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Francisco M. Couto is currently an associate professor with habilitation at Universidade de Lisboa (Faculty of Sciences) and a researcher at LASIGE. He graduated (2000) and has a master (2001) in Informatics and Computer Engineering from the IST. He concluded his doctorate (2006) in Informatics, specialization Bioinformatics, from the Universidade de Lisboa. He was an invited researcher at EBI, AFMB-CNRS, BioAlma during his doctoral studies. His main research contributions cover several key aspects of bioinformatics and knowledge management, namely in proposing and developing: various text mining solutions that explore the semantics encoded in ontologies; semantic similarity measures and tools using biomedical ontologies; and ontology and linked data matching systems. Until August 2022, he published 2 books; was co-author of 10 chapters, 64 journal papers (49 Q1 Scimago), and 33 conference papers (10 core A and A*); and was the supervisor of 10 PhD theses and of 52 master theses. At that same date, he had more than 6 thousand citations with an h-index of 36 at Google Scholar. He received the Young Engineer Innovation Prize 2004 from the Portuguese Engineers Guild, and an honorable mention in 2017 and the prize in 2018 of the ULisboa/Caixa Geral de Depósitos (CGD) Scientific Prizes.
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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@edu.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
2022/01/01
Concluded
 Informática (Doutoramento)
Major in Sem especialidade
Universidade de Lisboa Faculdade de Ciências, Portugal
"Recommender system to support comprehensive exploration of large scale scientific datasets" (THESIS/DISSERTATION)
2019
Concluded
 Biologia (Doutoramento)
Major in Especialidade: Biologia de Sistemas
Universidade de Lisboa Faculdade de Ciências, Portugal
""Development of a text mining approach to disease network discovery"" (THESIS/DISSERTATION)
2016/05/23
Concluded
 Informática (Título de Agregado)
Major in Engenharia Informática
Universidade de Lisboa Faculdade de Ciências, Portugal
 Aprovado por unanimidade
2014
Concluded
 Bioinformática e Biologia Computacional (Mestrado)
Major in Área de especialização: Bioinformática
Universidade de Lisboa Faculdade de Ciências, Portugal
"Identifying interactions between chemical entities in text" (THESIS/DISSERTATION)
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
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
Projects

Grant

Designation Funders
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
Principal investigator
Fundação para a Ciência e a Tecnologia, I.P.
2011/01 - 2014/06 In silico reconstruction of Streptococcus pneumoniae cellular networks and their impact on virulence
Provided by PTCRIS: 113824
113824
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
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.
2011 - 2013 SPNET: In silico reconstruction of Streptococcus pneumoniae cellular networks and their impact on virulence
PTDC/EBB-EBI/113824/2009
Researcher
Fundação para a Ciência e a Tecnologia
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
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
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. 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
  2. Diana Sousa; Francisco M. Couto. "BiOnt: Deep Learning Using Multiple Biomedical Ontologies for Relation Extraction". 367-374. Springer International Publishing, 2020.
    10.1007/978-3-030-45442-5_46
  3. Márcia Barros; André Moitinho; Francisco M. Couto; Barros M; Moitinho A; Couto FM. "Hybrid Semantic Recommender System for Chemical Compounds". 94-101. Springer International Publishing, 2020.
    10.1007/978-3-030-45442-5_12
  4. 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)". 654-659. Springer International Publishing, 2020.
    10.1007/978-3-030-45442-5_87
  5. Couto, Francisco M. "Semantic similarity definition". 2019.
    https://doi.org/10.1016/B978-0-12-809633-8.20401-9
  6. Couto, Francisco M. "Text Mining for Bioinformatics using Biomedical Literature". 2019.
    https://doi.org/10.1016/B978-0-12-809633-8.20409-3
  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. 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. Couto, Francisco M. "DRecPy: A Python Framework for Developing Deep Learning-Based Recommenders". 2020.
    10.1145/3383313.3418483
  2. Couto, Francisco M. "Report of the First International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages". 2020.
  3. 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.
  4. Couto, Francisco M. "Biomedical Question Answering using Extreme Multi-Label Classification and Ontologies in the Multilingual Panorama". 2020.
  5. Couto, Francisco M. "Towards a Multilingual Corpus for Named Entity Linking Evaluation in the Clinical Domain". 2020.
  6. Couto, Francisco M. "An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents". 2020.
  7. Couto, Francisco M. "COVID-19: A Semantic-Based Pipeline for Recommending Biomedical Entities". 2020.
  8. Couto, Francisco M. "LasigeBioTM at CANTEMIST: Named Entity Recognition and Normalization of Tumour Morphology Entities and Clinical Coding of Spanish Health-related Documents". 2020.
  9. Couto, Francisco M. "Privacy-Preserving Processing of Filtered DNA Reads". 2019.
  10. Couto, Francisco M. "Metadata Analyser: measuring metadata quality". 2017.
    https://doi.org/10.1007/978-3-319-60816-7_24
  11. Couto, Francisco M. "Cloud-Assisted Read Alignment and Privacy". 2017.
    https://doi.org/10.1007/978-3-319-60816-7_27
  12. Couto, Francisco M. "Anthropometric Data Analytics: a Portuguese Case Study". 2017.
    https://doi.org/10.1007/978-3-319-60816-7_12
  13. Couto, Francisco M. "How can photo sharing inspire sharing genomes?". 2017.
    https://doi.org/10.1007/978-3-319-60816-7_10
  14. 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
  15. 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
  16. Couto, Francisco M. "Friendsourcing the Unmet Needs of People with Dementia". 2014.
    https://doi.org/10.1145/2596695.2596716
  17. 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
  18. Couto, Francisco M. "Towards visualizing the alignment of large biomedical ontologies". 2014.
    https://doi.org/10.1007/978-3-319-08590-6_10
  19. Couto, Francisco M. "Towards annotating potential incoherences in BioPortal mappings". 2014.
    https://doi.org/10.1007/978-3-319-11915-1_2
  20. Couto, Francisco M. "Learning Temporal-Dependent Ranking Models". 2014.
    https://doi.org/10.1145/2600428.2609619
  21. 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
  22. Couto, Francisco M. "The AgreementMakerLight Ontology Matching System". 2013.
    https://doi.org/10.1007/978-3-642-41030-7_38
  23. Couto, Francisco M. "Toponym Disambiguation using Ontology-based Semantic Similarity". 2012.
    https://doi.org/10.1007/978-3-642-28885-2_20
  24. Couto, Francisco M. "Toward a Translational Medicine Approach for Hypertrophic Cardiomyopathy". 2012.
    https://doi.org/10.1007/978-3-642-32395-9_12
  25. Couto, Francisco M. "MEDCollector: Multisource Epidemic Data Collector". 2010.
    https://doi.org/10.1007/978-3-642-15020-3_2
  26. Couto, Francisco M. "Epidemic Marketplace: An Information Management System for Epidemiological Data". 2010.
    https://doi.org/10.1007/978-3-642-15020-3_3
  27. Couto, Francisco M. "Identifying Bioentity Recognition Errors of Rule-Based Text-Mining Systems". 2008.
    https://doi.org/10.1109/ICDIM.2008.4746791
  28. Couto, Francisco M. "Validating Associations in Biological Databases". 2006.
    https://doi.org/10.1145/1183614.1183639
  29. Couto, Francisco M. "Semantic Similarity over the Gene Ontology: Family Correlation and Selecting Disjunctive Ancestors". 2005.
    https://doi.org/10.1145/1099554.1099658
  30. Couto, Francisco M. "Classifying biological articles using web resources". 2004.
    https://doi.org/10.1145/967900.967925
Journal article
  1. 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
  2. Asif M; Martiniano HFMC; Lamurias A; Kausar S; Couto FM. "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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. Couto FM. "Introduction.". Advances in experimental medicine and biology (2019): http://europepmc.org/abstract/med/31183816.
    10.1007/978-3-030-13845-5_1
  19. Couto FM. "Resources.". Advances in experimental medicine and biology (2019): http://europepmc.org/abstract/med/31183817.
    10.1007/978-3-030-13845-5_2
  20. 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
  21. Couto, Francisco M. "Multi-domain semantic similarity in biomedical research". BMC Bioinformatics (2019):
    https://doi.org/10.1186/s12859-019-2810-9
  22. 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
  23. 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
  24. 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
  25. Couto, Francisco M. "Using research literature to generate datasets of implicit feedback for recommending scientific items". IEEE Access (2019):
    https://doi.org/10.1109/ACCESS.2019.2958002
  26. Marcia Barros; Andre Moitinho; Francisco M. Couto. "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
  27. 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
  28. Couto, Francisco M. "Tackling the Challenges of Matching Biomedical Ontologies". Journal of Biomedical Semantics (2018):
    https://doi.org/10.1186/s13326-017-0170-9
  29. 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
  30. 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
  31. 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
  32. 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
  33. Couto, Francisco M. "Extracting MicroRNA-Gene Relations from Biomedical Literature using Distant Supervision". PLoS ONE (2017):
    https://doi.org/10.1371/journal.pone.0171929
  34. 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
  35. 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
  36. Couto, Francisco M. "Assessing public metabolomics metadata, towards improving quality". Journal of Integrative Bioinformatics (2017):
    https://doi.org/10.1515/jib-2017-0054
  37. Couto, Francisco M. "Generating a Tolerogenic Cell Therapy Knowledge Graph from Literature". Frontiers in Immunology (2017):
    https://doi.org/10.3389/fimmu.2017.01656
  38. 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
  39. Couto, Francisco M. "Functional Coherence Metrics in Protein Families". Journal of Biomedical Semantics (2016):
    https://doi.org/10.1186/s13326-016-0076-y
  40. 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
  41. 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
  42. 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
  43. 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
  44. 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
  45. Couto, Francisco M. "Ontology alignment repair through modularization and confidence-based heuristics". PLoS ONE (2015):
    https://doi.org/10.1371/journal.pone.0144807
  46. Couto, Francisco M. "Automatic Background Knowledge Selection for Matching Biomedical Ontologies". PLoS ONE (2014):
    https://doi.org/10.1371/journal.pone.0111226
  47. 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
  48. 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
  49. Couto, Francisco M. "Tracking Politics with POWER". Program: electronic library and information systems (2013):
    https://doi.org/10.1108/00330331311313708
  50. 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
  51. Couto, Francisco M. "Enrichment analysis applied to disease prognosis". Journal of Biomedical Semantics (2013):
    https://doi.org/10.1186/2041-1480-4-21
  52. Couto, Francisco M. "Annotation extension through protein family annotation coherence metrics". Frontiers in Genetics (2013):
    https://doi.org/10.3389/fgene.2013.00201
  53. 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
  54. Couto, Francisco M. "Exploiting disjointness axioms to improve semantic similarity measures". Bioinformatics, Oxford Univ Press (2013):
    https://doi.org/10.1093/bioinformatics/btt491
  55. 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
  56. Couto, Francisco M. "Chemical Entity Recognition and Resolution to ChEBI". ISRN Bioinformatics (2012):
    https://doi.org/10.5402/2012/619427
  57. Couto, Francisco M. "Predicting the Extension of Biomedical Ontologies". PLoS Computational Biology (2012):
    https://doi.org/10.1371/journal.pcbi.1002630
  58. 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
  59. 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
  60. 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
  61. 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
  62. Couto, Francisco M. "Semantic Similarity for Automatic Classification of Chemical Compounds". PLoS Computational Biology (2010):
    https://doi.org/10.1371/journal.pcbi.1000937
  63. Couto, Francisco M. "Semantic Similarity in Biomedical Ontologies". PLoS Computational Biology (2009):
    https://doi.org/10.1371/journal.pcbi.1000443
  64. Couto, Francisco M. "Handling Self-citations using Google Scholar". Cybermetrics 13 1 (2009):
    https://doi.org/10451/14427
  65. 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
  66. 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
  67. 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
  68. 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
  69. 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. Asif M; Martiniano HF; Lamurias A; Kausar S; Couto FM. "DGH-GO: Dissecting the Genetic Heterogeneity of complex diseases using Gene Ontology". Preprint. 2022. http://europepmc.org/abstract/PPR/PPR562428.
    10.1101/2022.10.20.513077
  2. Andrade VD; Ruas P; Couto FM. "Named Entity Recognition and Linking: a Portuguese and Spanish Oncological Parallel Corpus". Preprint. 2021. http://europepmc.org/abstract/PPR/PPR397960.
    10.1101/2021.09.16.460605
Report
  1. Couto, Francisco M. 2013. Benchmarking some Portuguese S&T system research units: 2nd Edition.
    https://doi.org/10451/14123
  2. Couto, Francisco M. 2011. Desenvolvimento de Sistemas de Informação baseados em PHP e MySQL, e Java e Oracle.
    https://doi.org/10451/15281
  3. Couto, Francisco M. 2010. Benchmarking some Portuguese S&T system research units.
    https://doi.org/10451/14175
  4. Couto, Francisco M. 2010. Chemical and Metabolic Pathway Semantic Similarity.
    https://doi.org/10451/14249
  5. Couto, Francisco M. 2010. The Geo-Net-PT/Yahoo! GeoPlanet (TM) concordance.
    https://doi.org/10451/14174
  6. Couto, Francisco M. 2010. Desenvolvimento de Aplicações Web baseadas em SOA e AJAX.
    https://doi.org/10451/15279
  7. Couto, Francisco M. 2007. ProteInOn: a Web Tool for Protein Semantic Similarity.
    https://doi.org/10451/14140
  8. Couto, Francisco M. 2007. Semantic Similarity Match for Data Quality.
    https://doi.org/10451/14158
  9. Couto, Francisco M. 2005. Validation of Automated Protein Annotation.
    https://doi.org/10451/14744
  10. Couto, Francisco M. 2003. Implementation of a Functional Semantic Similarity Measure between Gene-Products.
    https://doi.org/10451/14410
  11. 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
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
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
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

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