Member

Acronym	Title	Funding Entity	Start Date	End Date
MicroGenAI	Generative Language Models for Unearthing Resilient Microbes in Regenerative Agriculture	FCT \| LASIGE	01/12/2025	31/05/2026
DeST	Deep Semantic Tagger	FCT	01/10/2018	30/09/2022
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

Canelhas, Maria Madalena Girão, Couto, Francisco José Moreira, Fortes, Ana Margarida da Costa Macedo. MiCRA : a minimal pipeline for functional microbiome information retrieval using Natural Language Processing and Biomedical Ontologies. Master's dissertation, 2025 [Biblios]

Pedro Simões Ruas, Francisco José Moreira Couto. Deep semantic entity linking. PhD thesis, 2025 [Biblios]

Anaya, Christopher, Couto, Francisco José Moreira, Fernandes, Maria Isabel Mou Sequeira . LLM fine-tuning with biomedical open-source data. Master's dissertation, 2025 [Biblios]

Ligia Moriguchi Watanabe, Lisete Sousa, Francisco M. Couto, Natália Yumi Noronha, Marcela Augusta de Souza Pinhel, Gleyson Francisco da Silva Carvalho, Guilherme da Silva Rodrigues, Carlos Roberto Bueno Júnior, Leslie Domenici Kulikowski, Fernando Barbosa Júnior, Carla Barbosa Nonino. Genome-Wide Admixture and Association Study of Serum Selenium Deficiency to Identify Genetic Variants Indirectly Linked to Selenium Regulation in Brazilian Adults. Nutrients, 16(11), MDPI AG, 2024 [Biblios]

Matilde Pato, Márcia Barros, Francisco M. Couto. Survey on Recommender Systems for Biomedical Items in Life and Health Sciences. ACM Computing Surveys, 56(6):1-32, Association for Computing Machinery (ACM), 2024 [Biblios]

Cassanheira, Rodrigo de Castro Sampaio, Couto, Francisco José Moreira. Relation extraction for gene and chemical compounds. Master's dissertation, 2024 [Biblios]

Silvestre, Pedro Moisés Marques, Couto, Francisco José Moreira. Identifying negative results using biomedical relation extraction systems. Master's dissertation, 2024 [Biblios]

Christopher Anaya, Maria Fernandes, Francisco M Couto. LLM Fine-Tuning With Biomedical Open-Source Data. In CLEF 2024: Conference and Labs of the Evaluation Forum, 2024 [Biblios]

Daniel Faria, Emanuel Santos, Booma Sowkarthiga Balasubramani, Marta C. Silva, Francisco M. Couto, Catia Pesquita. AgreementMakerLight. Semantic Web, 1-13, IOS Press, 2023 [Biblios]

Muhammad Asif, Hugo F. M. C. Martiniano, Andre Lamurias, Samina Kausar, Francisco M. Couto. DGH-GO: dissecting the genetic heterogeneity of complex diseases using gene ontology. BMC Bioinformatics, 24(1), Springer Science and Business Media LLC, 2023 [Biblios]

Diana F Sousa, Francisco M Couto. K-RET: knowledgeable biomedical relation extraction system. Bioinformatics, 39(4), Oxford University Press (OUP), 2023 [Biblios]

Matos, José Pedro Parracha de, David, Dezső, Couto, Francisco José Moreira. Development of machine learning tool for filtering artifacts in the identification of CNVs. Master's dissertation, 2023 [Biblios]

Monteiro, Ana Pereira de Brito Líbano, Fonseca, Maria Carmo, Couto, Francisco José Moreira. Unveiling co-transcriptional splicing kinetics using novel nascent transcriptomic techniques. Master's dissertation, 2023 [Biblios]

Maria Fernandes, Jérémie Decouchant, Francisco M. Couto. Security, privacy, and trust management in DNA computing, In Perspective of DNA Computing in Computer Science,Advances in Computers, pages 39 - 81. Elsevier, 2023 [Biblios]

Pedro Ruas, Diana F. Sousa, André Neves, Carlos Cruz, Francisco M. Couto. LASIGE and UNICAGE solution to the NASA LitCoin NLP Competition, arxiv, 2023 [Biblios]

Sofia I. R. Conceição, Diana F. Sousa, Pedro Silvestre, Francisco M Couto. lasigeBioTM at SemEval-2023 Task 7: Improving Natural Language Inference Baseline Systems with Domain Ontologies. In Proceedings of the The 17th International Workshop on Semantic Evaluation (SemEval-2023). Association for Computational Linguistics, 2023 [Biblios]

S. Conceicao, D. Sousa, P. Silvestre, F. Couto. BioRED track lasigeBioTM submission: Relation extraction using domain ontologies with BioRED. In BioCreative VIII Challenge Evaluation, 2023 [Biblios]

Sousa, Diana Francisco de, Couto, Francisco José Moreira. Deep learning system for biomedical relation extraction combining external sources of knowledge. PhD thesis, 2023 [Biblios]

Marcia Barros, André Moitinho, Francisco M. Couto. SeEn: Sequential enriched datasets for sequence-aware recommendations. Scientific Data, 9(1), Springer Science and Business Media LLC, 2022 [Biblios]

Pedro Ruas, Francisco M. Couto. NILINKER: Attention-based approach to NIL Entity Linking. Journal of Biomedical Informatics, 132, Elsevier BV, 2022 [Biblios]

Diana Sousa, Francisco M. Couto. Biomedical Relation Extraction With Knowledge Graph-Based Recommendations. IEEE Journal of Biomedical and Health Informatics, 26(8):4207-4217, Institute of Electrical and Electronics Engineers (IEEE), 2022 [Biblios]

Barros, Márcia Cristina Afonso, Couto, Francisco José Moreira, Almeida, André Moitinho de. Recommender system to support comprehensive exploration of large scale scientific datasets. PhD thesis, 2022 [Biblios]

Ilhéu, Ana Cristina Gonçalves, Couto, Francisco José Moreira, Asif, Muhammad. A computational pipeline to identify phenotypic manifestations related to genes. Master's dissertation, 2022 [Biblios]

Leonor Horta Torcato, Francisco José Moreira Couto. Extracting Negative Biomedical Relations from Literature. Master's dissertation, 2021 [Biblios]

Ana Rodrigues, João Santinha, Bernardo Galvão, Celso Matos, Francisco M. Couto, Nickolas Papanikolaou. Prediction of Prostate Cancer Disease Aggressiveness Using Bi-Parametric Mri Radiomics. Cancers, 13(23), MDPI AG, 2021 [Biblios]

Ana Carolina Vitorino Rodrigues, Nikolaos Papanikolaou, Francisco José Moreira Couto. Prostate MRI Radiomics for Prediction of Gleason Score. Master's dissertation, 2021 [Biblios]

Vítor Daniel Torres Andrade, Francisco José Moreira Couto. Named Entity Recognition and Linking in a Multilingual Biomedical Setting. Master's dissertation, 2021 [Biblios]

Márcia Barros, Pedro Ruas, Diana Sousa, Ali Haider Bangash, Francisco M. Couto. COVID-19 recommender system based on an annotated multilingual corpus. Genomics & Informatics, 19(3), Korea Genome Organization, 2021 [Biblios]

Sofia I. R. Conceição, Francisco M. Couto. Text Mining for Building Biomedical Networks Using Cancer as a Case Study. Biomolecules, 11(10), MDPI AG, 2021 [Biblios]

Andre Lamurias, Sofia Jesus, Vanessa Neveu, Reza M. Salek, Francisco M. Couto. Information Retrieval Using Machine Learning for Biomarker Curation in the Exposome-Explorer. Frontiers in Research Metrics and Analytics, 6, Frontiers Media SA, 2021 [Biblios]

Miguel Ângelo Conde Vieira, Francisco José Moreira Couto, André Francisco Martins Lamúrias. Development of a Corpus for User-based Scientific Question Answering. Master's dissertation, 2021 [Biblios]

Robert West, Smriti Bhagat, Paul Groth, Marinka Zitnik, Francisco M. Couto, Pasquale Lisena, Albert Meroño-Peñuela, Xiangyu Zhao, Wenqi Fan, Dawei Yin, Jiliang Tang, Linjun Shou, Ming Gong, Jian Pei, Xiubo Geng, Xingjie Zhou, Daxin Jiang, Benjamin Ricaud, Nicolas Aspert, Volodymyr Miz, Jennifer Dy, Stratis Ioannidis, ?lkay Y?ld?z, Rezvaneh Rezapour, Samin Aref, Ly Dinh, Jana Diesner, Alexey Drutsa, Dmitry Ustalov, Nikita Popov, Daria Baidakova, Shubhanshu Mishra, Arjun Gopalan, Da-Cheng Juan, Cesar Ilharco Magalhaes, Chun-Sung Ferng, Allan Heydon, Chun-Ta Lu, Philip Pham, George Yu, Yicheng Fan, Yueqi Wang, Florian Laurent, Yanick Schraner, Christian Scheller, Sharada Mohanty, Jiawei Chen, Xiang Wang, Fuli Feng, Xiangnan He, Irene Teinemaa, Javier Albert, Dmitri Goldenberg, Flavian Vasile, David Rohde, Olivier Jeunen, Amine Benhalloum, Otmane Sakhi, Yu Rong, Wenbing Huang, Tingyang Xu, Yatao Bian, Hong Cheng, Fuchun Sun, Junzhou Huang, Shobeir Fakhraei, Christos Faloutsos, Onur Çelebi, Martin Müller, Manuel Schneider, Olesia Altunina, Wolfram Wingerath, Benjamin Wollmer, Felix Gessert, Stephan Succo, Norbert Ritter, Evann Courdier, Tudor Mihai Avram, Dragan Cvetinovic, Levan Tsinadze, Johny Jose, Rose Howell, Mario Koenig, Michaël Defferrard, Krishnaram Kenthapadi, Ben Packer, Mehrnoosh Sameki, Nashlie Sephus. Summary of Tutorials at The Web Conference 2021. In Companion Proceedings of the Web Conference 2021. ACM, 2021 [Biblios]

Marcia Barros, Andre Moitinho, Francisco M. Couto. Hybrid semantic recommender system for chemical compounds in large-scale datasets. Journal of Cheminformatics, 13(1), Springer Science and Business Media LLC, 2021 [Biblios]

M. Barros, A. Moitinho, F. Couto. Recommender systems for scientific fields. In 19th International Symposium on Intelligent Data Analysis (IDA), 2021 [Biblios]

D. Faria, B. Lima, M. Silva, F. Couto, C. Pesquita. AML and AMLC results for OAEI 2021. In 16th International Workshop on Ontology Matching (OM-2021), 2021 [Biblios]

D. Sousa, R. Cassanheira, F. Couto. lasigeBioTM at BioCreative VII Track 1: Text mining drug and chemical-protein interactions using biomedical ontologies. In BioCreative VII Challenge Evaluation, 2021 [Biblios]

M. Campos, 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 [Biblios]

P. Ruas, V. Andrade, 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 [Biblios]

P. Ruas, V. Andrade, 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 [Biblios]

Fábio Colaço, Márcia Barros, Francisco M. Couto. DRecPy: A Python Framework for Developing Deep Learning-Based Recommenders. In Fourteenth ACM Conference on Recommender Systems. ACM, 2020 [Biblios]

Pedro Ruas, Andre Lamurias, Francisco M. Couto. Linking chemical and disease entities to ontologies by integrating PageRank with extracted relations from literature. Journal of Cheminformatics, 12(1), Springer Science and Business Media LLC, 2020 [Biblios]

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, 2020 [Biblios]

Diana Sousa, Andre Lamurias, Francisco M. Couto. Improving accessibility and distinction between negative results in biomedical relation extraction. Genomics & Informatics, 18(2), Korea Genome Organization, 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]

Muhammad Asif, Hugo F. M. C. Martiniano, Ana Rita Marques, João Xavier Santos, Joana Vilela, Celia Rasga, Guiomar Oliveira, Francisco M. Couto, Astrid M. Vicente. Identification of biological mechanisms underlying a multidimensional ASD phenotype using machine learning. Translational Psychiatry, 10(1), Springer Science and Business Media LLC, 2020 [Biblios]

Pedro Jorge Mendes dos Santos, Francisco José Moreira Couto, João Diogo Silva Ferreira. Validation of Automatic Similarity Measures. Master's dissertation, 2020 [Biblios]

Fábio Iúri Gaspar Colaço, Francisco José Moreira Couto. Recommender Systems Based on Deep Learning Techniques. Master's dissertation, 2020 [Biblios]

Neves, André Daniel Costa das, Couto, Francisco José Moreira, Lamúrias, André Francisco Martins. Applying deep learning extreme multi-label classification to the biomedical and multilingual panoramas. Master's dissertation, 2020 [Biblios]

Diana Sousa, Andre Lamurias, Francisco M Couto. A hybrid approach toward biomedical relation extraction training corpora: combining distant supervision with crowdsourcing. Database, 2020, Oxford University Press (OUP), 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]

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, Francisco M. Couto, J. Copara, N. Naderi, J. Knafou, P. Ruch, D. Teodoro, D. Lowe, J. Mayfield, A. Köksal, H. Dönmez, E. Özk?r?ml?, 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 [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]

Sérgio Nunes, Suzanne Little, Sumit Bhatia, Ludovico Boratto, Guillaume Cabanac, Ricardo Campos, Francisco M. Couto, Stefano Faralli, Ingo Frommholz, Adam Jatowt, Alípio Jorge, Mirko Marras, Philipp Mayr, Giovanni Stilo. ECIR 2020 workshops: assessing the impact of going online. ACM SIGIR Forum, 54(1), Association for Computing Machinery (ACM), 2020 [Biblios]

Francisco M. Couto, Martin Krallinger. First International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages (SIIRH), CEUR Workshop Proceedings, 2020 [Biblios]

Francisco M. Couto, Martin 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, pages 654-659. Springer International Publishing, 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]

Andre Lamurias, Pedro Ruas, Francisco M. Couto. PPR-SSM: personalized PageRank and semantic similarity measures for entity linking. BMC Bioinformatics, 20(1), Springer Science and Business Media LLC, 2019 [Biblios]

Muhammad Asif, Astrid M. Vicente, Francisco M. Couto. FunVar: A systematic pipeline to unravel the convergence patterns of genetic variants in ASD, a paradigmatic complex disease. Journal of Biomedical Informatics, 98, Elsevier BV, 2019 [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]

Andre Lamurias, Diana Sousa, Luka A. Clarke, Francisco M. Couto. BO-LSTM: classifying relations via long short-term memory networks along biomedical ontologies. BMC Bioinformatics, 20(1), Springer Science and Business Media LLC, 2019 [Biblios]

Lamúrias, André Francisco Martins, Couto, Francisco Jose Moreira , Clarke, Luka Alexander . Development of a text mining approach to disease network discovery. PhD thesis, 2019 [Biblios]

Ruas, Pedro Simões, Couto, Francisco José Moreira. Exploring Biomedical Ontologies, Personalized PageRank and Semantic Similarity in the Entity Linking task. Master's dissertation, 2019 [Biblios]

Jesus, Sofia Pinheiro Rodrigues de, Couto, Francisco José Moreira. Information Retrieval using Machine Learning for Database Curation. Master's dissertation, 2019 [Biblios]

Diana Francisco de Sousa, Couto, Francisco José Moreira. Extracting phenotype-gene relations from biomedical literature using distant supervision and deep learning. Master's dissertation, 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]

Marcia Barros, Andre Moitinho, Francisco M. Couto. Using Research Literature to Generate Datasets of Implicit Feedback for Recommending Scientific Items. IEEE Access, 7, Institute of Electrical and Electronics Engineers (IEEE), 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 Couto. Introdução à Bioinformática Via Linha de Comando, Gradiva, 2019 [Biblios]

Francisco M. Couto. Data and Text Processing for Health and Life Sciences, Springer, Advances in Experimental Medicine and Biology, 2019 [Biblios]

Muhammad Asif, Hugo F. M. C. M. Martiniano, Astrid M. Vicente, Francisco M. Couto. Identifying disease genes using machine learning and gene functional similarities, assessed through Gene Ontology. PLOS ONE, 13(12), Public Library of Science (PLoS), 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 Nature, 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]

Juliano Oliveira Santana, Karina Peres Gramacho, Katiúcia Tícila de Souza Eduvirgens Ferreira, Rachel Passos Rezende, Pedro Antônio Oliveira Mangabeira, Ricardo Pedro Moreira Dias, Francisco M. Couto, Carlos Priminho Pirovani. Witches’ broom resistant genotype CCN51 shows greater diversity of symbiont bacteria in its phylloplane than susceptible genotype catongo. BMC Microbiology, 18(1), Springer Nature, 2018 [Biblios]

Tânia Sofia Guerreiro Maldonado, Francisco José Moreira Couto. Extracting biomedical relations from biomedical literature. Master's dissertation, 2018 [Biblios]

Muhammad Asif, Asdrid Moura Vicente, Francisco José Moreira Couto. A System medicine approach to study autism spectrum disorder, based on genomic, and clinical data. PhD thesis, 2018 [Biblios]

Jérémie Decouchant, Maria Fernandes, Marcus Völp, Francisco M Couto, Paulo Esteves-Veríssimo. Accurate filtering of privacy-sensitive information in raw genomic data. Journal of Biomedical Informatics, 82, Elsevier BV, 2018 [Biblios]

Daniel Faria, Catia Pesquita, Isabela Mott, Catarina Martins, Francisco M. Couto, Isabel F. Cruz. Tackling the challenges of matching biomedical ontologies. Journal of Biomedical Semantics, 9(1), Springer Nature, 2018 [Biblios]

Rui Sérgio de Sousa Luís, Fonseca, M. Carmo, Couto, Francisco José Moreira. The role of antisense transcription on regulation of gene expression. Master's dissertation, 2018 [Biblios]

M. Asif, H. Martiniano, F. Couto, 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 [Biblios]

R. Dias, C. Pesquita, J. Rebelo, A. Pedrosa, C. Santos, J. Adonis, V. Mendes, F. Couto, R. Tenreiro. 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 [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]

Andre Lamurias, João D. Ferreira, Luka A. Clarke, Francisco M. Couto. Generating a Tolerogenic Cell Therapy Knowledge Graph from Literature. Frontiers in Immunology, 8, Frontiers Media SA, 2017 [Biblios]

Luis Filipe Leal Campos, Couto, Francisco José Moreira, Pedro, Vasco Calais. Semantic annotation of electronic health records in a multilingual environment. Master's dissertation, 2017 [Biblios]

Miguel Jorge Vitorino Sousa Rodrigues, Couto, Francisco José Moreira. Biomedical semantic question and answering system. Master's dissertation, 2017 [Biblios]

Manuel Stapleton Garcia De Vasconcelos Lobo, Couto, Francisco José Moreira. Identifying human phenotype terms in text using a machine learning approach. PhD thesis, 2017 [Biblios]

António Pedro Pereira Barata, Couto, Francisco José Moreira, Monteiro, Lucília da Conceição Mourão de Carvalho Cáceres. Anthropometric data analytics: a portuguese case study. Master's dissertation, 2017 [Biblios]

Pedro De Almeida Martins, Couto, Francisco José Moreira, Amaral, Margarida. Previsão da localização subcelular de Proteínas Humanas com base em Aprendizagem Automática. Master's dissertation, 2017 [Biblios]

Andre Lamurias, Luka A. Clarke, Francisco M. Couto. Extracting microRNA-gene relations from biomedical literature using distant supervision. PLOS ONE, 12(3), Public Library of Science (PLoS), 2017 [Biblios]

Luís Campos, Vasco Pedro, Francisco Couto. Impact of translation on named-entity recognition in radiology texts. Database, 2017, Oxford University Press (OUP), 2017 [Biblios]

Manuel Lobo, Andre Lamurias, Francisco M. Couto. Identifying Human Phenotype Terms by Combining Machine Learning and Validation Rules. BioMed Research International, 2017, Hindawi Limited, 2017 [Biblios]

L. Campos, F. Couto. MRA – proof of concept of a multilingual report annotator web application, Tech. Rep. arXiv:1704.01748 [cs.DL], arXiv.org, 2017 [Biblios]

M. Asif, H. Martiniano, C. Rasga, A. Marques, J. Santos, F. Couto, 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 [Biblios]

M. Asif, H. Martiniano, C. Rasga, A. Marques, J. Santos, G. Oliveira, F. Couto, 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 [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]

L. Campos, V. Pedro, F. Couto. Semantic annotation of electronic health records in a multilingual environment. In Bioinformatics Open Days, University of Minho, 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]

L. Campos, A. Lamurias, 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 [Biblios]

F. Couto, L. Campos, and A. Lamurias. MER: a minimal named-entity recognition tagger and annotation server. In BioCreative V.5 Challenge Evaluation, 2017 [Biblios]

A. Lamurias, L. Campos, F. Couto. IBEnt: Chemical entity mentions in patents using ChEBI. In BioCreative V.5 Challenge Evaluation, 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]

A. Lamurias, Diana Sousa, S. Pereira, L.A. Clarke, 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 [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]

Florêncio, Rita João Martinho , Couto, Francisco José Moreira, Matela, Nuno Miguel de Pinto Lobo e. Radiation monitoring system in clinical imaging. Master's dissertation, 2016 [Biblios]

Silva, Rodolfo José Machado, Couto, Francisco José Moreira, Teixeira, Jorge Filipe Pinheiro Guerra de Ribeiro. Desenvolvimento de uma rede social desportiva. Master's dissertation, 2016 [Biblios]

M. Barros, F.M. Couto. Knowledge Representation and Management: a Linked Data Perspective. Yearbook of Medical Informatics, 25(01):178-183, Georg Thieme Verlag KG, 2016 [Biblios]

Inácio, Bruno Filipe Prudêncio, Couto, Francisco José Moreira, Ferreira, João Diogo Silva. Qanto valem os metadados?. Master's dissertation, 2016 [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]

M. Asif, I. Conceição, K. Kwiatkowska, C. Rasga, C. Café, L. Sousa, G. Oliveira, F. Couto, A. Vicente. Increased frequency of the autism broader phenotype in mothers transmitting etiological CNVs to sons affected by Autism Spectrum Disorder (ASD). European Journal of Human Genetics, 24(E-Suppl 1):184-184, Nature Publishing Group, 2016 [Biblios]

João Diogo Silva Ferreira, Couto, Francisco José Moreira. Semantic Similarity Across Biomedical Ontologies. PhD thesis, 2016 [Biblios]

Mónica Isabel Henriques Abreu, Francisco José Moreira Couto. Impacto das obras musicais lusófonas nas redes sociais. Master's dissertation, 2016 [Biblios]

Aparício, Tiago Miguel Marques, Guerreiro, Tiago, Couto, Francisco José Moreira. Aplicações na web para validação e classificação de notícias pela crowd. Master's dissertation, 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]

M. Rodriques, M. Fale, 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 [Biblios]

M. Asif, I. Conceição, K. Kwiatkowska, C. Rasga, F. Couto, A. Vicente. Maternal copy number variants (CNV) transmission to their Autism Spectrum Disorder (ASD) sons correlates with phenotypic traits. In 13th International Congress of Human Genetics (ICHG), 2016 [Biblios]

H. Curado, M. Cândido, M. Silva, J. Carriço, 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 [Biblios]

M. Lobo, A. Lamurias, F. Couto. Identifying human phenotype terms in text using a machine learning approach. In Bioinformatics Open Days, University of Minho, 2016 [Biblios]

P. Martins, L. Clarke, M. Amaral, F. Couto. Exploring machine learning algorithms to predict subcellular localizations. In Bioinformatics Open Days, University of Minho, 2016 [Biblios]

M. Barros, A. Lamúrias, M. Antunes, J. Teixeira, G. Figueiró, A. Pinheiro, F. Couto. Extraction of temporal expressions and clinical events from clinical notes. In Bioinformatics Open Days, University of Minho, 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]

M. Barros, F. Couto, H. Savietto, C. Barata, M. Domingos, A. Krone-Martins, A. Moitinho. A pipeline for producing a scientifically accurate visualisation of the Milky Way. In INForum - Simpósio de Informática, 2016 [Biblios]

A. Lamurias, M. Rodrigues, L. Clarke, F. Couto. Extraction of regulatory events using kernel-based classifiers and distant supervision. In ACL proceedings of the 4th BioNLP Shared Task Workshop, 2016 [Biblios]

M. Barros, A. Lamurias, G. Figueiro, M. Antunes, J. Teixeira, A. Pinheiro, F. Couto, M. Barros. 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 [Biblios]

Hugo Bastos, L. Sousa, L. Clarke, Francisco Couto. GRYFUN: A web application for GO term annotation visualization and analysis in protein sets. PLOS ONE, 10(3), Public Library of Science (PLoS) , 2015 [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]

João Oliveira, Francisco José Moreira Couto, Bruno Emanuel da Graça Martins. Análise de corpora jornalístico através das ocorrências de N-gramas. Master's dissertation, 2015 [Biblios]

Diogo Gonçalves, Francisco José Moreira Couto, Paulo Ricardo Pacheco Rodrigues Trezentos. Recommendation system for modern television. Master's dissertation, 2015 [Biblios]

Vítor Martins, Francisco José Moreira Couto, Paulo Ricardo Pacheco Rodrigues Trezentos. Towards an engaging social TV on a second screen. Master's dissertation, 2015 [Biblios]

André Leal, Francisco José Moreira Couto, Bruno Emanuel da Graça Martins. Recognition and normalization of biomedical entities within clinical notes. Master's dissertation, 2015 [Biblios]

Luís Oliveira, António Emanuel Magalhães Duarte Pereira dos Santos, Francisco José Moreira Couto. Desenvolvimento de Aplicação Web de Pesquisa, Gestão e Partilha de Eventos. Master's dissertation, 2015 [Biblios]

Maria Fernandes, João Pedro de Magalhães, Francisco M. Couto. Anti and Pro-longevity Genes Differentiation and Overlap with Age-related Diseases. Master's dissertation, 2015 [Biblios]

Luis Simões, Ana Rita Fialho Grosso, Francisco José Moreira Couto. Assessing pseudogene expression during neural differentiation by RNA-Seq. Master's dissertation, 2015 [Biblios]

Miguel Gomes, André Maria da Silva Dias Moitinho de Almeida, Francisco José Moreira Couto. 3D Visualization of Very Large Databases – Integrating and expanding the state of the art in Bioinformatics and Astroinformatics. Master's dissertation, 2015 [Biblios]

Natacha Leitão, Francisco José Moreira Couto, João Carlos Antunes Leitão. Development of a scalable, precise, and high-coverage genomics mapping tool for NGS. Master's dissertation, 2015 [Biblios]

Hugo Bastos, Francisco José Moreira Couto, Luka Alexander Clarke. Functional coherence and annotation agreement metrics for enzyme families. PhD thesis, 2015 [Biblios]

Daniel Faria, Catarina Martins, A. Nanavaty, Daniela Oliveira, B. S. Balasubramani, A. Taheri, Cátia Pesquita, Francisco Couto, Isabel Cruz. AML results for OAEI 2015, 2015 [Biblios]

Alastair Francisco Couto, Janna Hastings. Proocedings of the International Conference on Biomedical Ontologies (ICBO), 2015 [Biblios]

Carlos Barata, Mónica Abreu, Pedro Torres, Jorge Teixeira, Tiago Guerreiro, Francisco Couto. Social impact – identifying quotes of literary works in social networks. In 17th Portuguese Conference on Artificial Intelligence (EPIA), 2015 [Biblios]

André Leal, Bruno Martins, Francisco Couto. Recognition and normalization of biomedical entities based on ontologies. In Bioinformatics Open Days, 2015 [Biblios]

Francisco Couto. Metarate – incentivize data integration and sharing by rating and rewarding metadata annotation. In European Data Forum (EDF), 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 Lamurias, V. Pedro, L. Clarke, Francisco Couto. Annotating biomedical terms in electronic health records using crowd-sourcing. In International Conference on Biomedical Ontologies (ICBO), 2015 [Biblios]

André Lamúrias, Manuel Lobo, M. Antunes, L. Clarke, Francisco Couto. Identifying chemical entities in patents using brown clustering and semantic similarity. In 5th BioCreative Challenge Evaluation, 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]

Tudor Groza, Sebastian Kohler, Sandra Doelken, Nigel Collier, Anika Oellrich, Damian Smedley, Francisco M. Couto, Gareth Baynam, Andreas Zankl, Peter N. Robinson. Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora. DATABASE (OXFORD), 2015( bav005):1-13, 2015 [Biblios]

Martin Krallinger, Obdulia Rabal, Florian Leitner, Miguel Vazquez, David Salgado, Zhiyong Lu, Robert Leaman, Yanan Lu, Donghong Ji, Daniel M. Lowe, Roger A. Sayle, Riza Theresa Batista-Navarro, Rafal Rak, Torsten Huber, Tim Rocktäschel, Sérgio Matos, David Campos, Buzhou Tang, Hua Xu, Tsendsuren Munkhdalai, Keun Ho Ryu, S.V. Ramanan, Senthil Nathan, Slavko Žitnik, Marko Bajec, Lutz Weber, Matthias Irmer, Saber A. Akhondi, Jan A. Kors, Shuo Xu, Xin An, Utpal Kumar Sikdar, Asif Ekbal, Masaharu Yoshioka, Thaer M. Dieb, Miji Choi, Karin Verspoor, Madian Khabsa, C. Lee Giles, Hongfang Liu, Komandur Elayavilli Ravikumar, André Lamúrias, Francisco M. Couto, Hong-Jie Dai, Richard Tzong-Han Tsai, Caglar Ata, Tolga Can, Anabel Usié, Rui Alves, Isabel Segura-Bedmar, Paloma Martínez, Julen Oyarzabal, Alfonso Valencia. The CHEMDNER corpus of chemicals and drugs and its annotation principles. JOURNAL OF CHEMINFORMATICS, 7(1):1-20, 2015 [Biblios]

Emanuel Santos, Daniel Faria, Cátia Pesquita, Francisco Couto. Ontology alignment repair through modularization and confidence-based heuristics. PLOS ONE, 10(12):1-19, 2015 [Biblios]

Cátia Machado, Dietrich Rebholz-Schuhmann, Ana Freitas, Francisco Couto. The semantic web in translational medicine: current applications and future directions. BRIEFINGS IN BIOINFORMATICS, 16(1):89-103, 2015 [Biblios]

André Lamúrias, João Ferreira, Francisco Couto. Improving chemical entity recognition through h-index based semantic similarity. JOURNAL OF CHEMINFORMATICS, 7(1):1-20, 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]

Costa, Miguel Ângelo Leal da, Silva, Mário J. Gaspar da, Couto, Francisco José Moreira. Information Search in Web Archives. PhD thesis, 2014 [Biblios]

Machado, Cátia Maria, Couto, Francisco José Moreira, Freitas, Ana Teresa. Knowledge representation for data integration and exploration in translational medicine. PhD thesis, 2014 [Biblios]

Silva, Mickael Santos da, Carriço, João André Nogueira Custódio, Couto, Francisco José Moreira. NGSOnto – Proposta de uma ontologia para descrever o processo de Sequenciação de Alto Desempenho. Master's dissertation, 2014 [Biblios]

Lamúrias, André Francisco Martins, Couto, Francisco José Moreira . Identifying interactions between chemical entities in text. Master's dissertation, 2014 [Biblios]

Barata, Carlos André Freitas, Couto, Francisco José Moreira, Guerreiro, Tiago. Impacto de obras literárias nas redes sociais. Master's dissertation, 2014 [Biblios]

Carilho, José Alberto Barreto Duarte, Guerreiro, Tiago, Couto, Francisco José Moreira. Towards an intelligent biographical cognitive prosthesis. Master's dissertation, 2014 [Biblios]

José Carilho, Oliver Schnell, João Martins, Luís Carriço, Carlos Duarte, Francisco M Couto, Tiago Guerreiro. Predicting Relevant Events in the Life of a Person with Alzheime. In Bioinformatics Open Days, 2014 [Biblios]

Richard Norman, Francisco M Couto. Using Google Scholar to predict self-citation: A case study in health economics, 2014 [Biblios]

Daniel Faria, Cátia Pesquita, Emanuel Santos, Isabel Cruz, Francisco Couto. Automatic Background Knowledge Selection for Matching Biomedical Ontologies. PLOS ONE, 9(11), 2014 [Biblios]

Catia Pesquita, Michelle Cheatham, Daniel Faria, Joana Barros, Emanuel Santos, Francisco M. 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 at ISWC 2014, 2014 [Biblios]

Tiago Mendes, Bruno Rodrigues, André Moitinho, Miguel Gomes, Francisco Couto, Tiago Guerreiro, Alberto Krone-Martins. Exploração visual online de bases de dados astronómicas. In 6th Simpósio de Informática (INFORUM), 2014 [Biblios]

Andre Leal Diogo Gonçalves, Bruno Martins, Francisco Couto. Ulisboa: Identification and classification of medical concepts. In 7th International Workshop on Semantic Evaluation (SemEval), 2014 [Biblios]

Daniel Faria, Cátia Pesquita, Emanuel Santos, Isabel Cruz, Francisco Couto. AgreementMakerLight: A Scalable Automated Ontology Matching System. In DILS 2014, 2014 [Biblios]

Daniel Faria, E. Jiménez-Ruiz, Cátia Pesquita, Emanuel Santos, Francisco Couto. Towards annotating potential incoherences in BioPortal mappings. In 13th International Semantic Web Conference (ISWC), pages 17-32, 2014 [Biblios]

João Martins, José Carilho, Oliver Schnell, Carlos Duarte, Francisco M. Couto, Luís Carriço, Tiago Guerreiro. Friendsourcing the unmet needs of people with dementia. In 11th Web for All Conference (W4A '14), 2014 [Biblios]

Hugo P. Bastos, Luka A. Clarke, Francisco M. Couto. Annotation extension through protein family annotation coherence metrics. Frontiers in Genetics, 4, Frontiers Media SA, 2013 [Biblios]

Vera Maria Leal Carvalho, Couto, Francisco José Moreira, Hansen, Martin Asser. Metagenomic analysis of Mariana Trench sediment samples. Master's dissertation, 2013 [Biblios]

Tiago Filipe Francisco Santos, Catita, Cristina Maria Sousa, Couto, Francisco José Moreira. Implementação de uma Base de Dados Geográficos para a Gestão das Matérias-Primas do grupo Cimpor. Master's dissertation, 2013 [Biblios]

André Filipe Agostinho Lopes, Couto, Francisco José Moreira, Silva, Mário J. Gaspar da. A tool for ontology instance matching. Master's dissertation, 2013 [Biblios]

Tiago Daniel Pereira Grego, Couto, Francisco José Moreira. Identifying Chemical Entities on Literature: a Machine Learning Approach using Dictionaries as Domain Knowledge. PhD thesis, 2013 [Biblios]

Francisco Couto, Daniel Faria, Bruno Tavares, Pedro Gonçalves, Paulo Verissimo. Benchmarking some portuguese S&T system research units: 2nd edition, 2013 [Biblios]

Emanuel Santos, Daniel Faria, Cátia Pesquita, Francisco Couto. Ontology alignment repair through modularization and confidence-based heuristics, 2013 [Biblios]

Mário Silva, C. Vaz, A. Francisco, M. Ramirez, Francisco Couto, 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), 2013 [Biblios]

João Ferreira, Francisco Couto. Semantic similarity in the biomedical domain. In Molecular Biology in Portugal and EMBL (and EMBL Alumni), 2013 [Biblios]

C. Alonso, Francisco Couto, 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), 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]

S. Moreira, J. Filgueiras, Bruno Martins, Francisco Couto, Mário Silva. REACTION: A naive machine learning approach for sentiment classification. 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]

João Ferreira, Cátia Pesquita, Francisco Couto, Mário Silva. Digital preservation of epidemic resources: coupling metadata and ontologies. In 10th International Conference on Preservation of Digital Objects, 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, Emanuel Santos, Francisco 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 [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]

André Lamurias, Tiago Grego, Francisco Couto. Chemical compound and drug name recognition using crfs and semantic similarity based on chebi. In 4th BioCreative Challenge Evaluation, 2013 [Biblios]

Tiago Grego, Francisco Couto. Enhancement of chemical entity identification in text using semantic similarity validation. PLOS ONE, 8(5), 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 Ferreira, J. Hastings, Francisco Couto. Exploiting disjointness axioms to improve semantic similarity measures. BIOINFORMATICS, 29(21):2781-2787, 2013 [Biblios]

Hugo Bastos, L. Clarke, Francisco Couto. Annotation extension through protein family annotation coherence metrics, 2013 [Biblios]

Francisco Couto, H. Pinto. The next generation of similarity measures that fully explore the semantics in biomedical ontologies. JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 11(5):1-12, 2013 [Biblios]

Cátia Machado, A. Freitas, Francisco Couto. Enrichment analysis applied to disease prognosis. JOURNAL OF BIOMEDICAL SEMANTICS, 4(21), 2013 [Biblios]

Daniel Faria, Cátia Pesquita, Emanuel Santos, Francisco Couto, C. Stroe, Isabel Cruz. Testing the AgreementMaker system in the anatomy task of OAEI 2012, 2012 [Biblios]

Catia Pesquita, Francisco M. Couto. Predicting the Extension of Biomedical Ontologies. PLOS COMPUTATIONAL BIOLOGY, 9(8), 2012 [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]

Tiago Grego, Catia Pesquita, Hugo Bastos, Francisco M. Couto. Chemical Entity Recognition and Resolution to ChEBI, 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]

Francisco M Couto, João D Ferreira, João Zamite, Carlos Santos, Tiago Posse, Paulo Graça, Dulce Domingos, Mário J Silva. The Epidemic Marketplace Platform: towards semantic characterization of epidemiological resources using biomedical ontologies. In International Conference on Biomedical Ontologies,, 2012 [Biblios]

H. Bastos, F. Couto, P. Coutinho. Exploring gene ontology relationships in enzyme families: An application to polysaccharide lyases. In 9th Carbohydrate Bioengineering Meeting (CBM9), 2011 [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]

João Ferreira, David Batista, Francisco Couto, Mário J. Silva. The Geo-Net- PT/Yahoo! GeoPlanet (TM) concordance, 2010 [Biblios]

Tiago Grego, João D. Ferreira, Cátia Pesquita, Hugo Bastos, Diogo Vila Viçosa, João Freire, Francisco Couto. Chemical and Metabolic Pathway SemanticSimilarity, 2010 [Biblios]

Fabrício A.B. Silva, Mário J. Silva, Francisco Couto. Epidemic Marketplace: an e-Science Platform for Epidemic Modelling and Analysis, 2010 [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 Pesquita, Cosmin Stroe, Isabel F. Cruz, Francisco Couto. BLOOMS on AgreementMaker: results for OAEI 2010. In ISWC Workshop on Ontology Matching, 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]

Patricia Gomes-Alves, Francisco Couto, Cátia Pesquita, AV Coelho, Deborah 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, 1804(4):856-865, 2010 [Biblios]

João D. Ferreira, Francisco Couto. Semantic similarity for automatic classification of chemical compounds. PLOS COMPUTATIONAL BIOLOGY, 6(9), 2010 [Biblios]

Luis Filipe Lopes, João Zamite, Bruno Tavares, Francisco Couto, Fabrício A.B. Silva, Mário J. Silva. Automated Social Network Epidemic Data Collector. In INForum - Simpósio de Informática 2009 , 2009 [Biblios]

Hugo Bastos, Tiago Grego, Francisco Couto, Pedro M. Coutinho. Enzyme family coherence assessment: validation and prediction. In JB'2009 - Challenges in Bioinformatics , 2009 [Biblios]

Ana Teixeira, Rui C Santos, Francisco Couto. ThermInfo: Collecting and Presenting Thermochemical Properties. In INForum - Simpósio de Informática 2009 , 2009 [Biblios]

Tiago Grego, Piotr Pezik, Francisco Couto, Dietrich Rebholz-Schuhmann. Identification of Chemical Entities in Patent Documents. In 3rd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB'09), 2009 [Biblios]

Daniel Faria, Catia Pesquita, Francisco Couto, André Falcão. GOclasses: molecular function as viewed by proteins. In BioOntologies SIG at ISMB/ECCB - 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) , 2009 [Biblios]

Catia Pesquita, Tiago Grego, Francisco M. Couto. Identifying Gene Ontology Areas for Automated Enrichment. In 3rd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB'09), 2009 [Biblios]

Catia Pesquita, Francisco Couto. GO where we need it to go: focused automated enrichment of the Gene Ontology.Student Council Symposium. In Student Council Symposium at ISMB/ECCB 2009, 2009 [Biblios]

Catia Pesquita, Delphine Pessoa, Daniel Faria, Francisco Couto. Collaborative Evaluation of GO-based Similarity Measures. In 12th Annual Bio-Ontologies Meeting at ISMB/ECCB 2009, 2009 [Biblios]

Catia Pesquita, Daniel Faria, Rui Lopes, Francisco M. Couto. Measuring coherence between electronic and manual annotations in biological databases. In SAC '09: Proceedings of the 2009 ACM Symposium on Applied Computing 2009, 2009 [Biblios]

Catia Machado, Hugo Bastos, Francisco Couto. GREAT: Gene Regulation EvAluation Tool. In 3rd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB'09) , 2009 [Biblios]

Cátia Pesquita, Daniel Faria, André O. Falcão, P. Lord, Francisco M. Couto. Semantic Similarity in Biomedical Ontologies. PLOS COMPUTATIONAL BIOLOGY, 5(7), 2009 [Biblios]

P.M. Coutinho, C. Rancurel, M. Stam, T. Bernard, Francisco Couto, E.G.J. Danchin, B. Henrissat. Carbohydrate-Active Enzymes Database: Principles and Classification of Glycosyltransferases, In In Bioinformatics for Glycobiology and Glycomics . Wiley, 2009 [Biblios]

Francisco M. Couto, Mário J. Silva. Biomedical research line of LASIGE, 2008 [Biblios]

Francisco Couto, Tiago Grego, Catia Pesquita, Hugo Bastos, R. Torres, P. Sanchez, L. Pascual, C. Blaschke. Identifying Bioentity Recognition Errors of Rule-Based Text-Mining Systems. In IEEE Third International Conference on Digital Information Management (ICDIM), 2008 [Biblios]

Catia Pesquita, Daniel Faria, Hugo Bastos, António Ferreira, André Falcão, Francisco Couto. Metrics for GO based protein semantic similarity: a systematic evaluation. BMC BIOINFORMATICS, 5(9), 2008 [Biblios]

Catia Pesquita, Daniel Faria, Tiago Grego, Francisco Couto, Mário J. Silva. Untangling BioOntologies for Mining Biomedical Information. Idea Group Inc., 2008 [Biblios]

Francisco M. Couto, Tiago Grego, Rafael Torres, Pablo Sanchez, Leandro Pascual, Christian Blaschke. Filtering Bioentity Recognition Errors in Bioliterature using a Casebased Approach. In ISMB/ECCB, 2007 [Biblios]

Cátia Pesquita, Daniel Faria, Hugo Bastos, André O. Falcão, Francisco M. Couto. Evaluating GO-based Semantic Similarity Measures. In ISMB/ECCB 2007, 2007 [Biblios]

Francisco Couto, Mário J. Silva, Pedro M. Coutinho. Measuring semantic similarity between gene ontology terms. DATA & KNOWLEDGE ENGINEERING, 61(1):137-152, 2007 [Biblios]

Francisco Couto, Mário J. Silva, V. Lee, E. Dimmer, E. Camon, R. Apweiler, H. Kirsch, D. Rebholz-Schuhmann. GOAnnotator: linking electronic protein GO annotation to evidence text, 2005 [Biblios]

Francisco Couto, Mário J. Silva, Pedro M. Coutinho. Validation of Automated Protein Annotation, 2005 [Biblios]

Francisco Couto, Mário J. Silva, Pedro Fernandes. Bioinformatics: Knowledge Discovery in Biology, 2005 [Biblios]

Pooja Jain, Francisco Couto, Mário J. Silva, Jorg D. Becker. Literature Based Functional Annotation of Genes. In BKDB2005 – Bioinformatics: knowledge discovery in biology, 2005 [Biblios]

Francisco Couto, Mário J. Silva, Pedro Coutinho. Semantic Similarity over the Gene Ontology: Family Correlation and Selecting Disjunctive Ancestors. In ACM CIKM 05 - Conference in Information and Knowledge Management, 2005 [Biblios]

Francisco Couto, Mário J. Silva, Pedro Coutinho. Finding Genomic Ontology Terms in Text using Evidence Content. BMC BIOINFORMATICS, 6(1), 2005 [Biblios]

D. Rebholz-Schuhmann, H. Kirsch, Francisco Couto. Facts from text: Is Text Mining ready to deliver?. PLOS BIOLOGY, 3(2), 2005 [Biblios]

Francisco Couto, Mário J. Silva. Mining the BioLiterature: towards automatic annotation of genes and proteins. Idea Group Inc., 2005 [Biblios]

Francisco Couto, Bruno Martins, Mário J. Silva, Pedro Coutinho. Classifying Biomedical Articles using Web Resources. In 19th ACM Symposium on Applied Computing (SAC), 2004 [Biblios]

Francisco Couto, Mário J. Silva, Pedro Coutinho. FiGO: Finding GO terms in unstructured text. In Critical Assessment of Information Extraction systems in Biology (BioCreative), 2004 [Biblios]

Francisco Couto, Bruno Martins, Mário J. Silva, Pedro Coutinho. Classifying Biomedical Articles using Web Resources: application to KDD Cup 02, 2003 [Biblios]

Francisco Couto, Mário J. Silva, Pedro Coutinho. Implementation of a Functional Semantic Similarity Measure between Gene-Products, 2003 [Biblios]

Francisco Couto, Mário J. Silva. Bioinformática – Exploração da Informação, 2003 [Biblios]

Francisco Couto, Mário J. Silva, Pedro Coutinho. Improving Information Extraction through Biological Correlation. In Data Mining and Text Mining for Bioinformatics Workshop at the ECML/PKDD2003, 2003 [Biblios]

Francisco Couto, Mário J. Silva, Pedro Coutinho. ReBIL: Relating Biological Information through Literature. In Intelligent Systems for Molecular Biology (ISMB), 2003 [Biblios]

Francisco Couto, Mário J. Silva, Pedro Coutinho. Curating Extracted Information through the Correlation between Structure and Function. In Third meeting of the special interest group on Text Mining at the Intelligent Systems for Molecular Biology (ISMB), 2003 [Biblios]

Francisco Couto, Mário J. Silva, Pedro Coutinho. ProFAL: PROtein Functional Annotation through Literature. In JISBD 2003 - VIII Jornadas de Ingeniería del Software y Bases de Datos, 2003 [Biblios]

Francisco Couto, Pooja Jain, Mário J. Silva, Pedro Coutinho. ReBIL: Relating Biological Information through Literature. In 1rst Annual Meeting of Portuguese Proteomic Network - ProCura: Functional Genomics And Proteomics, 2003 [Biblios]