologs orthology benchmark service in 2022. - Yannis Nevers; Tamsin E. M. Jones; Dushyanth Jyothi; Bethan Yates; Meritxell Ferret; Laura Portell-Silva; Laia Codó; Salvatore Cosentino; Marina Marcet-Houben; Anna Vlasova; Laetitia Poidevin; Arnaud Kress; et al. (Nucleic Acids Res., 2022)

InterPro in 2022. - Typhaine Paysan-Lafosse; Matthias Blum; Sara Chuguransky; Tiago Grego; Beatriz Lázaro Pinto; Gustavo A. Salazar; Maxwell L. Bileschi; Peer Bork; Alan J. Bridge; Lucy J. Colwell; Julian Gough; Daniel H. Haft; et al. (Nucleic Acids Res., 2023)

Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy. - Karina Martinez; Jon Agirre; Yukie Akune; Kiyoko F. Aoki-Kinoshita; Cecilia N. Arighi; Kristian B. Axelsen; Evan Bolton; Emily Bordeleau; Nathan J. Edwards; Elisa Fadda; Ten Feizi; Catherine A. Hayes; et al. (Database J. Biol. Databases Curation, 2024)