| 2021 | KDD | Creating Recommender Systems Datasets in Scientific Fields. | Mrcia Barros, Francisco M. Couto, Matilde Pato, Pedro Ruas |
| 2020 | ECIR | Hybrid Semantic Recommender System for Chemical Compounds. | Mrcia Barros, Andr Moitinho, Francisco M. Couto |
| 2020 | ECIR | 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 |
| 2020 | ECIR | 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 |
| 2020 | ECIR | Biomedical Question Answering using Extreme Multi-Label Classification and Ontologies in the Multilingual Panorama. | Andr Neves, Andr Lamrias, Francisco M. Couto |
| 2020 | ECIR | Towards a Multilingual Corpus for Named Entity Linking Evaluation in the Clinical Domain. | Pedro Ruas, Andr Lamrias, Francisco M. Couto |
| 2020 | ECIR | BiOnt: Deep Learning Using Multiple Biomedical Ontologies for Relation Extraction. | Diana F. Sousa, Francisco M. Couto |
| 2020 | EMNLP | COVID-19: A Semantic-Based Pipeline for Recommending Biomedical Entities. | Mrcia Barros, Andre Lamurias, Diana F. Sousa, Pedro Ruas, Francisco M. Couto |
| 2020 | RecSys | DRecPy: A Python Framework for Developing Deep Learning-Based Recommenders. | Fbio Colao, Mrcia Barros, Francisco M. Couto |
| 2019 | NAACL | A Silver Standard Corpus of Human Phenotype-Gene Relations. | Diana F. Sousa, Andre Lamurias, Francisco M. Couto |
| 2017 | PACBB | Anthropometric Data Analytics: A Portuguese Case Study. | Antnio Barata, Luclia Carvalho, Francisco M. Couto |
| 2017 | PACBB | How Can Photo Sharing Inspire Sharing Genomes? | Vinicius Vielmo Cogo, Alysson Bessani, Francisco M. Couto, Margarida Gama-Carvalho, Maria Fernandes, Paulo Jorge Esteves Verssimo |
| 2017 | PACBB | Cloud-Assisted Read Alignment and Privacy. | Maria Fernandes, Jrmie Decouchant, Francisco M. Couto, Paulo Jorge Esteves Verssimo |
| 2017 | PACBB | Metadata Analyser: Measuring Metadata Quality. | Bruno Incio, Joo D. Ferreira, Francisco M. Couto |
| 2015 | EPIA | Social Impact - Identifying Quotes of Literary Works in Social Networks. | Carlos Barata, Mnica Abreu, Pedro Torres, Jorge Teixeira, Tiago Joo Guerreiro, Francisco M. Couto |
| 2014 | PACBB | Chemical Named Entity Recognition: Improving Recall Using a Comprehensive List of Lexical Features. | Andre Lamurias, Joo D. Ferreira, Francisco M. Couto |
| 2014 | SIGIR | Learning temporal-dependent ranking models. | Miguel Costa, Francisco M. Couto, Mrio J. Silva |
| 2013 | WWW | A survey of web archive search architectures. | Miguel Costa, Daniel Gomes, Francisco M. Couto, Mrio J. Silva |
| 2009 | IWANN | Identification of Chemical Entities in Patent Documents. | Tiago Grego, Piotr Pezik, Francisco M. Couto, Dietrich Rebholz-Schuhmann |
| 2009 | IWANN | GREAT: Gene Regulation EvAluation Tool. | Catia M. Machado, Hugo P. Bastos, Francisco M. Couto |
| 2009 | IWANN | Identifying Gene Ontology Areas for Automated Enrichment. | Catia Pesquita, Tiago Grego, Francisco M. Couto |
| 2009 | SAC | Measuring coherence between electronic and manual annotations in biological databases. | Catia Pesquita, Daniel Faria, Francisco M. Couto |
| 2006 | CIKM | Validating associations in biological databases. | Francisco M. Couto, Mrio J. Silva, Pedro Coutinho |
| 2005 | CIKM | Semantic similarity over the gene ontology: family correlation and selecting disjunctive ancestors. | Francisco M. Couto, Mrio J. Silva, Pedro Coutinho |
| 2004 | SAC | Classifying biological articles using web resources. | Francisco M. Couto, Bruno Martins, Mrio J. Silva |