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Lopes, L. F., F. Silva, F. Couto, MJ. Silva, and D3. Epiwork, "1: Meta-model Initial Specification", Catalogue of Relevant Data, Platform Requirements. 30th September, 2009.
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Decouchant, J., M. Fernandes, M. Völp, F. M. Couto, and P. Esteves-Verissimo, "Accurate filtering of privacy-sensitive information in raw genomic data", Journal of biomedical informatics, vol. 82: Elsevier, pp. 1–12, 2018.
Couto, F., and M. J. Silva, "Advanced Data Mining Techonologies in Bioinformatics, chapter Mining the BioLiterature: towards automatic annotation of genes and proteins", Idea Group Inc, 2006.
Faria, D., C. Pesquita, E. Santos, I.. Cruz, and F. Couto, "AgreementMakerLight 2.0: Towards Efficient Large-Scale Ontology Matching", International Semantic Web Conference (ISWC), 2014.
Faria, D., C. Pesquita, E. Santos, I. F. Cruz, and F. Couto, "AgreementMakerLight: A Scalable Automated Ontology Matching System", DILS 2014, pp. 29, 2014.
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.", OM, pp. 101–108, 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. Martins, A.. Nanavaty, A.. Taheriand, C. Pesquita, E. Santos, I.. Cruz, and F. Couto, "AgreementMakerLight results for OAEI 2014", The Ninth International Workshop on Ontology Matching (OM-2013), 2014.
Bastos, H., L. A. Clarke, and F. Couto, "Annotation extension through protein family annotation coherence metrics", Frontiers in genetics, vol. 4: Frontiers Media SA, 2013.
Barata, A., L. Carvalho, and F. M. Couto, "Anthropometric data analytics: a portuguese case study", International Conference on Practical Applications of Computational Biology & Bioinformatics: Springer, pp. 92–100, 2017.
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.
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.
Formella, A., F. Couto, JS. Silva, and P. Fernandes, "Approximate point set match for partial protein structure alignment", Proceedings of Bioinformatics: Knowledge Discovery in Biology (BKDB2005). Facultade Ciencias Lisboa da Universidade de Lisboa, pp. 53–57, 2005.
Ferreira, J. D., B. Inácio, R. M. Salek, and F. M. Couto, "Assessing Public Metabolomics Metadata, Towards Improving Quality", Journal of integrative bioinformatics, vol. 14, no. 4: De Gruyter, 2017.
Asif, M., F. Couto, and A. M. Vicente, "Associação entre variantes genéticas e perfil cl{ínico multidimensional de doentes com perturbação do espetro do autismo: uma abordagem integrativa", Boletim Epidemiológico Observações, vol. 7, no. 22: Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, pp. 38–42, 2018.
Lopes, L. F., J. Zamite, B. Tavares, F. Couto, F. Silva, and M. J. Silva, "Automated social network epidemic data collector", INForum informatics symposium. Lisboa, 2009.
Faria, D., C. Pesquita, E. Santos, I. F. Cruz, and F. Couto, "Automatic Background Knowledge Selection for Matching Biomedical Ontologies", PloS one, vol. 9, no. 11: Public Library of Science, pp. e111226, 2014.
Groza, T.., 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, vol. 2015, pp. 1-13, 2015.
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Couto, F., D. Faria, B. Tavares, P. Gonçalves, and P. Verissimo, "Benchmarking some Portuguese S&T system research units", arXiv preprint arXiv:1302.0420, 2013.
Couto, F., I. Andrade, P. Gonçalves, and P. Verissimo, Benchmarking some Portuguese S&T system research units, , 2010.
Couto, F., D. Faria, B. Tavares, P. Gonçalves, and P. Verissimo, "Benchmarking some Portuguese S&T system research units: 2nd Edition", arXiv preprint arXiv:1302.0420, 2013.
Couto, F., and M. J. Silva, Bioinformática-Exploração da Informação, : centroatlantico. pt magazine, 2003.
Couto, F., M. J. Silva, and P. Fernandes, Bioinformatics: Knowledge Discovery in Biology, : Bioinformatics: Knowledge Discovery in Biology-Workshop Proceedings, 2005.
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.
Cruz, I. F., C. Stroe, C. Pesquita, F. Couto, and V. Cross, "Biomedical Ontology Matching Using the AgreementMaker System.", ICBO, 2011.
Couto, F., and M. J. Silva, Biomedical research line of LASIGE, , 2008.
Pesquita, C., C. Stroe, I. F. Cruz, and F. Couto, "BLOOMS on AgreementMaker: results for OAEI 2010", Ontology Matching, pp. 134, 2010.
Lamurias, A., L. A. Clarke, and F. M. Couto, "BO-LSTM: Classifying relations via long short-term memory networks along biomedical ontologies", bioRxiv: Cold Spring Harbor Laboratory, pp. 336719, 2018.
Ferreira, J., C. Pesquita, F. Couto, and M. J. Silva, "Bringing epidemiology into the Semantic Web.", ICBO, 2012.
Silva, M. J., F. Silva, L. Filipe Lopes, and F. Couto, "Building a digital library for epidemic modelling", Proceedings of ICDL, pp. 23–27, 2010.
Pesquita, C., M. Cheatham, D. Faria, J. Barros, E. Santos, and F. Couto, "Building reference alignments for compound matching of multiple ontologies using OBO cross-products", Ontology Matching Workshop at ISWC 2014, 2014.
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Coutinho, P. M., C. Rancurel, M. Stam, T. Bernard, F. Couto, E. G. J. Danchin, and B. Henrissat, "Carbohydrate-Active Enzymes Database: Principles and Classification of Glycosyltransferases", Bioinformatics for Glycobiology and Glycomics: An Introduction: John Wiley & Sons, Ltd, pp. 89–118, 2009.
Pesquita, C., D. Pessoa, D. Faria, and F. Couto, "CESSM: collaborative evaluation of semantic similarity measures", JB2009: Challenges in Bioinformatics, 2009.
Krallinger, M.., O.. Rabal, F.. Leitner, M.. Vazquez, D.. Salgado, Z.. Lu, R.. Leaman, Y.. Lu, D.. Ji, D.. Lowe, et al., "The CHEMDNER corpus of chemicals and drugs and its annotation principles", Journal of Cheminformatics, vol. 7, pp. S2, 1-20, 2015.
Grego, T., J. Ferreira, C. Pesquita, H. Bastos, D. Vila Viçosa, J. Freire, and F. Couto, Chemical and Metabolic Pathway Semantic Similarity, , 2010.
Lamurias, A., T. Grego, and F. Couto, "Chemical compound and drug name recognition using CRFs and semantic similarity based on ChEBI", BioCreative Challenge Evaluation Workshop, vol. 2, pp. 75, 2013.
Grego, T., C. Pesquita, H. Bastos, and F. Couto, "Chemical entity recognition and resolution to ChEBI", International Scholarly Research Notices, vol. 2012: Hindawi Publishing Corporation, 2012.
Lamurias, A., J. Ferreira, and F. Couto, "Chemical Named Entity Recognition: Improving Recall Using a Comprehensive List of Lexical", Bioinformatics (Pacbb 2014), vol. 294: Springer, pp. 253, 2014.
Lamurias, A., J. Ferreira, and F. Couto, "Chemical named entity recognition: Improving recall using a comprehensive list of lexical features", 8th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2014): Springer International Publishing, pp. 253–260, 2014.
Couto, F., "CIDS country rankings: comparing documents and citations of USA, UK and China top researchers", arXiv preprint arXiv:1310.5597, 2013.
Couto, F., B. Martins, and M. J. Silva, "Classifying biological articles using web resources", Proceedings of the 2004 ACM symposium on Applied computing: ACM, pp. 111–115, 2004.
Couto, F., B. Martins, M. J. Silva, and P. Coutinho, Classifying biomedical articles using web resources, : 19th ACM Symposium on Applied Computing (SAC), 2004.
Couto, F., B. Martins, M. J. Silva, and P. M. Coutinho, Classifying Biomedical Articles using Web Resources: application to KDD Cup 02, : Department of Informatics, University of Lisbon, 2003.
Fernandes, M., J. Decouchant, F. M. Couto, and P. Esteves-Verissimo, "Cloud-Assisted Read Alignment and Privacy", 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, vol. 616: Springer, pp. 220, 2017.
Pesquita, C., D. Pessoa, D. Faria, and F. Couto, Collaborative Evaluation of GO-based Similarity Measures, : 12th Annual Bio-Ontologies Meeting at ISMB/ECCB 2009, 2009.
Couto, F., M. J. Silva, and P. Coutinho, "Curating extracted information through the correlation between structure and function", third meeting of the special interest group on Text Data Mining: Citeseer, 2003.
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Grego, T., and F. Couto, "Enhancement of chemical entity identification in text using semantic similarity validation", PloS one, vol. 8, no. 5: Public Library of Science, pp. e62984, 2013.
Machado, C. M., A. T. Freitas, and F. Couto, "Enrichment analysis applied to disease prognosis.", J. Biomedical Semantics, vol. 4, pp. 21, 2013.
Bastos, H., T. Grego, F. Couto, and P. M. Coutinho, Enzyme family coherence assessment: validation and prediction, : JB'2009-Challenges in Bioinformatics, 2009.
Silva, F., M. J. Silva, and F. Couto, "Epidemic Marketplace: an e-Science Platform for Epidemic Modelling and Analysis", ERCIM News, 2010.
Lopes, L. F., F. Silva, F. Couto, J. Zamite, H. Ferreira, C. Sousa, and M. J. Silva, "Epidemic marketplace: an information management system for epidemiological data", Information Technology in Bio-and Medical Informatics, ITBAM 2010: Springer Berlin Heidelberg, pp. 31–44, 2010.
Couto, F., J. Ferreira, J. Zamite, C. Santos, T. Posse, P. Graça, D. Domingos, and M. J. Silva, "The Epidemic Marketplace Platform: towards semantic characterization of epidemiological resources using biomedical ontologies.", ICBO, 2012.
Couto, F., J. Ferreira, J. Zamite, C. Santos, T. Posse, P. Graça, D. Domingos, and M. J. Silva, "The Epidemic Marketplace Platform: towards semantic characterization of epidemiological resources using biomedical ontologies", International Conference on Biomedical Ontologies, 2012.
Pesquita, C., J. Ferreira, F. Couto, and M. J. Silva, "The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources", Journal of biomedical semantics, vol. 5: BioMed Central, pp. 4, 2014.
Lopes, L. F., F. Silva, F. Couto, and M. J. Silva, Epiwork D3. 1: Meta-model Initial Specification, Catalogue of Relevant Data, Platform Requirements, , 2009.
Pesquita, C., D. Faria, H. Bastos, A. O. Falcao, and F. Couto, "Evaluating gobased semantic similarity measures", Proc. 10th Annual Bio-Ontologies Meeting, vol. 2007, pp. 37–40, 2007.
Pesquita, C., D. Faria, H. Bastos, A. O. Falcao, and F. Couto, "Evaluating go-based semantic similarity measures", Proc. 10th Annual Bio-Ontologies Meeting, vol. 37, no. 40, pp. 38, 2007.
Pesquita, C., D. Faria, H. Bastos, A. O. Falcao, and F. Couto, "Evaluating GO-based Semantic Similarity Measures. ISMB/ECCB 2007 SIG Meeting Program Materials", International Society for Computational Biology, 2007.
Leitão, N., J.. Leitão, and F. Couto, "Expansão do Espaço de Procura em Mapeamento Genómico de Alto Rendimento", INForum - Simp{ó}sio de Inform{á}tica, 2014.
Ferreira, J., J. Hastings, and F. Couto, "Exploiting disjointness axioms to improve semantic similarity measures", Bioinformatics, vol. 29, no. 21: Oxford University Press, pp. 2781–2787, 2013.
Mendes, T.., B.. Rodrigues, A.. Moitinho, M.. Gomes, F. Couto, T. Guerreiro, and A.. Krone-Martins, "Exploração Visual Online de Bases de Dados Astronómicas", INForum - Simpósio de Informática, 2014.
Lamurias, A., L. A. Clarke, and F. M. Couto, "Extracting microRNA-gene relations from biomedical literature using distant supervision", PloS one, vol. 12, no. 3: Public Library of Science, pp. e0171929, 2017.
Lamurias, A., M. J. Rodrigues, L. A. Clarke, and F. M. Couto, "Extraction of Regulatory Events using Kernel-based Classifiers and Distant Supervision", ACL 2016, pp. 88, 2016.
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Rebholz-Schuhmann, D., H. Kirsch, and F. Couto, "Facts from text–Is text mining ready to deliver?", PLoS Biology, vol. 3, no. 2: Public Library of Science, pp. e65, 2005.
Couto, F., M. J. Silva, and P. Coutinho, "Figo: Finding go terms in unstructured text", Proc. of BioCreative Workshop, 2004.
Couto, F., M. J. Silva, and P. Coutinho, "FIGO: findings GO terms in unStructured text", Proc. of BioCreative Workshop, 2004.
Couto, F., T. Grego, R. Torres, P. Sánchez, L. Pascual, and C. Blaschke, "Filtering bioentity recognition errors in bioliterature using a case-based approach", BioLINK SIG, ISMB/ECCB, 2007.
Couto, F., M. J. Silva, and P. Coutinho, "Finding genomic ontology terms in text using evidence content", BMC bioinformatics, vol. 6, no. Suppl 1: BioMed Central Ltd, pp. S21, 2005.
Gonçalves, D., M. Costa, and F. M. Couto, "A Flexible Recommendation System for Cable TV", arXiv preprint arXiv:1609.02451, 2016.
Martins, J., J. Carilho, O. Schnell, C. Duarte, F. Couto, L. Carriço, and T. Guerreiro, "Friendsourcing the unmet needs of people with dementia", Proceedings of the 11th Web for All Conference: ACM, pp. 35, 2014.
Ferreira, J., B.. Bono, and F. Couto, "From data to knowledge: a tool for clustering multi-scale resources for physiology research", Virtual Physiological Human (VPH), 2014.
Bastos, H. P., L. Sousa, L. A. Clarke, and F. M. Couto, "Functional coherence metrics in protein families", Journal of biomedical semantics, vol. 7, no. 1: BioMed Central, pp. 41, 2016.
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Lamurias, A., J. D. Ferreira, L. A. Clarke, and F. M. Couto, "Generating a Tolerogenic Cell Therapy Knowledge Graph from Literature", Frontiers in Immunology, vol. 8: Frontiers, pp. 1656, 2017.
Ferreira, J., and F. Couto, "Generic Semantic Relatedness Measure for Biomedical Ontologies.", ICBO, vol. 833, 2011.
Batista, D. S., M. J. Silva, F. Couto, and B. Behera, "Geographic signatures for semantic retrieval", Proceedings of the 6th Workshop on Geographic Information Retrieval: ACM, pp. 19, 2010.
Ferreira, J., D. S. Batista, F. Couto, and M. J. Silva, The Geo-Net-PT/Yahoo! GeoPlanet (TM) concordance, , 2010.
Pesquita, C., and F. Couto, GO where we need it to go: focused automated enrichment of the Gene Ontology. Student Council Symposium, : Student Council Symposium at ISMB/ECCB 2009, 2009.
Couto, F., M. J. Silva, V. Lee, E. Dimmer, E. Camon, R. Apweiler, H. Kirsch, and D. Rebholz-Schuhmann, GOAnnotator: linking electronic protein GO annotation to evidence text, , 2005.
Couto, F., M. J. Silva, V. Lee, E. Dimmer, E. Camon, R. Apweiler, H. Kirsch, and D. Rebholz-Schuhmann, "GOAnnotator: linking protein GO annotations to evidence text", Journal of Biomedical Discovery and Collaboration, vol. 1, no. 1: BioMed Central Ltd, pp. 19, 2006.
Faria, D., C. Pesquita, F. Couto, and A. O. Falcao, "GOclasses: molecular function as viewed by proteins", The 12th Annual Bio-Ontologies, 2009.
Machado, C. M., H. Bastos, and F. Couto, "GREAT: gene regulation evaluation tool", Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living: Springer Berlin Heidelberg, pp. 930–933, 2009.
Bastos, H., 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, pp. 1-20, 2015.
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Couto, F., T. Grego, C. Pesquita, and P. Verissimo, Handling self-citations using Google Scholar, : International Journal of Scientometrics, Informetrics and Bibliometrics, 2009.
Cogo, V., A. Bessani, F. Couto, and P. Verissimo, "A High-Throughput Method to Detect Privacy-Sensitive Human Genomic Data", Workshop on Privacy in the Electronic Society (WPES), 2015.
Cogo, V. V., A. Bessani, F. M. Couto, M. Gama-Carvalho, M. Fernandes, and P. Esteves-Verissimo, "How can photo sharing inspire sharing genomes?", International Conference on Practical Applications of Computational Biology & Bioinformatics: Springer, pp. 74–82, 2017.
Cogo, V. V., A. Bessani, F. M. Couto, M. Gama-Carvalho, M. Fernandes, and P. Esteves-Verissimo, "How Can Photo Sharing Inspire Sharing Genomes?", 11th International Conference on Practical Applications of Computational Biology & Bioinformatics, vol. 616: Springer, pp. 74, 2017.
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Grego, T., P. Pęzik, F. Couto, and D. Rebholz-Schuhmann, "Identification of chemical entities in patent documents", Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living: Springer, pp. 942–949, 2009.
Couto, F., T. Grego, H. Bastos, C. Pesquita, R. Torres, P. Sánchez, L. Pascual, and C. Blaschke, "Identifying bioentity recognition errors of rule-based text-mining systems", Digital Information Management, 2008. ICDIM 2008. Third International Conference on: IEEE, pp. 733–738, 2008.
Grego, T., F. R. Pinto, and F. Couto, "Identifying Chemical Entities based on ChEBI.", ICBO, 2012.
Lamurias, A., M.. Lobo, M.. Antunes, L.. Clarke, and F. Couto, "Identifying chemical entities in patents using brown clustering and semantic similarity", 5th BioCreative Challenge Evaluation, 2015.
Pesquita, C., T. Grego, and F. Couto, "Identifying Gene Ontology Areas for Automated Enrichment", Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living: Springer, pp. 934–941, 2009.
Lobo, M., A. Lamurias, and F. M. Couto, "Identifying Human Phenotype Terms by Combining Machine Learning and Validation Rules", BioMed Research International, vol. 2017: Hindawi, 2017.
Lamurias, A., J. Ferreira, and F. Couto, "Identifying interactions between chemical entities in biomedical text", Journal of integrative bioinformatics, vol. 11, no. 3, pp. 247, 2014.

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