Identifying bioentity recognition errors of rule-based text-mining systems. - Francisco M. Couto; Tiago Grego; Hugo P. Bastos; Catia Pesquita; Rafael P. Torres; Pablo Sanchez; Leandro Pascual; Christian Blaschke (ICDIM, 2008)

BOLOS: BLAST & Ontology Linked-hOmologue Stars. - Hugo P. Bastos; Catia Pesquita; Daniel Faria; André O. Falcão (SAC, 2008)

Metrics for GO based protein semantic similarity: a systematic evaluation. - Catia Pesquita; Daniel Faria; Hugo P. Bastos; António E. N. Ferreira; André O. Falcão; Francisco M. Couto (BMC Bioinform., 2008)

GREAT: Gene Regulation EvAluation Tool. - Catia M. Machado; Hugo P. Bastos; Francisco M. Couto (IWANN (2), 2009)

The Biomedical Ontology Applications (BOA) Framework. - Bruno Tavares; Hugo P. Bastos; Daniel Faria; João D. Ferreira; Tiago Grego; Catia Pesquita; Francisco M. Couto (ICBO, 2011)

Functional coherence metrics in protein families. - Hugo P. Bastos; Lisete Sousa; Luka A. Clarke; Francisco M. Couto (J. Biomed. Semant., 2016)