List of Publications

| Chapters | Journal papers | Conference papers | Workshop papers | Extended Abstracts | Magazine papers | Technical reports | Theses |

Chapters

[1] A. Lamurias and F. Couto, “Text mining for bioinformatics using biomedical literature,” in Reference Module in Life Sciences (Encyclopedia of Bioinformatics and Computational Biology), pp. 1–31, Elsevier, 2018. [ bib | DOI | pdf ]
[2] F. Couto and A. Lamurias, “Semantic similarity definition,” in Reference Module in Life Sciences (Encyclopedia of Bioinformatics and Computational Biology), pp. 1–17, Elsevier, 2018. [ bib | DOI | pdf ]
[3] H. Bastos, B. Tavares, C. Pesquita, D. Faria, and F. Couto, “Application of Gene Ontology to gene identification,” in In Silico Tools for Gene Discovery, Methods in Molecular Biology (B. Yu and M. Hinchcliffe, eds.), Humana Press, 2011. [ bib | DOI | pdf | pubmed | scholar ]
[4] P. Coutinho, C. Rancurel, M. Stam, T. Bernard, F. Couto, E. Danchin, and B. Henrissat, “Carbohydrate-active enzymes database: Principles and classification of glycosyltransferases,” in In Bioinformatics for Glycobiology and Glycomics (C. Lieth, T. Lutteke, and M. Frank, eds.), Wiley, 2009. [ bib | DOI | scholar ]
[5] F. Couto, M. Silva, V. Lee, E. Dimmer, E. Camon, R. Apweiler, H. Kirsch, and D. Rebholz-Schuhmann, “Verification of uncurated protein annotations,” in Information Retrieval in Biomedicine: Natural Language Processing for Knowledge Integration (V. Prince and M. Roche, eds.), Idea Group Inc, 2009. [ bib | DOI | pdf | scholar ]
[6] C. Pesquita, D. Faria, T. Grego, F. Couto, and M. Silva, “Untangling BioOntologies for mining biomedical information,” in Handbook of Research on Text and Web Mining Technologies (M. Song and Y. Wu, eds.), Idea Group Inc., 2009. [ bib | DOI | pdf | scholar ]
[7] F. Couto and M. Silva, “Mining the bioliterature: towards automatic annotation of genes and proteins,” in Advanced Data Mining Techonologies in Bioinformatics (H. Hsu, ed.), Idea Group Inc., 2006. [ bib | DOI | pdf | scholar ]

Journal papers

[1] J. Decouchant, M. Fernandes, M. Völp, F. Couto, and P. Veríssimo, “Accurate filtering of privacy-sensitive information in raw genomic data,” Journal of Biomedical Informatics, vol. (in press), pp. 1–35, 2018. [ bib | DOI | pdf | pubmed | scholar ]
[2] D. Faria, C. Pesquita, I. Mott, C. Martins, F. Couto, and I. Cruz, “Tackling the challenges of matching biomedical ontologies,” Journal of Biomedical Semantics, vol. 9, no. 4, pp. 1–25, 2018. [ bib | DOI | pdf | pubmed | scholar ]
[3] A. Lamurias, J. Ferreira, L. Clarke, and F. Couto, “Generating a tolerogenic cell therapy knowledge graph from literature,” Frontiers in Immunology, vol. 8, no. 1656, pp. 1–23, 2017. [ bib | DOI | pdf | pubmed | scholar ]
[4] J. Ferreira, B. Inácio, R. Salek, and F. Couto, “Assessing public metabolomics metadata, towards improving quality,” Journal of Integrative Bioinformatics, vol. 14, no. 4, pp. 1–28, 2017. [ bib | DOI | pdf | pubmed | scholar ]
[5] M. Lobo, A. Lamurias, and F. Couto, “Identifying human phenotype terms by combining machine learning and validation rules,” BioMed Research International, vol. 2017, pp. 1–14, 2017. [ bib | DOI | pdf | pubmed | scholar ]
[6] L. Campos, V. Pedro, and F. Couto, “Impact of translation on named-entity recognition in radiology texts,” Database: The Journal of Biological Databases and Curation, vol. 2017, no. bax064, pp. 1–9, 2017. [ bib | DOI | pdf | pubmed | scholar ]
[7] A. Lamurias, L. Clarke, and F. Couto, “Extracting microRNA-gene relations from biomedical literature using distant supervision,” PLoS ONE, vol. 12, no. 3, pp. 1–20, 2017. [ bib | DOI | pdf | pubmed | scholar ]
[8] M. Barros and F. Couto, “Knowledge representation and management: a linked data perspective,” IMIA Yearbook of Medical Informatics, pp. 178–183, 2016. [ bib | DOI | pdf | pubmed | scholar ]
[9] H. Bastos, L. Sousa, L. Clarke, and F. Couto, “Functional coherence metrics in protein families,” Journal of Biomedical Semantics, vol. 7, no. 1, pp. 41–51, 2016. [ bib | DOI | pdf | pubmed | scholar ]
[10] E. Santos, D. Faria, C. Pesquita, and F. Couto, “Ontology alignment repair through modularization and confidence-based heuristics,” PLoS ONE, vol. 10, no. 12, pp. 1–19, 2015. [ bib | DOI | pdf | pubmed | scholar ]
[11] H. Bastos, L. Sousa, L. Clarke, and F. Couto, “GRYFUN: A web application for GO term annotation visualization and analysis in protein sets,” PLoS ONE, vol. 10, no. 3, pp. 1–20, 2015. [ bib | DOI | pdf | pubmed | scholar ]
[12] T. Groza, S. Köhler, S. Doelken, N. Collier, A. Oellrich, D. Smedley, F. Couto, G. Baynam, A. Zankl, and P. Robinson, “Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora,” Database: The Journal of Biological Databases and Curation, vol. 2015, no. bav005, pp. 1–13, 2015. [ bib | DOI | pdf | pubmed | scholar ]
[13] A. Lamurias, J. Ferreira, and F. Couto, “Improving chemical entity recognition through h-index based semantic similarity,” Journal of Cheminformatics, vol. 7, no. Suppl 1, pp. S13, 1–20, 2015. [ bib | DOI | pdf | pubmed | scholar ]
[14] M. Krallinger, O. Rabal, F. Leitner, M. Vazquez, D. Salgado, Z. Lu, R. Leaman, Y. Lu, D. Ji, D. Lowe, R. Sayle, R. Batista-Navarro, R. Rak, T. Huber, T. Rocktaschel, S. Matos, D. Campos, B. Tang, H. Xu, T. Munkhdalai, K. Ryu, S. Ramanan, S. Nathan, S. Zitnik, M. Bajec, L. Weber, M. Irmer, S. Akhondi, J. Kors, S. Xu, X. An, U. Sikdar, A. Ekbal, M. Yoshioka, T. Dieb, M. Choi, K. Verspoor, M. Khabsa, C. Giles, H. Liu, K. Ravikumar, A. Lamurias, F. Couto, H. Dai, R. Tsai, C. Ata, T. Can, A. Usié, R. Alves, I. Segura-Bedmar, P. Martínez, J. Oryzabal, and A. Valencia, “The CHEMDNER corpus of chemicals and drugs and its annotation principles,” Journal of Cheminformatics, vol. 7, no. Suppl 1, pp. S2, 1–20, 2015. [ bib | DOI | pdf | pubmed | scholar ]
[15] C. Machado, D. Rebholz-Schuhmann, A. Freitas, and F. Couto, “The semantic web in translational medicine: current applications and future directions,” Briefings in Bioinformatics, Oxford University Press, vol. 16, no. 1, pp. 89–103, 2015. [ bib | DOI | pdf | pubmed | scholar ]
[16] D. Faria, C. Pesquita, E. Santos, I. Cruz, and F. Couto, “Automatic background knowledge selection for matching biomedical ontologies,” PLoS ONE, vol. 9, no. 11, pp. 1–9, 2014. [ bib | DOI | pdf | pubmed | scholar ]
[17] A. Lamurias, J. Ferreira, and F. Couto, “Identifying interactions between chemical entities in biomedical text,” Journal of Integrative Bioinformatics, vol. 11, no. 3, pp. 1–16, 2014. [ bib | DOI | pdf | pubmed | scholar ]
[18] C. Pesquita, J. Ferreira, F. Couto, and M. Silva, “The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources,” Journal of Biomedical Semantics, vol. 5, no. 4, pp. 1–17, 2014. [ bib | DOI | pdf | pubmed | scholar ]
[19] J. Ferreira, J. Hastings, and F. Couto, “Exploiting disjointness axioms to improve semantic similarity measures,” Bioinformatics, Oxford Univ Press, vol. 29, no. 21, pp. 2781–2787, 2013. [ bib | DOI | pdf | pubmed | scholar ]
[20] H. Bastos, L. Clarke, and F. Couto, “Annotation extension through protein family annotation coherence metrics,” Frontiers in Genetics, vol. 4, no. 201, pp. 1–10, 2013. [ bib | DOI | pdf | pubmed | scholar ]
[21] F. Couto and H. Pinto, “The next generation of similarity measures that fully explore the semantics in biomedical ontologies,” Journal of Bioinformatics and Computational Biology, vol. 11, no. 1371001, pp. 1–12, 2013. [ bib | DOI | pdf | pubmed | scholar ]
[22] C. Machado, A. Freitas, and F. Couto, “Enrichment analysis applied to disease prognosis,” Journal of Biomedical Semantics, vol. 4, no. 21, pp. 1–26, 2013. [ bib | DOI | pdf | pubmed | scholar ]
[23] T. Grego and F. Couto, “Enhancement of chemical entity identification in text using semantic similarity validation,” PLoS ONE, vol. 8, no. 5 (e62984), pp. 1–13, 2013. [ bib | DOI | pdf | pubmed | scholar ]
[24] S. Moreira, D. Batista, P. Carvalho, F. Couto, and M. Silva, “Tracking politics with POWER,” Program: electronic library and information systems, vol. 47, no. 2, pp. 120–135, 2013. [ bib | DOI | scholar ]
[25] J. Ferreira, D. Paolotti, F. Couto, and M. Silva, “On the usefulness of ontologies in epidemiologic research and practice,” Journal of Epidemiology and Community Health, vol. 67, pp. 385–388, 2013. [ bib | DOI | pubmed | scholar ]
[26] C. Pesquita and F. Couto, “Predicting the extension of biomedical ontologies,” PLoS Computational Biology, vol. 8, no. 9 (e1002630), pp. 1–16, 2012. [ bib | DOI | pubmed | scholar ]
[27] T. Grego, C. Pesquita, H. Bastos, and F. Couto, “Chemical entity recognition and resolution to ChEBI,” ISRN Bioinformatics, vol. 2012, no. 619427, pp. 1–9, 2012. [ bib | DOI | pdf | scholar ]
[28] F. Couto and M. Silva, “Disjunctive shared information between ontology concepts: application to Gene Ontology,” Journal of Biomedical Semantics, vol. 2, no. 5, pp. 1–16, 2011. [ bib | DOI | code | pt | pubmed | scholar ]
[29] T. Simões, N. Charro, J. Blonder, D. Faria, F. Couto, K. Chan, T. Waybright, H. Isaaq, T. Veenstra, and D. Penque, “Molecular profiling of the human nasal epithelium: A proteomics approach,” Journal of Proteomics, vol. 75, no. 1, pp. 56–69, 2011. [ bib | DOI | pubmed | scholar ]
[30] N. Charro, B. Hood, D. Faria, P. Pacheco, P. Azevedo, C. Lopes, A. Almeida, F. Couto, T. Conrads, and D. Penque, “Serum proteomics signature of Cystic Fibrosis patients: A complementary 2-DE and LC-MS/MS approach,” Journal of Proteomics, vol. 74, no. 1, pp. 110–126, 2011. [ bib | DOI | pubmed | scholar ]
[31] J. Ferreira and F. Couto, “Semantic similarity for automatic classification of chemical compounds,” PLoS Computational Biology, vol. 6, no. 9 (e1000937), pp. 1–11, 2010. [ bib | DOI | pubmed | scholar ]
[32] P. Gomes-Alves, F. Couto, C. Pesquita, A. Coelho, and D. Penque, “Rescue of F508del-CFTR by RXR motif inactivation triggers proteome modulation associated with the unfolded protein response,” Biochimica et Biophysica Acta, Proteins and Proteomics, vol. 1804, no. 4, pp. 856–865, 2010. [ bib | DOI | pubmed | scholar ]
[33] C. Pesquita, D. Faria, A. Falcão, P. Lord, and F. Couto, “Semantic similarity in biomedical ontologies,” PLoS Computational Biology, vol. 5, no. 7 (e1000443), pp. 1–11, 2009. [ bib | DOI | pubmed | scholar ]
[34] F. Couto, C. Pesquita, T. Grego, and P. Verissimo, “Handling self-citations using Google Scholar,” Cybermetrics, vol. 13, no. 1, pp. 1–7, 2009. [ bib | pdf | scholar ]
[35] C. Pesquita, D. Faria, A. Ferreira, A. Falcão, and F. Couto, “Metrics for GO based protein semantic similarity: a systematic evaluation,” BMC Bioinformatics, vol. 9, no. 5 (S4), pp. 1–16, 2008. [ bib | DOI | pubmed | scholar ]
[36] F. Couto, M. Silva, and P. Coutinho, “Measuring semantic similarity between Gene Ontology terms,” Data and Knowledge Engineering, vol. 61, no. 1, pp. 137–152, 2007. [ bib | DOI | pdf | scholar ]
[37] F. Couto, M. Silva, V. Lee, E. Dimmer, E. Camon, R. Apweiler, H. Kirsch, and D. Rebholz-Schuhmann, “GOAnnotator: linking electronic protein GO annotation to evidence text,” Journal of Biomedical Discovery and Collaboration, vol. 19, no. 1, pp. 1–6, 2006. [ bib | DOI | pubmed | scholar ]
[38] F. Couto, M. Silva, and P. Coutinho, “Finding genomic ontology terms in text using evidence content,” BMC Bioinformatics, vol. 6, no. S1( S21), pp. 1–6, 2005. [ bib | DOI | pubmed | scholar ]
[39] D. Rebholz-Schuhmann, H. Kirsch, and F. Couto, “Facts from text – is text mining ready to deliver?,” PLoS Biology, vol. 3, no. 2 (e65), pp. 1–8, 2005. [ bib | DOI | pubmed | scholar ]

Conference papers

[1] M. Fernandes, J. Decouchant, F. Couto, and P. Verissimo, “Cloud-assisted read alignment and privacy,” in Practical Applications of Computational Biology and Bioinformatics (PACBB), pp. 220–227, 2017. [ bib | DOI | pdf | scholar ]
[2] B. Inácio, J. Ferreira, and F. Couto, “Metadata analyser: measuring metadata quality,” in Practical Applications of Computational Biology and Bioinformatics (PACBB), pp. 197–204, 2017. [ bib | DOI | pdf | scholar ]
[3] A. Barata, L. Carvalho, and F. Couto, “Anthropometric data analytics: a portuguese case study,” in Practical Applications of Computational Biology and Bioinformatics (PACBB), pp. 92–100, 2017. [ bib | DOI | pdf | scholar ]
[4] V. Cogo, A. Bessani, F. Couto, M. Gama-Carvalho, M. Fernandes, and P. Verissimo, “How can photo sharing inspire sharing genomes?,” in Practical Applications of Computational Biology and Bioinformatics (PACBB), pp. 74–82, 2017. [ bib | DOI | pdf | scholar ]
[5] A. Lamurias, L. Clarke, and F. Couto, “IICE: web tool for automatic identification of chemical entities and interactions,” in European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD), Demo Track, pp. 285–288, 2015. [ bib | DOI | pdf | url | scholar ]
[6] A. Lamurias, V. Pedro, L. Clarke, and F. Couto, “Annotating biomedical terms in electronic health records using crowd-sourcing,” in International Conference on Biomedical Ontologies (ICBO), Early Career, 2015. [ bib | pdf | url | scholar ]
[7] C. Barata, M. Abreu, P. Torres, J. Teixeira, T. Guerreiro, and F. Couto, “Social impact – identifying quotes of literary works in social networks,” in 17th Portuguese Conference on Artificial Intelligence (EPIA), pp. 789–795, 2015. [ bib | DOI | pdf | scholar ]
[8] D. Faria, E. Jiménez-Ruiz, C. Pesquita, E. Santos, I. Cruz, and F. Couto, “Towards annotating potential incoherences in BioPortal mappings,” in International Semantic Web Conference (ISWC), pp. 17–32, 2014. [ bib | DOI | pdf | scholar ]
[9] M. Costa, F. Couto, and M. Silva, “Learning temporal-dependent ranking models,” in The 37th annual international ACM Special Interest Group On Information Retrieval conference (ACM SIGIR), pp. 757–766, 2014. [ bib | DOI | pdf | url | scholar ]
[10] C. Pesquita, D. Faria, E. Santos, J. Neefs, and F. Couto, “Towards visualizing the alignment of large biomedical ontologies,” in The 10th International Conference on Data Integration in the Life Sciences (DILS) (short paper), pp. 104–111, 2014. [ bib | DOI | pdf | scholar ]
[11] A. Lamurias, J. Ferreira, and F. Couto, “Chemical named entity recognition: Improving recall using a comprehensive list of lexical features,” in Practical Applications of Computational Biology and Bioinformatics (PACBB), vol. 294, pp. 253–260, Lecture Notes in Computer Science, 2014. [ bib | DOI | pdf | scholar ]
[12] J. Martins, J. Carilho, O. Schnell, C. Duarte, F. Couto, L. Carriço, and T. Guerreiro, “Friendsourcing the unmet needs of people with dementia,” in The 11th Web for All Conference (W4A), pp. 1–4, 2014. [ bib | DOI | pdf | scholar ]
[13] D. Faria, C. Pesquita, E. Santos, M. Palmonari, I. Cruz, and F. Couto, “The AgreementMakerLight ontology matching system,” in The 12th International Conference on Ontologies, DataBases, and Applications of Semantics (ODBASE), pp. 527–541, 2013. [ bib | DOI | pdf | scholar ]
[14] C. Pesquita, D. Faria, C. Stroe, E. Santos, I. Cruz, and F. Couto, “What’s in a `nym’? synonyms in biomedical ontology matching,” in International Semantic Web Conference (ISWC), pp. 526–541, 2013. [ bib | DOI | pdf | scholar ]
[15] C. Machado, F. Couto, A. Fernandes, S. Santos, and A. Freitas, “Toward a translational medicine approach for hypertrophic cardiomyopathy,” in International Conference on Information Technology in Bio and Medical Informatics (ITBAM – DEXA), pp. 151–165, 2012. [ bib | DOI | pdf | scholar ]
[16] J. Ferreira, C. Pesquita, M. Silva, and F. Couto, “Bringing epidemiology into the semantic web,” in International Conference on Biomedical Ontologies (ICBO), pp. 1–5, 2012. [ bib | pdf | url | scholar ]
[17] D. Batista, J. Ferreira, F. Couto, and M. Silva, “Toponym disambiguation using ontology-based semantic similarity,” in Computational Processing of the Portuguese Language (PROPOR), pp. 179–185, 2012. [ bib | DOI | pdf | scholar ]
[18] J. Ferreira and F. Couto, “Generic semantic relatedness measure for biomedical ontologies,” in International Conference on Biomedical Ontologies (ICBO), pp. 1–10, 2011. [ bib | pdf | url | scholar ]
[19] C. Pesquita and F. Couto, “Where GO is going and what it means for ontology extension,” in International Conference on Biomedical Ontologies (ICBO), pp. 1–10, 2011. [ bib | pdf | url | scholar ]
[20] L. Lopes, F. Silva, F. Couto, J. Zamite, H. Ferreira, C. Sousa, and M. Silva, “Epidemic marketplace: An information management system for epidemiological data,” in International Conference on Information Technology in Bio and Medical Informatics (ITBAM – DEXA), pp. 31–44, 2010. [ bib | DOI | pdf | scholar ]
[21] J. Zamite, F. Silva, F. Couto, and M. Silva, “MEDCollector: Multisource epidemic data collector,” in International Conference on Information Technology in Bio and Medical Informatics (ITBAM – DEXA), pp. 16–30, 2010. [ bib | DOI | pdf ]
[22] M. Silva, F. Silva, L. Lopes, and F. Couto, “Building a digital library for epidemic modelling,” in The International Conference on Digital Libraries (ICDL), pp. 1–13, 2010. [ bib | pdf | scholar ]
[23] F. Couto, T. Grego, C. Pesquita, H. Bastos, R. Torres, P. Sanchez, L. Pascual, and C. Blaschke, “Identifying bioentity recognition errors of rule-based text-mining systems,” in IEEE Third International Conference on Digital Information Management (ICDIM), pp. 1–6, 2008. [ bib | DOI | pdf | scholar ]
[24] F. Couto, M. Silva, and P. Coutinho, “Validating associations in biological databases,” in ACM Conference in Information and Knowledge Management (CIKM), pp. 42–151, 2006. [ bib | DOI | pdf | scholar ]
[25] F. Couto, M. Silva, and P. Coutinho, “Semantic similarity over the gene ontology: Family correlation and selecting disjunctive ancestors,” in ACM Conference in Information and Knowledge Management (CIKM) (as a short paper), pp. 343–344, 2005. [ bib | DOI | pdf | scholar ]
[26] F. Couto, B. Martins, and M. Silva, “Classifying biological articles using web resources,” in 2004 ACM Symposium on Applied Computing (SAC), pp. 111–115, 2004. [ bib | DOI | pdf | scholar ]
[27] F. Couto, M. Silva, and P. Coutinho, “ProFAL: Protein functional annotation through literature,” in 8th Conference on Software Engineering and Databases (JISBD), p. 747–756, 2003. [ bib | pdf | scholar ]

Workshop papers

[1] M. Fernandes, J. Decouchant, F. Couto, and P. Veríssimo, “Accurate filtering of privacy-sensitive information in raw genomic data,” in The Twelfth EuroSys Doctoral Workshop (EuroDW 2018), 2018. [ bib | pdf | url ]
[2] D. Faria, B. Balasubramani, V. Shivaprabhu, I. Mott, C. Pesquita, F. Couto, and I. Cruz, “Results of AML in OAEI 2017,” in The Twelfth International Workshop on Ontology Matching (OM-2017), 2017. [ bib | pdf | url ]
[3] L. Campos, A. Lamurias, and F. Couto, “Can the wisdom of the crowd be used to improve the creation of gold-standard for text mining applications?,” in INForum – Simpósio de Informática, 2017. [ bib | pdf ]
[4] F. Couto, L. Campos, and A. Lamurias, “MER: a minimal named-entity recognition tagger and annotation server,” in BioCreative V.5 Challenge Evaluation, 2017. [ bib | pdf | url ]
[5] A. Lamurias, L. Campos, and F. Couto, “IBEnt: Chemical entity mentions in patents using ChEBI,” in BioCreative V.5 Challenge Evaluation, 2017. [ bib | pdf | url ]
[6] M. Rodrigues and F. Couto, “MoRS at SemEval-2017 task 3: Easy to use SVM in ranking tasks,” in 10th International Workshop on Semantic Evaluation (SemEval), 2017. [ bib | pdf | url ]
[7] A. Lamurias, D. Sousa, S. Pereira, L. Clarke, and F. Couto, “ULISBOA at SemEval-2017 Task 12: Extraction and classification of temporal expressions and events,” in 10th International Workshop on Semantic Evaluation (SemEval), 2017. [ bib | pdf | url ]
[8] D. Faria, C. Pesquita, B. Balasubramani, C. Martins, J. Cardoso, H. Curado, F. Couto, and I. Cruz, “OAEI 2016 results of AML,” in The Eleventh International Workshop on Ontology Matching (OM-2016), 2016. [ bib | pdf | url ]
[9] D. Goncalves, M. Costa, and F. Couto, “A large-scale characterization of user behaviour in cable TV,” in 3rd Workshop on Recommendation Systems for Television and online Video (RecSysTV), 2016. [ bib | pdf ]
[10] D. Goncalves, M. Costa, and F. Couto, “A flexible recommendation system for cable TV,” in 3rd Workshop on Recommendation Systems for Television and online Video (RecSysTV), 2016. [ bib | pdf ]
[11] M. Barros, F. Couto, H. Savietto, C. Barata, M. Domingos, A. Krone-Martins, and A. Moitinho, “A pipeline for producing a scientifically accurate visualisation of the Milky Way,” in INForum – Simpósio de Informática, 2016. [ bib | pdf ]
[12] A. Lamurias, M. Rodrigues, L. Clarke, and F. Couto, “Extraction of regulatory events using kernel-based classifiers and distant supervision,” in ACL proceedings of the 4th BioNLP Shared Task Workshop, 2016. [ bib | pdf | url ]
[13] M. Barros, A. Lamurias, G. Figueiro, M. Antunes, J. Teixeira, A. Pinheiro, and F. Couto, “ULISBOA at SemEval-2016 task 12: Extraction of temporal expressions, clinical events and relations using IBEnt,” in 9th International Workshop on Semantic Evaluation (SemEval), 2016. [ bib | pdf | url ]
[14] V. Cogo, A. Bessani, F. Couto, and P. Verissimo, “A high-throughput method to detect privacy-sensitive human genomic data,” in Workshop on Privacy in the Electronic Society (WPES), 2015. [ bib | pdf | url ]
[15] A. Lamurias, M. Lobo, M. Antunes, L. Clarke, and F. Couto, “Identifying chemical entities in patents using brown clustering and semantic similarity,” in 5th BioCreative Challenge Evaluation, 2015. [ bib | pdf | url ]
[16] A. Leal, B. Martins, and F. Couto, “ULisboa: Recognition and normalization of medical concepts,” in 8th International Workshop on Semantic Evaluation (SemEval), 2015. [ bib | pdf | url ]
[17] D. Faria, C. Martins, A. Nanavaty, D. Oliveira, B. Sowkarthiga, A. Taheri, C. Pesquita, F. Couto, and I. Cruz, “AgreementMakerLight results for OAEI 2015,” in The Tenth International Workshop on Ontology Matching (OM-2015), 2014. [ bib | pdf | url ]
[18] D. Faria, C. Martins, A. Nanavaty, A. Taheriand, C. Pesquita, E. Santos, I. Cruz, and F. Couto, “AgreementMakerLight results for OAEI 2014,” in The Ninth International Workshop on Ontology Matching (OM-2014), 2014. [ bib | pdf | url ]
[19] F. Couto, “Rating, recognizing and rewarding metadata integration and sharing on the semantic web,” in 3rd International Workshop on Methods for Establishing Trust of (Open) Data (METHOD), 2014. [ bib | pdf | url ]
[20] T. Mendes, B. Rodrigues, A. Moitinho, M. Gomes, F. Couto, T. Guerreiro, and A. Krone-Martins, “Exploração visual online de bases de dados astronómicas,” in INForum – Simpósio de Informática, 2014. [ bib | pdf ]
[21] A. Leal, D. Gonçalves, B. Martins, and F. Couto, “Ulisboa: Identification and classification of medical concepts,” in 7th International Workshop on Semantic Evaluation (SemEval), 2014. [ bib | pdf | url ]
[22] C. Pesquita, D. Faria, E. Santos, and F. Couto, “To repair or not to repair: reconciling correctness and coherence in ontology reference alignments,” in The Eighth International Workshop on Ontology Matching (OM-2013), 2013. [ bib | pdf | url ]
[23] D. Faria, C. Pesquita, E. Santos, I. Cruz, and F. Couto, “AgreementMakerLight results for OAEI 2013,” in The Eighth International Workshop on Ontology Matching (OM-2013), 2013. [ bib | pdf | url ]
[24] A. Lamurias, T. Grego, and F. Couto, “Chemical compound and drug name recognition using CRFs and semantic similarity based on ChEBI,” in 4th BioCreative Challenge Evaluation, 2013. [ bib | pdf | url ]
[25] M. Costa, D. Gomes, F. Couto, and M. Silva, “A survey of web archive search architectures,” in 3rd Temporal Web Analytics Workshop (TempWeb), 2013. [ bib | pdf | url ]
[26] T. Grego, F. Pinto, and F. Couto, “LASIGE: using conditional random fields and ChEBI ontology,” in 7th International Workshop on Semantic Evaluation (SemEval), 2013. [ bib | pdf | url ]
[27] S. Moreira, J. Filgueiras, B. Martins, F. Couto, and M. Silva, “REACTION: A naive machine learning approach for sentiment classification,” in 7th International Workshop on Semantic Evaluation (SemEval), 2013. [ bib | pdf | url ]
[28] C. Machado, A. Freitas, and F. Couto, “Enrichment analysis applied to disease prognosis,” in Ontologies in Biomedicine and Life Sciences (OBML), 2012. [ bib | pdf | url ]
[29] T. Grego, F. Pinto, and F. Couto, “Identifying chemical entities based on ChEBI,” in Software Demonstration at the International Conference on Biomedical Ontologies (ICBO), 2012. [ bib | pdf | url ]
[30] F. Couto, J. Ferreira, J. Zamite, C. Santos, T. Posse, P. Graça, D. Domingos, and M. Silva, “The epidemic marketplace platform: towards semantic characterization of epidemiological resources using biomedical ontologies,” in Software Demonstration at the International Conference on Biomedical Ontologies (ICBO), 2012. [ bib | pdf | url ]
[31] I. Cruz, C. Stroe, F. Caimi, A. Fabiani, C. Pesquita, F. Couto, and M. Palmonari, “Using AgreementMaker to align ontologies for OAEI 2011,” in The Sixth International Workshop on Ontology Matching (OM-2011), 2011. [ bib | pdf | url ]
[32] S. Domingos, C. Pesquita, F. Couto, L. Goulao, C. Oliveira, and F. Couto, “Improving gene functional analysis in ethylene-induced leaf abscission using GO and ProteInOn,” in INForum – Simpósio de Informática, 2011. [ bib | pdf ]
[33] B. Tavares, H. Bastos, D. Faria, J. Ferreira, T. Grego, C. Pesquita, and F. Couto, “The biomedical ontology applications (BOA) framework,” in Software Demonstration at the International Conference on Biomedical Ontologies (ICBO), 2011. [ bib | pdf | url ]
[34] I. Cruz, C. Stroe, C. Pesquita, F. Couto, and V. Cross, “Biomedical ontology matching using the AgreementMaker system,” in Software Demonstration at the International Conference on Biomedical Ontologies (ICBO), 2011. [ bib | pdf | url ]
[35] S. Moreira, D. Batista, P. Carvalho, F. Couto, and M. Silva, “POWER: Politics ontology for web entity retrieval,” in 5th International Workshop on Ontology, Models, Conceptualization and Epistemology in Social, Artificial and Natural Systems (ONTOSE), 2011. [ bib | pdf ]
[36] C. Machado, F. Couto, A. Fernandes, S. Santos, N. Cardim, and A. Freitas, “Semantic characterization of hypertrophic cardiomyopathy disease,” in First Workshop on Knowledge Engineering, Discovery and Dissemination in Health (KEDDH), 2010. [ bib | pdf ]
[37] C. Pesquita, C. Stroe, I. Cruz, and F. Couto, “BLOOMS on AgreementMaker: results for OAEI 2010,” in ISWC Workshop on Ontology Matching, 2010. [ bib | pdf ]
[38] D. Batista, M. Silva, F. Couto, and B. Behera, “Geographic signatures for semantic retrieval,” in 6th Workshop on Geographic Information Retrieval (GIR), 2010. [ bib | pdf ]
[39] D. Faria, C. Pesquita, F. Couto, and A. Falcão, “GOclasses: molecular function as viewed by proteins,” in The 12th Annual Bio-Ontologies Meeting at ISMB/ECCB, 2009. [ bib | pdf ]
[40] C. Pesquita and F. Couto, “Taking GO where we need it to go: focused automated enrichment of the gene ontology,” in Student Council Symposium at ISMB/ECCB, 2009. [ bib | pdf ]
[41] C. Pesquita, D. Pessoa, D. Faria, and F. Couto, “CESSM: Collaborative evaluation of semantic similarity measures,” in Jornadas em Bioinformatica, 2009. [ bib | pdf ]
[42] H. Bastos, T. Grego, F. Couto, and P. Coutinho, “Enzyme family coherence assessment: validation and prediction,” in Jornadas em Bioinformatica, 2009. [ bib | pdf ]
[43] A. Teixeira, R. Santos, and F. Couto, “ThermInfo: Collecting and presenting thermochemical properties,” in INForum – Simpósio de Informática, 2009. [ bib | pdf ]
[44] L. F. Lopes, J. Zamite, B. Tavares, F. Couto, F. Silva, and M. Silva, “Automated social network epidemic data collector,” in INForum – Simpósio de Informática, 2009. [ bib | pdf ]
[45] C. Pesquita, T. Grego, and F. Couto, “Identifying gene ontology areas for automated enrichment,” in Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB), vol. 5518, pp. 934–941, Lecture Notes in Computer Science, 2009. [ bib | pdf ]
[46] T. Grego, P. Pezik, F. Couto, and D. Rebholz-Schuhmann, “Identification of chemical entities in patent documents,” in Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB), vol. 5518, pp. 942–949, Lecture Notes in Computer Science, 2009. [ bib | pdf ]
[47] C. Machado, H. Bastos, and F. Couto, “Great: Gene regulation evaluation tool,” in Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB), vol. 5518, pp. 930–933, Lecture Notes in Computer Science, 2009. [ bib | pdf ]
[48] C. Pesquita, D. Faria, H. Bastos, A. Falcão, and F. Couto, “Evaluating GO-based semantic similarity measures,” in BioOntologies SIG co-located with Internacional Conference on Intelligent Systems for Molecular Biology (ISMB), 2007. [ bib | pdf ]
[49] F. Couto, T. Grego, R. Torres, P. Sanchez, L. Pascual, and C. Blaschke, “Filtering bioentity recognition errors in bioliterature using a case-based approach,” in BioLINK SIG co-located with co-located with Internacional Conference on Intelligent Systems for Molecular Biology (ISMB), 2007. [ bib | pdf ]
[50] P. Jain, F. Couto, M. Silva, and J. Becker, “Literature based functional annotation of genes,” in Bioinformatics: Knowledge Discovery in Biology Workshop (BKDB), 2005. [ bib | pdf ]
[51] F. Couto, M. Silva, and P. Coutinho, “FiGO: Finding GO terms in unstructured text,” in BioCreAtIvE Challenge Evaluation Workshop, 2004. [ bib | pdf ]
[52] F. Couto, M. Silva, and P. Coutinho, “Improving information extraction through biological correlation,” in Data Mining and Text Mining for Bioinformatics Workshop co-located with 7th European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD), 2003. [ bib | pdf ]
[53] F. Couto, M. Silva, and P. Coutinho, “Curating extracted information through the correlation between structure and function,” in Text Data Mining SIG co-located with Internacional Conference on Intelligent Systems for Molecular Biology (ISMB), 2003. [ bib | pdf ]
[54] F. Couto, “The development of a computer application that identifies reusable components through formal specifications,” in 1st International Workshop on Automated Verification of Infinite-State Systems (AVIS’01) co-located with the 10th European Conference organised by Formal Methods Europe (FME), 2001. [ bib | pdf ]

Extended Abstracts

[1] M. Asif, C. Rasga, H. Martiniano, J. Santos, A. Marques, F. Couto, and A. Vicente, “An integrative system biology approach for dissecting autism spectrum disorder,” in 2º Dia do Jovem Investigador do Instituto Nacional de Saúde Doutor Ricardo Jorge, 2017. [ bib | pdf ]
[2] L. Campos, V. Pedro, and F. Couto, “Semantic annotation of electronic health records in a multilingual environment,” in Bioinformatics Open Days, University of Minho, 2017. [ bib | pdf ]
[3] A. Lamurias, L. Clarke, and F. Couto, “Development of a text mining framework for systems biology,” in Bioinformatics Open Days, University of Minho, 2017. [ bib | pdf ]
[4] G. Figueiró, F. Couto, and A. Moitinho, “3d identification of clusters: a cancer cell case-study,” in Bioinformatics Open Days, University of Minho, 2017. [ bib | pdf ]
[5] M. Rodriques, M. Fale, and F. Couto, “WS4A: a biomedical question and answering system based on public web services and ontologies,” in ACL proceedings of the 4th BioASQ Workshop, 2016. [ bib | pdf | url ]
[6] M. Asif, I. Conceição, K. Kwiatkowska, C. Rasga, C. Café, L. Sousa, G. Oliveira, F. Couto, and A. Vicente, “Increased frequency of the autism broader phenotype in mothers transmitting etiological CNVs to sons affected by Autism Spectrum Disorder (ASD),” in European Human Genetics Conference (ESHG), 2016. [ bib | pdf ]
[7] M. Asif, I. Conceição, K. Kwiatkowska, C. Rasga, F. Couto, and A. Vicente, “Maternal copy number variants (CNV) transmission to their Autism Spectrum Disorder (ASD) sons correlates with phenotypic traits,” in The 13th International Congress of Human Genetics (ICHG), 2016. [ bib | pdf ]
[8] H. Curado, M. Cândido, M. Silva, J. Carriço, and F. Couto, “A proposal for allele validation tool (AVT) for whole genome multilocus sequence typing (wgMLST) schemas,” in Bioinformatics Open Days, University of Minho, 2016. [ bib | pdf ]
[9] M. Lobo, A. Lamurias, and F. Couto, “Identifying human phenotype terms in text using a machine learning approach,” in Bioinformatics Open Days, University of Minho, 2016. [ bib | pdf ]
[10] R. Florencio, F. Couto, N. Matela, and J. Afonso, “Radiation monitoring system in clinical imaging,” in Bioinformatics Open Days, University of Minho, 2016. [ bib | pdf ]
[11] P. Martins, L. Clarke, M. Amaral, and F. Couto, “Exploring machine learning algorithms to predict subcellular localizations,” in Bioinformatics Open Days, University of Minho, 2016. [ bib | pdf ]
[12] M. Barros, A. Lamúrias, M. Antunes, J. Teixeira, G. Figueiró, A. Pinheiro, and F. Couto, “Extraction of temporal expressions and clinical events from clinical notes,” in Bioinformatics Open Days, University of Minho, 2016. [ bib | pdf ]
[13] A. Barata, F. Couto, and L. Carvalho, “Anthropometric data analytics: Portuguese case-study,” in Bioinformatics Open Days, University of Minho, 2016. [ bib | pdf ]
[14] F. Couto, “Metarate – incentivize data integration and sharing by rating and rewarding metadata annotation,” in European Data Forum (EDF), 2015. [ bib | pdf ]
[15] A. Leal, B. Martins, and F. Couto, “Recognition and normalization of biomedical entities based on ontologies,” in Bioinformatics Open Days, University of Lisbon, 2015. [ bib | pdf ]
[16] M. Asif, I. Conceição, C. Café, J. Almeida, S. Mouga, G. Oliveira, F. Couto, and A. Vicente, “Use of machine learning approaches to explore genetic and phenotypic associations for Autism Spectrum Disorder,” in 18th Meeting of The Portuguese Society of Human Genetics (SPGH), 2014. [ bib | pdf ]
[17] J. Ferreira, B. Bono, and F. Couto, “From data to knowledge: a tool for clustering multi-scale resources for physiology research,” in Virtual Physiological Human (VPH), 2014. [ bib | pdf ]
[18] C. Pesquita, M. Cheatham, D. Faria, J. Barros, E. Santos, and F. Couto, “Building reference alignments for compound matching of multiple ontologies using obo cross-products,” in The Ninth International Workshop on Ontology Matching (OM-2014), 2014. [ bib | pdf | url ]
[19] D. Faria, C. Pesquita, E. Santos, I. Cruz, and F. Couto, “Agreementmakerlight: A scalable automated ontology matching system,” in The 10th International Conference on Data Integration in the Life Sciences (DILS), 2014. [ bib | pdf | url ]
[20] N. Leitão, J. Leitão, and F. Couto, “Expansão do espaço de procura em mapeamento genómico de alto rendimento,” in INForum – Simpósio de Informática, 2014. [ bib | pdf ]
[21] D. Faria, C. Pesquita, E. Santos, I. Cruz, and F. Couto, “AgreementMakerLight 2.0: Towards efficient large-scale ontology matching,” in International Semantic Web Conference (ISWC), 2014. [ bib | pdf ]
[22] A. Moitinho, T. Mendes, B. Rodrigues, M. Gomes, A. Krone-Martins, and F. Couto, “Veja – visual exploration just anywhere,” in International Astronomical Union Symposium (IAUS), 2014. [ bib | pdf ]
[23] L. Silva, F. Couto, H. Manso, and A. Vicente, “Development of a semantic model for cerebrovascular accident (CVA) patients,” in Bioinformatics Open Days, University of Minho, 2014. [ bib | pdf ]
[24] J. Carilho, O. Schnell, J. Martins, L. Carriço, C. Duarte, F. Couto, and T. Guerreiro, “Predicting relevant events in the life of a person with alzheimer,” in Bioinformatics Open Days, University of Minho, 2014. [ bib | pdf ]
[25] N. Leitão, J. Leitão, and F. Couto, “Llc-gnumap: Scalable, precise, and high-coverage genomics mapping,” in Bioinformatics Open Days, University of Minho, 2014. [ bib | pdf ]
[26] A. Lamurias and F. Couto, “Identifying interactions between chemical entities in text,” in Bioinformatics Open Days, University of Minho, 2014. [ bib | pdf ]
[27] C. Machado, F. Couto, and A. Freitas, “Exploring ontological knowledge for translational medicine,” in Workshop on Machine Learning for Clinical Data Analysis and Healthcare (NIPS), 2013. [ bib | pdf ]
[28] J. Ferreira, C. Pesquita, F. Couto, and M. Silva, “Digital preservation of epidemic resources: coupling metadata and ontologies,” in 10th International Conference on Preservation of Digital Objects, 2013. [ bib | pdf ]
[29] C. Pesquita, J. Ferreira, F. Couto, and M. Silva, “Semi-automated annotation of epidemiological resources,” in Epiwork International Workshop on Digital Epidemiology, Turin, 2013. [ bib | pdf ]
[30] M. Silva, C. Vaz, A. Francisco, M. Ramirez, F. Couto, and J. Carriço, “NGSOnto – keeping track of the ngs pipeline process using an ontological approach and its application on molecular epidemiology,” in Molecular Biology in Portugal and EMBL (and EMBL Alumni), FCUL, 2013. [ bib | pdf ]
[31] J. Ferreira and F. Couto, “Semantic similarity in the biomedical domain,” in Molecular Biology in Portugal and EMBL (and EMBL Alumni), FCUL, 2013. [ bib | pdf ]
[32] C. Alonso, F. Couto, and R. Dias, “Comparative genomics of bacillus spp.: can core genome be the key for new therapeutics? assessment of the core genome of bacillus spp. and its stability,” in Molecular Biology in Portugal and EMBL (and EMBL Alumni), FCUL, 2013. [ bib | pdf ]
[33] T. Grego and F. Couto, “Recognition and resolution of chemical entities to ChEBI,” in Bioinformatics Open Days, University of Minho, 2012. [ bib | pdf ]
[34] J. Ferreira and F. Couto, “Semantic similarity in the biomedical domain,” in Bioinformatics Open Days, University of Minho, 2012. [ bib | pdf ]
[35] H. Bastos, F. Couto, and P. Coutinho, “Exploring gene ontology relationships in enzyme families: An application to polysaccharide lyases,” in 9th Carbohydrate Bioengineering Meeting (CBM9), 2011. [ bib | pdf ]
[36] C. Pesquita, J. Ferreira, and F. Couto, “FLORAL: Semantic and lexical matching of biomedical ontologies,” in 1st Virtual Physiological Human Conference (VPH), 2010. [ bib | pdf ]
[37] C. Pesquita, D. Pessoa, D. Faria, and F. Couto, “Collaborative evaluation of GO-based similarity measures,” in The 12th Annual Bio-Ontologies Meeting at ISMB/ECCB, 2009. [ bib | pdf ]
[38] C. Pesquita, D. Faria, R. Lopes, and F. Couto, “Measuring coherence between electronic and manual annotations in biological databases,” in SAC ’09: Proceedings of the 2009 ACM Symposium on Applied Computing, 2009. [ bib | pdf ]
[39] P. Gomes-Alves, A. Coelho, F. Couto, P. Nogueira, and D. Penque, “Proteins potentially involved in F508del-CFTR trafficking restoration process,” in HUPO 7th Annual World Congress, 2008. [ bib | pdf ]
[40] C. Pesquita, F. Couto, and M. Silva, “Automated enrichment of bioontologies,” in First Portuguese Forum on Computational Biology, 2008. [ bib | pdf ]
[41] H. Bastos, C. Machado, A. Freitas, and F. Couto, “Retrieving relevant documents from bioliterature for the curation of yeast gene regulatory networks,” in First Portuguese Forum on Computational Biology, 2008. [ bib | pdf ]
[42] D. Faria, C. Pesquita, F. Couto, and A. Falcão, “ProteInOn: Web tool for protein semantic similarity,” in 15th Internacional Conference on Intelligent Systems for Molecular Biology (ISMB) as a poster, 2007. [ bib | pdf ]
[43] F. Couto, “ReBIL: Relating biological information through literature,” in I Annual Meeting of Portuguese Proteomic Network – ProCura: Functional Genomics And Proteomics, 2003. [ bib | pdf ]
[44] F. Couto, M. Silva, and P. Coutinho, “ReBIL: Relating biological information through literature,” in 11th Internacional Conference on Intelligent Systems for Molecular Biology (ISMB) as a poster, 2003. [ bib | pdf ]
[45] F. Couto, “Category theory based identification of reusable components through formal specifications,” in 5th European Conference on Research and Advanced Technology for Digital Libraries as a poster, 2001. [ bib | pdf ]

Magazine papers

[1] F. Couto, “Exploiting biomedical information through literature and ontologies,” El País – Sociedad, 2011. [ bib | url ]
[2] C. Machado, F. Couto, A. Fernandes, S. Santos, N. Cardim, and A. Freitas, “Unraveling hypertrophic cardiomyopathy variability,” ERCIM News 82 – Special Theme: Computational Biology, 2010. [ bib | url ]
[3] F. Silva, M. Silva, and F. Couto, “Epidemic marketplace: an e-science platform for epidemic modelling and analysis,” ERCIM News 82 – Special Theme: Computational Biology, 2010. [ bib | url ]
[4] F. Couto and M. Silva, “Bioinformática – exploração da informação,” centroatlantico.pt magazine, vol. 3, 2003. [ bib | pdf ]

Technical reports

[1] L. Campos and F. Couto, “MRA – proof of concept of a multilingual report annotator web application,” Tech. Rep. arXiv:1704.01748 [cs.DL], arXiv.org, April 2017. [ bib | pdf | url ]
[2] C. Ramos, M. Louro, M. Santos, and F. Couto, “Knowledge ratings in MetaboLights,” Tech. Rep. arXiv:1604.07997 [cs.DL], arXiv.org, April 2016. [ bib | pdf | url ]
[3] R. Norman and F. Couto, “Using Google Scholar to predict self-citation: A case study in health economics,” Tech. Rep. arXiv:1406.5241 [stat.OT], arXiv.org, July 2014. [ bib | pdf | url ]
[4] F. Couto, “CIDS country rankings: comparing documents and citations of USA, UK and China top researchers,” Tech. Rep. arXiv:1310.5597 [cs.DL], arXiv.org, July 2013. [ bib | pdf | url ]
[5] E. Santos, D. Faria, C. Pesquita, and F. Couto, “Ontology alignment repair through modularization and confidence-based heuristics,” Tech. Rep. arXiv:1307.5322 [cs.AI], arXiv.org, July 2013. [ bib | pdf | url ]
[6] F. Couto, D. Faria, B. Tavares, P. Gonçalves, and P. Verissimo, “Benchmarking some portuguese S&T system research units: 2nd edition,” DI/FCUL TR 13–03, Department of Informatics, University of Lisbon, February 2013. [ bib | DOI | pdf ]
[7] D. Faria, C. Pesquita, E. Santos, F. Couto, C. Stroe, and I. Cruz, “Testing the AgreementMaker system in the anatomy task of OAEI 2012,” Tech. Rep. arXiv:1212.1625 [cs.IR], arXiv.org, December 2012. [ bib | pdf | url ]
[8] J. Ferreira, D. Batista, F. Couto, and M. Silva, “The Geo-Net-PT/Yahoo! GeoPlanet (TM) concordance,” DI/FCUL TR 10–05, Department of Informatics, University of Lisbon, September 2010. [ bib | DOI | pdf ]
[9] T. Grego, J. Ferreira, C. Pesquita, H. Bastos, D. Viçosa, J. Freire, and F. Couto, “Chemical and metabolic pathway semantic similarity,” DI/FCUL TR 10–01, Department of Informatics, University of Lisbon, March 2010. [ bib | DOI | pdf ]
[10] F. Couto, I. Andrade, P. Gonçalves, and P. Verissimo, “Benchmarking some portuguese S&T system research units,” DI/FCUL TR 10–07, Department of Informatics, University of Lisbon, March 2010. [ bib | DOI | pdf ]
[11] F. Martins, A. Falcão, and F. Couto, “Semantic similarity match for data quality,” DI/FCUL TR 07–25, Department of Informatics, University of Lisbon, October 2007. [ bib | DOI | pdf ]
[12] D. Faria, C. Pesquita, F. Couto, and A. Falcão, “ProteInOn: a web tool for protein semantic similarity,” DI/FCUL TR 07–6, Department of Informatics, University of Lisbon, March 2007. [ bib | DOI | pdf ]
[13] F. Couto, M. Silva, V. Lee, E. Dimmer, E. Camon, R. Apweiler, H. Kirsch, and D. Rebholz-Schuhmann, “GOAnnotator: linking electronic protein GO annotation to evidence text,” DI/FCUL TR 05–25, Department of Informatics, University of Lisbon, December 2005. [ bib | DOI | pdf ]
[14] F. Couto, M. Silva, and P. Coutinho, “Validation of automated protein annotation,” DI/FCUL TR 05–24, Department of Informatics, University of Lisbon, December 2005. [ bib | DOI | pdf ]
[15] F. Couto, M. Silva, and P. Coutinho, “Implementation of a functional semantic similarity measure between gene-products,” DI/FCUL TR 03–29, Department of Informatics, University of Lisbon, November 2003. [ bib | DOI | pdf ]
[16] F. Couto, B. Martins, M. Silva, and P. Coutinho, “Classifying biomedical articles using web resources: application to KDD Cup 02,” DI/FCUL TR 03–24, Department of Informatics, University of Lisbon, July 2003. [ bib | DOI | pdf ]
[17] F. Couto, “Representação categorial de especificações de espécie Única,” trabalho final de curso, Instituto Superior Técnico da Universidade Técnica de Lisboa, July 2000. [ bib | pdf ]

Theses

[1] F. Couto, ReBIL: Relating Biological Information through Literature. PhD thesis, Faculdade de Ciências da Universidade de Lisboa, January 2006. [ bib | DOI | pdf ]
[2] F. Couto, “Identificação de componentes reutilizáveis através de especificações formais,” Master’s thesis, Instituto Superior Técnico da Universidade Técnica de Lisboa, July 2001. [ bib | pdf ]