| Books | Chapters | Journal papers | Conference papers | Workshop papers | Extended Abstracts | Magazine papers | Technical reports | Theses | Talks and Tutorials | Proceedings |

Books

[1] F. Couto, Data and Text Processing for Health and Life Sciences. No. 1137 in Advances in Experimental Medicine and Biology, Springer, 2019. [ bib | DOI | pdf | scholar ]
[2] F. Couto, Introdução à Bioinformática Via Linha de Comando. Trajectos / Ciência, Gradiva, 2019. [ bib | url ]

Chapters

[1] M. Fernandes, J. Decouchant, and F. Couto, “Security, privacy and trust management in DNA computing,” in Perspective of DNA Computing in Computer Science (S. Namasudra, ed.), vol. 129, pp. 39--81, Elsevier, 2023. [ bib | DOI | pdf | scholar ]
[2] D. Sousa, A. Lamurias, and F. Couto, “Using neural networks for relation extraction from biomedical literature,” in Artificial Neural Networks. Methods in Molecular Biology (H. Cartwright, ed.), vol. 2190, pp. 289--305, Humana, New York, NY, 2020. [ bib | DOI | pdf | scholar ]
[3] J. Ferreira and F. Couto, “Semantic similarity in cheminformatics,” in Cheminformatics and its Applications (A. Stefaniu, ed.), IntechOpen, 2019. [ bib | DOI | pdf | scholar ]
[4] A. Lamurias and F. Couto, “Text mining for bioinformatics using biomedical literature,” in Encyclopedia of Bioinformatics and Computational Biology (S. Ranganathan, K. Nakai, C. Schönbach, and M. Gribskov, eds.), vol. 1, pp. 602--611, Oxford: Elsevier, 2019. [ bib | DOI | pdf | scholar ]
[5] F. Couto and A. Lamurias, “Semantic similarity definition,” in Encyclopedia of Bioinformatics and Computational Biology (S. Ranganathan, K. Nakai, C. Schönbach, and M. Gribskov, eds.), vol. 1, pp. 870--876, Oxford: Elsevier, 2019. [ bib | DOI | pdf | scholar ]
[6] 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 ]
[7] 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 ]
[8] 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 ]
[9] 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 ]
[10] 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] D. Sousa and F. Couto, “K-RET: Knowledgeable biomedical relation extraction system,” Bioinformatics, Oxford Univ Press, vol. 39, no. 4, pp. 1--8, 2023. [ bib | DOI | Q1 2022 Computer Science Applications | pdf | pubmed | scholar ]
[2] M. Asif, H. Martiniano, A. Lamurias, S. Kausar, and F. Couto, “DGH‑GO: dissecting the genetic heterogeneity of complex diseases using Gene Ontology,” BMC Bioinformatics, vol. 24, no. 171, pp. 1--20, 2023. [ bib | DOI | Q1 2022 Computer Science Applications | pdf | pubmed | scholar ]
[3] D. Faria, E. S. B. Balasubramani, M. Silva, F. Couto, and C. Pesquita, “AgreementMakerLight,” Semantic Web, IOS Press, vol. Pre-press, no. Pre-press, pp. 1--13, 2023. [ bib | DOI | Q2 2022 Information Systems | pdf ]
[4] M. Barros, A. Moitinho, and F. Couto, “SeEn: Sequential enriched datasets for sequence-aware recommendations,” Scientific Data, vol. 9, no. 1, pp. 1--12, 2022. [ bib | DOI | Q1 2021 Information Systems | pdf | pubmed | scholar ]
[5] P. Ruas and F. Couto, “NILINKER: Attention-based approach to NIL entity linking,” Journal of Biomedical Informatics, vol. 132, no. 104137, pp. 1--11, 2022. [ bib | DOI | Q1 2021 Computer Science Applications | pdf | pubmed | scholar ]
[6] D. Sousa and F. Couto, “Biomedical relation extraction with knowledge graph-based recommendations,” IEEE Journal of Biomedical and Health Informatics, vol. 26, no. 8, pp. 4207--4217, 2022. [ bib | DOI | Q1 2021 Computer Science Applications | pdf | pubmed | scholar ]
[7] S. Conceição and F. Couto, “Text mining for building biomedical networks using cancer as a case study,” biomolecules, vol. 11, no. 10, pp. 1430 (1--12), 2021. [ bib | DOI | Q2 2020 Molecular Biology | pdf | pubmed | scholar ]
[8] A. Rodrigues, J. Santinha, B. Galvão, C. Matos, F. Couto, and N. Papanikolaou, “Prediction of prostate cancer disease aggressiveness using bi-parametric mri radiomics,” cancers, vol. 13, no. 23, pp. 6065 (1--17), 2021. [ bib | DOI | Q1 2020 Oncology | pdf | pubmed | scholar ]
[9] M. Barros, P. Ruas, D. Sousa, A. Bangash, and F. Couto, “COVID-19 recommender system based on an annotated multilingual corpus,” Genomics & Informatics, vol. 19, no. 3, pp. e24 (1--7), 2021. [ bib | DOI | Q2 2020 Ecology, Evolution, Behavior and Systematics | pdf | pubmed | scholar ]
[10] A. Lamurias, S. Jesus, V. Neveu, R. Salek, and F. Couto, “Information retrieval using machine learning for biomarker curation in the exposome-explorer,” Frontiers in Research Metrics and Analytics, vol. 6, no. 55, pp. 1--10, 2021. [ bib | DOI | pdf | pubmed | scholar ]
[11] M. Barros, A. Moitinho, and F. Couto, “Hybrid semantic recommender system for chemical compounds in large‐scale datasets,” Journal of Cheminformatics, vol. 13, no. 15, pp. 1--15, 2021. [ bib | DOI | Q1 2020 Computer Science Applications | pdf | pubmed | scholar ]
[12] D. Sousa, A. Lamurias, and F. Couto, “A hybrid approach toward biomedical relation extraction training corpora: combining distant supervision with crowdsourcing,” Database: The Journal of Biological Databases and Curation, vol. 2020, no. baaa104, pp. 1--15, 2020. [ bib | DOI | Q1 2020 Information Systems | pdf | pubmed | scholar ]
[13] P. Ruas, A. Lamurias, and F. Couto, “Linking chemical and disease entities to ontologies by integrating PageRank with extracted relations from literature,” Journal of Cheminformatics, vol. 12, no. 57, pp. 1--15, 2020. [ bib | DOI | Q1 2020 Computer Science Applications | pdf | pubmed | scholar ]
[14] A. Lamurias, D. Sousa, and F. Couto, “Generating biomedical question answering corpora from Q&A forums,” IEEE Access, vol. 8, no. 0, pp. 161042--161051, 2020. [ bib | DOI | Q1 2020 Computer Science (miscellaneous) | pdf | scholar ]
[15] S. Nunes, S. Little, S. Bhatia, L. Boratto, G. Cabanac, R. Campos, F. Couto, S. Faralli, I. Frommholz, A. Jatowt, A. Jorge, M. Marras, P. Mayr, and G. Stilo, “ECIR 2020 workshops: Assessing the impact of going online,” SIGIR Forum, vol. 54, no. 1, pp. 1--11, 2020. [ bib | DOI | Q1 2006 Management Information Systems | pdf | scholar ]
[16] D. Sousa, A. Lamurias, and F. Couto, “Improving accessibility and distinction between negative results in biomedical relation extraction,” Genomics & Informatics, vol. 18, no. 1, pp. e15 (1--4), 2020. [ bib | DOI | Q2 2020 Ecology, Evolution, Behavior and Systematics | pdf | pubmed | scholar ]
[17] M. Fernandes, J. Decouchant, M. Völp, F. Couto, and P. Veríssimo, “DNA-SeAl: Sensitivity levels to optimize the performance of privacy-preserving DNA alignment,” IEEE Journal of Biomedical and Health Informatics, vol. 24, no. 3, pp. 907--915, 2020. [ bib | DOI | Q1 2020 Computer Science Applications | pdf | pubmed | scholar ]
[18] M. Asif, H. Martiniano, A. Marques, J. Santos, J. Vilela, C. Rasga, G. Oliveira, F. Couto, and A. Vicente, “Identification of biological mechanisms underlying a multidimensional ASD phenotype using machine learning,” Translational Psychiatry, vol. 10, no. 43, pp. 1--12, 2020. [ bib | DOI | Q1 2020 Biological Psychiatry | pdf | pubmed | scholar ]
[19] M. Barros, A. Moitinho, and F. Couto, “Using research literature to generate datasets of implicit feedback for recommending scientific items,” IEEE Access, vol. 7, no. 0, pp. 176668--176680, 2019. [ bib | DOI | Q1 2019 Engineering (miscellaneous) | pdf | scholar ]
[20] A. Lamurias, P. Ruas, and F. Couto, “PPR-SSM: personalized PageRank and semantic similarity measures for entity linking,” BMC Bioinformatics, vol. 20, no. 534, pp. 1--12, 2019. [ bib | DOI | Q1 2019 Computer Science Applications | pdf | pubmed | scholar ]
[21] M. Asif, A. Vicente, and F. Couto, “Funvar: A systematic pipeline to unravel the convergence patterns of genetic variants in ASD, a paradigmatic complex disease,” Journal of Biomedical Informatics, pp. 1--29, 2019. [ bib | DOI | Q1 2019 Computer Science Applications | pdf | pubmed | scholar ]
[22] J. Ferreira and F. Couto, “Multi-domain semantic similarity in biomedical research,” BMC Bioinformatics, vol. 20, no. 246, pp. 1--9, 2019. [ bib | DOI | Q1 2019 Computer Science Applications | pdf | pubmed | scholar ]
[23] A. Lamurias, D. Sousa, L. Clarke, and F. Couto, “BO-LSTM: classifying relations via long short-term memory networks along biomedical ontologies,” BMC Bioinformatics, vol. 20, no. 10, pp. 1--12, 2019. [ bib | DOI | Q1 2019 Computer Science Applications | pdf | pubmed | scholar ]
[24] F. Couto and A. Lamurias, “MER: a shell script and annotation server for minimal named entity recognition and linking,” Journal of Cheminformatics, vol. 10, no. 58, pp. 1--10, 2018. [ bib | DOI | Q1 2018 Computer Science Applications | pdf | pubmed | scholar ]
[25] M. Asif, H. Martiniano, A. Vicente, and F. Couto, “Identifying disease genes using machine learning and gene functional similarities, assessed through Gene Ontology,” PLoS ONE, vol. 13, no. 12, pp. 1--15, 2018. [ bib | DOI | Q1 2018 Biochemistry, Genetics and Molecular Biology (miscellaneous) | pdf | pubmed | scholar ]
[26] J. Santana, K. Gramacho, K. Ferreira, R. Rezende, P. Mangabeira, R. Dias, F. Couto, and C. Pirovani, “Witches' broom resistant genotype CCN51 shows greater diversity of symbiont bacteria in its phylloplane than susceptible genotype catongo,” BMC Microbiology, vol. 18, no. 1, pp. 194 (1--10), 2018. [ bib | DOI | Q2 2018 Microbiology | pdf | pubmed | scholar ]
[27] 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. 82, pp. 1--12, 2018. [ bib | DOI | Q1 2018 Computer Science Applications | pdf | pubmed | scholar ]
[28] 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 | Q1 2018 Computer Science Applications | pdf | pubmed | scholar ]
[29] 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 | Q1 2017 Immunology | pdf | pubmed | scholar ]
[30] 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 | Q3 2017 Medicine (miscellaneous) | pdf | pubmed | scholar ]
[31] 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 | Q1 2017 Biochemistry, Genetics and Molecular Biology (miscellaneous) | pdf | pubmed | scholar ]
[32] 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 | Q1 2017 Information Systems | pdf | pubmed | scholar ]
[33] 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 | Q1 2017 Biochemistry, Genetics and Molecular Biology (miscellaneous) | pdf | pubmed | scholar ]
[34] M. Barros and F. Couto, “Knowledge representation and management: a linked data perspective,” IMIA Yearbook of Medical Informatics, pp. 178--183, 2016. [ bib | DOI | Q2 2016 Medicine (miscellaneous) | pdf | pubmed | scholar ]
[35] 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 | Q1 2016 Computer Science Applications | pdf | pubmed | scholar ]
[36] 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 | Q1 2015 Biochemistry, Genetics and Molecular Biology (miscellaneous) | pdf | pubmed | scholar ]
[37] 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 | Q1 2015 Biochemistry, Genetics and Molecular Biology (miscellaneous) | pdf | pubmed | scholar ]
[38] 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 | Q1 2015 Information Systems | pdf | pubmed | scholar ]
[39] 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 | Q1 2015 Computer Science Applications | pdf | pubmed | scholar ]
[40] 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 | Q1 2015 Computer Science Applications | pdf | pubmed | scholar ]
[41] 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 | Q1 2015 Information Systems | pdf | pubmed | scholar ]
[42] 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 | Q1 2014 Biochemistry, Genetics and Molecular Biology (miscellaneous) | pdf | pubmed | scholar ]
[43] 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 | Q2 2014 Medicine (miscellaneous) | pdf | pubmed | scholar ]
[44] 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 | Q1 2014 Information Systems | pdf | pubmed | scholar ]
[45] 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 | Q1 2013 Computational Mathematics | pdf | pubmed | scholar ]
[46] 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 | Q2 2013 Genetics | pdf | pubmed | scholar ]
[47] 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 | Q2 2013 Computer Science Applications | pdf | pubmed | scholar ]
[48] 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 | Q1 2013 Information Systems | pdf | pubmed | scholar ]
[49] 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 | Q1 2013 Biochemistry, Genetics and Molecular Biology (miscellaneous) | pdf | pubmed | scholar ]
[50] 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 | Q2 2013 Information Systems | scholar ]
[51] 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 | Q1 2013 Epidemiology | pubmed | scholar ]
[52] 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 | Q1 2012 Computational Theory and Mathematics | pubmed | scholar ]
[53] 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 ]
[54] 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 | Q1 2011 Information Systems | pubmed | scholar ]
[55] 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 | Q1 2011 Biophysics | pubmed | scholar ]
[56] 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 | Q1 2011 Biophysics | pubmed | scholar ]
[57] 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 | Q1 2010 Computational Theory and Mathematics | pubmed | scholar ]
[58] 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 | Q1 2010 Biophysics | pubmed | scholar ]
[59] 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 | Q1 2009 Computational Theory and Mathematics | pubmed | scholar ]
[60] 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 | DOI | Q1 2009 Library and Information Sciences | pdf | scholar ]
[61] 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 | Q1 2008 Computer Science Applications | pubmed | scholar ]
[62] 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 | Q2 2007 Information Systems and Management | pdf | scholar ]
[63] 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 | Q2 2007 History and Philosophy of Science | pubmed | scholar ]
[64] 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 | Q1 2005 Computer Science Applications | pubmed | scholar ]
[65] 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 | Q1 2005 Biochemistry, Genetics and Molecular Biology (miscellaneous) | pubmed | scholar ]

Conference papers

[1] R. West, S. Bhagat, P. Groth, M. Zitnik, F. M. Couto, P. Lisena, A. M. no Peñuela, X. Zhao, W. Fan, D. Yin, J. Tang, L. Shou, M. Gong, J. Pei, X. Geng, X. Zhou, D. Jiang, B. Ricaud, N. Aspert, V. Miz, J. Dy, S. Ioannidis, I. Yildiz, R. Rezapour, S. Aref, L. Dinh, J. Diesner, A. Drutsa, D. Ustalov, N. Popov, D. Baidakova, S. Mishra, A. Gopalan, D. Juan, C. I. Magalhaes, C. Ferng, A. Heydon, C. Lu, P. Pham, G. Yu, Y. Fan, Y. Wang, F. Laurent, Y. Schraner, C. Scheller, S. Mohanty, J. Chen, X. Wang, F. Feng, X. He, I. Teinemaa, J. Albert, D. Goldenberg, F. Vasile, D. Rohde, O. Jeunen, A. Benhalloum, O. Sakhi, Y. Rong, W. Huang, T. Xu, Y. Bian, H. Cheng, F. Sun, J. Huang, S. Fakhraei, C. Faloutsos, O. Çelebi, M. Müller, M. Schneider, O. Altunina, W. Wingerath, B. Wollmer, F. Gessert, S. Succo, N. Ritter, E. Courdier, T. M. Avram, D. Cvetinovic, L. Tsinadze, J. Jose, R. Howell, M. Koenig, M. Defferrard, K. Kenthapadi, B. Packer, M. Sameki, and N. Sephus, “Summary of tutorials at The Web Conference 2021,” in Companion Proceedings of the Web Conference 2021, p. 727–733, 2021. [ bib | Core2021 A* (companion) | pdf | url | scholar ]
[2] F. Colaço, M. Barros, and F. Couto, “DRecPy: A python framework for developing deep learning-based recommenders,” in 14th ACM Conference on Recommender Systems (RECSYS 2020) (Late-breaking results), p. 675–680, 2020. [ bib | Core2020 B | pdf | url | scholar ]
[3] M. Barros, A. Moitinho, and F. Couto, “Hybrid semantic recommender system for chemical compounds,” in 42nd European Conference on Information Retrieval (ECIR 2020), vol. 12036, pp. 1--8, 2020. [ bib | Core2020 A | pdf | url | scholar ]
[4] D. Sousa and F. Couto, “BiOnt: Deep learning using multiple biomedical ontologies for relation extraction,” in 42nd European Conference on Information Retrieval (ECIR 2020), vol. 12036, pp. 1--8, 2020. [ bib | Core2020 A | pdf | url | scholar ]
[5] F. Couto and M. Krallinger, “Proposal of the first international workshop on semantic indexing and information retrieval for health from heterogeneous content types and languages (SIIRH),” in 42nd European Conference on Information Retrieval (ECIR 2020), vol. 12036, pp. 1--6, 2020. [ bib | Core2020 A | pdf | url | scholar ]
[6] D. Sousa, A. Lamurias, and F. Couto, “A silver standard corpus of human phenotype-gene relations,” in Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies (NAACL 2019), vol. N19-1152, p. 1487–1492, 2019. [ bib | Core2018 A | pdf | url | scholar ]
[7] 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 ]
[8] 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 ]
[9] 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 ]
[10] 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 ]
[11] 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 | Core2014 A | pdf | url | scholar ]
[12] 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 ]
[13] 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 ]
[14] 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 | Core2014 A | pdf | scholar ]
[15] 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 | Core2014 A* | pdf | url | scholar ]
[16] 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 ]
[17] 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 ]
[18] 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 ]
[19] 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 ]
[20] 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 | Core2013 A | pdf | scholar ]
[21] 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 | Core2010 B | pdf | scholar ]
[22] 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 ]
[23] 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 ]
[24] 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 ]
[25] 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 ]
[26] 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 | Core2010 B | pdf | scholar ]
[27] 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 | Core2010 B | pdf ]
[28] 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 ]
[29] 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 ]
[30] 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 | Core2008 A | pdf | scholar ]
[31] 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 | Core2008 A | pdf | scholar ]
[32] 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 | Core2008 B | pdf | scholar ]
[33] 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] S. Conceicao, D. Sousa, P. Silvestre, and F. Couto, “BioRED track lasigeBioTM submission: Relation extraction using domain ontologies with BioRED,” in BioCreative VIII Challenge Evaluation, 2023. [ bib | pdf | url ]
[2] S. Conceicao, D. Sousa, P. Silvestre, and F. Couto, “lasigeBioTM at SemEval-2023 Task 7: Improving natural language inference baseline systems with domain ontologies,” in 17th International Workshop on Semantic Evaluation (SemEval), 2023. [ bib | pdf | url ]
[3] D. Faria, B. Lima, M. Silva, F. Couto, and C. Pesquita, “AML and AMLC results for OAEI 2021,” in 16th International Workshop on Ontology Matching (OM-2021), 2021. [ bib | pdf | url ]
[4] D. Sousa, R. Cassanheira, and F. Couto, “lasigeBioTM at BioCreative VII Track 1: Text mining drug and chemical-protein interactions using biomedical ontologies,” in BioCreative VII Challenge Evaluation, 2021. [ bib | pdf | url ]
[5] M. Campos and F. Couto, “Post-processing BioBERT and using voting methods for biomedical question answering,” in 9th edition of BioASQ: Large-scale Biomedical Semantic Indexing and Question Answering (CLEF 2021 Working Notes), 2021. [ bib | pdf | url ]
[6] P. Ruas, V. Andrade, and F. Couto, “LASIGE-BioTM at MESINESP2: entity linking with semantic similarity and extreme multi-label classification on spanish biomedical documents,” in 9th edition of BioASQ: Large-scale Biomedical Semantic Indexing and Question Answering (CLEF 2021 Working Notes), 2021. [ bib | pdf | url ]
[7] P. Ruas, V. Andrade, and F. Couto, “Lasige-BioTM at ProfNER: BiLSTM-CRF and contextual spanish embeddings for named entity recognition and tweet binary classification,” in 6th Social Media Mining for Health Workshop, 2021. [ bib | pdf | url ]
[8] M. Barros, A. Lamurias, D. Sousa, P. Ruas, and F. Couto, “COVID-19: A semantic-based pipeline for recommending biomedical entities,” in 1st Workshop on NLP for COVID-19 (Part 2) at EMNLP 2020, 2020. [ bib | pdf | url ]
[9] B. Lima, D. Faria, F. Couto, I. Cruz, and C. Pesquita, “OAEI 2020 results for AML and AMLC,” in 15th International Workshop on Ontology Matching (OM-2020), 2020. [ bib | pdf | url ]
[10] A. Neves, A. Lamurias, and F. Couto, “Biomedical question answering using extreme multi-label classification and ontologies in the multilingual panorama,” in 8th edition of BioASQ: Large-scale Biomedical Semantic Indexing and Question Answering (CLEF 2020 Working Notes), 2020. [ bib | pdf | url ]
[11] P. Ruas, A. Lamurias, and F. Couto, “LasigeBioTM team at CLEF2020 ChEMU evaluation lab: Named entity recognition and event extraction from chemical reactions described in patents using BioBERT NER and RE,” in The workshop ChEMU: Named Entity Recognition and Event Extraction of Chemical Reactions from Patents (CLEF 2020 Working Notes), 2020. [ bib | pdf | url ]
[12] J. He, D. Nguyen, S. Akhondi, C. Druckenbrodt, C. Thorne, R. Hoessel, Z. Afzal, Z. Zhai, B. Fang, H. Yoshikawa, A. Albahem, J. Wang, Y. Ren, Z. Zhang, Y. Zhang, M. Dao, P. Ruas, A. Lamurias, F. Couto, J. Copara, N. Naderi, J. Knafou, P. Ruch, D. Teodoro, D. Lowe, J. Mayfield, A. Köksal, H. Dönmez, E. Özkırımlı, A. Özgür, D. Mahendran, G. Gurdin, N. Lewinski, C. Tang, B. McInnes, M. C.S., P. Rao, S. Devi, L. Cavedon, T. Cohn, T. Baldwin, and K. Verspoor, “An extended overview of the CLEF 2020 ChEMU lab: Information extraction of chemical reactions from patents,” in The workshop ChEMU: Named Entity Recognition and Event Extraction of Chemical Reactions from Patents (CLEF 2020 Working Notes), 2020. [ bib | pdf | url ]
[13] P. Ruas, A. Neves, V. Andrade, and F. Couto, “LasigeBioTM at CANTEMIST: Named entity recognition and normalization of tumour morphology entities and clinical coding of spanish health-related documents,” in The Iberian Languages Evaluation Forum (IberLEF 2020), 2020. [ bib | pdf | url ]
[14] A. Neves, A. Lamurias, and F. Couto, “Biomedical question answering using extreme multi-label classification and ontologies in the multilingual panorama,” in 1st International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages (SIIRH), 2020. [ bib | pdf | url ]
[15] P. Ruas, A. Lamurias, and F. Couto, “Towards a multilingual corpus for named entity linking evaluation in the clinical domain,” in 1st International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages (SIIRH), 2020. [ bib | pdf | url ]
[16] F. Couto and M. Krallinger, “Report of the first international workshop on semantic indexing and information retrieval for health from heterogeneous content types and languages,” in 1st International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages (SIIRH), 2020. [ bib | pdf | url ]
[17] M. Fernandes, J. Decouchant, M. Volp, F. Couto, and P. Veríssimo, “Privacy-preserving processing of filtered DNA reads,” in 6th International Workshop on Genome Privacy and Security (GenoPri-2019), 2019. [ bib | pdf | url ]
[18] D. Faria, C. Pesquita, T. Tervo, F. Couto, and I. Cruz, “AML and AMLC results for OAEI 2019,” in 14th International Workshop on Ontology Matching (OM-2019), 2019. [ bib | pdf | url ]
[19] A. Lamurias and F. Couto, “LasigeBioTM at MEDIQA 2019: Biomedical question answering using bidirectional transformers and named entity recognition,” in 18th ACL Workshop on Biomedical Natural Language Processing (BioNLP 2019), 2019. [ bib | pdf | url ]
[20] J. Ferreira and F. Couto, “Multi-domain semantic similarity in biomedical research,” in 12th Data and Text Mining in Biomedical Informatics (DTMBIO 2018), 2018. [ bib | pdf | url ]
[21] D. Faria, C. Pesquita, B. Balasubramani, T. Tervo, D. Carriço, R. Garrilha, F. Couto, and I. Cruz, “Results of AML in OAEI 2018,” in 13th International Workshop on Ontology Matching (OM-2018), 2018. [ bib | pdf | url ]
[22] M. Fernandes, J. Decouchant, F. Couto, and P. Veríssimo, “Privacy-preserving algorithms and workflows for next-generation genomics,” in The Twelfth EuroSys Doctoral Workshop (EuroDW 2018), 2018. [ bib | pdf | url ]
[23] D. Faria, B. Balasubramani, V. Shivaprabhu, I. Mott, C. Pesquita, F. Couto, and I. Cruz, “Results of AML in OAEI 2017,” in 12th International Workshop on Ontology Matching (OM-2017), 2017. [ bib | pdf | url ]
[24] 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 ]
[25] 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 ]
[26] 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 ]
[27] 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 ]
[28] 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 ]
[29] 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 ]
[30] 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 ]
[31] 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 ]
[32] 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 ]
[33] 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 ]
[34] 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 ]
[35] 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 ]
[36] 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 ]
[37] 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 ]
[38] 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 ]
[39] 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 ]
[40] 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 ]
[41] 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 ]
[42] 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 ]
[43] 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 ]
[44] 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 ]
[45] 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 ]
[46] 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 ]
[47] 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 ]
[48] 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 ]
[49] 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 ]
[50] 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 ]
[51] 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 ]
[52] 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 ]
[53] 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 ]
[54] 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 ]
[55] 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 ]
[56] 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 ]
[57] 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 ]
[58] 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 ]
[59] 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 ]
[60] 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 ]
[61] 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 ]
[62] C. Pesquita, D. Pessoa, D. Faria, and F. Couto, “CESSM: Collaborative evaluation of semantic similarity measures,” in Jornadas em Bioinformatica, 2009. [ bib | pdf ]
[63] H. Bastos, T. Grego, F. Couto, and P. Coutinho, “Enzyme family coherence assessment: validation and prediction,” in Jornadas em Bioinformatica, 2009. [ bib | pdf ]
[64] A. Teixeira, R. Santos, and F. Couto, “ThermInfo: Collecting and presenting thermochemical properties,” in INForum - Simpósio de Informática, 2009. [ bib | pdf ]
[65] 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 ]
[66] 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 ]
[67] 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 ]
[68] 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 ]
[69] 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 ]
[70] 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 ]
[71] 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 ]
[72] F. Couto, M. Silva, and P. Coutinho, “FiGO: Finding GO terms in unstructured text,” in BioCreAtIvE Challenge Evaluation Workshop, 2004. [ bib | pdf ]
[73] 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 ]
[74] 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 ]
[75] 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] F. Couto, “Data and text processing for sustainability,” in 2nd edition of the INternational CongRess on Engineering and Sustainability in the XXI cEntury (INCREaSE), 2023. [ bib | pdf ]
[2] F. Couto, “Data and text processing for development and stem cells,” in FENS Regional Meeting (FRM), 2023. [ bib | pdf ]
[3] F. Couto, “DeST: Deep semantic tagger,” in 2nd Joint Meeting of Spanish, French and Portuguese Proteomics Societies (ProteoVilamoura 2022), 2022. [ bib | pdf ]
[4] M. Asif, H. Martiniano, and F. Couto, “DGH-GO dissecting the genetic heterogeneity of complex diseases using Gene Ontology, an interactive and user-friendly web application,” in 55th European Society of Human Genetics Conference (ESHG), 2022. [ bib | pdf ]
[5] M. Barros, A. Moitinho, and F. Couto, “Recommender systems for scientific fields,” in 19th International Symposium on Intelligent Data Analysis (IDA), 2021. [ bib | pdf ]
[6] A. Ilhéu, M. Asif, and F. Couto, “Establishing genotype-phenotype associations for ASD,” in 52nd European Society of Human Genetics Conference (ESHG), 2019. [ bib | pdf ]
[7] M. Asif, H. Martiniano, C. Rasga, A. Marques, J. Santo, G. Oliveira, F. Couto, and A. Vicente, “An integrative approach to correlate clinical presentation patterns in autism spectrum disorder with biological processes disrupted by Copy Number Variants (CNV) in brain genes,” in 51st European Society of Human Genetics Conference (ESHG), 2018. [ bib | pdf ]
[8] R. Dias, C. Pesquita, J. Rebelo, A. Pedrosa, C. Santos, J. Adonis, V. Mendes, F. Couto, R. Tenreiro, and P. Sousa, “RESISTIR - intelligent decision support systems for personalized prevention and clinical management of infectious diseases,” in Ciência 2018 - Encontro com a Ciência e Tecnologia em Portugal, 2018. [ bib | pdf ]
[9] M. Asif, H. Martiniano, C. Rasga, A. Marques, J. Santos, F. Couto, and A. Vicente, “An integrative system biology approach to delineate complex genotype phenotype associations in Autism Spectrum Disorder,” in EMBO EMBL Symposia - From Single to Multiomics: Applications and Challenges in Data Integration, 2017. [ bib | pdf ]
[10] M. Asif, H. Martiniano, C. Rasga, A. Marques, J. Santos, G. Oliveira, F. Couto, and A. Vicente, “Translating the complex ASD genetic architecture into clinical phenotype using an integrative system biology approach,” in Annual meeting of the International Society for Autism Research (INSAR 2017), 2017. [ bib | pdf ]
[11] 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 ]
[12] 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 ]
[13] 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 ]
[14] 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 ]
[15] 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 ]
[16] 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 49th European Human Genetics Conference (ESHG), 2016. [ bib | pdf ]
[17] 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 ]
[18] 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 ]
[19] 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 ]
[20] 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 ]
[21] 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 ]
[22] 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 ]
[23] A. Barata, F. Couto, and L. Carvalho, “Anthropometric data analytics: Portuguese case-study,” in Bioinformatics Open Days, University of Minho, 2016. [ bib | pdf ]
[24] F. Couto, “METARATE - incentivize data integration and sharing by rating and rewarding metadata annotation,” in European Data Forum (EDF), 2015. [ bib | pdf ]
[25] 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 ]
[26] 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 ]
[27] 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 ]
[28] 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 ]
[29] 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 ]
[30] 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 ]
[31] 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 ]
[32] 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 ]
[33] 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 ]
[34] 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 ]
[35] 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 ]
[36] A. Lamurias and F. Couto, “Identifying interactions between chemical entities in text,” in Bioinformatics Open Days, University of Minho, 2014. [ bib | pdf ]
[37] 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 ]
[38] 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 ]
[39] 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 ]
[40] 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 ]
[41] 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 ]
[42] 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 ]
[43] T. Grego and F. Couto, “Recognition and resolution of chemical entities to ChEBI,” in Bioinformatics Open Days, University of Minho, 2012. [ bib | pdf ]
[44] J. Ferreira and F. Couto, “Semantic similarity in the biomedical domain,” in Bioinformatics Open Days, University of Minho, 2012. [ bib | pdf ]
[45] 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 ]
[46] 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 ]
[47] 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 ]
[48] 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 ]
[49] 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 ]
[50] C. Pesquita, F. Couto, and M. Silva, “Automated enrichment of BioOntologies,” in First Portuguese Forum on Computational Biology, 2008. [ bib | pdf ]
[51] 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 ]
[52] 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 ]
[53] F. Couto, “ReBIL: Relating biological information through literature,” in I Annual Meeting of Portuguese Proteomic Network - ProCura: Functional Genomics And Proteomics, 2003. [ bib | pdf ]
[54] 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 ]
[55] 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] M. Asif, H. Martiniano, F. Couto, and A. Vicente, “Associação entre variantes genéticas e perfil clínico multidimensional de doentes com perturbação do espetro do autismo: uma abordagem integrativa,” Observações Boletim Epidemiológico, 2018. [ bib | url ]
[2] F. Couto, “Exploiting biomedical information through literature and ontologies,” El País - Sociedad, 2011. [ bib | url ]
[3] 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 ]
[4] 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 ]
[5] F. Couto and M. Silva, “Bioinformática - exploração da informação,” centroatlantico.pt magazine, vol. 3, 2003. [ bib | pdf ]

Technical reports

[1] P. Ruas, D. Sousa, A. Neves, C. Cruz, and F. Couto, “LASIGE and UNICAGE at NASA LitCoin NLP Competition,” Tech. Rep. arXiv:2308.05609 [cs.CL], arXiv.org, Aug 2023. [ bib | pdf | url ]
[2] 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 ]
[3] 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 ]
[4] 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 ]
[5] 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 ]
[6] 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 ]
[7] 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 ]
[8] 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 ]
[9] 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 ]
[10] 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 ]
[11] 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 ]
[12] 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 ]
[13] 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 ]
[14] 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 ]
[15] 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 ]
[16] 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 ]
[17] 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 ]
[18] 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 ]

Talks and Tutorials

[1] F. Couto, “Interpretação de dados biológicos.” Tutorial nas Jornadas de Biologia do Instituto Superior de Agronomia, Lisboa, March 2022. [ bib ]
[2] F. Couto, “Bioinformatics: interpretation of biological data.” Tutorial na Semana da Bioengenharia no Instituto Superior Técnico, Lisboa, March 2022. [ bib ]
[3] M. Barros, F. Couto, M. Pato, and P. Ruas, “Creating recommender systems datasets in scientific fields.” Tutorial at the 30th The Web Conference (KDD2021), Singapore, August 2021. [ bib ]
[4] F. Couto, “Exploring biomedical web resources using shell scripting.” Tutorial at the 30th The Web Conference (WWW2021), Ljubljana, Slovenia, April 2021. [ bib ]
[5] F. Couto, “Biomedical text processing using semantics.” Tutorial at the 43rd European Conference on Information Retrieval (ECIR2021), Lucca, Italy, March 2021. [ bib ]
[6] F. Couto, “Why analyze biomedical text if we have data?.” Talk at Data Science Seminars, Universidade de Lisboa, December 2020. [ bib ]
[7] F. Couto, “Biomedical text mining: exploring semantic resources.” Talk at Bioinformatics and Computational Biology Seminars, Universidade de Lisboa, October 2020. [ bib ]
[8] F. Couto, “Multilingual resources and community Q&A forums.” Participation in the Discussion Panel of the 8th BioASQ 2020 Workshop, September 2020. [ bib ]
[9] F. Couto, “Biomedical data and text processing using shell scripting.” Tutorial at the 19th European Conference on Computational Biology (ECCB2020), Barcelona, Spain, September 2020. [ bib ]
[10] F. Couto, “Bioinformática: processamento de dados e texto biológico via linha de comando.” Palestra na II Semana de Biologia da Universidade Federal do Sul da Bahia, Brazil, September 2020. [ bib ]
[11] F. Couto, “Multilingual text mining: Overcoming the lack of clinical NLP resources.” Talk at the First Multilingual clinical NLP workshop (MUCLIN), Geneva, Switzerland, July 2020. [ bib ]
[12] F. Couto, “Introdução à bioinformática via linha de comando.” Tutorial na Faculdade de Ciências e Tecnologias da Universidade Nova de Lisboa, Caparica, December 2019. [ bib ]
[13] F. Couto, “Introdução à bioinformática via linha de comando.” Tutorial no V Encontro de Ecologia, Universidade de Coimbra, November 2019. [ bib ]
[14] F. Couto, “Data and text processing in health and life sciences: an example driven workshop using shell scripting.” Tutorial na Universidade do Algarve, Faro, July 2019. [ bib ]
[15] F. Couto, “Data and text processing in health and life sciences: an example driven workshop using shell scripting.” Tutorial at the Bioinformatics Open Days, Universidade do Minho, Braga, February 2019. [ bib ]
[16] F. Couto, “Exploration, sharing and privacy of data: Linked data - challenges for imagiology and radiology.” Palestra no Encontro Nacional de Física Médica, FISMED2017, Coimbra, 2017. [ bib ]
[17] F. Couto, “Towards a privacy-preserving environment for genomic data analysis.” Talk at the Computational Biology and Bioinformatics Seminar, IMM, Lisboa, 2016. [ bib ]
[18] F. Couto, “Master in bioinformatics and computational biology.” Talk at the Bioinformatics Open Days, Braga, 2016. [ bib ]
[19] F. Couto, “Identifying interactions between chemical entities in text.” Talk at the Innovation and Business Creation Pitch Session, EIT Health, Lisboa, 2015. [ bib ]
[20] F. Couto, “Master in bioinformatics and computational biology.” Talk at the Bioinformatics Open Days, Lisboa, 2015. [ bib ]
[21] F. Couto, “Recognizing and rewarding data sharing through KnowldegeCoins.” Talk at the Data sharing in peer review, PEERE workshop, Lisboa, 2015. [ bib ]
[22] F. Couto, “Biomedical ontologies and optimization challenges.” Palestra no 3º workshop em bio-optimização, Instituto Superior de Agronomia, 2014. [ bib ]
[23] F. Couto, “Current research themes on the area of information systems: The case of biomedical text mining.” Talk at the Research Topics Class, IST, 2014. [ bib ]
[24] F. Couto, “Rewarding and recognizing metadata sharing and integration on the semantic web using ontologies.” Talk at the RDA Europe Workshop about Data Sharing and Interoperability, Brussels, 2014. [ bib ]
[25] F. Couto, “KnowledgeCoin (KC): a reward and recognition mechanism to incentivize proper data integration and sharing.” Talk at the SAPO Labs, Lisboa, 2014. [ bib ]
[26] F. Couto, “The BiobankCloud.” Talk at the Meeting on IT/Informatics BBMRI-ERIC, Austria, 2014. [ bib ]
[27] F. Couto, “How can biomedical ontologies assist biological systems, functional & integrative genomics research?.” Talk at the BioSys/BioFIG Research Seminar, University of Lisbon, 2014. [ bib ]
[28] F. Couto, “O Mundo em Pessoa 2.0.” Talk at the SAPO Labs, Lisboa, 2014. [ bib ]
[29] F. Couto, “Master in bioinformatics and computational biology at FCUL.” Talk at the Bioinformatics Open Days, University of Minho, 2014. [ bib ]
[30] F. Couto, “O Mundo em Pessoa.” Palestra na 1ª Semana Ciências em Movimento, FCUL, 2014. [ bib ]
[31] F. Couto, “Privacy-preserving genome annotation.” Talk at the 3rd Biobank Technical Meeting, University of Lisbon, 2013. [ bib ]
[32] F. Couto, “How biomedical ontologies can assist computational and theoretical biology research?.” Talk at the Seminars on Computational and Theoretical Biology, Instituto Gulbenkian de Ciência, 2013. [ bib ]
[33] F. Couto, “Biomedical ontologies: semantic annotation and similarity.” Palestra no Instituto de Biofísica e Engenharia Biomédica (IBEB), 2013. [ bib ]
[34] F. Couto, “Semantic similarity in biomedical ontologies: Measurement, assessment and applications.” Talk at the Workshop on Ontologies in Biomedicine and Life Sciences (OBML), Dresden, Germany, 2012. [ bib ]
[35] F. Couto, “Semantic ontology matching using external resources.” Palestra no Centro de Ciências e Tecnologias de Computação (CCTC) Seminar, University of Minho, 2012. [ bib ]
[36] F. Couto, “Exploring the semantics of biomedical ontologies.” Talk at the Bioinformatics Open Days, University of Minho, 2012. [ bib ]
[37] F. Couto, “Bioinformática.” Palestra no Ciclo de Seminários Web, Universidade dos Açores, 2011. [ bib ]
[38] F. Couto, “Untangling biomedical ontologies.” Talk at the Workshop on Bioinformatics and Systems Modelling, University of Lisbon, 2011. [ bib ]
[39] F. Couto, “Exploring the semantics of biomedical ontologies.” Talk at the External Seminar at European Bioinformatics Institute, Hinxton, UK, 2011. [ bib ]
[40] F. Couto, “Biomedical informatics.” Talk at the Translational Bioinformatics, IGC, Oeiras, 2010. [ bib ]
[41] F. Couto, “Untangling BioOntologies for effectively exploring biomedical information.” Talk at the IMM Bioinformatics nanocourse, Lisboa, 2010. [ bib ]
[42] F. Couto, “Gene ontology.” Talk at the FLUP Escola de Verão, Lisboa, 2010. [ bib ]
[43] F. Couto, “Biomedical research line.” Talk at the First INTERAC workshop, Braga, 2008. [ bib ]
[44] F. Couto, “Untangling BioOntologies for mining biomedical information.” Talk at the First Portuguese forum on computational biology, IGC, Oeiras, 2008. [ bib ]
[45] F. Couto, “ReBIL: Relating biological information through literature.” Talk at the Workshop: Algoritmos de bioinformatica na Faculdade de Medicina da Universidade do Porto, 2008. [ bib ]
[46] F. Couto, “Bioinformática - exploração da informação genómica.” Palestra no Instituto Politécnico de Tomar, 2006. [ bib ]
[47] F. Couto, “Machine learning.” Talk at the BioAlma Seminar, Madrid, 2006. [ bib ]
[48] F. Couto, “Identificação automática de evidências que suportem anotações de proteínas na literatura científica.” Palestra na Entrega do Prémio Inovação Jovem Engenheiro 2004, Ordem dos Engenheiros, Lisboa, Portugal, October 2005. [ bib ]
[49] F. Couto, “Caracterização bioquímica de genes e proteínas: Bases de dados e ferramentas de anotação automática.” Palestra no II Encontro Nacional de Estudantes Bioquímicos (II ENeBIOQ), Faculdade de Ciências da Universidade de Lisboa, Portugal, April 2005. [ bib ]
[50] F. Couto, “ReBIL: Relating biological information through literature.” Palestra no Seminário do Programa Estudos Avançados de Oeiras (EAO seminar), IGC, Oeiras, 2005. [ bib ]
[51] F. Couto, “ReBIL: Relating biological information through literature.” II Annual Meeting of Portuguese Proteomic Network (ProCura) Functional Genomics And Proteomics, Inst. Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal, November 2004. [ bib ]
[52] F. Couto, “Automatic identification in literature of evidences that support electronic GOA annotations.” Talk at the Seminary of the Sequence Database Group, European Bioinformatics Institute, Hinxton, UK, October 2004. [ bib ]
[53] F. Couto, “ReBIL : Relating biological information through literature.” Talk at the Seminary of the AFMB laboratory, AFMB-CNRS, Marseille, France, December 2003. [ bib ]
[54] F. Couto, “Extracting biological information through literature: automatic annotation of FlyBase and CAZy databases.” Talk at the Scientific Meeting on Bioinformatics (satellite to the EMBnet AGM02), Instituto Gulbenkian de Ciência, Oeiras, Portugal, September 2002. [ bib ]

Proceedings

[1] F. Couto and M. Krallinger, eds., First International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages (SIIRH), vol. 2619, CEUR Workshop Proceedings (CEUR-WS.org), 2020. [ bib | url ]
[2] F. Couto and J. Hastings, eds., The Sixth International Conference on Biomedical Ontologies (ICBO), vol. 1515, CEUR Workshop Proceedings (CEUR-WS.org), 2015. [ bib | url ]