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)

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)

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)

Applications of Pathway Logic Modeling to Target Identification. - Anupama Panikkar; Merrill Knapp; Huaiyu Mi; Dave Anderson; Krishna Kodukula; Amit K. Galande; Carolyn L. Talcott (Formal Modeling: Actors, Open Systems, Biological Systems, 2011)

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

Software support for SBGN maps: SBGN-ML and LibSBGN. - Martijn P. van Iersel; Alice Villéger; Tobias Czauderna; Sarah E. Boyd; Frank T. Bergmann; Augustin Luna; Emek Demir; Anatoly A. Sorokin; Ugur Dogrusöz; Yukiko Matsuoka; Akira Funahashi; Mirit I. Aladjem; et al. (Bioinform., 2012)

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)

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)

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)

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2 . - Huaiyu Mi; Falk Schreiber; Stuart L. Moodie; Tobias Czauderna; Emek Demir; Robin Haw; Augustin Luna; Nicolas Le Novère; Anatoly A. Sorokin; Alice Villéger (J. Integr. Bioinform., 2015)

Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3. - Stuart L. Moodie; Nicolas Le Novère; Emek Demir; Huaiyu Mi; Alice Villéger (J. Integr. Bioinform., 2015)

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2. - Anatoly A. Sorokin; Nicolas Le Novère; Augustin Luna; Tobias Czauderna; Emek Demir; Robin Haw; Huaiyu Mi; Stuart L. Moodie; Falk Schreiber; Alice Villéger (J. Integr. Bioinform., 2015)

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 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)

Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0. - Adrien Rougny; Vasundra Touré; Stuart L. Moodie; Irina Balaur; Tobias Czauderna; Hanna Borlinghaus; Ugur Dogrusoz; Alexander Mazein; Andreas Dräger; Michael L. Blinov; Alice Villéger; Robin Haw; et al. (J. Integr. Bioinform., 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)

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 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)

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)

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)