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 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)

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

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)

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)

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)

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)

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 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)

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)