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]
Hugo P. Bastos, Lisete Sousa, Luka A. Clarke, Francisco M. Couto. Functional coherence metrics in protein families. Journal of Biomedical Semantics, 7(41), Springer Nature, 2016 [Biblios]
C. Ramos, M. Louro, M. Santos, F. Couto. Knowledge ratings in MetaboLights, Tech. Rep. arXiv:1604.07997 [cs.DL], arXiv.org, 2016 [Biblios]
A. Barata, F. Couto, L. Carvalho. Anthropometric data analytics: Portuguese case-study. In Bioinformatics Open Days, University of Minho, 2016 [Biblios]
D. Faria, C. Pesquita, B. Balasubramani, C. Martins, J. Cardoso, H. Curado, F. Couto, I. Cruz. OAEI 2016 results of AML. In The Eleventh International Workshop on Ontology Matching (OM-2016), 2016 [Biblios]
D. Goncalves, M. Costa, 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 [Biblios]
D. Goncalves, M. Costa, F. Couto. A flexible recommendation system for cable TV. In 3rd Workshop on Recommendation Systems for Television and online Video (RecSysTV), 2016 [Biblios]
Andre Lamurias, João D Ferreira, Francisco M Couto. Improving chemical entity recognition through h-index based semantic similarity. Journal of Cheminformatics, 7(S1), Springer Science and Business Media LLC, 2015 [Biblios]
Andre Lamurias, Luka A. Clarke, Francisco M. Couto. IICE: Web Tool for Automatic Identification of Chemical Entities and Interactions. In Machine Learning and Knowledge Discovery in Databases,Lecture Notes in Computer Science, pages 285-288. Springer International Publishing, 2015 [Biblios]
Andre Lamurias, Luka A. Clarke, Francisco M. Couto. IICE: Web Tool for Automatic Identification of Chemical Entities and Interactions. In Machine Learning and Knowledge Discovery in Databases,Lecture Notes in Computer Science, pages 285-288. Springer International Publishing, 2015 [Biblios]
Vinicius Vielmo Cogo, Alysson Bessani, Francisco M. Couto, Paulo Veríssimo. A high-throughput method to detect privacy-sensitive human genomic data. In WPES 2015 - Workshop on Privacy in the Electronic Society (together with ACM CCS’15), 2015 [Biblios]
André Leal, Bruno Martins, Francisco Couto. ULisboa: Recognition and normalization of medical concepts. In 8th International Workshop on Semantic Evaluation (SemEval), 2015 [Biblios]
Daniel Faria, Ernesto Jiménez-Ruiz, Catia Pesquita, Emanuel Santos, Francisco M. Couto. Towards Annotating Potential Incoherences in BioPortal Mappings. In The Semantic Web – ISWC 2014,Lecture Notes in Computer Science, pages 17-32. Springer International Publishing, 2014 [Biblios]
João Ferreira, Francisco Couto. Semantic similarity in the biomedical domain. In Molecular Biology in Portugal and EMBL (and EMBL Alumni), 2013 [Biblios]
Tiago Grego, F. Pinto, Francisco Couto. LASIGE: using conditional random fields and chebi ontology. In 7th International Workshop on Semantic Evaluation (SemEval), 2013 [Biblios]
Miguel Costa, Daniel Gomes, Francisco Couto, Mário Silva. A survey of web archive search architectures. In 3rd Temporal Web Analytics Workshop (TempWeb), 2013 [Biblios]
Daniel Faria, Cátia Pesquita, Emanuel Santos, M. Palmonari, I. Cruz, Francisco Couto. The AgreementMakerLight ontology matching system. In On The Move (OTM) Federated International Conference, pages 527-541, 2013 [Biblios]
Cátia Pesquita, João Ferreira, Francisco Couto, Mário Silva. Semi-automated annotation of epidemiological resources. In Epiwork International Workshop on Digital Epidemiology, 2013 [Biblios]
Cátia Pesquita, Daniel Faria, C. Stroe, Emanuel Santos, I. Cruz, Francisco Couto. What's in a `nym'? synonyms in biomedical ontology matching. In 12th International Semantic Web Conference (ISWC), pages 526-541, 2013 [Biblios]
Cátia Machado, Francisco Couto, A. Freitas. Exploring ontological knowledge for translational medicine. In Workshop on Machine Learning for Clinical Data Analysis and Healthcare (NIPS), 2013 [Biblios]
Silvio Moreira, David Batista, Paula Carvalho, Francisco Couto, Mário Silva. Tracking politics with POWER. PROGRAM-ELECTRONIC LIBRARY AND INFORMATION SYSTEMS, 47(2):120-135, 2013 [Biblios]
João D. Ferreira, Catia Pesquita, Francisco M. Couto, Mário J. Silva. Bringing epidemiology into the Semantic Web. In International Conference on Biomedical Ontologies (ICBO), 2012 [Biblios]
F. Couto. Semantic Similarity in Biomedical Ontologies: measurement, assessment and applications. In 4th Workshop of Ontologies in Biomedicine and Life Sciences (OBML), 2012 [Biblios]
S. Moreira, D. Batista, P. Carvalho, F. Couto, 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 [Biblios]
I. Cruz, C. Stroe, C. Pesquita, F. Couto, V. Cross. Biomedical ontology matching using the AgreementMaker system. In International Conference on Biomedical Ontologies (ICBO), 2011, 2011 [Biblios]
C. Pesquita, F. Couto. Where GO is going and what it means for ontology extension. In International Conference on Biomedical Ontologies (ICBO), 2011 [Biblios]
J. Ferreira, F. Couto. Generic semantic relatedness measure for biomedical ontologies. In International Conference on Biomedical Ontologies (ICBO), 2011 [Biblios]
Mário J. Silva, Fabrício A.B. Silva, Luís Filipe Lopes, Francisco Couto. Building a Digital Library for Epidemic Modelling. In Proceedings of ICDL 2010 - The International Conference on Digital Libraries, 2010 [Biblios]
Luis Filipe Lopes, Fabrício Silva, Francisco Couto, João Zamite, Hugo Ferreira, Carla Sousa, Mário J. Silva. Epidemic Marketplace: An Information Management System for Epidemiological Data. In Proceedings of the ITBAM - 1st International Conference on Information Technology in Bio and Medical Informatics - DEXA 2010, pages 31-44, 2010 [Biblios]
João Zamite, Fabrício Silva, Francisco Couto, Mário J. Silva. MEDCollector: Multisource Epidemic Data Collector. In Proceedings of ITBAM'10 - 1st International Conference on Information Technology in Bio and Medical Informatics - DEXA 2010, 2010 [Biblios]
David Batista, Mário J. Silva, Francisco Couto, Bibek Behera. Geographic Signatures for Semantic Retrieval. In 6th ACM Workshop on Geographic Information Retrieval , 2010 [Biblios]
Cátia M. Machado, Francisco Couto, Alexandra R. Fernandes, Susana Santos, Nuno Cardim, Ana T. Freitas. Semantic Characterization of Hypertrophic Cardiomyopathy Disease. In First Workshop on Knowledge Engineering, Discovery and Dissemination in Health (KEDDH10), held in conjunction with The IEEE International Conference on Bioinformatics & Biomedicine (BIBM 2010) , 2010 [Biblios]