Faria, D., C. Pesquita, E. Santos, M. Palmonari, I. F. Cruz, and F. Couto, "The agreementmakerlight ontology matching system", On the Move to Meaningful Internet Systems: OTM 2013 Conferences: Springer Berlin Heidelberg, pp. 527–541, 2013.
Faria, D., C. Pesquita, E. Santos, I. F. Cruz, and F. Couto, "AgreementMakerLight Results for OAEI 2013", Ontology Matching, pp. 101, 2013.
Faria, D., C. Pesquita, E. Santos, I. F. Cruz, and F. Couto, "AgreementMakerLight results for OAEI 2013.", OM, pp. 101–108, 2013.
Pesquita, C., D. Faria, C. Stroe, E. Santos, I. F. Cruz, and F. Couto, "What's in a 'nym'? Synonyms in Biomedical Ontology Matching", The Semantic Web–ISWC 2013: Springer Berlin Heidelberg, pp. 526–541, 2013.
Bastos, H., B. Tavares, C. Pesquita, D. Faria, and F. Couto, "Application of Gene Ontology to gene identification", In Silico Tools for Gene Discovery: Humana Press, pp. 141–157, 2011.
Bastos, H., B. Tavares, C. Pesquita, D. Faria, and F. Couto, "Application of gene ontology to gene identification.", Methods in molecular biology (Clifton, NJ), vol. 760: Springer, pp. 141–157, 2011.
Faria, D., A. E. N. Ferreira, and A. O. Falcao, "Enzyme classification with peptide programs: a comparative study", BMC bioinformatics, vol. 10, no. 1: BioMed Central Ltd, pp. 231, 2009.
Pesquita, C., D. Faria, and F. Couto, "Measuring coherence between electronic and manual annotations in biological databases", Proceedings of the 2009 ACM symposium on Applied Computing: ACM, pp. 806–807, 2009.
Pesquita, C., D. Faria, A. O. Falcao, P. Lord, and F. Couto, "Semantic similarity in biomedical ontologies", PLoS computational biology, vol. 5, no. 7: Public Library of Science, pp. e1000443, 2009.
Pesquita, C., D. Faria, T. Grego, F. Couto, and M. J. Silva, "Untangling BioOntologies for Mining Biomedical Information", Handbook of research on text and Web mining technologies: Information Science Reference, 2009.
Tavares, B., H. Bastos, D. Faria, J. Ferreira, T. Grego, C. Pesquita, and F. Couto, "The Biomedical Ontology Applications (BOA) framework", evaluation, vol. 9, no. S5, pp. S4, 2008.
Bastos, H., C. Pesquita, D. Faria, and A. O. Falcao, "BOLOS: BLAST & Ontology Linked-hOmologue Stars", Proceedings of the 2008 ACM symposium on Applied computing: ACM, pp. 1278–1281, 2008.
Falcao, A. O., D. Faria, and A. Ferreira, "Peptide programs: applying fragment programs to protein classification", Proceedings of the 2nd international workshop on Data and text mining in bioinformatics: ACM, pp. 37–44, 2008.
Silva, M. J., F. Couto, T. Grego, D. Faria, and C. Pesquita, Untangling BioOntologies for Mining Biomedical Information, : Handbook of Research on Text and Web Mining Technologies, IGI Global Publishing, 2008.
Bastos, H., D. Faria, C. Pesquita, and A. O. Falcao, "Using GO terms to evaluate protein clustering", BioOntologies SIG at ISMB/ECCB-15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), 2007.