???global.info.a_carregar???
Francisco M. Couto is an associate professor with habilitation at the Universidade de Lisboa (Faculty of Sciences) and a researcher at LASIGE. He earned his PhD (2006) in Informatics, specializing in Bioinformatics, from the Universidade de Lisboa, after graduating (2000) and completing his master's (2001) in Informatics and Computer Engineering from IST. He served as an invited researcher at EBI, AFMB-CNRS, and BioAlma. His research bridges bioinformatics, knowledge management, and information retrieval, driving innovations in semantic similarity, named entity recognition and linking and relation extraction.. As of December 2025, he has authored 2 books; co-authored 12 chapters, 68 journal papers (48 Q1 Scimago), and 33 conference papers (10 core A/A*); and supervised 12 PhDs and 59 master's theses to completion. His publications have amassed 7,073 citations with an h-index of 39 on Google Scholar. Awards include the 2004 Young Engineer Innovation Prize from the Portuguese Engineers Guild and ULisboa/CGD Scientific Prizes (honorable mention 2017; winner 2018). He ranks among top Computer Science researchers on Research.com (2024/2025) and the global top 2% most cited scientists by Elsevier/Stanford (2025). He has shone in international challenges like BioCreative, BioASQ, SemEval, ACM KDD Cup, and OAEI, plus 7th place ($5,000 USD) in the 2022 LitCoin NLP Challenge with Unicage, fostering academia-industry ties to accelerate medical breakthroughs.
Read full resume ↓
Identification

Personal identification

Full name
Francisco Couto

Citation names

  • Couto, Francisco
  • Couto, Francisco M

Author identifiers

Ciência ID
AB14-EC64-0200
ORCID iD
0000-0003-0627-1496
Google Scholar ID
9_78rfMAAAAJ
Scopus Author Id
6603489917

Email addresses

  • fjcouto@ciencias.ulisboa.pt (Professional)

Addresses

  • LASIGE, Departamento de Informática, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Lisboa, Portugal (Professional)

Websites

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Exact Sciences - Computer and Information Sciences - Information Science

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Education
Degree Classification
2016/05/23
Concluded
 Informática (Título de Agregado)
Major in Engenharia Informática
Universidade de Lisboa Faculdade de Ciências, Portugal
 Aprovado por unanimidade
2006/05/04
Concluded
 Informática (Doutoramento)
Major in Bioinformática
Universidade de Lisboa Faculdade de Ciências, Portugal
"ReBIL: Relating Biological Information through Literature" (THESIS/DISSERTATION)
 Dinstinção e Louvor
2000/09/01 - 2001/07
Concluded
 Engenharia Informática e Computadores (Mestrado integrado)
Universidade de Lisboa Instituto Superior Técnico, Portugal
"Identificação de Componentes Reutilizáveis através de Especificações Formais" (THESIS/DISSERTATION)
 5 (escala de 0 a 5)
1995/09/01 - 2000/07/31
Concluded
 Engenharia Informática e Computadores (Licenciatura)
Universidade de Lisboa Instituto Superior Técnico, Portugal
 18
Affiliation

Science

Category
Host institution 		Employer
2001/09/01 - Current Researcher (Research) Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal
2016/01/01 - 2016/06/01 Visiting Researcher (Research) Bioalma, Spain
2003/01/01 - 2005/12/31 Visiting Researcher (Research) AFMB, France
2004/01/01 - 2004/06/01 Visiting Researcher (Research) European Bioinformatics Institute, United Kingdom

Teaching in Higher Education

Category
Host institution 		Employer
2013/12/31 - Current Associate Professor (University Teacher) Universidade de Lisboa Faculdade de Ciências, Portugal
2016 - 2019 Associate Professor (University Teacher) Universidade de Lisboa, Portugal
2013 - 2016 Associate Professor (University Teacher) Universidade de Lisboa Faculdade de Ciências, Portugal
2006/05/04 - 2013/12/30 Assistant Professor (University Teacher) Universidade de Lisboa Faculdade de Ciências, Portugal
2001/09/01 - 2006/09/01 Lecturer (University Teacher) Universidade de Lisboa Faculdade de Ciências, Portugal
2000/09/01 - 2001/09/01 Lecturer (University Teacher) Universidade de Lisboa Instituto Superior Técnico, Portugal
1998/09/01 - 2000/09/01 Tutor (University Teacher) Universidade de Lisboa Instituto Superior Técnico Departamento de Matemática, Portugal

Positions / Appointments

Category
Host institution 		Employer
2016 - 2019 Coordenação ou direção de centro de investigação, departamento ou equivalente Universidade de Lisboa, Portugal
2015 - 2016 Coordenação ou direção de centro de investigação, departamento ou equivalente Universidade de Lisboa Faculdade de Ciências, Portugal
Projects

Grant

Designation Funders
2023 - 2024 Microdrygrape: Seeking functional microbiome by assessing impact of water availability in grapevine health, physiological plasticity, and associated soil microbial communities
N/A
Co-Principal Investigator (Co-PI)
FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências
2019 - 2022 GEnvIA: Gene-Environment Interaction in Autism Spectrum Disorder
02/SAICT/2017
Researcher
Associação para a Inovação e Desenvolvimento da FCT
2018/10 - 2021/09 DeST: Deep Semantic Tagger
PTDC/CCI-BIO/28685/2017
Principal investigator
Fundação para a Ciência e a Tecnologia
2018 - 2018 Classifying Relations via Long Short-Term Memory Networks along Biomedical Ontologies
654021
Principal investigator
EU Framework Programme for Research and Innovation Research Infrastructures and E-Infrastructures
2012 - 2015 BiobankCloud: Scalable, Secure Storage of Biobank Data
317871
Researcher
European Commission Seventh Framework Programme for Research and Technological Development Information and Communication Technologies
2012/03 - 2014/10 SOMER: Semantic Ontology Matching using External Resources
119119
Provided by PTCRIS: 119119
PTDC/EIA-EIA/119119/2010
Principal investigator
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal

LASIGE Laboratório de Sistemas Informáticos de Grande Escala, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Universidade de Lisboa Faculdade de Ciências, Portugal
Fundação para a Ciência e a Tecnologia, I.P.

Fundação para a Ciência e a Tecnologia
Concluded
2011/01 - 2014/06 In silico reconstruction of Streptococcus pneumoniae cellular networks and their impact on virulence
Provided by PTCRIS: 113824
113824
PTDC/EBB-EBI/113824/2009
Researcher
Fundação para a Ciência e a Tecnologia, I.P.

Fundação para a Ciência e a Tecnologia
2010/10 - 2014/04 REACTION - Retrieval, Extraction, and Aggregation Computing Technology for Integrating and Organizing News
Provided by PTCRIS: 110545
110545
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
2010 - 2012 VPH: Virtual Physiological Human Network of Excellence
223920
Researcher
European Commission Seventh Framework Programme for Research and Technological Development
2009 - 2012 EPIWORK: Developing the Framework for an Epidemic Forecast infrastructure
231807
Researcher
European Commission Seventh Framework Programme for Research and Technological Development Information and Communication Technologies
2008/01 - 2010/12 ARN - Algorithms for the identification of genetic Regulatory Networks
67722
Provided by PTCRIS: 67722
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
2008/01 - 2010/10 GREASE-II - Geographic Reasoning for Search Engines
Provided by PTCRIS: 73614
73614
Researcher
Fundação para a Ciência e a Tecnologia, I.P.

Contract

Designation Funders
2022/01/01 - 2023/06/30 Deep graph learning approaches to personalized medicine
EXPL/CCI-BIO/0126/2021
FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal

Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal

Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2019/01/01 - 2019/12/31 LABORATÓRIO DE SISTEMAS INFORMÁTICOS DE GRANDE-ESCALA
UID/CEC/00408/2019
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal

FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal

Universidade de Lisboa Faculdade de Ciências, Portugal

LASIGE Laboratório de Sistemas Informáticos de Grande Escala, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2017 - 2018 Unbabel 2017: Um novo ecossistema de Machine and Crowd Translation
LISBOA-01-0247-FEDER-010432
Principal investigator
Agência Nacional de Inovação SA
Concluded
2011/01/01 - 2013/12/31 Strategic Project - UI 408 - 2011-2012
PEst-OE/EEI/UI0408/2011
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal

LASIGE Laboratório de Sistemas Informáticos de Grande Escala, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2008/01/01 - 2010/12/31 ARN - Algoritmos para a identificação de redes de regulação genética
PTDC/EIA/67722/2006
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal

Universidade de Lisboa Instituto Superior Técnico, Portugal

Universidade de Lisboa Faculdade de Ciências, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Book
  1. Couto, Francisco M. Introdução à Bioinformática Via Linha de Comando. Gradiva. 2019.
  2. Couto, Francisco M. Data and Text Processing for Health and Life Sciences. Springer. 2019.
    https://doi.org/10.1007/978-3-030-13845-5
Book chapter
  1. M. Fernandes; J. Decouchant; F. Couto; Suyel Namasudra. "Security, Privacy and Trust Management in DNA Computing". edited by Suyel Namasudra. Elsevier, 2023.
    https://doi.org/10.1016/bs.adcom.2022.08.009
  2. Diana Sousa; Andre Lamurias; Francisco M. Couto. "Using Neural Networks for Relation Extraction from Biomedical Literature". 289-305. Springer {US, 2021.
    10.1007/978-1-0716-0826-5_14
  3. Márcia Barros; André Moitinho; Francisco M. Couto; Barros M; Moitinho A; Couto FM; M. Barros; A. Moitinho; F. Couto. "Hybrid Semantic Recommender System for Chemical Compounds". In 42nd European Conference on Information Retrieval (ECIR 2020), 94-101. Springer International Publishing, 2020.
    10.1007/978-3-030-45442-5_12
  4. Couto, Francisco M. "Semantic similarity definition". 2019.
    https://doi.org/10.1016/B978-0-12-809633-8.20401-9
  5. Couto, Francisco M. "Text Mining for Bioinformatics using Biomedical Literature". 2019.
    https://doi.org/10.1016/B978-0-12-809633-8.20409-3
  6. J. Ferreira; F. Couto; A. Stefaniu. "Semantic Similarity in Cheminformatics". edited by A. Stefaniu. IntechOpen, 2019.
    https://doi.org/10.5772/intechopen.89032
  7. Couto, Francisco M. "Application of Gene Ontology to Gene Identification". 2011.
    http://dx.doi.org/10.1007/978-1-61779-176-5_9
  8. Couto, Francisco M. "Carbohydrate-Active Enzymes Database: Principles and Classification of Glycosyltransferases". 2009.
    http://dx.doi.org/10.1002/9780470029619.ch5
  9. Couto, Francisco M. "Untangling BioOntologies for Mining Biomedical Information". 2009.
    http://dx.doi.org/10.4018/978-1-59904-990-8
  10. Couto, Francisco M. "Verification of Uncurated Protein Annotations". 2009.
    http://dx.doi.org/10.4018/978-1-60566-274-9
  11. Pesquita, Catia; Grego, Tiago; Couto, Francisco. "Identifying Gene Ontology Areas for Automated Enrichment". In Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living, 934-941. Springer Berlin Heidelberg, 2009.
    10.1007/978-3-642-02481-8_143
  12. Couto, Francisco M. "Mining the BioLiterature: towards automatic annotation of genes and proteins". 2006.
    http://dx.doi.org/10.4018/978-1-59140-863-5
Conference paper
  1. Anaya, Christopher; Couto, Francisco M. "LLM Fine-Tuning With Biomedical Open-Source Data". Paper presented in CLEF 2024, Grenoble, 2024.
    Published
  2. S. Conceicao; D. Sousa; P. Silvestre; F. Couto. "lasigeBioTM at SemEval-2023 Task 7: Improving Natural Language Inference Baseline Systems with Domain Ontologies". 2023.
  3. S. Conceicao; D. Sousa; P. Silvestre; F. Couto. "BioRED track lasigeBioTM submission: Relation extraction using Domain Ontologies with BioRED". 2023.
  4. Barros, Márcia; Couto, Francisco M; Matilde Pato; RUAS, PEDRO. "Creating Recommender Systems Datasets in Scientific Fields". Paper presented in KDD ¿21: The 27th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2021.
    In press • 10.1145/3447548.3470805
  5. R. West; S. Bhagat; P. Groth; M. Zitnik; F. M. Couto; P. Lisena; A. Meroño-Peñuela; et al. "Summary of Tutorials at The Web Conference 2021". 2021.
  6. D. Sousa; R. Cassanheira; F. Couto. "lasigeBioTM at BioCreative VII Track 1: Text mining drug and chemical-protein interactions using biomedical ontologies". 2021.
  7. P. Ruas; V. Andrade; F. Couto. "LASIGE-BioTM at MESINESP2: entity linking with semantic similarity and extreme multi-label classification on Spanish biomedical documents". 2021.
  8. D. Faria; B. Lima; M. Silva; F. Couto; C. Pesquita. "AML and AMLC results for OAEI 2021". 2021.
  9. P. Ruas; V. Andrade; F. Couto. "Lasige-BioTM at ProfNER: BiLSTM-CRF and contextual Spanish embeddings for Named Entity Recognition and Tweet Binary Classification". 2021.
  10. M. Campos; F. Couto. "Post-processing BioBERT And Using Voting Methods for Biomedical Question Answering". 2021.
  11. Couto, Francisco M. "Report of the First International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages". 2020.
  12. Couto, Francisco M. "LasigeBioTM Team at CLEF2020 ChEMU Evaluation Lab: Named Entity Recognition and Event extraction from chemical reactions described in patents using BioBERT NER and RE". 2020.
  13. Couto, Francisco M. "Biomedical Question Answering using Extreme Multi-Label Classification and Ontologies in the Multilingual Panorama". 2020.
  14. Couto, Francisco M. "Towards a Multilingual Corpus for Named Entity Linking Evaluation in the Clinical Domain". 2020.
  15. Couto, Francisco M. "An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents". 2020.
  16. Couto, Francisco M. "COVID-19: A Semantic-Based Pipeline for Recommending Biomedical Entities". 2020.
  17. Couto, Francisco M. "LasigeBioTM at CANTEMIST: Named Entity Recognition and Normalization of Tumour Morphology Entities and Clinical Coding of Spanish Health-related Documents". 2020.
  18. F. Couto; M. Krallinger. "First International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages (SIIRH)". 2020.
  19. D. Sousa; F. Couto; Diana Sousa; Francisco M. Couto. "BiOnt: Deep Learning using Multiple Biomedical Ontologies for Relation Extraction". 2020.
    10.1007/978-3-030-45442-5_46
  20. F. Colaço; M. Barros; F. Couto; Couto, Francisco M. "DRecPy: A Python Framework for Developing Deep Learning-Based Recommenders". 2020.
    10.1145/3383313.3418483
  21. B. Lima; D. Faria; F. Couto; I. Cruz; C. Pesquita. "OAEI 2020 results for AML and AMLC". 2020.
  22. F. Couto; M. Krallinger; 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)". 2020.
    10.1007/978-3-030-45442-5_87
  23. Couto, Francisco M. "Privacy-Preserving Processing of Filtered DNA Reads". 2019.
  24. Sousa, Diana; Lamurias, Andre; Couto, Francisco M; D. Sousa; A. Lamurias; F. Couto. "A Silver Standard Corpus of Human Phenotype-Gene Relations". Paper presented in Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Minneapolis, 2019.
    Published • 10.18653/v1/N19-1152
  25. D. Faria; C. Pesquita; T. Tervo; F. Couto; I. Cruz. "AML and AMLC Results for OAEI 2019". 2019.
  26. A. Lamurias; F. Couto. "LasigeBioTM at MEDIQA 2019: Biomedical Question Answering using Bidirectional Transformers and Named Entity Recognition". 2019.
  27. Faria, Daniel; Pesquita, Cátia; Balasubramani, Booma Sowkarthiga; Teemu, Tervo; Teixeira, David; Garrilha, Rodrigo; Couto, Francisco M; Cruz, Isabel F. "Results of AML participation in OAEI 2018". Paper presented in Proceedings of the 13th International Workshop on Ontology Matching, 2018.
    Published
  28. M. Fernandes; J. Decouchant; F. Couto; P. Veríssimo. "Privacy-preserving algorithms and workflows for next-generation genomics". 2018.
  29. Couto, Francisco M. "Metadata Analyser: measuring metadata quality". 2017.
    https://doi.org/10.1007/978-3-319-60816-7_24
  30. Couto, Francisco M. "Cloud-Assisted Read Alignment and Privacy". 2017.
    https://doi.org/10.1007/978-3-319-60816-7_27
  31. Couto, Francisco M. "Anthropometric Data Analytics: a Portuguese Case Study". 2017.
    https://doi.org/10.1007/978-3-319-60816-7_12
  32. Couto, Francisco M. "How can photo sharing inspire sharing genomes?". 2017.
    https://doi.org/10.1007/978-3-319-60816-7_10
  33. Lamurias, Andre; Sousa, Diana; Pereira, Sofia; Clarke, Luka; Couto, Francisco M; A. Lamurias; D. Sousa; et al. "ULISBOA at SemEval-2017 Task 12: Extraction and classification of temporal expressions and events". 2017.
    Published • 10.18653/v1/s17-2179
  34. D. Faria; B. Balasubramani; V. Shivaprabhu; I. Mott; C. Pesquita; F. Couto; I. Cruz. "Results of AML in OAEI 2017". 2017.
  35. A. Lamurias; L. Campos; F. Couto. "IBEnt: Chemical Entity Mentions in Patents using ChEBI". 2017.
  36. F. Couto; L. Campos; A. Lamurias. "MER: a Minimal Named-Entity Recognition Tagger and Annotation Server". 2017.
  37. M. Rodrigues; F. Couto. "MoRS At SemEval-2017 Task 3: Easy To Use SVM In Ranking Tasks". 2017.
  38. D. Faria; C. Pesquita; B. Balasubramani; C. Martins; J. Cardoso; H. Curado; F. Couto; I. Cruz. "OAEI 2016 Results of AML". 2016.
  39. A. Lamurias; M. Rodrigues; L. Clarke; F. Couto. "Extraction of Regulatory Events using Kernel-based Classifiers and Distant Supervision". 2016.
  40. M. Barros; A. Lamurias; G. Figueiro; M. Antunes; J. Teixeira; A. Pinheiro; F. Couto. "ULISBOA at SemEval-2016 Task 12: Extraction of temporal expressions, clinical events and relations using IBEnt". 2016.
  41. M. Rodriques; M. Fale; F. Couto. "WS4A: a Biomedical Question and Answering System based on public web services and ontologies". 2016.
  42. Couto, Francisco M. "IICE: web tool for automatic identification of chemical entities and interactions". 2015.
    https://doi.org/10.1007/978-3-319-23461-8_31
  43. Couto, Francisco M. "Social Impact - Identifying Quotes of Literary Works in Social Networks". 2015.
    https://doi.org/10.1007/978-3-319-23485-4_79
  44. A. Lamurias; M. Lobo; M. Antunes; L. Clarke; F. Couto. "Identifying chemical entities in patents using brown clustering and semantic similarity". 2015.
  45. F. Couto; J. Hastings. "The Sixth International Conference on Biomedical Ontologies (ICBO)". 2015.
  46. A. Lamurias; V. Pedro; L. Clarke; F. Couto. "Annotating biomedical terms in electronic health records using crowd-sourcing". 2015.
  47. A. Leal; B. Martins; F. Couto. "ULisboa: Recognition and Normalization of Medical Concepts". 2015.
  48. V. Cogo; A. Bessani; F. Couto; P. Verissimo. "A High-Throughput Method to Detect Privacy-Sensitive Human Genomic Data". 2015.
  49. Couto, Francisco M. "Friendsourcing the Unmet Needs of People with Dementia". 2014.
    https://doi.org/10.1145/2596695.2596716
  50. Couto, Francisco M. "Chemical Named Entity Recognition: Improving Recall Using a Comprehensive List of Lexical Features". 2014.
    https://doi.org/10.1007/978-3-319-07581-5_30
  51. Couto, Francisco M. "Towards visualizing the alignment of large biomedical ontologies". 2014.
    https://doi.org/10.1007/978-3-319-08590-6_10
  52. Couto, Francisco M. "Towards annotating potential incoherences in BioPortal mappings". 2014.
    https://doi.org/10.1007/978-3-319-11915-1_2
  53. Couto, Francisco M. "Learning Temporal-Dependent Ranking Models". 2014.
    https://doi.org/10.1145/2600428.2609619
  54. F. Couto. "Rating, recognizing and rewarding metadata integration and sharing on the semantic web". 2014.
  55. D. Faria; C. Pesquita; E. Santos; I. Cruz; F. Couto. "AgreementMakerLight: A Scalable Automated Ontology Matching System". 2014.
  56. C. Pesquita; M. Cheatham; D. Faria; J. Barros; E. Santos; F. Couto. "Building reference alignments for compound matching of multiple ontologies using OBO cross-products". 2014.
  57. A. Leal; D. Gonçalves; B. Martins; F. Couto. "ULisboa: Identification and Classification of Medical Concepts". 2014.
  58. D. Faria; C. Martins; A. Nanavaty; A. Taheriand; C. Pesquita; E. Santos; I. Cruz; F. Couto. "AgreementMakerLight results for OAEI 2014". 2014.
  59. D. Faria; C. Martins; A. Nanavaty; D. Oliveira; B. Sowkarthiga; A. Taheri; C. Pesquita; F. Couto; I. Cruz. "AgreementMakerLight results for OAEI 2015". 2014.
  60. Couto, Francisco M. "What's in a `nym'? Synonyms in Biomedical Ontology Matching". 2013.
    https://doi.org/10.1007/978-3-642-41335-3_33
  61. Couto, Francisco M. "The AgreementMakerLight Ontology Matching System". 2013.
    https://doi.org/10.1007/978-3-642-41030-7_38
  62. T. Grego; F. Pinto; F. Couto. "LASIGE: using Conditional Random Fields and ChEBI ontology". 2013.
  63. C. Pesquita; D. Faria; E. Santos; F. Couto. "To repair or not to repair: reconciling correctness and coherence in ontology reference alignments". 2013.
  64. S. Moreira; J. Filgueiras; B. Martins; F. Couto; M. Silva. "REACTION: A naive machine learning approach for sentiment classification". 2013.
  65. M. Costa; D. Gomes; F. Couto; M. Silva. "A survey of web archive search architectures". 2013.
  66. A. Lamurias; T. Grego; F. Couto. "Chemical compound and drug name recognition using CRFs and semantic similarity based on ChEBI". 2013.
  67. D. Faria; C. Pesquita; E. Santos; I. Cruz; F. Couto. "AgreementMakerLight results for OAEI 2013". 2013.
  68. Couto, Francisco M. "Toponym Disambiguation using Ontology-based Semantic Similarity". 2012.
    https://doi.org/10.1007/978-3-642-28885-2_20
  69. Couto, Francisco M. "Toward a Translational Medicine Approach for Hypertrophic Cardiomyopathy". 2012.
    https://doi.org/10.1007/978-3-642-32395-9_12
  70. T. Grego; F. Pinto; F. Couto. "Identifying Chemical Entities based on ChEBI". 2012.
  71. J. Ferreira; C. Pesquita; M. Silva; F. Couto. "Bringing epidemiology into the Semantic Web". 2012.
  72. F. Couto; J. Ferreira; J. Zamite; C. Santos; T. Posse; P. Graça; D. Domingos; M. Silva. "The Epidemic Marketplace Platform: towards semantic characterization of epidemiological resources using biomedical ontologies". 2012.
  73. C. Machado; A. Freitas; F. Couto; Couto, Francisco M. "Enrichment analysis applied to disease prognosis". 2012.
    https://doi.org/10.1186/2041-1480-4-21
  74. I. Cruz; C. Stroe; C. Pesquita; F. Couto; V. Cross. "Biomedical Ontology Matching Using the AgreementMaker System". 2011.
  75. I. Cruz; C. Stroe; F. Caimi; A. Fabiani; C. Pesquita; F. Couto; M. Palmonari. "Using AgreementMaker to Align Ontologies for OAEI 2011". 2011.
  76. J. Ferreira; F. Couto. "Generic semantic relatedness measure for biomedical ontologies". 2011.
  77. C. Pesquita; F. Couto. "Where GO is going and what it means for ontology extension". 2011.
  78. B. Tavares; H. Bastos; D. Faria; J. Ferreira; T. Grego; C. Pesquita; F. Couto. "The Biomedical Ontology Applications (BOA) framework". 2011.
  79. Moreira, Silvio; Batista, David; Carvalho, Paula; Couto, Francisco; Silva, Mário. "POWER - Politics Ontology for Web Entity Retrieval". Paper presented in ONTOSE 2011: 5th International Workshop on Ontology, Models, Conceptualization and Epistemology in Social, Artificial and Natural Systems, Londres, 2011.
    Published • 10.1007/978-3-642-22056-2_51
  80. Couto, Francisco M. "MEDCollector: Multisource Epidemic Data Collector". 2010.
    https://doi.org/10.1007/978-3-642-15020-3_2
  81. Couto, Francisco M. "Epidemic Marketplace: An Information Management System for Epidemiological Data". 2010.
    https://doi.org/10.1007/978-3-642-15020-3_3
  82. Couto, Francisco M. "Identifying Bioentity Recognition Errors of Rule-Based Text-Mining Systems". 2008.
    https://doi.org/10.1109/ICDIM.2008.4746791
  83. Couto, Francisco M. "Validating Associations in Biological Databases". 2006.
    https://doi.org/10.1145/1183614.1183639
  84. Couto, Francisco M. "Semantic Similarity over the Gene Ontology: Family Correlation and Selecting Disjunctive Ancestors". 2005.
    https://doi.org/10.1145/1099554.1099658
  85. Couto, Francisco M. "Classifying biological articles using web resources". 2004.
    https://doi.org/10.1145/967900.967925
Journal article
  1. Fernando Gallego; Pedro Ruas; Francisco M. Couto; Francisco J. Veredas. "Enhancing cross-encoders using knowledge graph hierarchy for medical entity linking in zero- and few-shot scenarios". Knowledge-Based Systems (2025): https://doi.org/10.1016/j.knosys.2025.113211.
    10.1016/j.knosys.2025.113211
  2. Matilde Pato; Márcia Barros; Francisco M. Couto. "Survey on Recommender Systems for Biomedical Items in Life and Health Sciences". ACM Computing Surveys (2024): https://doi.org/10.1145/3639047.
    10.1145/3639047
  3. 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; et al. "Genome-Wide Admixture and Association Study of Serum Selenium Deficiency to Identify Genetic Variants Indirectly Linked to Selenium Regulation in Brazilian Adults". Nutrients (2024): https://doi.org/10.3390/nu16111627.
    10.3390/nu16111627
  4. Watanabe, Ligia Moriguchi; Sousa, Lisete; Noronha, Natália; Pinhel, Marcela; Carvalho, Gleyson; Rodrigues, Guilherme; Couto, Francisco; et al. "Genome-wide case-control association study identifies a locus connecting NRF2-ARE regulation and selenium deficiency". Free Radical Biology and Medicine 208 (2023): S23-S24. http://dx.doi.org/10.1016/j.freeradbiomed.2023.10.054.
    Published • 10.1016/j.freeradbiomed.2023.10.054
  5. Diana F Sousa; Francisco M Couto; Jonathan Wren. "K-RET: knowledgeable biomedical relation extraction system". Bioinformatics (2023): https://doi.org/10.1093/bioinformatics/btad174.
    10.1093/bioinformatics/btad174
  6. Asif M; Martiniano HFMC; Lamurias A; Kausar S; Couto FM; Martiniano HF. "DGH-GO: dissecting the genetic heterogeneity of complex diseases using gene ontology.". BMC bioinformatics (2023): http://europepmc.org/abstract/med/37101154.
    10.1186/s12859-023-05290-4
  7. D. Faria; E. Santos B. Balasubramani; M. Silva; F. Couto; C. Pesquita. "AgreementMakerLight". Semantic Web, IOS Press Pre-press Pre-press (2023):
    https://doi.org/10.3233/SW-233304
  8. Pedro Ruas; Francisco M. Couto. "NILINKER: Attention-based approach to NIL Entity Linking". Journal of Biomedical Informatics 132 (2022): 104137-104137. https://doi.org/10.1016/j.jbi.2022.104137.
    10.1016/j.jbi.2022.104137
  9. Diana Sousa; Francisco M. Couto. "Biomedical Relation Extraction With Knowledge Graph-Based Recommendations". IEEE Journal of Biomedical and Health Informatics (2022): https://doi.org/10.1109/JBHI.2022.3173558.
    10.1109/JBHI.2022.3173558
  10. Barros M; Moitinho A; Couto FM. "SeEn: Sequential enriched datasets for sequence-aware recommendations.". Scientific data (2022): http://europepmc.org/abstract/med/35927282.
    10.1038/s41597-022-01598-7
  11. Rodrigues A; Santinha J; Galvão B; Matos C; Couto FM; Papanikolaou N. "Prediction of Prostate Cancer Disease Aggressiveness Using Bi-Parametric Mri Radiomics.". Cancers (2021): http://europepmc.org/abstract/med/34885175.
    10.3390/cancers13236065
  12. Márcia Barros; Pedro Ruas; Diana Sousa; Ali Haider Bangash; Francisco M. Couto. "COVID-19 recommender system based on an annotated multilingual corpus". Genomics & Informatics (2021): https://doi.org/10.5808/gi.21008.
    10.5808/gi.21008
  13. Sofia I. R. Conceição; Francisco M. Couto. "Text Mining for Building Biomedical Networks Using Cancer as a Case Study". Biomolecules 11 10 (2021): 1430-1430. https://doi.org/10.3390/biom11101430.
    10.3390/biom11101430
  14. Lamurias A; Jesus S; Neveu V; Salek RM; Couto FM. "Information Retrieval Using Machine Learning for Biomarker Curation in the Exposome-Explorer.". Frontiers in research metrics and analytics (2021): http://europepmc.org/abstract/med/34490412.
    10.3389/frma.2021.689264
  15. Couto, Francisco M. "Hybrid semantic recommender system for chemical compounds in large-scale datasets.". Journal of cheminformatics (2021): https://doi.org/10.1186/s13321-021-00495-2.
    10.1186/s13321-021-00495-2
  16. Couto, Francisco M. "A hybrid approach toward biomedical relation extraction training corpora: combining distant supervision with crowdsourcing.". Database : the journal of biological databases and curation (2020): https://europepmc.org/articles/PMC7706181.
    10.1093/database/baaa104
  17. Ruas, Pedro; Lamurias, Andre; Couto, Francisco M.. "Linking chemical and disease entities to ontologies by integrating PageRank with extracted relations from literature". Journal of Cheminformatics 12 1 (2020): http://dx.doi.org/10.1186/s13321-020-00461-4.
    10.1186/s13321-020-00461-4
  18. Diana Sousa; Andre Lamurias; Francisco M. Couto. "Improving accessibility and distinction between negative results in biomedical relation extraction". Genomics & Informatics (2020): https://doi.org/10.5808/GI.2020.18.2.e20.
    10.5808/GI.2020.18.2.e20
  19. Couto, Francisco M. "Identification of biological mechanisms underlying a multidimensional ASD phenotype using machine learning". Translational Psychiatry (2020):
    https://doi.org/10.1038/s41398-020-0721-1
  20. Andre Lamurias; Diana Sousa; Francisco M. Couto. "Generating Biomedical Question Answering Corpora From Q&A Forums". IEEE Access 8 (2020): 161042-161051. https://doi.org/10.1109/ACCESS.2020.3020868.
    10.1109/ACCESS.2020.3020868
  21. S. Nunes; S. Little; S. Bhatia; L. Boratto; G. Cabanac; R. Campos; F. Couto; et al. "ECIR 2020 Workshops: Assessing the Impact of Going Online". SIGIR Forum 54 1 (2020):
    http://sigir.org/wp-content/uploads/2020/06/p09.pdf
  22. Couto FM. "Text Processing.". Advances in experimental medicine and biology (2019): http://europepmc.org/abstract/med/31183819.
    10.1007/978-3-030-13845-5_4
  23. Couto FM. "Semantic Processing.". Advances in experimental medicine and biology (2019): http://europepmc.org/abstract/med/31183820.
    10.1007/978-3-030-13845-5_5
  24. Couto FM. "Introduction.". Advances in experimental medicine and biology (2019): http://europepmc.org/abstract/med/31183816.
    10.1007/978-3-030-13845-5_1
  25. Couto FM. "Resources.". Advances in experimental medicine and biology (2019): http://europepmc.org/abstract/med/31183817.
    10.1007/978-3-030-13845-5_2
  26. Couto FM. "Data Retrieval.". Advances in experimental medicine and biology (2019): http://europepmc.org/abstract/med/31183818.
    10.1007/978-3-030-13845-5_3
  27. Couto, Francisco M; J. Ferreira; F. Couto. "Multi-domain semantic similarity in biomedical research". BMC Bioinformatics (2019):
    https://doi.org/10.1186/s12859-019-2810-9
  28. Couto, Francisco M; 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 (2019): 907-915. https://doi.org/10.1109/JBHI.2019.2914952.
    https://doi.org/10.1109/JBHI.2019.2914952
  29. Couto, Francisco M. "FunVar: A Systematic Pipeline to Unravel the Convergence Patterns of Genetic Variants in ASD, a Paradigmatic Complex Disease". Journal of Biomedical Informatics (2019):
    https://doi.org/10.1016/j.jbi.2019.103273
  30. Couto, Francisco M. "BO-LSTM: classifying relations via long short-term memory networks along biomedical ontologies". BMC Bioinformatics (2019):
    https://doi.org/10.1186/s12859-018-2584-5
  31. Marcia Barros; Andre Moitinho; Francisco M. Couto; Couto, Francisco M. "Using Research Literature to Generate Datasets of Implicit Feedback for Recommending Scientific Items". IEEE Access 7 (2019): 176668-176680. https://doi.org/10.1109/ACCESS.2019.2958002.
    10.1109/ACCESS.2019.2958002
  32. Couto, Francisco M. "PPR-SSM: personalized PageRank and semantic similarity measures for entity linking". BMC Bioinformatics (2019):
    https://doi.org/10.1186/s12859-019-3157-y
  33. Couto, Francisco M. "Tackling the Challenges of Matching Biomedical Ontologies". Journal of Biomedical Semantics (2018):
    https://doi.org/10.1186/s13326-017-0170-9
  34. Couto, Francisco M. "Accurate Filtering of Privacy-Sensitive Information in Raw Genomic Data". Journal of Biomedical Informatics (2018):
    https://doi.org/10.1016/j.jbi.2018.04.006
  35. Couto, Francisco M. "Identifying disease genes using machine learning and gene functional similarities, assessed through Gene Ontology". PLoS ONE (2018):
    https://doi.org/10.1371/journal.pone.0208626
  36. Couto, Francisco M. "MER: a Shell Script and Annotation Server for Minimal Named Entity Recognition and Linking". Journal of Cheminformatics (2018):
    https://doi.org/10.1186/s13321-018-0312-9
  37. Couto, Francisco M. "Witches' broom resistant genotype CCN51 shows greater diversity of symbiont bacteria in its phylloplane than susceptible genotype catongo". BMC Microbiology 18 1 (2018):
    https://doi.org/10.1186/s12866-018-1339-9
  38. 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): http://www.insa.min-saude.pt/category/informacao-e-cultura-cientifica/publicacoes/boletim-epidemiologico-observacoes-numero-22/.
  39. Couto, Francisco M. "Extracting MicroRNA-Gene Relations from Biomedical Literature using Distant Supervision". PLoS ONE (2017):
    https://doi.org/10.1371/journal.pone.0171929
  40. Couto, Francisco M. "Impact of translation on named-entity recognition in radiology texts". Database: The Journal of Biological Databases and Curation (2017):
    https://doi.org/10.1093/database/bax064
  41. Couto, Francisco M. "Identifying Human Phenotype Terms by Combining Machine Learning and Validation Rules". BioMed Research International (2017):
    https://doi.org/10.1155/2017/8565739
  42. Couto, Francisco M. "Assessing public metabolomics metadata, towards improving quality". Journal of Integrative Bioinformatics (2017):
    https://doi.org/10.1515/jib-2017-0054
  43. Couto, Francisco M. "Generating a Tolerogenic Cell Therapy Knowledge Graph from Literature". Frontiers in Immunology (2017):
    https://doi.org/10.3389/fimmu.2017.01656
  44. Couto, Francisco M. "Knowledge Representation and Management: a linked data perspective". IMIA Yearbook of Medical Informatics (2016):
    https://doi.org/10.15265/IY-2016-022
  45. Couto, Francisco M. "Functional Coherence Metrics in Protein Families". Journal of Biomedical Semantics (2016):
    https://doi.org/10.1186/s13326-016-0076-y
  46. Couto, Francisco M. "The semantic web in translational medicine: current applications and future directions". Briefings in Bioinformatics, Oxford University Press (2015):
    https://doi.org/10.1093/bib/bbt079
  47. Couto, Francisco M. "The CHEMDNER corpus of chemicals and drugs and its annotation principles". Journal of Cheminformatics (2015):
    https://doi.org/10.1186/1758-2946-7-S1-S2
  48. Couto, Francisco M. "Improving chemical entity recognition through h-index based semantic similarity". Journal of Cheminformatics (2015):
    https://doi.org/10.1186/1758-2946-7-S1-S13
  49. Couto, Francisco M. "Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora". Database: The Journal of Biological Databases and Curation (2015):
    https://doi.org/10.1093/database/bav005
  50. Couto, Francisco M. "GRYFUN: A Web Application for GO Term Annotation Visualization and Analysis in Protein Sets". PLoS ONE (2015):
    https://doi.org/10.1371/journal.pone.0119631
  51. Couto, Francisco M; E. Santos; D. Faria; C. Pesquita; F. Couto. "Ontology alignment repair through modularization and confidence-based heuristics". PLoS ONE (2015): https://arxiv.org/abs/1307.5322v1.
    https://doi.org/10.1371/journal.pone.0144807
  52. Couto, Francisco M. "Automatic Background Knowledge Selection for Matching Biomedical Ontologies". PLoS ONE (2014):
    https://doi.org/10.1371/journal.pone.0111226
  53. Couto, Francisco M. "The epidemiology ontology: an ontology for the semantic annotation of epidemiological resources". Journal of Biomedical Semantics (2014):
    https://doi.org/10.1186/2041-1480-5-4
  54. Couto, Francisco M. "Identifying interactions between chemical entities in biomedical text". Journal of Integrative Bioinformatics (2014):
    https://doi.org/10.2390/biecoll-jib-2014-247
  55. Couto, Francisco M. "Tracking Politics with POWER". Program: electronic library and information systems (2013):
    https://doi.org/10.1108/00330331311313708
  56. Couto, Francisco M. "Enhancement of Chemical Entity Identification in Text using Semantic Similarity Validation". PLoS ONE (2013):
    https://doi.org/10.1371/journal.pone.0062984
  57. Couto, Francisco M. "Annotation extension through protein family annotation coherence metrics". Frontiers in Genetics (2013):
    https://doi.org/10.3389/fgene.2013.00201
  58. Couto, Francisco M. "The Next Generation of Similarity Measures that fully explore the Semantics in Biomedical Ontologies". Journal of Bioinformatics and Computational Biology (2013):
    https://doi.org/10.1142/S0219720013710017
  59. Couto, Francisco M. "Exploiting disjointness axioms to improve semantic similarity measures". Bioinformatics, Oxford Univ Press (2013):
    https://doi.org/10.1093/bioinformatics/btt491
  60. Couto, Francisco M. "On the usefulness of ontologies in epidemiologic research and practice". Journal of Epidemiology and Community Health (2013):
    https://doi.org/10.1136/jech-2012-201142
  61. Couto, Francisco M. "Chemical Entity Recognition and Resolution to ChEBI". ISRN Bioinformatics (2012):
    https://doi.org/10.5402/2012/619427
  62. Couto, Francisco M. "Predicting the Extension of Biomedical Ontologies". PLoS Computational Biology (2012):
    https://doi.org/10.1371/journal.pcbi.1002630
  63. Couto, Francisco M. "Serum proteomics signature of Cystic Fibrosis patients: A complementary 2-DE and LC-MS/MS approach". Journal of Proteomics (2011):
    https://doi.org/10.1016/j.jprot.2010.10.001
  64. Couto, Francisco M. "Molecular profiling of the human nasal epithelium: A proteomics approach". Journal of Proteomics (2011):
    https://doi.org/10.1016/j.jprot.2011.05.012
  65. Couto, Francisco M. "Disjunctive Shared Information between Ontology Concepts: application to Gene Ontology". Journal of Biomedical Semantics (2011):
    https://doi.org/10.1186/2041-1480-2-5
  66. F. Couto. "Exploiting Biomedical Information through Literature and Ontologies". El País - Sociedad (2011): http://sociedad.elpais.com/sociedad/2011/11/07/actualidad/1320620406_850215.html.
  67. Couto, Francisco M. "Rescue of F508del-CFTR by RXR motif inactivation triggers proteome modulation associated with the unfolded protein response". Biochimica et Biophysica Acta, Proteins and Proteomics (2010):
    https://doi.org/10.1016/j.bbapap.2009.12.013
  68. Couto, Francisco M. "Semantic Similarity for Automatic Classification of Chemical Compounds". PLoS Computational Biology (2010):
    https://doi.org/10.1371/journal.pcbi.1000937
  69. C. Machado; F. Couto; A. Fernandes; S. Santos; N. Cardim; A. Freitas. "Unraveling Hypertrophic Cardiomyopathy Variability". ERCIM News 82 - Special Theme: Computational Biology (2010): http://ercim-news.ercim.eu/en82/special/unraveling-hypertrophic-cardiomyopathy-variability.
  70. F. Silva; M. Silva; F. Couto. "Epidemic Marketplace: an e-Science Platform for Epidemic Modelling and Analysis". ERCIM News 82 - Special Theme: Computational Biology (2010): http://ercim-news.ercim.eu/en82/special/epidemic-marketplace-an-e-science-platform-for-epidemic-modelling-and-analysis.
  71. Couto, Francisco M. "Semantic Similarity in Biomedical Ontologies". PLoS Computational Biology (2009):
    https://doi.org/10.1371/journal.pcbi.1000443
  72. Couto, Francisco M. "Handling Self-citations using Google Scholar". Cybermetrics 13 1 (2009):
    https://doi.org/10451/14427
  73. Couto, Francisco M. "Metrics for GO based protein semantic similarity: a systematic evaluation". BMC Bioinformatics (2008):
    https://doi.org/10.1186/1471-2105-9-S5-S4
  74. Couto, Francisco M. "Measuring Semantic Similarity between Gene Ontology Terms". Data and Knowledge Engineering (2007):
    https://doi.org/10.1016/j.datak.2006.05.003
  75. Couto, Francisco M. "GOAnnotator: linking electronic protein GO annotation to evidence text". Journal of Biomedical Discovery and Collaboration 19 1 (2006):
    https://doi.org/10451/14956
  76. Couto, Francisco M. "Finding Genomic Ontology Terms in Text using Evidence Content". BMC Bioinformatics (2005):
    https://doi.org/10.1186/1471-2105-6-S1-S21
  77. Couto, Francisco M. "Facts from text - Is Text Mining ready to deliver?". PLoS Biology (2005):
    https://doi.org/10.1371/journal.pbio.0030065
Preprint
  1. David da Costa Correia; Francisco M. Couto; Hugo Martiniano. "Predicting non-coding RNA function using Artificial Intelligence". 2024. https://doi.org/10.1101/2024.12.30.630736.
    10.1101/2024.12.30.630736
  2. Andrade VD; Ruas P; Couto FM. "Named Entity Recognition and Linking: a Portuguese and Spanish Oncological Parallel Corpus". 2021. http://europepmc.org/abstract/PPR/PPR397960.
    10.1101/2021.09.16.460605
Report
  1. P. Ruas; D. Sousa; A. Neves; C. Cruz; F. Couto. 2023. LASIGE and UNICAGE at NASA LitCoin NLP Competition. https://arxiv.org/abs/2308.05609.
  2. L. Campos; F. Couto. 2017. MRA - Proof of Concept of a Multilingual Report Annotator Web Application. https://arxiv.org/abs/1704.01748.
  3. C. Ramos; M. Louro; M. Santos; F. Couto. 2016. Knowledge Ratings in MetaboLights. https://arxiv.org/abs/1604.07997.
  4. R. Norman; F. Couto. 2014. Using Google Scholar to Predict Self-Citation: A Case Study in Health Economics. https://arxiv.org/abs/1406.5241.
  5. Couto, Francisco M. 2013. Benchmarking some Portuguese S&T system research units: 2nd Edition.
    https://doi.org/10451/14123
  6. F. Couto. 2013. CIDS country rankings: comparing documents and citations of USA, UK and China top researchers. https://arxiv.org/abs/1310.5597.
  7. D. Faria; C. Pesquita; E. Santos; F. Couto; C. Stroe; I. Cruz. 2012. Testing the AgreementMaker System in the Anatomy Task of OAEI 2012. https://arxiv.org/abs/1212.1625.
  8. Couto, Francisco M. 2011. Desenvolvimento de Sistemas de Informação baseados em PHP e MySQL, e Java e Oracle.
    https://doi.org/10451/15281
  9. Couto, Francisco M. 2010. Benchmarking some Portuguese S&T system research units.
    https://doi.org/10451/14175
  10. Couto, Francisco M. 2010. Chemical and Metabolic Pathway Semantic Similarity.
    https://doi.org/10451/14249
  11. Couto, Francisco M. 2010. The Geo-Net-PT/Yahoo! GeoPlanet (TM) concordance.
    https://doi.org/10451/14174
  12. Couto, Francisco M. 2010. Desenvolvimento de Aplicações Web baseadas em SOA e AJAX.
    https://doi.org/10451/15279
  13. Couto, Francisco M. 2007. ProteInOn: a Web Tool for Protein Semantic Similarity.
    https://doi.org/10451/14140
  14. Couto, Francisco M. 2007. Semantic Similarity Match for Data Quality.
    https://doi.org/10451/14158
  15. Couto, Francisco M. 2005. Validation of Automated Protein Annotation.
    https://doi.org/10451/14744
  16. Couto, Francisco M. 2003. Implementation of a Functional Semantic Similarity Measure between Gene-Products.
    https://doi.org/10451/14410
  17. Couto, Francisco M. 2003. Classifying Biomedical Articles using Web Resources: application to KDD Cup 02.
    https://doi.org/10451/14322
Thesis / Dissertation
  1. Couto, Francisco M. "ReBIL: Relating Biological Information through Literature". 2006.
    https://doi.org/10451/14312
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2022/03 Interpretação de dados biológicos Jornadas de Biologia do Instituto Superior de Agronomia
2022/03 Bioinformatics: interpretation of biological data Semana da Bioengenharia no Instituto Superior Técnico
2020/12 Why analyze biomedical text if we have data? Data Science Seminars, Universidade de Lisboa
2020/10 Biomedical text mining: exploring semantic resources Bioinformatics and Computational Biology Seminars, Universidade de Lisboa
2020/09/04 Multilingual text mining: Overcoming the lack of clinical NLP resources First Multilingual clinical NLP workshop (MUCLIN)
2020/09 Multilingual resources and community Q&A forums Discussion Panel of the 8th BioASQ 2020 Workshop
2020/09 Bioinformática: processamento de dados e texto biológico via linha de comando II Semana de Biologia da Universidade Federal do Sul da Bahia
2019/11 Introdução à bioinformática via linha de comando V Encontro de Ecologia, Universidade de Coimbra
2017 Exploration, sharing and privacy of data: Linked data - challenges for imagiology and radiology Encontro Nacional de Física Médica, FISMED2017
2016 Towards a privacy-preserving environment for genomic data analysis Computational Biology and Bioinformatics Seminar, IMM

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2025 - 2025 MiCRA: a minimal pipeline for functional microbiome information retrieval using Natural Language Processing and Biomedical Ontologies
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2025 - 2025 Hybrid Recommender Systems for Protein Ligand Interaction Prediction
Co-supervisor
 Informática (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2024 - 2024 Relation Extraction for Gene and Chemical Compounds
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2024 - 2024 Predicting non-coding RNA function using Artificial Intelligence
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2024 - 2024 Identifying negative results using biomedical relation extraction systems
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2023 - 2023 Development of machine learning tool for filtering artifacts in the identification of CNVs
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2023 - 2023 Unveiling co-transcriptional splicing kinetics using novel nascent transcriptomic techniques
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2023 - 2023 Development of a recommender system based on life and health sciences literature
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2023 - 2023 External knowledge in n-ary relation extraction
Supervisor
 Informática (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2022 - 2022 A computational pipeline to identify phenotypic manifestations related to genes
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2022 - 2022 Deep Semantic Entity Linking
Supervisor
 Informática (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2018 - 2022 Recommender system to support comprehensive exploration of large scale scientific datasets
Co-supervisor
 Informática (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - 2021 Prostate MRI Radiomics for Prediction of Gleason Score
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - 2021 Extracting Negative Biomedical Relations from Literature
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - 2021 Named Entity Recognition and Linking in a Multilingual Biomedical Setting
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021 - 2021 Development of a Corpus for User-based Scientific Question Answering
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2020 Applying deep learning extreme multi-label classification to the biomedical and multilingual panoramas
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2020 Recommender Systems Based on Deep Learning Techniques
Supervisor
 Ciência de Dados (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020 - 2020 Deep Learning System for Biomedical Ralation Extraction Combining External Sources of Knowledge
Supervisor
 Informática (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 - 2019 The role of antisense transcription on regulation of gene expression
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 - 2019 Extracting phenotype-gene relations from biomedical literature using distant supervision and deep learning
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 - 2019 Exploring Biomedical Ontologies, Personalized PageRank and Semantic Similarity in the Entity Linking task
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 - 2019 Information Retrieval using Machine Learning for Database Curation
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2016 - 2019 "Development of a text mining approach to disease network discovery"
Supervisor
 Biologia (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2018 - 2018 Extracting biomedical relations from biomedical literature
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - 2018 " A System medicine approach to study autism spectrum disorder, based on genomic, and clinical data"
Co-supervisor
 Biologia (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2017 - 2017 Previsão da localização subcelular de Proteínas Humanas com base em Aprendizagem Automática
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2017 - 2017 Anthropometric data analytics: a portuguese case study
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2017 - 2017 Semantic annotation of electronic health records in a multilingual environment
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2017 - 2017 Identifying human phenotype terms in text using a machine learning approach
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2017 - 2017 Biomedical semantic question and answering system
Supervisor
 Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2016 - 2016 Aplicações na web para validação e classificação de notícias pela crowd
Co-supervisor
 Engenharia Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2016 - 2016 Impacto das obras musicais lusófonas nas redes sociais
Supervisor
 Engenharia Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2016 - 2016 Quanto valem os metadados?
Supervisor
 Engenharia Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2016 - 2016 Desenvolvimento de uma rede social desportiva
Supervisor
 Engenharia Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2016 - 2016 Radiation monitoring system in clinical imaging
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2010 - 2016 "Semantic Similarity Across Biomedical Ontologies"
Supervisor
 Informática (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - 2015 3D Visualization of Very Large Databases - Integrating and expanding the state of the art in Bioinformatics and Astroinformatics
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - 2015 Development of a scalable, precise, and high-coverage genomics mapping tool for NGS
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - 2015 Análise de corpora jornalístico através das ocorrências de N-gramas
Co-supervisor
 Engenharia Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - 2015 Towards an engaging social TV on a second screen
Co-supervisor
 Engenharia Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - 2015 Recommendation system for modern television
Co-supervisor
 Engenharia Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - 2015 Recognition and normalization of biomedical entities within clinical notes
Supervisor
 Engenharia Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - 2015 Desenvolvimento de aplicação web de pesquisa, gestão e partilha de eventos
Co-supervisor
 Engenharia Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - 2015 Anti and pro-longevity genes differentiation and overlap with age-related diseases
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2015 - 2015 Assessing pseudogene expression during neural differentiation by RNA-Seq
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2009 - 2015 Functional coherence and annotation agreement metrics for enzyme families
Supervisor
 Informática (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2014 - 2014 NGSOnto: proposta de uma ontologia para descrever o processo de sequenciação de alto desempenho
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2014 - 2014 Identifying interactions between chemical entities in text
Supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2014 - 2014 Impacto de obras literárias nas redes sociais
Supervisor
 Engenharia Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2014 - 2014 Towards an intelligent biographical cognitive prosthesis
Co-supervisor
 Engenharia Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2010 - 2014 Knowledge representation for data integration and exploration in translational medicine
Co-supervisor
 Informática (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2008 - 2014 "Information search in Web Archives"
Co-supervisor
 Informática (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2013 - 2013 Metagenomic analysis of Mariana Trench sediment samples
Co-supervisor
 Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2013 - 2013 A tool for ontology instance matching
Co-supervisor
 Informática (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2013 - 2013 Implementação de uma base de dados geográficos para a gestão das matérias-primas do grupo Cimpor
Co-supervisor
 Sistemas de Informação Geográfica - Tecnologias e Aplicações (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2008 - 2013 Identifying Chemical Entities on Literature: a Machine Learning Approach using Dictionaries as Domain Knowledge
Supervisor
 Informática (PhD)
Universidade de Lisboa, Portugal
2008 - 2008 Automated extension of Biomedical Ontologies
Supervisor
 Informática (PhD)
Universidade de Lisboa, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2021/09/21 - 2021/09/21 Iberian Health and Food Language Technologies workshop. Held in conjunction with the XXXVII International Conference of the Spanish Society for Natural Language Processing (SEPLN2021) (2021/09/21 - 2021/09/21)
Workshop (Co-organisor)
2021/08/15 - 2021/08/15 Creating Recommender Systems Datasets in Scientific Fields. Tutorial at ACM Conference on Knowledge Discovery and Data Mining (KDD). (2021/08/15 - 2021/08/15)
Workshop (Co-organisor)
2021/04/12 - 2021/04/12 Exploring Biomedical Web Resources using Shell Scripting. Tutorial at 30th The Web Conference (WWW '21) (2021/04/12 - 2021/04/12)
Workshop (Co-organisor)
2021/03/28 - 2021/03/28 Biomedical Text Processing using Semantics. Tutorial at the 43rd European Conference on Information Retrieval (ECIR 2021) (2021/03/28 - 2021/03/28)
Workshop (Co-organisor)
2020/09/04 - 2020/09/04 Biomedical Data and Text Processing using Shell Scripting. Tutorial at the 19th European Conference on Computational Biology (ECCB '20) (2020/09/04 - 2020/09/04)
Workshop (Co-organisor)
2020/04/14 - 2020/04/14 Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages Held in conjunction with the 42nd European Conference on Information Retrieval (ECIR2020) (2020/04/14 - 2020/04/14)
Workshop (Co-organisor)
 Universidade de Lisboa Laboratório de Sistemas Informáticos de Grande Escala, Portugal

Centro Nacional de Supercomputación, Spain
2019/02 - 2019/02 Data and text processing in health and life sciences: an example driven workshop using shell scripting. Tutorial at the Bioinformatics Open Days, Universidade do Minho (2019/02 - 2019/02)
Workshop (Co-organisor)
2015/09/27 - 2015/09/30 6th International Conference on Biomedical Ontology (ICBO 2015). (2015/09/27 - 2015/09/30)
Conference (Co-organisor)

Evaluation committee

Activity description
Role 		Institution / Organization Funding entity
2023 - 2023 Review of Project Proposals
Evaluator
 Schweizerischer Nationalfonds zur Förderung der wissenschaftlichen Forschung
2023 - 2023 Review of Project Proposals
Evaluator
 HFRI - Hellenic Foundation for Research & Innovation
2020 - 2020 Review of Research Proposals
Evaluator
 King Abdullah University of Science and Technology
2020 - 2020 Review of Research Proposals
Evaluator
 Schweizerischer Nationalfonds zur Förderung der wissenschaftlichen Forschung
Distinctions

Award

2022 7th Prize, LitCoin NLP Challenge
NASA, United States

National Center for Advancing Translational Sciences, United States
2018 Scientific Prize in Computer Science and Computer Engineering
Caixa Geral de Depositos, Portugal
2017 Honorable mention in Computer Science and Computer Engineering
Caixa Geral de Depositos, Portugal
2004 Young Engineer Innovation Prize
Ordem dos Engenheiros, Portugal

Other distinction

2025 Top 40 Portuguese scientists in the computer science field
Research.com, United States
2025 World's Top 2% Scientists (Stanford-Elsevier List)
Elsevier BV, Netherlands
2024 Top 40 Portuguese scientists in the computer science field
Research.com, United States