Francisco Couto

Book Chapter
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.
Book Chapter
Moreira, S., D. S. Batista, P. Carvalho, F. Couto, and M. J. Silva, "POWER-Politics Ontology for Web Entity Retrieval", Advanced Information Systems Engineering Workshops: Springer Berlin Heidelberg, pp. 489–500, 2011.
Book Chapter
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.
Conference Paper
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.
Book Chapter
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.
Journal Article
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.
Conference Paper
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.
Journal Article
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.
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.
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.
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.
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.
Bastos, H., T. Grego, F. Couto, and P. M. Coutinho, Enzyme family coherence assessment: validation and prediction, : JB'2009-Challenges in Bioinformatics, 2009.
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., 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.
Faria, D., C. Pesquita, F. Couto, and A. O. Falcao, "GOclasses: molecular function as viewed by proteins", The 12th Annual Bio-Ontologies, 2009.
Book Chapter
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.
Journal Article
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.
Conference Paper
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.
Journal Article
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.
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, 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.
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.
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.
Couto, F., and M. J. Silva, Biomedical research line of LASIGE, , 2008.
Conference Paper
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.
Journal Article
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.
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, 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.
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. M. Coutinho, "Measuring semantic similarity between Gene Ontology terms", Data & knowledge engineering, vol. 61, no. 1: Elsevier, pp. 137–152, 2007.
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.
Martins, F., A. O. Falcao, and F. Couto, Semantic Similarity Match for Data Quality, : Department of Informatics, University of Lisbon, 2007.
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.
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., 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.
Thesis
Couto, F., ReBIL: Relating Biological Information through Literature, : Tese de Doutoramento, Faculdade de Ciências, Departamento de Informática, Universidade de Lisboa, 2006.
Conference Paper
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.
Journal Article
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.
Couto, F., M. J. Silva, and P. Fernandes, Bioinformatics: Knowledge Discovery in Biology, : Bioinformatics: Knowledge Discovery in Biology-Workshop Proceedings, 2005.
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, "Finding genomic ontology terms in text using evidence content", BMC bioinformatics, vol. 6, no. Suppl 1: BioMed Central Ltd, pp. S21, 2005.
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.
Jain, P., F. Couto, M. J. Silva, and J. D. Becker, "Literature based functional annotation of genes", BKDB2005-Bioinformatics: Knowledge Discovery in Biology, 2005.
Silva, M. J., P. Fernandes, and F. Couto, Proceedings of Bioinformatics: Knowledge Discovery in Biology Workshop (BKDB 2005), , 2005.
Conference Paper
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.
Journal Article
Couto, F., M. J. Silva, and P. M. Coutinho, Validation of Automated Protein Annotation, : Department of Informatics, University of Lisbon, 2005.
Conference Paper
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.
Journal Article
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., 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., and M. J. Silva, Bioinformática-Exploração da Informação, : centroatlantico. pt magazine, 2003.
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.
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.
Couto, F., M. J. Silva, and P. Coutinho, DI–FCUL TR–03–29, , 2003.
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.
Couto, F., M. J. Silva, and P. Coutinho, "Improving information extraction through biological correlation", Data Mining and Text Mining for Bioinformatics, pp. 8, 2003.
Journal Article
Couto, F., M. J. Silva, and P. Coutinho, "Rebil: Relating biological information through literature", Intelligent Systems for Molecular Biology, 2003.

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