MEMBER

Francisco Couto

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ONGOING

Acronym Title Funding Entity Start Date End Date
DeST Deep Semantic Tagger FCT 01/10/2018 30/06/2022

PAST

Acronym Title Funding Entity Start Date End Date
RESISTIR Sistema de Informação para controlo de infecção inteligente e antibioterapia personalizada P2020 01/04/2016 01/04/2019
Biobank Cloud Scalable, Secure Storage of Biobank Data EU FP7 01/12/2012 30/11/2015
SOMER SOMER - Semantic Ontology Matching using External Resources FCT 19/03/2012 31/10/2014
SP-Net SP-Net - In silico reconstruction of Streptococcus pneumoniae cellular networks and their impact on virulence FCT 01/01/2011 30/06/2014
REACTION Retrieval, Extraction, and Aggregation Computing Technology for Integrating and Organizing News FCT 01/01/2010 30/09/2013
EPIWork EPIWork - Developing the Framwork for an Epidemic Forecast Infrastructure EU FP7 01/02/2009 31/07/2013
ARN Algorithms for the identification of genetic Regulatory Networks FCT 01/11/2007 31/10/2010
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Diana Sousa, Andre Lamurias, Francisco M. Couto. Using Neural Networks for Relation Extraction from Biomedical Literature, In Methods in Molecular Biology,Artificial Neural Networks, pages 289-305. Springer US, 2020 [Biblios]
Maria Fernandes, Jeremie Decouchant, Marcus Volp, Francisco M. Couto, Paulo Esteves-Verissimo. DNA-SeAl: Sensitivity Levels to Optimize the Performance of Privacy-Preserving DNA Alignment. IEEE Journal of Biomedical and Health Informatics, 24(3):907-915, Institute of Electrical and Electronics Engineers (IEEE), 2020 [Biblios]
Francisco M. Couto, Martin Krallinger. Report of the first international workshop on semantic indexing and information retrieval for health from heterogeneous content types and languages. In The First International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages (SIIRH), 2020 [Biblios]
P. Ruas, A. Lamurias, Francisco M. Couto. Towards a multilingual corpus for named entity linking evaluation in the clinical domain. In The First International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages (SIIRH), 2020 [Biblios]
P. Ruas, A. Lamurias, Francisco M. 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 [Biblios]
A. Neves, A. Lamurias, Francisco M. Couto. Biomedical question answering using extreme multi-label classification and ontologies in the multilingual panorama. In The Eighth edition of BioASQ: Large-scale Biomedical Semantic Indexing and Question Answering (CLEF 2020 Working Notes), 2020 [Biblios]
Márcia Barros, André Moitinho, Francisco M. Couto. Hybrid Semantic Recommender System for Chemical Compounds. In 42nd European Conference on Information Retrieval, pages 94-101. Springer International Publishing, 2020 [Biblios]
Diana Sousa, Francisco M. Couto. BiOnt: Deep Learning Using Multiple Biomedical Ontologies for Relation Extraction. In 42nd European Conference on Information Retrieval, pages 367-374. Springer International Publishing, 2020 [Biblios]
Andre Lamurias, Diana Sousa, Francisco M. Couto. Generating Biomedical Question Answering Corpora From Q&A Forums. IEEE Access, 8, Institute of Electrical and Electronics Engineers (IEEE), 2020 [Biblios]
João D. Ferreira, Francisco M. Couto. Semantic Similarity in Cheminformatics, In Cheminformatics and its Applications [Working Title]. IntechOpen, 2019 [Biblios]
João D. Ferreira, Francisco M. Couto. Multi-domain semantic similarity in biomedical research. BMC Bioinformatics, 20(S10), Springer Science and Business Media LLC, 2019 [Biblios]
M. Fernandes, J. Decouchant, M. Volp, Francisco M. Couto, Paulo Verissímo. Privacy-preserving processing of filtered DNA reads. In The Sixth International Workshop on ?Genome Privacy and Security (GenoPri-2019), 2019 [Biblios]
Diana Sousa, Andre Lamurias, Francisco M. Couto. A Silver Standard Corpus of Human Phenotype-Gene Relations. In Proceedings of the 2019 Conference of the North. Association for Computational Linguistics, 2019 [Biblios]
Andre Lamurias, Francisco M Couto. LasigeBioTM at MEDIQA 2019: Biomedical Question Answering using Bidirectional Transformers and Named Entity Recognition. In Proceedings of the 18th BioNLP Workshop and Shared Task. Association for Computational Linguistics, 2019 [Biblios]
Andre Lamurias, Francisco M. Couto. Text Mining for Bioinformatics Using Biomedical Literature, In Encyclopedia of Bioinformatics and Computational Biology, pages 602-611. Elsevier, 2019 [Biblios]
Francisco M. Couto, Andre Lamurias. Semantic Similarity Definition, In Encyclopedia of Bioinformatics and Computational Biology, pages 870-876. Elsevier, 2019 [Biblios]
Diana Sousa, Andre Lamurias, Francisco M. Couto. A Silver Standard Corpus of Human Phenotype-Gene Relations. In Proceedings of the 2019 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long and Short Papers). Association for Computational Linguistics, 2019 [Biblios]
Maria Fernandes, Jeremie Decouchant, Marcus Volp, Francisco M. Couto, Paulo Verissimo. DNA-SeAl: Sensitivity Levels to Optimize the Performance of Privacy-Preserving DNA Alignment. IEEE Journal of Biomedical and Health Informatics, 1-1, Institute of Electrical and Electronics Engineers (IEEE), 2019 [Biblios]
Francisco M. Couto. Data and Text Processing for Health and Life Sciences, Springer International Publishing, Advances in Experimental Medicine and Biology, 2019 [Biblios]
Francisco M. Couto, Andre Lamurias. MER: a shell script and annotation server for minimal named entity recognition and linking. Journal of Cheminformatics, 10(1), Springer Science and Business Media LLC, 2018 [Biblios]
Francisco M. Couto, Andre Lamurias. MER: a shell script and annotation server for minimal named entity recognition and linking. Journal of Cheminformatics, 10(1), Springer Science and Business Media LLC, 2018 [Biblios]
J. Ferreira, F. Couto. Multi-domain semantic similarity in biomedical research. In The Twelfth Data and Text Mining in Biomedical Informatics (DTMBIO 2018), 2018 [Biblios]
D. Faria, C. Pesquita, B. Balasubramani, T. Tervo, D. Carriço, R. Garrilha, F. Couto, I. Cruz. Results of AML in OAEI 2018. In The Thirteen International Workshop on Ontology Matching (OM-2018), 2018 [Biblios]
João D. Ferreira, Bruno Inácio, Reza M. Salek, Francisco M. Couto. Assessing Public Metabolomics Metadata, Towards Improving Quality. Journal of Integrative Bioinformatics, 14(4), Walter de Gruyter GmbH, 2017 [Biblios]
M. Asif, C. Rasga, H. Martiniano, J. Santos, A. Marques, F. Couto, 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 [Biblios]
A. Lamurias, L. Clarke, F. Couto. Development of a text mining framework for systems biology. In Bioinformatics Open Days, University of Minho, 2017 [Biblios]
G. Figueiró, F. Couto, A. Moitinho. 3D identification of clusters: a cancer cell case-study. In Bioinformatics Open Days, University of Minho, 2017 [Biblios]
D. Faria, B. Balasubramani, V. Shivaprabhu, I. Mott, C. Pesquita, F. Couto, I. Cruz. Results of AML in OAEI 2017. In The Twelfth International Workshop on Ontology Matching (OM-2017), 2017 [Biblios]
M. Rodrigues, F. Couto. MoRS at SemEval-2017 task 3: Easy to use SVM in ranking tasks. In 10th International Workshop on Semantic Evaluation (SemEval), 2017 [Biblios]
Vinicius V. Cogo, Alysson Bessani, Francisco M. Couto, Margarida  Gama-Carvalho, Maria Fernandes, Paulo Esteves-Verissimo. How Can Photo Sharing Inspire Sharing Genomes?. In Practical Applications of Computational Biology and Bioinformatics (PACBB), pages 74-82. Springer International Publishing, 2017 [Biblios]
Bruno Inácio, João D. Ferreira, Francisco M. Couto. Metadata Analyser: Measuring Metadata Quality. In Practical Applications of Computational Biology and Bioinformatics (PACBB), pages 197-204. Springer International Publishing, 2017 [Biblios]
António Barata, Lucília Carvalho, Francisco M. Couto. Anthropometric Data Analytics: A Portuguese Case Study. In Practical Applications of Computational Biology and Bioinformatics (PACBB), pages 92-100. Springer International Publishing, 2017 [Biblios]
Maria Fernandes, Jérémie Decouchant, Francisco M. Couto, Paulo Esteves-Verissimo. Cloud-Assisted Read Alignment and Privacy. In Practical Applications of Computational Biology and Bioinformatics (PACBB), pages 220-227. Springer International Publishing, 2017 [Biblios]