Publications

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Journal Article
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.
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.
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.
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.
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.
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.
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.
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.
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.
Couto, F., T. Grego, C. Pesquita, and P. Verissimo, Handling self-citations using Google Scholar, : International Journal of Scientometrics, Informetrics and Bibliometrics, 2009.
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.
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.
Campos, L., V. Pedro, and F. Couto, "Impact of translation on named-entity recognition in radiology texts", Database, vol. 2017: Oxford University Press, 2017.
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.
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. Coutinho, "Improving information extraction through biological correlation", Data Mining and Text Mining for Bioinformatics, pp. 8, 2003.
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.
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.
Barros, M., F. M. Couto, and , "Knowledge Representation and Management: a linked data perspective", IMIA Yearbook: Schattauer Publishers, pp. 178–183, 2016.
Gonçalves, D., M. Costa, and F. M. Couto, "A Large-Scale Characterization of User Behaviour in Cable TV", arXiv preprint arXiv:1609.02453, 2016.
Grego, T., F. Pinto, and F. Couto, "LASIGE: using conditional random fields and chebi ontology", Proceedings of SemEval, pp. 660–666, 2013.
Jain, P., F. Couto, M. J. Silva, and J. D. Becker, "Literature based functional annotation of genes", BKDB2005-Bioinformatics: Knowledge Discovery in Biology, 2005.
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, 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.
Couto, F., and M. J. Silva, "Mining BioLiterature: Toward Automatic", Advanced Data Mining Technologies in Bioinformatics: IGI Global, pp. 283, 2006.
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.
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.
Campos, L., and F. Couto, "MRA-Proof of Concept of a Multilingual Report Annotator Web Application", arXiv preprint arXiv:1704.01748, 2017.
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.
Santos, E., D. Faria, C. Pesquita, and F. Couto, "Ontology alignment repair through modularization and confidence-based heuristics", arXiv preprint arXiv:1307.5322, 2013.
Pesquita, C., and F. Couto, "Predicting the extension of biomedical ontologies", PLoS computational biology, vol. 8, no. 9: Public Library of Science, pp. e1002630, 2012.
Silva, M. J., P. Fernandes, and F. Couto, Proceedings of Bioinformatics: Knowledge Discovery in Biology Workshop (BKDB 2005), , 2005.
Faria, D., C. Pesquita, F. Couto, and A. O. Falcao, Proteinon: A web tool for protein semantic similarity, : Department of Informatics, University of Lisbon, 2007.
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.
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., M. J. Silva, and P. Coutinho, "Rebil: Relating biological information through literature", Intelligent Systems for Molecular Biology, 2003.
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.
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.
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, and F. Couto, "Semantic similarity in biomedical ontologies", PLoS computational biology, vol. 5, no. 7: Public Library of Science, pp. e1000443, 2009.
Martins, F., A. O. Falcao, and F. Couto, Semantic Similarity Match for Data Quality, : Department of Informatics, University of Lisbon, 2007.
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.
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.
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.
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.
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.
Teixeira, A. L., R. C. Santos, and F. Couto, "ThermInfo: Collecting and Presenting Thermochemical Properties", methods, vol. 1, pp. 3, 2009.
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.
Faria, D., E. Jiménez-Ruiz, C. Pesquita, E. Santos, and F. Couto, "Towards annotating potential incoherences in BioPortal mappings", International Semantic Web Conference, 2014.
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.
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.
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.
Leal, A., D. Gonçalves, B. Martins, and F. Couto, "ULisboa: Identification and Classification of Medical Concepts", SemEval 2014, pp. 711, 2014.
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.
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.
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.
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.
Norman, R., and F. Couto, "Using Google Scholar to predict self citation: A case study in Health Economics", arXiv preprint arXiv:1406.5241, 2014.
Couto, F., M. J. Silva, and P. M. Coutinho, Validation of Automated Protein Annotation, : Department of Informatics, University of Lisbon, 2005.
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.
Rodrigues, M. J., M. Falé, A. Lamurias, and F. M. Couto, "WS4A: a biomedical question and answering system based on public web services and ontologies", arXiv preprint arXiv:1609.08492, 2016.
Thesis
Couto, F., ReBIL: Relating Biological Information through Literature, : Tese de Doutoramento, Faculdade de Ciências, Departamento de Informática, Universidade de Lisboa, 2006.

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