ProFAL: PROtein Functional Annotation through Literature. - Francisco M. Couto; Mário J. Silva; Pedro Coutinho 001 (JISBD, 2003)

Classifying biological articles using web resources. - Francisco M. Couto; Bruno Martins 001; Mário J. Silva (SAC, 2004)

Semantic similarity over the gene ontology: family correlation and selecting disjunctive ancestors. - Francisco M. Couto; Mário J. Silva; Pedro Coutinho 001 (CIKM, 2005)

Finding genomic ontology terms in text using evidence content. - Francisco M. Couto; Mário J. Silva; Pedro Coutinho 001 (BMC Bioinform., 2005)

Validating associations in biological databases. - Francisco M. Couto; Mário J. Silva; Pedro Coutinho 001 (CIKM, 2006)

ReBIL: Relating Biological Information through Literature - Francisco M. Couto (2006)

Measuring semantic similarity between Gene Ontology terms. - Francisco M. Couto; Mário J. Silva; Pedro Coutinho 001 (Data Knowl. Eng., 2007)

Identifying bioentity recognition errors of rule-based text-mining systems. - Francisco M. Couto; Tiago Grego; Hugo P. Bastos; Catia Pesquita; Rafael P. Torres; Pablo Sanchez; Leandro Pascual; Christian Blaschke (ICDIM, 2008)

Metrics for GO based protein semantic similarity: a systematic evaluation. - Catia Pesquita; Daniel Faria; Hugo P. Bastos; António E. N. Ferreira; André O. Falcão; Francisco M. Couto (BMC Bioinform., 2008)

Verification of Uncurated Protein Annotations. - Francisco M. Couto; Mário J. Silva; Vivian Lee; Emily Dimmer; Evelyn Camon; Rolf Apweiler (Information Retrieval in Biomedicine, 2009)

Identification of Chemical Entities in Patent Documents. - Tiago Grego; Piotr Pezik; Francisco M. Couto; Dietrich Rebholz-Schuhmann (IWANN (2), 2009)

GREAT: Gene Regulation EvAluation Tool. - Catia M. Machado; Hugo P. Bastos; Francisco M. Couto (IWANN (2), 2009)

Identifying Gene Ontology Areas for Automated Enrichment. - Catia Pesquita; Tiago Grego; Francisco M. Couto (IWANN (2), 2009)

Measuring coherence between electronic and manual annotations in biological databases. - Catia Pesquita; Daniel Faria; Francisco M. Couto (SAC, 2009)

Semantic Similarity in Biomedical Ontologies. - Catia Pesquita; Daniel Faria; André O. Falcão; Phillip W. Lord; Francisco M. Couto (PLoS Comput. Biol., 2009)

Semantic characterization of hypertrophic cardiomyopathy disease. - Catia M. Machado; Francisco M. Couto; Alexandra R. Fernandes; Susana Santos; Nuno Cardim; Ana T. Freitas (BIBM Workshops, 2010)

Geographic signatures for semantic retrieval. - David S. Batista; Mário J. Silva; Francisco M. Couto; Bibek Behera (GIR, 2010)

Epidemic Marketplace: An Information Management System for Epidemiological Data. - Luis F. Lopes; Fabrício A. B. da Silva; Francisco M. Couto; João Zamite; Hugo Alexandre Ferreira; Carla Sousa; Mário J. Silva (ITBAM, 2010)

BLOOMS on AgreementMaker: results for OAEI 2010. - Catia Pesquita; Cosmin Stroe; Isabel F. Cruz; Francisco M. Couto (OM, 2010)

Unraveling Hypertrophic Cardiomyopathy Variability. - Catia M. Machado; Francisco M. Couto; Alexandra R. Fernandes; Susana Santos; Nuno Cardim; Ana T. Freitas (ERCIM News, 2010)

Epidemic Marketplace: An e-Science Platform for Epidemic Modelling and Analysis. - Fabrício A. B. da Silva; Mário J. Silva; Francisco M. Couto (ERCIM News, 2010)

Semantic Similarity for Automatic Classification of Chemical Compounds. - João D. Ferreira; Francisco M. Couto (PLoS Comput. Biol., 2010)

Biomedical Ontology Matching Using the AgreementMaker System. - Isabel F. Cruz; Cosmin Stroe; Catia Pesquita; Francisco M. Couto; Valerie Cross (ICBO, 2011)

Generic Semantic Relatedness Measure for Biomedical Ontologies. - João D. Ferreira; Francisco M. Couto (ICBO, 2011)

Where GO is Going and What it Means for Ontology Extension. - Catia Pesquita; Francisco M. Couto (ICBO, 2011)

The Biomedical Ontology Applications (BOA) Framework. - Bruno Tavares; Hugo P. Bastos; Daniel Faria; João D. Ferreira; Tiago Grego; Catia Pesquita; Francisco M. Couto (ICBO, 2011)

Using AgreementMaker to align ontologies for OAEI 2011. - Isabel F. Cruz; Cosmin Stroe; Federico Caimi; Alessio Fabiani; Catia Pesquita; Francisco M. Couto; Matteo Palmonari (OM, 2011)

REACTION at the Entity Linking task in KBP 2011. - David S. Batista; Silvio Moreira; Mário J. Silva; Paula Carvalho 001; Francisco M. Couto (TAC, 2011)

Disjunctive shared information between ontology concepts: application to Gene Ontology. - Francisco M. Couto; Mário J. Silva (J. Biomed. Semant., 2011)

MEDCollector: Multisource Epidemic Data Collector. - João Zamite; Fabrício A. B. da Silva; Francisco M. Couto; Mário J. Silva (Trans. Large Scale Data Knowl. Centered Syst., 2011)

The Epidemic Marketplace Platform: towards semantic characterization of epidemiological resources using biomedical ontologies. - Francisco M. Couto; João D. Ferreira; João Zamite; Carlos Santos; Tiago Posse; Paulo M. L. A. Graça; Dulce Domingos; Mário J. Silva (ICBO, 2012)

Bringing epidemiology into the Semantic Web. - João D. Ferreira; Catia Pesquita; Francisco M. Couto; Mário J. Silva (ICBO, 2012)

Identifying Chemical Entities based on ChEBI. - Tiago Grego; Francisco R. Pinto; Francisco M. Couto (ICBO, 2012)

Toward a Translational Medicine Approach for Hypertrophic Cardiomyopathy. - Catia M. Machado; Francisco M. Couto; Alexandra R. Fernandes; Susana Santos; Ana T. Freitas (ITBAM, 2012)

Toponym Disambiguation Using Ontology-Based Semantic Similarity. - David S. Batista; João D. Ferreira; Francisco M. Couto; Mário J. Silva (PROPOR, 2012)

Testing the AgreementMaker System in the Anatomy Task of OAEI 2012 - Daniel Faria; Catia Pesquita; Emanuel Santos; Francisco M. Couto; Cosmin Stroe; Isabel F. Cruz (CoRR, 2012)

Predicting the Extension of Biomedical Ontologies. - Catia Pesquita; Francisco M. Couto (PLoS Comput. Biol., 2012)

Digital preservation of epidemic resources: coupling metadata and ontologies. - João D. Ferreira; Catia Pesquita; Francisco M. Couto; Mário J. Silva (iPRES, 2013)

The AgreementMakerLight Ontology Matching System. - Daniel Faria; Catia Pesquita; Emanuel Santos; Matteo Palmonari; Isabel F. Cruz; Francisco M. Couto (OTM Conferences, 2013)

LASIGE: using Conditional Random Fields and ChEBI ontology. - Tiago Grego; Francisco R. Pinto; Francisco M. Couto (SemEval@NAACL-HLT, 2013)

REACTION: A naive machine learning approach for sentiment classification. - Silvio Moreira; João Filgueiras; Bruno Martins 001; Francisco M. Couto; Mário J. Silva (SemEval@NAACL-HLT, 2013)

AgreementMakerLight results for OAEI 2013. - Daniel Faria; Catia Pesquita; Emanuel Santos; Isabel F. Cruz; Francisco M. Couto (OM, 2013)

To repair or not to repair: reconciling correctness and coherence in ontology reference alignments. - Catia Pesquita; Daniel Faria; Emanuel Santos; Francisco M. Couto (OM, 2013)

What's in a 'nym'? Synonyms in Biomedical Ontology Matching. - Catia Pesquita; Daniel Faria; Cosmin Stroe; Emanuel Santos; Isabel F. Cruz; Francisco M. Couto (ISWC (1), 2013)

A survey of web archive search architectures. - Miguel Costa; Daniel Gomes; Francisco M. Couto; Mário J. Silva (WWW (Companion Volume), 2013)

Exploiting disjointness axioms to improve semantic similarity measures. - João D. Ferreira; Janna Hastings; Francisco M. Couto (Bioinform., 2013)

Enrichment analysis applied to disease prognosis. - Catia M. Machado; Ana T. Freitas; Francisco M. Couto (J. Biomed. Semant., 2013)

CIDS country rankings: comparing documents and citations of USA, UK and China top researchers. - Francisco M. Couto (CoRR, 2013)

Ontology alignment repair through modularization and confidence-based heuristics. - Emanuel Santos; Daniel Faria; Catia Pesquita; Francisco M. Couto (CoRR, 2013)

Benchmarking some Portuguese S&T system research units - Francisco M. Couto; Daniel Faria; Bruno Tavares; Pedro Gonçalves; Paulo Veríssimo (CoRR, 2013)

The Next Generation of Similarity Measures that Fully Explore the Semantics in Biomedical Ontologies. - Francisco M. Couto; Helena Sofia Pinto (J. Bioinform. Comput. Biol., 2013)

Tracking politics with POWER. - Silvio Moreira; David S. Batista; Paula Carvalho 001; Francisco M. Couto; Mário J. Silva (Program, 2013)

Towards Visualizing the Alignment of Large Biomedical Ontologies. - Catia Pesquita; Daniel Faria; Emanuel Santos; Jean-Marc Neefs; Francisco M. Couto (DILS, 2014)

Chemical Named Entity Recognition: Improving Recall Using a Comprehensive List of Lexical Features. - Andre Lamurias; João D. Ferreira; Francisco M. Couto (PACBB, 2014)

ULisboa: Identification and Classification of Medical Concepts. - André Leal; Diogo Gonçalves 002; Bruno Martins 001; Francisco M. Couto (SemEval@COLING, 2014)

Rating, Recognizing and Rewarding Metadata Integration and Sharing on the Semantic Web. - Francisco M. Couto (URSW, 2014)

Towards Annotating Potential Incoherences in BioPortal Mappings. - Daniel Faria; Ernesto Jiménez-Ruiz; Catia Pesquita; Emanuel Santos; Francisco M. Couto (ISWC (2), 2014)

AgreementMakerLight results for OAEI 2014. - Daniel Faria; Catarina Martins; Amruta Nanavaty; Aynaz Taheri; Catia Pesquita; Emanuel Santos; Isabel F. Cruz; Francisco M. Couto (OM, 2014)

AgreementMakerLight 2.0: Towards Efficient Large-Scale Ontology Matching. - Daniel Faria; Catia Pesquita; Emanuel Santos; Isabel F. Cruz; Francisco M. Couto (ISWC (Posters & Demos), 2014)

Building reference alignments for compound matching of multiple ontologies using OBO cross-products. - Catia Pesquita; Michelle Cheatham; Daniel Faria; Joana Barros; Emanuel Santos; Francisco M. Couto (OM, 2014)

Learning temporal-dependent ranking models. - Miguel Costa; Francisco M. Couto; Mário J. Silva (SIGIR, 2014)

Friendsourcing the unmet needs of people with dementia. - João Martins; José Carilho; Oliver Schnell; Carlos Duarte; Francisco M. Couto; Luís Carriço; Tiago João Guerreiro 001 (W4A, 2014)

The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources. - Catia Pesquita; João D. Ferreira; Francisco M. Couto; Mário J. Silva (J. Biomed. Semant., 2014)

Identifying interactions between chemical entities in biomedical text. - Andre Lamurias; João D. Ferreira; Francisco M. Couto (J. Integr. Bioinform., 2014)

Social Impact - Identifying Quotes of Literary Works in Social Networks. - Carlos Barata; Mónica Abreu; Pedro Torres 005; Jorge Teixeira; Tiago João Guerreiro 001; Francisco M. Couto (EPIA, 2015)

Annotating biomedical ontology terms in electronic health records using crowd-sourcing. - Andre Lamurias; Vasco Pedro; Luka A. Clarke; Francisco M. Couto (ICBO, 2015)

IICE: Web Tool for Automatic Identification of Chemical Entities and Interactions. - Andre Lamurias; Luka A. Clarke; Francisco M. Couto (ECML/PKDD (3), 2015)

ULisboa: Recognition and Normalization of Medical Concepts. - André Leal; Bruno Martins 001; Francisco M. Couto (SemEval@NAACL-HLT, 2015)

AML results for OAEI 2015. - Daniel Faria; Catarina Martins; Amruta Nanavaty; Daniela Oliveira 002; Booma Sowkarthiga; Aynaz Taheri; Catia Pesquita; Francisco M. Couto; Isabel F. Cruz (OM, 2015)

A High-Throughput Method to Detect Privacy-Sensitive Human Genomic Data. - Vinicius Vielmo Cogo; Alysson Bessani; Francisco M. Couto; Paulo Veríssimo (WPES@CCS, 2015)

The semantic web in translational medicine: current applications and future directions. - Catia M. Machado; Dietrich Rebholz-Schuhmann; Ana T. Freitas; Francisco M. Couto (Briefings Bioinform., 2015)

Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora. - Tudor Groza; Sebastian Köhler 001; Sandra C. Doelken; Nigel Collier; Anika Oellrich; Damian Smedley; Francisco M. Couto; Gareth Baynam; Andreas Zankl; Peter N. Robinson (Database J. Biol. Databases Curation, 2015)

The CHEMDNER corpus of chemicals and drugs and its annotation principles. - 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; et al. (J. Cheminformatics, 2015)

Improving chemical entity recognition through h-index based semantic similarity. - Andre Lamurias; João D. Ferreira; Francisco M. Couto (J. Cheminformatics, 2015)

Extraction of Regulatory Events using Kernel-based Classifiers and Distant Supervision. - Andre Lamurias; Miguel J. Rodrigues; Luka A. Clarke; Francisco M. Couto (BioNLP (Shared Task), 2016)

ULISBOA at SemEval-2016 Task 12: Extraction of temporal expressions, clinical events and relations using IBEnt. - Márcia Barros; Andre Lamurias; Gonçalo Figueiró; Marta Antunes; Joana Teixeira; Alexandre Pinheiro; Francisco M. Couto (SemEval@NAACL-HLT, 2016)

OAEI 2016 results of AML. - Daniel Faria; Catia Pesquita; Booma S. Balasubramani; Catarina Martins; João Cardoso 002; Hugo Curado; Francisco M. Couto; Isabel F. Cruz (OM@ISWC, 2016)

Functional coherence metrics in protein families. - Hugo P. Bastos; Lisete Sousa; Luka A. Clarke; Francisco M. Couto (J. Biomed. Semant., 2016)

A Flexible Recommendation System for Cable TV. - Diogo Gonçalves 002; Miguel Costa; Francisco M. Couto (CoRR, 2016)

A Large-Scale Characterization of User Behaviour in Cable TV. - Diogo Gonçalves 002; Miguel Costa; Francisco M. Couto (CoRR, 2016)

Knowledge Ratings in MetaboLights. - Camila Ramos; Marco Louro; Miguel Santos; Francisco M. Couto (CoRR, 2016)

WS4A: a Biomedical Question and Answering System based on public Web Services and Ontologies. - Miguel J. Rodrigues; Miguel Falé; Andre Lamurias; Francisco M. Couto (CoRR, 2016)

Anthropometric Data Analytics: A Portuguese Case Study. - António Barata; Lucília Carvalho; Francisco M. Couto (PACBB, 2017)

How Can Photo Sharing Inspire Sharing Genomes? - Vinicius Vielmo Cogo; Alysson Bessani; Francisco M. Couto; Margarida Gama-Carvalho; Maria Fernandes; Paulo Jorge Esteves Veríssimo (PACBB, 2017)

Cloud-Assisted Read Alignment and Privacy. - Maria Fernandes; Jérémie Decouchant; Francisco M. Couto; Paulo Jorge Esteves Veríssimo (PACBB, 2017)

Metadata Analyser: Measuring Metadata Quality. - Bruno Inácio; João D. Ferreira; Francisco M. Couto (PACBB, 2017)

ULISBOA at SemEval-2017 Task 12: Extraction and classification of temporal expressions and events. - Andre Lamurias; Diana F. Sousa; Sofia Pereira; Luka A. Clarke; Francisco M. Couto (SemEval@ACL, 2017)

MoRS at SemEval-2017 Task 3: Easy to use SVM in Ranking Tasks. - Miguel J. Rodrigues; Francisco M. Couto (SemEval@ACL, 2017)

Results of AML in OAEI 2017. - Daniel Faria; Booma S. Balasubramani; Vivek R. Shivaprabhu; Isabela Mott; Catia Pesquita; Francisco M. Couto; Isabel F. Cruz (OM@ISWC, 2017)

Impact of translation on named-entity recognition in radiology texts. - Luís Campos; Vasco Pedro; Francisco M. Couto (Database J. Biol. Databases Curation, 2017)

MRA - Proof of Concept of a Multilingual Report Annotator Web Application. - Luís Campos; Francisco M. Couto (CoRR, 2017)

Assessing Public Metabolomics Metadata, Towards Improving Quality. - João D. Ferreira; Bruno Inácio; Reza M. Salek; Francisco M. Couto (J. Integr. Bioinform., 2017)

Results of AML participation in OAEI 2018. - Daniel Faria; Catia Pesquita; Booma Sowkarthiga Balasubramani; Teemu Tervo; David Carriço; Rodrigo Garrilha; Francisco M. Couto; Isabel F. Cruz (OM@ISWC, 2018)

Tackling the challenges of matching biomedical ontologies. - Daniel Faria; Catia Pesquita; Isabela Mott; Catarina Martins; Francisco M. Couto; Isabel F. Cruz (J. Biomed. Semant., 2018)

Accurate filtering of privacy-sensitive information in raw genomic data. - Jérémie Decouchant; Maria Fernandes; Marcus Völp; Francisco M. Couto; Paulo Jorge Esteves Veríssimo (J. Biomed. Informatics, 2018)

MER: a shell script and annotation server for minimal named entity recognition and linking. - Francisco M. Couto; Andre Lamurias (J. Cheminformatics, 2018)

LasigeBioTM at MEDIQA 2019: Biomedical Question Answering using Bidirectional Transformers and Named Entity Recognition. - Andre Lamurias; Francisco M. Couto (BioNLP@ACL, 2019)

A Silver Standard Corpus of Human Phenotype-Gene Relations. - Diana F. Sousa; Andre Lamurias; Francisco M. Couto (NAACL-HLT (1), 2019)

AML and AMLC Results for OAEI 2019. - Daniel Faria; Catia Pesquita; Teemu Tervo; Francisco M. Couto; Isabel F. Cruz (OM@ISWC, 2019)

Using Research Literature to Generate Datasets of Implicit Feedback for Recommending Scientific Items. - Márcia Barros; André Moitinho; Francisco M. Couto (IEEE Access, 2019)

Multi-domain semantic similarity in biomedical research. - João D. Ferreira; Francisco M. Couto (BMC Bioinform., 2019)

PPR-SSM: personalized PageRank and semantic similarity measures for entity linking. - Andre Lamurias; Pedro Ruas; Francisco M. Couto (BMC Bioinform., 2019)

Using Neural Networks for Relation Extraction from Biomedical Literature. - Diana F. Sousa; Andre Lamurias; Francisco M. Couto (CoRR, 2019)

Semantic Similarity Definition. - Francisco M. Couto; Andre Lamurias (Encyclopedia of Bioinformatics and Computational Biology (1), 2019)

Text Mining for Bioinformatics Using Biomedical Literature. - Andre Lamurias; Francisco M. Couto (Encyclopedia of Bioinformatics and Computational Biology (1), 2019)

BO-LSTM: classifying relations via long short-term memory networks along biomedical ontologies. - Andre Lamurias; Diana F. Sousa; Luka A. Clarke; Francisco M. Couto (BMC Bioinform., 2019)

An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents. - Jiayuan He 002; Dat Quoc Nguyen; Saber A. Akhondi; Christian Druckenbrodt; Camilo Thorne; Ralph Hoessel; Zubair Afzal; Zenan Zhai; Biaoyan Fang; Hiyori Yoshikawa; Ameer Albahem; Jingqi Wang; et al. (CLEF (Working Notes), 2020)

Extreme Multi-Label Classification applied to the Biomedical and Multilingual Panorama. - André Neves; André Lamúrias; Francisco M. Couto (CLEF (Working Notes), 2020)

LasigeBioTM Team at CLEF2020 ChEMU Evaluation Lab: Named Entity Recognition and Event extraction from chemical reactions described in patents using BioBERT NER and RE. - Pedro Ruas; Andre Lamurias; Francisco M. Couto (CLEF (Working Notes), 2020)

Hybrid Semantic Recommender System for Chemical Compounds. - Márcia Barros; André Moitinho; Francisco M. Couto (ECIR (2), 2020)

Proposal of the First International Workshop on Semantic Indexing and Information Retrieval for Health from Heterogeneous Content Types and Languages (SIIRH). - Francisco M. Couto; Martin Krallinger (ECIR (2), 2020)

Report of the First International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages. - Francisco M. Couto; Martin Krallinger (SIIRH@ECIR, 2020)

Biomedical Question Answering using Extreme Multi-Label Classification and Ontologies in the Multilingual Panorama. - André Neves; André Lamúrias; Francisco M. Couto (SIIRH@ECIR, 2020)

Towards a Multilingual Corpus for Named Entity Linking Evaluation in the Clinical Domain. - Pedro Ruas; André Lamúrias; Francisco M. Couto (SIIRH@ECIR, 2020)

BiOnt: Deep Learning Using Multiple Biomedical Ontologies for Relation Extraction. - Diana F. Sousa; Francisco M. Couto (ECIR (2), 2020)

COVID-19: A Semantic-Based Pipeline for Recommending Biomedical Entities. - Márcia Barros; Andre Lamurias; Diana F. Sousa; Pedro Ruas; Francisco M. Couto (NLP4COVID@EMNLP, 2020)

DRecPy: A Python Framework for Developing Deep Learning-Based Recommenders. - Fábio Colaço; Márcia Barros; Francisco M. Couto (RecSys, 2020)

OAEI 2020 results for AML and AMLC. - Beatriz Lima; Daniel Faria; Francisco M. Couto; Isabel F. Cruz; Catia Pesquita (OM@ISWC, 2020)

LasigeBioTM at CANTEMIST: Named Entity Recognition and Normalization of Tumour Morphology Entities and Clinical Coding of Spanish Health-related Documents. - Pedro Ruas; André Neves; Vitor D. T. Andrade; Francisco M. Couto (IberLEF@SEPLN, 2020)

Generating Biomedical Question Answering Corpora From Q&A Forums. - Andre Lamurias; Diana F. Sousa; Francisco M. Couto (IEEE Access, 2020)

A hybrid approach toward biomedical relation extraction training corpora: combining distant supervision with crowdsourcing. - Diana F. Sousa; Andre Lamurias; Francisco M. Couto (Database J. Biol. Databases Curation, 2020)

Generating Scientific Question Answering Corpora from Q&A forums. - Andre Lamurias; Diana F. Sousa; Francisco M. Couto (CoRR, 2020)

Linking chemical and disease entities to ontologies by integrating PageRank with extracted relations from literature. - Pedro Ruas; Andre Lamurias; Francisco M. Couto (J. Cheminformatics, 2020)

ECIR 2020 workshops: assessing the impact of going online. - Sérgio Nunes 001; Suzanne Little; Sumit Bhatia; Ludovico Boratto; Guillaume Cabanac; Ricardo Campos 001; Francisco M. Couto; Stefano Faralli 001; Ingo Frommholz; Adam Jatowt; Alípio Jorge; Mirko Marras; et al. (SIGIR Forum, 2020)

DNA-SeAl: Sensitivity Levels to Optimize the Performance of Privacy-Preserving DNA Alignment. - Maria Fernandes; Jérémie Decouchant; Marcus Völp; Francisco M. Couto; Paulo Jorge Esteves Veríssimo (IEEE J. Biomed. Health Informatics, 2020)

Using Neural Networks for Relation Extraction from Biomedical Literature. - Diana F. Sousa; Andre Lamurias; Francisco M. Couto (Artificial Neural Networks, 3rd Edition, 2021)

Post-processing BioBERT And Using Voting Methods for Biomedical Question Answering. - Margarida M. Campos; Francisco M. Couto (CLEF (Working Notes), 2021)

LASIGE-BioTM at MESINESP2: entity linking with semantic similarity and extreme multi-label classification on Spanish biomedical documents. - Pedro Ruas; Vitor D. T. Andrade; Francisco M. Couto (CLEF (Working Notes), 2021)

Creating Recommender Systems Datasets in Scientific Fields. - Márcia Barros; Francisco M. Couto; Matilde Pato; Pedro Ruas (KDD, 2021)

AML and AMLC results for OAEI 2021. - Daniel Faria; Beatriz Lima; Marta Contreiras Silva; Francisco M. Couto; Catia Pesquita (OM@ISWC, 2021)

Lasige-BioTM at ProfNER: BiLSTM-CRF and contextual Spanish embeddings for Named Entity Recognition and Tweet Binary Classification. - Pedro Ruas; Vitor D. T. Andrade; Francisco M. Couto (SMM4H@NAACL-HLT, 2021)

Information Retrieval Using Machine Learning for Biomarker Curation in the Exposome-Explorer. - Andre Lamurias; Sofia Jesus; Vanessa Neveu; Reza M. Salek; Francisco M. Couto (Frontiers Res. Metrics Anal., 2021)

Hybrid semantic recommender system for chemical compounds in large-scale datasets. - Márcia Barros; André Moitinho; Francisco M. Couto (J. Cheminformatics, 2021)

NILINKER: Attention-based approach to NIL Entity Linking. - Pedro Ruas; Francisco M. Couto (J. Biomed. Informatics, 2022)

Biomedical Relation Extraction With Knowledge Graph-Based Recommendations. - Diana F. Sousa; Francisco M. Couto (IEEE J. Biomed. Health Informatics, 2022)

lasigeBioTM at SemEval-2023 Task 7: Improving Natural Language Inference Baseline Systems with Domain Ontologies. - Sofia I R. Conceição; Diana F. Sousa; Pedro Silvestre; Francisco M. Couto (SemEval@ACL, 2023)

Chapter Two - Security, privacy, and trust management in DNA computing. - Maria Fernandes; Jérémie Decouchant; Francisco M. Couto (Adv. Comput., 2023)

LASIGE and UNICAGE solution to the NASA LitCoin NLP Competition. - Pedro Ruas; Diana F. Sousa; André Neves; Carlos Cruz; Francisco M. Couto (CoRR, 2023)

K-RET: knowledgeable biomedical relation extraction system. - Diana F. Sousa; Francisco M. Couto (Bioinform., 2023)

DGH-GO: dissecting the genetic heterogeneity of complex diseases using gene ontology. - Muhammad Asif 009; Hugo F. M. C. Martiniano; Andre Lamurias; Samina Kausar; Francisco M. Couto (BMC Bioinform., 2023)

LLM Fine-Tuning With Biomedical Open-Source Data. - Christopher Anaya; Maria Fernandes; Francisco M. Couto (CLEF (Working Notes), 2024)

Hybrid X-Linker: Automated Data Generation and Extreme Multi-label Ranking for Biomedical Entity Linking. - Pedro Ruas; Fernando Gallego Donoso; Francisco J. Veredas 001; Francisco M. Couto (CoRR, 2024)

Survey on Recommender Systems for Biomedical Items in Life and Health Sciences. - Matilde Pato; Márcia Barros; Francisco M. Couto (ACM Comput. Surv., 2024)

Enhancing cross-encoders using knowledge graph hierarchy for medical entity linking in zero- and few-shot scenarios. - Fernando Gallego Donoso; Pedro Ruas; Francisco M. Couto; Francisco J. Veredas 001 (Knowl. Based Syst., 2025)