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Rebholz-Schuhmann, D., H. Kirsch, R. Apweiler, E. Camon, E. Dimmer, V. Lee, M. J. Silva, and F. Couto, Verification of Uncurated Protein Annotations, : Information Retrieval in Biomedicine: Natural Language Processing for Knowledge Integration, IGI Global Publishing, 2009.
Moitinho, A.., T.. Mendes, B.. Rodrigues, M.. Gomes, A.. Krone-Martins, and F. Couto, "VEJA - Visual Exploration Just Anywhere", International Astronomical Union Symposium (IAUS), 2014.
Couto, F., M. J. Silva, and P. M. Coutinho, Validation of Automated Protein Annotation, : Department of Informatics, University of Lisbon, 2005.
Couto, F., M. J. Silva, and P. M. Coutinho, "Validating associations in biological databases", Proceedings of the 15th ACM international conference on Information and knowledge management: ACM, pp. 142–151, 2006.
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Norman, R., and F. Couto, "Using Google Scholar to predict self citation: A case study in Health Economics", arXiv preprint arXiv:1406.5241, 2014.
Cruz, I. F., C. Stroe, F. Caimi, A. Fabiani, C. Pesquita, F. Couto, and M. Palmonari, "Using AgreementMaker to align ontologies for OAEI 2011", Proceedings of the Sixth International Workshop on Ontology Matching, pp. 114–121, 2011.
Ferreira, J., D. Paolotti, F. Couto, and M. J. Silva, "On the usefulness of ontologies in epidemiology research and practice", Journal of epidemiology and community health: BMJ Publishing Group Ltd, pp. jech–2012, 2012.
Asif, M., 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", 18th Meeting of The Portuguese Society of Human Genetics (SPGH), 2014.
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.
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.
Leal, A.., B.. Martins, and F. Couto, "ULisboa: Recognition and Normalization of Medical Concepts", 8th International Workshop on Semantic Evaluation (SemEval), 2015.
Leal, A., D. Gonçalves, B. Martins, and F. Couto, "ULisboa: Identification and Classification of Medical Concepts", SemEval 2014, pp. 711, 2014.
Lamurias, A., D. Sousa, S. Pereira, L. Clarke, and F. M. Couto, "ULISBOA at SemEval-2017 Task 12: Extraction and classification of temporal expressions and events", Proceedings of the 11th International Workshop on Semantic Evaluation (SemEval-2017), pp. 1019–1023, 2017.
Barros, M., A. Lamurias, G. Figueiró, M. Antunes, J. Teixeira, A. Pinheiro, and F. M. Couto, "ULISBOA at SemEval-2016 Task 12: Extraction of temporal expressions, clinical events and relations using IBEnt.", SemEval@ NAACL-HLT, pp. 1263–1267, 2016.
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Asif, M., H. F. Martiniano, C. Rasga, A. R. Marques, J. X. Santos, F. M. Couto, and AM. Vicente, "Translating the complex ASD genetic architecture into clinical phenotype using an integrative system biology approach", European Society of Human Genetics, 16-19 june, 2018: Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, 2018.
Moreira, S., D. S. Batista, P. Carvalho, F. Couto, and M. J. Silva, "Tracking politics with POWER", Program, vol. 47, no. 2: Emerald Group Publishing Limited, pp. 120–135, 2013.
Pesquita, C., D. Faria, E. Santos, J-M. Neefs, and F. Couto, "Towards visualizing the alignment of large biomedical ontologies", Data Integration in the Life Sciences (DILS), 2014.
Faria, D., E. Jiménez-Ruiz, C. Pesquita, E. Santos, and F. Couto, "Towards annotating potential incoherences in BioPortal mappings", International Semantic Web Conference, 2014.
Machado, C. M., F. Couto, A. R. Fernandes, S. Santos, and A. T. Freitas, "Toward a translational medicine approach for hypertrophic cardiomyopathy", Information Technology in Bio-and Medical Informatics: Springer Berlin Heidelberg, pp. 151–165, 2012.
Batista, D. S., J. Ferreira, F. Couto, and M. J. Silva, "Toponym disambiguation using ontology-based semantic similarity", Computational Processing of the Portuguese Language: Springer Berlin Heidelberg, pp. 179–185, 2012.
Pesquita, C., D. Faria, E. Santos, and F. Couto, "To repair or not to repair: reconciling correctness and coherence in ontology reference alignments.", OM, pp. 13–24, 2013.
Pesquita, C., D. Faria, E. Santos, and F. Couto, "To repair or not to repair: reconciling correctness and coherence in ontology reference alignments", Ontology Matching, pp. 13, 2013.
Teixeira, A. L., R. C. Santos, and F. Couto, "ThermInfo: Collecting and Presenting Thermochemical Properties", methods, vol. 1, pp. 3, 2009.
Faria, D., C. Pesquita, E. Santos, F. Couto, C. Stroe, and I. F. Cruz, "Testing the AgreementMaker System in the Anatomy Task of OAEI 2012", arXiv preprint arXiv:1212.1625, 2012.
Faria, D., C. Pesquita, I. Mott, C. Martins, F. M. Couto, and I. F. Cruz, "Tackling the challenges of matching biomedical ontologies", Journal of biomedical semantics, vol. 9, no. 1: BioMed Central, pp. 4, 2018.
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Barata, C., M. Abreu, P. Torres, J. Teixeira, T. Guerreiro, and F. Couto, "Social Impact-Identifying Quotes of Literary Works in Social Networks", Progress in Artificial Intelligence: Springer, pp. 789–795, 2015.
Charro, N., B. L. Hood, D. Faria, P. Pacheco, P. Azevedo, C. Lopes, A. Bugalho de Almeida, F. Couto, T. P. 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: Elsevier, pp. 110–126, 2011.
Fernandes, M., J. Decouchant, M. Voelp, F. M. Couto, and P. Esteves-Verissimo, "Sensitivity Levels: Optimizing the Performance of Privacy Preserving DNA Alignment", bioRxiv: Cold Spring Harbor Laboratory, pp. 292227, 2018.
Machado, C. M., D. Rebholz-Schuhmann, A. T. Freitas, and F. Couto, "The semantic web in translational medicine: current applications and future directions", Briefings in bioinformatics, vol. 16, no. 1: Oxford University Press, pp. 89–103, 2015.
Couto, F., M. J. Silva, and P. M. Coutinho, "Semantic similarity over the gene ontology: family correlation and selecting disjunctive ancestors", Proceedings of the 14th ACM international conference on Information and knowledge management: ACM, pp. 343–344, 2005.
Martins, F., A. O. Falcao, and F. Couto, Semantic Similarity Match for Data Quality, : Department of Informatics, University of Lisbon, 2007.
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.
Ferreira, J., and F. Couto, "Semantic similarity for automatic classification of chemical compounds", PLoS computational biology, vol. 6, no. 9: Public Library of Science, pp. e1000937, 2010.
Pesquita, C., D. Faria, A. O. Falcao, P. Lord, F. Couto, and , "Semantic Similarities in Biomedical Ontologies", IMIA Yearbook, vol. 5, pp. 84–84, 2010.
Machado, C. M., F. Couto, A. R. Fernandes, S. Santos, N. Cardim, and A. T. Freitas, "Semantic characterization of hypertrophic cardiomyopathy disease", Bioinformatics and Biomedicine Workshops (BIBMW), 2010 IEEE International Conference on: IEEE, pp. 432–439, 2010.
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Gomes-Alves, P., F. Couto, C. Pesquita, A. V. 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 (BBA)-Proteins & Proteomics, vol. 1804, no. 4: Elsevier, pp. 856–865, 2010.
Leal, A.., B. Martins, and F. Couto, "Recognition and Normalization of Biomedical Entities Based on Ontologies", Bioinformatics Open Days, University of Lisbon, 2015.
Couto, F., M. J. Silva, and P. Coutinho, "Rebil: Relating biological information through literature", Intelligent Systems for Molecular Biology, 2003.
Couto, F., ReBIL: Relating Biological Information through Literature, : Tese de Doutoramento, Faculdade de Ciências, Departamento de Informática, Universidade de Lisboa, 2006.
Moreira, S., J. Filgueiras, B. Martins, F. Couto, and M. J. Silva, "Reaction: A naive machine learning approach for sentiment classification", Second Joint Conference on Lexical and Computational Semantics (* SEM), vol. 2, pp. 490–494, 2013.
Couto, F., "Rating, recognizing and rewarding metadata integration and sharing on the semantic web", 10th International Workshop on Uncertainty Reasoning for the Semantic Web (URSW 2014), pp. 67, 2014.
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Couto, F., and S. 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. 05: The Authors, 2013.
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Campos, L., and F. Couto, "MRA-Proof of Concept of a Multilingual Report Annotator Web Application", arXiv preprint arXiv:1704.01748, 2017.
Rodrigues, M. J., and F. M. Couto, "MoRS at SemEval-2017 task 3: Easy to use SVM in ranking tasks", Proceedings of the 11th International Workshop on Semantic Evaluation (SemEval-2017), pp. 287–291, 2017.
Simões, T., N. Charro, J. Blonder, D. Faria, F. Couto, K. C. Chan, T. Waybright, H. J. Isaaq, T. D. Veenstra, and D. Penque, "Molecular profiling of the human nasal epithelium: A proteomics approach", Journal of proteomics, vol. 75, no. 1: Elsevier, pp. 56–69, 2011.
Silva, M. J., and F. Couto, Mining the BioLiterature: towards automatic annotation of genes and proteins, : Advanced Data Mining Technologies in Bioinformatics, Idea Group IncIdea Group Inc, 2006.
Couto, F., and M. J. Silva, "Mining BioLiterature: Toward Automatic", Advanced Data Mining Technologies in Bioinformatics: IGI Global, pp. 283, 2006.
Pesquita, C., D. Faria, H. Bastos, A. Ferreira, A. O. Falcao, and F. Couto, "Metrics for GO based protein semantic similarity: a systematic evaluation", BMC bioinformatics, vol. 9, no. Suppl 5: BioMed Central Ltd, pp. S4, 2008.
Inácio, B., J. D. Ferreira, and F. M. Couto, "Metadata Analyser: measuring metadata quality", International Conference on Practical Applications of Computational Biology & Bioinformatics: Springer, pp. 197–204, 2017.
Couto, F. M., L. Campos, and A. Lamurias, "MER: a minimal named-entity recognition tagger and annotation server", Proceedings of the BioCreative, Conference: BeCalm challenge evaluation workshop (Biocreative V.5), at Barcelona, Spain, vol. 5, 2017.
Zamite, J., F. Silva, F. Couto, and M. J. Silva, "MEDCollector: Multisource epidemic data collector", Information Technology in Bio-and Medical Informatics, ITBAM 2010: Springer, pp. 16–30, 2010.
Zamite, J., F. Silva, F. Couto, and M. J. Silva, "MEDCollector: Multisource epidemic data collector", Transactions on large-scale data-and knowledge-centered systems IV: Springer Berlin Heidelberg, pp. 40–72, 2011.
Couto, F., M. J. Silva, and P. M. Coutinho, "Measuring semantic similarity between Gene Ontology terms", Data & knowledge engineering, vol. 61, no. 1: Elsevier, pp. 137–152, 2007.
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.
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Leitão, N., J.. Leitão, and F. Couto, "LLC-GNUMAP: Scalable, Precise, and High-Coverage Genomics Mapping", Bioinformatics Open Days, University of Braga, 2014.
Jain, P., F. Couto, M. J. Silva, and J. D. Becker, "Literature based functional annotation of genes", BKDB2005-Bioinformatics: Knowledge Discovery in Biology, 2005.
Costa, M., F. Couto, and M. J. Silva, "Learning temporal-dependent ranking models", Proceedings of the 37th international ACM SIGIR conference on Research & development in information retrieval: ACM, pp. 757–766, 2014.
Grego, T., F. Pinto, and F. Couto, "LASIGE: using conditional random fields and chebi ontology", Proceedings of SemEval, pp. 660–666, 2013.
Gonçalves, D., M. Costa, and F. M. Couto, "A Large-Scale Characterization of User Behaviour in Cable TV", arXiv preprint arXiv:1609.02453, 2016.
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Barros, M., F. M. Couto, and , "Knowledge Representation and Management: a linked data perspective", IMIA Yearbook: Schattauer Publishers, pp. 178–183, 2016.
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Asif, M., H. F. Martiniano, C. Rasga, A. R. Marques, J. X. Santos, F. M. Couto, A. M. Vicente, and , "An integrative system biology approach to delineate complex genotype-phenotype associations in Autism Spectrum Disorder", 2nd BioSys Retreat 2017, 6-7 October, 2017: Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, 2017.
Asif, M., C. Rasga, H. Martiniano, JX. Santos, AR. Marques, FM. Couto, and AM. Vicente, "An integrative system biology approach for dissecting Autism Spectrum Disorder", 2º Dia do Jovem Investigador do Instituto Nacional de Saúde Doutor Ricardo Jorge, 8 maio 2017: Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, 2017.
Couto, F., M. J. Silva, and P. Coutinho, "Improving information extraction through biological correlation", Data Mining and Text Mining for Bioinformatics, pp. 8, 2003.
Lamurias, A., J. Ferreira, and F. Couto, "Improving chemical entity recognition through h-index based semantic similarity", Journal of Cheminformatics, vol. 7, pp. S13, 1-20, 2015.
Couto, F., M. J. Silva, and P. M. Coutinho, Implementation of a functional semantic similarity measure between gene-products, : Department of Informatics, University of Lisbon, 2003.
Campos, L., V. Pedro, and F. Couto, "Impact of translation on named-entity recognition in radiology texts", Database, vol. 2017: Oxford University Press, 2017.
Lamurias, A., L.. Clarke, and F. Couto, "IICE: web tool for automatic identification of chemical entities and interactions", European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD), Demo Track, 2015.
Lamurias, A., and F. Couto, "Identifying Interactions Between Chemical Entities in Text", Bioinformatics Open Days, University of Braga, 2014.
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.
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.
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.
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.
Grego, T., F. R. Pinto, and F. Couto, "Identifying Chemical Entities based on ChEBI.", ICBO, 2012.
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., 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.
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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.
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., 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.
Couto, F., T. Grego, C. Pesquita, and P. Verissimo, Handling self-citations using Google Scholar, : International Journal of Scientometrics, Informetrics and Bibliometrics, 2009.
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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.
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.
Faria, D., C. Pesquita, F. Couto, and A. O. Falcao, "GOclasses: molecular function as viewed by proteins", The 12th Annual Bio-Ontologies, 2009.
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.
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.
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.
Ferreira, J., D. S. Batista, F. Couto, and M. J. Silva, The Geo-Net-PT/Yahoo! GeoPlanet (TM) concordance, , 2010.
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., and F. Couto, "Generic Semantic Relatedness Measure for Biomedical Ontologies.", ICBO, vol. 833, 2011.

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