MOPAC: MOtif Finding by Preprocessing and Agglomerative Clustering from Microarrays. - R. Ganesh; Deborah A. Siegele; Thomas R. Ioerger (Pacific Symposium on Biocomputing, 2003)

The Ontology of Microbial Phenotypes (OMP): A Precomposed Ontology Based on Cross Products from Multiple External Ontologies that is Used for Guiding Microbial Phenotype Annotation. - Marcus C. Chibucos; Adrienne E. Zweifel; Deborah A. Siegele; Peter Uetz; Michelle G. Giglio; James C. Hu (ICBO, 2011)

EcoliWiki: a wiki-based community resource for Escherichia coli. - Brenley K. McIntosh; Daniel P. Renfro; Gwendowlyn S. Knapp; Chanchala R. Lairikyengbam; Nathan M. Liles; Lili Niu; Amanda M. Supak; Anand Venkatraman; Adrienne E. Zweifel; Deborah A. Siegele; James C. Hu (Nucleic Acids Res., 2012)

GONUTS: the Gene Ontology Normal Usage Tracking System. - Daniel P. Renfro; Brenley K. McIntosh; Anand Venkatraman; Deborah A. Siegele; James C. Hu (Nucleic Acids Res., 2012)

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)

Phenotype annotation with the ontology of microbial phenotypes (OMP). - Deborah A. Siegele; Sandra A. LaBonte; Peter I-Fan Wu; Marcus C. Chibucos; Suvarna Nandendla; Michelle G. Giglio; James C. Hu (J. Biomed. Semant., 2019)

ECO, the Evidence & Conclusion Ontology: community standard for evidence information. - Michelle G. Giglio; Rebecca Tauber; Suvarna Nadendla; James B. Munro; Dustin Olley; Shoshannah Ball; Elvira Mitraka; Lynn M. Schriml; Pascale Gaudet; Elizabeth T. Hobbs; Ivan Erill; Deborah A. Siegele; et al. (Nucleic Acids Res., 2019)

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)

Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO). - Jolene Ramsey; Brenley K. McIntosh; Daniel P. Renfro; Suzanne A. Aleksander; Sandra A. LaBonte; Curtis Ross; Adrienne E. Zweifel; Nathan Liles; Shabnam Farrar; Jason J. Gill; Ivan Erill; Sarah Ades; et al. (PLoS Comput. Biol., 2021)