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Publications for fjcouto (277)

2024
Identifying negative results using biomedical relation extraction systems (2024)
Silvestre, Pedro Moisés Marques
Couto, Francisco José Moreira
Academic documents
2024
Relation extraction for gene and chemical compounds (2024)
Cassanheira, Rodrigo de Castro Sampaio
Couto, Francisco José Moreira
Academic documents
2023
AgreementMakerLight (2023)
Daniel Faria et al., with 6 authors including:
Francisco M. Couto
Catia Pesquita
Journal articles
2023
DGH-GO: dissecting the genetic heterogeneity of complex diseases using gene ontology (2023)
Muhammad Asif
Hugo F. M. C. Martiniano
Andre Lamurias
Samina Kausar
Francisco M. Couto
Journal articles
2023
K-RET: knowledgeable biomedical relation extraction system (2023)
Diana F Sousa
Francisco M Couto
Journal articles
2023
Development of machine learning tool for filtering artifacts in the identification of CNVs (2023)
Matos, José Pedro Parracha de
David, Dezső
Couto, Francisco José Moreira
Academic documents
2023
BioRED track lasigeBioTM submission: Relation extraction using domain ontologies with BioRED (2023)
S. Conceicao
D. Sousa
P. Silvestre
F. Couto
Conference papers
2023
lasigeBioTM at SemEval-2023 Task 7: Improving Natural Language Inference Baseline Systems with Domain Ontologies (2023)
Sofia I. R. Conceição
Diana F. Sousa
Pedro Silvestre
Francisco M Couto
Conference papers
2023
LASIGE and UNICAGE solution to the NASA LitCoin NLP Competition (2023)
Pedro Ruas
Diana F. Sousa
André Neves
Carlos Cruz
Francisco M. Couto
Other
2023
Security, privacy, and trust management in DNA computing (2023)
Maria Fernandes
Jérémie Decouchant
Francisco M. Couto
Book chapters
2023
Deep learning system for biomedical relation extraction combining external sources of knowledge (2023)
Sousa, Diana Francisco de
Couto, Francisco José Moreira
Academic documents
2023
Unveiling co-transcriptional splicing kinetics using novel nascent transcriptomic techniques (2023)
Monteiro, Ana Pereira de Brito Líbano
Fonseca, Maria Carmo
Couto, Francisco José Moreira
Academic documents
2022
SeEn: Sequential enriched datasets for sequence-aware recommendations (2022)
Marcia Barros
André Moitinho
Francisco M. Couto
Journal articles
2022
Biomedical Relation Extraction With Knowledge Graph-Based Recommendations (2022)
Diana Sousa
Francisco M. Couto
Journal articles
2022
NILINKER: Attention-based approach to NIL Entity Linking (2022)
Pedro Ruas
Francisco M. Couto
Journal articles
2022
Recommender system to support comprehensive exploration of large scale scientific datasets (2022)
Barros, Márcia Cristina Afonso
Couto, Francisco José Moreira
Almeida, André Moitinho de
Academic documents
2022
A computational pipeline to identify phenotypic manifestations related to genes (2022)
Ilhéu, Ana Cristina Gonçalves
Couto, Francisco José Moreira
Asif, Muhammad
Academic documents
2021
Extracting Negative Biomedical Relations from Literature (2021)
Leonor Horta Torcato
Francisco José Moreira Couto
Academic documents
2021
Prediction of Prostate Cancer Disease Aggressiveness Using Bi-Parametric Mri Radiomics (2021)
Ana Rodrigues et al., with 6 authors including:
Francisco M. Couto
Journal articles
2021
Prostate MRI Radiomics for Prediction of Gleason Score (2021)
Ana Carolina Vitorino Rodrigues
Nikolaos Papanikolaou
Francisco José Moreira Couto
Academic documents
2021
Named Entity Recognition and Linking in a Multilingual Biomedical Setting (2021)
Vítor Daniel Torres Andrade
Francisco José Moreira Couto
Academic documents
2021
COVID-19 recommender system based on an annotated multilingual corpus (2021)
Márcia Barros
Pedro Ruas
Diana Sousa
Ali Haider Bangash
Francisco M. Couto
Journal articles
2021
Text Mining for Building Biomedical Networks Using Cancer as a Case Study (2021)
Sofia I. R. Conceição
Francisco M. Couto
Journal articles
2021
Information Retrieval Using Machine Learning for Biomarker Curation in the Exposome-Explorer (2021)
Andre Lamurias
Sofia Jesus
Vanessa Neveu
Reza M. Salek
Francisco M. Couto
Journal articles
2021
Development of a Corpus for User-based Scientific Question Answering (2021)
Miguel Ângelo Conde Vieira
Francisco José Moreira Couto
André Francisco Martins Lamúrias
Academic documents
2021
Summary of Tutorials at The Web Conference 2021 (2021)
Robert West et al., with 88 authors including:
Francisco M. Couto
Conference papers
2021
Hybrid semantic recommender system for chemical compounds in large-scale datasets (2021)
Marcia Barros
Andre Moitinho
Francisco M. Couto
Journal articles
2021
Lasige-BioTM at ProfNER: BiLSTM-CRF and contextual spanish embeddings for named entity recognition and tweet binary classification (2021)
P. Ruas
V. Andrade
F. Couto
Conference papers
2021
LASIGE-BioTM at MESINESP2: entity linking with semantic similarity and extreme multi-label classification on spanish biomedical documents (2021)
P. Ruas
V. Andrade
F. Couto
Conference papers
2021
Post-processing BioBERT and using voting methods for biomedical question answering (2021)
M. Campos
F. Couto
Conference papers
2021
lasigeBioTM at BioCreative VII Track 1: Text mining drug and chemical-protein interactions using biomedical ontologies (2021)
D. Sousa
R. Cassanheira
F. Couto
Conference papers
2021
AML and AMLC results for OAEI 2021 (2021)
D. Faria
B. Lima
M. Silva
F. Couto
C. Pesquita
Conference papers
2021
Recommender systems for scientific fields (2021)
M. Barros
A. Moitinho
F. Couto
Conference papers
2020
DRecPy: A Python Framework for Developing Deep Learning-Based Recommenders (2020)
Fábio Colaço
Márcia Barros
Francisco M. Couto
Conference papers
2020
Linking chemical and disease entities to ontologies by integrating PageRank with extracted relations from literature (2020)
Pedro Ruas
Andre Lamurias
Francisco M. Couto
Journal articles
2020
Using Neural Networks for Relation Extraction from Biomedical Literature (2020)
Diana Sousa
Andre Lamurias
Francisco M. Couto
Book chapters
2020
Improving accessibility and distinction between negative results in biomedical relation extraction (2020)
Diana Sousa
Andre Lamurias
Francisco M. Couto
Journal articles
2020
DNA-SeAl: Sensitivity Levels to Optimize the Performance of Privacy-Preserving DNA Alignment (2020)
Maria Fernandes
Jeremie Decouchant
Marcus Volp
Francisco M. Couto
Paulo Esteves-Verissimo
Journal articles
2020
Identification of biological mechanisms underlying a multidimensional ASD phenotype using machine learning (2020)
Muhammad Asif et al., with 9 authors including:
Francisco M. Couto
Journal articles
2020
Generating Biomedical Question Answering Corpora From Q&A Forums (2020)
Andre Lamurias
Diana Sousa
Francisco M. Couto
Journal articles
2020
BiOnt: Deep Learning Using Multiple Biomedical Ontologies for Relation Extraction (2020)
Diana Sousa
Francisco M. Couto
Conference papers
2020
Hybrid Semantic Recommender System for Chemical Compounds (2020)
Márcia Barros
André Moitinho
Francisco M. Couto
Conference papers
2020
Proposal of the First International Workshop on Semantic Indexing and Information Retrieval for Health from Heterogeneous Content Types and Languages (SIIRH) (2020)
Francisco M. Couto
Martin Krallinger
Conference papers
2020
First International Workshop on Semantic Indexing and Information Retrieval for Health from heterogeneous content types and languages (SIIRH) (2020)
Francisco M. Couto
Martin Krallinger
Books
2020
ECIR 2020 workshops: assessing the impact of going online (2020)
Sérgio Nunes et al., with 14 authors including:
Francisco M. Couto
Journal articles
2020
Biomedical question answering using extreme multi-label classification and ontologies in the multilingual panorama (2020)
A. Neves, A. Lamurias
Francisco M. Couto
Conference papers
2020
LasigeBioTM team at CLEF2020 ChEMU evaluation lab: Named entity recognition and event extraction from chemical reactions described in patents using BioBERT NER and RE (2020)
P. Ruas, A. Lamurias
Francisco M. Couto
Conference papers
2020
An extended overview of the CLEF 2020 ChEMU lab: Information extraction of chemical reactions from patents (2020)
J. He, D. Nguyen, S. Akhondi, C. Druckenbrodt, C. Thorne, R. Hoessel, Z. Afzal, Z. Zhai, B. Fang, H. Yoshikawa, A. Albahem, J. Wang, Y. Ren, Z. Zhang, Y. Zhang, M. Dao, P. Ruas, A. Lamurias
Francisco M. Couto
J. Copara, N. Naderi, J. Knafou, P. Ruch, D. Teodoro, D. Lowe, J. Mayfield, A. Köksal, H. Dönmez, E. Özk?r?ml?, A. Özgür, D. Mahendran, G. Gurdin, N. Lewinski, C. Tang, B. McInnes, M. C.S., P. Rao, S. Devi, L. Cavedon, T. Cohn, T. Baldwin, and K. Verspoor
Conference papers
2020
Towards a multilingual corpus for named entity linking evaluation in the clinical domain (2020)
P. Ruas, A. Lamurias
Francisco M. Couto
Conference papers
2020
Report of the first international workshop on semantic indexing and information retrieval for health from heterogeneous content types and languages (2020)
Francisco M. Couto
Martin Krallinger
Conference papers
2020
A hybrid approach toward biomedical relation extraction training corpora: combining distant supervision with crowdsourcing (2020)
Diana Sousa
Andre Lamurias
Francisco M Couto
Journal articles
2020
Validation of Automatic Similarity Measures (2020)
Pedro Jorge Mendes dos Santos
Francisco José Moreira Couto
João Diogo Silva Ferreira
Academic documents
2020
Applying deep learning extreme multi-label classification to the biomedical and multilingual panoramas (2020)
Neves, André Daniel Costa das
Couto, Francisco José Moreira
Lamúrias, André Francisco Martins
Academic documents
2020
Recommender Systems Based on Deep Learning Techniques (2020)
Fábio Iúri Gaspar Colaço
Francisco José Moreira Couto
Academic documents
2019
PPR-SSM: personalized PageRank and semantic similarity measures for entity linking (2019)
Andre Lamurias
Pedro Ruas
Francisco M. Couto
Journal articles
2019
FunVar: A systematic pipeline to unravel the convergence patterns of genetic variants in ASD, a paradigmatic complex disease (2019)
Muhammad Asif
Astrid M. Vicente
Francisco M. Couto
Journal articles
2019
Semantic Similarity in Cheminformatics (2019)
João D. Ferreira
Francisco M. Couto
Book chapters
2019
Multi-domain semantic similarity in biomedical research (2019)
João D. Ferreira
Francisco M. Couto
Journal articles
2019
BO-LSTM: classifying relations via long short-term memory networks along biomedical ontologies (2019)
Andre Lamurias
Diana Sousa
Luka A. Clarke
Francisco M. Couto
Journal articles
2019
Semantic Similarity Definition (2019)
Francisco M. Couto
Andre Lamurias
Book chapters
2019
Text Mining for Bioinformatics Using Biomedical Literature (2019)
Andre Lamurias
Francisco M. Couto
Book chapters
2019
LasigeBioTM at MEDIQA 2019: Biomedical Question Answering using Bidirectional Transformers and Named Entity Recognition (2019)
Andre Lamurias
Francisco M Couto
Conference papers
2019
Information Retrieval using Machine Learning for Database Curation (2019)
Jesus, Sofia Pinheiro Rodrigues de
Couto, Francisco José Moreira
Academic documents
2019
Exploring Biomedical Ontologies, Personalized PageRank and Semantic Similarity in the Entity Linking task (2019)
Ruas, Pedro Simões
Couto, Francisco José Moreira
Academic documents
2019
Using Research Literature to Generate Datasets of Implicit Feedback for Recommending Scientific Items (2019)
Marcia Barros
Andre Moitinho
Francisco M. Couto
Journal articles
2019
A Silver Standard Corpus of Human Phenotype-Gene Relations (2019)
Diana Sousa
Andre Lamurias
Francisco M. Couto
Conference papers
2019
Privacy-preserving processing of filtered DNA reads (2019)
M. Fernandes, J. Decouchant, M. Volp
Francisco M. Couto
Paulo Verissímo
Conference papers
2019
DNA-SeAl: Sensitivity Levels to Optimize the Performance of Privacy-Preserving DNA Alignment (2019)
Maria Fernandes
Jeremie Decouchant
Marcus Volp
Francisco M. Couto
Paulo Verissimo
Journal articles
2019
Using Research Literature to Generate Datasets of Implicit Feedback for Recommending Scientific Items (2019)
Marcia Barros
Andre Moitinho
Francisco M. Couto
Journal articles
2019
A Silver Standard Corpus of Human Phenotype-Gene Relations (2019)
Diana Sousa
Andre Lamurias
Francisco M. Couto
Conference papers
2019
Development of a text mining approach to disease network discovery (2019)
Lamúrias, André Francisco Martins
Couto, Francisco Jose Moreira
Clarke, Luka Alexander
Academic documents
2019
Extracting phenotype-gene relations from biomedical literature using distant supervision and deep learning (2019)
Diana Francisco de Sousa
Couto, Francisco José Moreira
Academic documents
2019
Data and Text Processing for Health and Life Sciences (2019)
Francisco M. Couto
Books
2019
Introdução à Bioinformática Via Linha de Comando (2019)
Francisco Couto
Books
2018
Identifying disease genes using machine learning and gene functional similarities, assessed through Gene Ontology (2018)
Muhammad Asif
Hugo F. M. C. M. Martiniano
Astrid M. Vicente
Francisco M. Couto
Journal articles
2018
MER: a shell script and annotation server for minimal named entity recognition and linking (2018)
Francisco M. Couto
Andre Lamurias
Journal articles
2018
MER: a shell script and annotation server for minimal named entity recognition and linking (2018)
Francisco M. Couto
Andre Lamurias
Journal articles
2018
MER: a shell script and annotation server for minimal named entity recognition and linking (2018)
Francisco M. Couto
Andre Lamurias
Journal articles
2018
Witches’ broom resistant genotype CCN51 shows greater diversity of symbiont bacteria in its phylloplane than susceptible genotype catongo (2018)
Juliano Oliveira Santana et al., with 8 authors including:
Francisco M. Couto
Journal articles
2018
Extracting biomedical relations from biomedical literature (2018)
Tânia Sofia Guerreiro Maldonado
Francisco José Moreira Couto
Academic documents
2018
A System medicine approach to study autism spectrum disorder, based on genomic, and clinical data (2018)
Muhammad Asif
Asdrid Moura Vicente
Francisco José Moreira Couto
Academic documents
2018
Accurate filtering of privacy-sensitive information in raw genomic data (2018)
Jérémie Decouchant
Maria Fernandes
Marcus Völp
Francisco M Couto
Paulo Esteves-Veríssimo
Journal articles
2018
Tackling the challenges of matching biomedical ontologies (2018)
Daniel Faria et al., with 6 authors including:
Daniel Faria
Catia Pesquita
Francisco M. Couto
Journal articles
2018
Results of AML in OAEI 2018 (2018)
D. Faria
C. Pesquita
B. Balasubramani, T. Tervo, D. Carriço, R. Garrilha
F. Couto
I. Cruz
Conference papers
2018
Multi-domain semantic similarity in biomedical research (2018)
J. Ferreira
F. Couto
Conference papers
2018
The role of antisense transcription on regulation of gene expression (2018)
Rui Sérgio de Sousa Luís
Fonseca, M. Carmo
Couto, Francisco José Moreira
Academic documents
2018
RESISTIR - intelligent decision support systems for personalized prevention and clinical management of infectious diseases (2018)
R. Dias et al., with 9 authors including:
C. Pesquita
J. Rebelo
A. Pedrosa
C. Santos
F. Couto
Conference papers
2018
Associação entre variantes genéticas e perfil clínico multidimensional de doentes com perturbação do espetro do autismo: uma abordagem integrativa (2018)
M. Asif
H. Martiniano
F. Couto
A. Vicente
Journal articles
2017
Assessing Public Metabolomics Metadata, Towards Improving Quality (2017)
João D. Ferreira
Bruno Inácio
Reza M. Salek
Francisco M. Couto
Journal articles
2017
Generating a Tolerogenic Cell Therapy Knowledge Graph from Literature (2017)
Andre Lamurias
João D. Ferreira
Luka A. Clarke
Francisco M. Couto
Journal articles
2017
Generating a Tolerogenic Cell Therapy Knowledge Graph from Literature (2017)
Andre Lamurias
João D. Ferreira
Luka A. Clarke
Francisco M. Couto
Journal articles
2017
Semantic annotation of electronic health records in a multilingual environment (2017)
Luis Filipe Leal Campos
Couto, Francisco José Moreira
Pedro, Vasco Calais
Academic documents
2017
Biomedical semantic question and answering system (2017)
Miguel Jorge Vitorino Sousa Rodrigues
Couto, Francisco José Moreira
Academic documents
2017
Identifying human phenotype terms in text using a machine learning approach (2017)
Manuel Stapleton Garcia De Vasconcelos Lobo
Couto, Francisco José Moreira
Academic documents
2017
Anthropometric data analytics: a portuguese case study (2017)
António Pedro Pereira Barata
Couto, Francisco José Moreira
Monteiro, Lucília da Conceição Mourão de Carvalho Cáceres
Academic documents
2017
Previsão da localização subcelular de Proteínas Humanas com base em Aprendizagem Automática (2017)
Pedro De Almeida Martins
Couto, Francisco José Moreira
Amaral, Margarida
Academic documents
2017
Extracting microRNA-gene relations from biomedical literature using distant supervision (2017)
Andre Lamurias
Luka A. Clarke
Francisco M. Couto
Journal articles
2017
Extracting microRNA-gene relations from biomedical literature using distant supervision (2017)
Andre Lamurias
Luka A. Clarke
Francisco M. Couto
Journal articles
2017
Impact of translation on named-entity recognition in radiology texts (2017)
Luís Campos
Vasco Pedro
Francisco Couto
Journal articles
2017
Identifying Human Phenotype Terms by Combining Machine Learning and Validation Rules (2017)
Manuel Lobo
Andre Lamurias
Francisco M. Couto
Journal articles
2017
Identifying Human Phenotype Terms by Combining Machine Learning and Validation Rules (2017)
Manuel Lobo
Andre Lamurias
Francisco M. Couto
Journal articles
2017
ULISBOA at SemEval-2017 Task 12: Extraction and classification of temporal expressions and events (2017)
A. Lamurias
Diana Sousa
S. Pereira
L.A. Clarke
F. Couto
Conference papers
2017
MoRS at SemEval-2017 task 3: Easy to use SVM in ranking tasks (2017)
M. Rodrigues
F. Couto
Conference papers
2017
IBEnt: Chemical entity mentions in patents using ChEBI (2017)
A. Lamurias, L. Campos
F. Couto
Conference papers
2017
MER: a minimal named-entity recognition tagger and annotation server (2017)
F. Couto
L. Campos, and A. Lamurias
Conference papers
2017
Can the wisdom of the crowd be used to improve the creation of gold-standard for text mining applications? (2017)
L. Campos, A. Lamurias
F. Couto
Conference papers
2017
Results of AML in OAEI 2017 (2017)
D. Faria, B. Balasubramani, V. Shivaprabhu, I. Mott
C. Pesquita
F. Couto
I. Cruz
Conference papers
2017
Cloud-Assisted Read Alignment and Privacy (2017)
Maria Fernandes
Jérémie Decouchant
Francisco M. Couto
Paulo Esteves-Verissimo
Conference papers
2017
Anthropometric Data Analytics: A Portuguese Case Study (2017)
António Barata
Lucília Carvalho
Francisco M. Couto
Conference papers
2017
Metadata Analyser: Measuring Metadata Quality (2017)
Bruno Inácio
João D. Ferreira
Francisco M. Couto
Conference papers
2017
How Can Photo Sharing Inspire Sharing Genomes? (2017)
Vinicius V. Cogo et al., with 6 authors including:
Vinicius V. Cogo
Alysson Bessani
Francisco M. Couto
Margarida  Gama-Carvalho
Conference papers
2017
3D identification of clusters: a cancer cell case-study (2017)
G. Figueiró
F. Couto
A. Moitinho
Conference papers
2017
Development of a text mining framework for systems biology (2017)
A. Lamurias, L. Clarke
F. Couto
Conference papers
2017
Semantic annotation of electronic health records in a multilingual environment (2017)
L. Campos, V. Pedro
F. Couto
Conference papers
2017
An integrative system biology approach for dissecting autism spectrum disorder (2017)
M. Asif et al., with 7 authors including:
H. Martiniano
F. Couto
Conference papers
2017
Translating the complex ASD genetic architecture into clinical phenotype using an integrative system biology approach (2017)
M. Asif et al., with 8 authors including:
H. Martiniano
F. Couto
Conference papers
2017
An integrative system biology approach to delineate complex genotype phenotype associations in Autism Spectrum Disorder (2017)
M. Asif et al., with 7 authors including:
H. Martiniano
F. Couto
Conference papers
2017
MRA - proof of concept of a multilingual report annotator web application (2017)
L. Campos
F. Couto
Other
2016
Radiation monitoring system in clinical imaging (2016)
Florêncio, Rita João Martinho
Couto, Francisco José Moreira
Matela, Nuno Miguel de Pinto Lobo e
Academic documents
2016
Desenvolvimento de uma rede social desportiva (2016)
Silva, Rodolfo José Machado
Couto, Francisco José Moreira
Teixeira, Jorge Filipe Pinheiro Guerra de Ribeiro
Academic documents
2016
Knowledge Representation and Management: a Linked Data Perspective (2016)
M. Barros
F.M. Couto
Journal articles
2016
Qanto valem os metadados? (2016)
Inácio, Bruno Filipe Prudêncio
Couto, Francisco José Moreira
Ferreira, João Diogo Silva
Academic documents
2016
Functional coherence metrics in protein families (2016)
Hugo P. Bastos
Lisete Sousa
Luka A. Clarke
Francisco M. Couto
Journal articles
2016
Increased frequency of the autism broader phenotype in mothers transmitting etiological CNVs to sons affected by Autism Spectrum Disorder (ASD) (2016)
M. Asif et al., with 9 authors including:
L. Sousa
F. Couto
Journal articles
2016
Semantic Similarity Across Biomedical Ontologies (2016)
João Diogo Silva Ferreira
Couto, Francisco José Moreira
Academic documents
2016
Impacto das obras musicais lusófonas nas redes sociais (2016)
Mónica Isabel Henriques Abreu
Francisco José Moreira Couto
Academic documents
2016
Aplicações na web para validação e classificação de notícias pela crowd (2016)
Aparício, Tiago Miguel Marques
Guerreiro, Tiago
Couto, Francisco José Moreira
Academic documents
2016
Radiation Monitoring System in Clinical Imaging (2016)
Florencio, R. M.
Couto, F. M.
Matela, N.
Afonso, J..
Conference papers
2016
ULISBOA at SemEval-2016 task 12: Extraction of temporal expressions, clinical events and relations using IBEnt (2016)
M. Barros, A. Lamurias, G. Figueiro, M. Antunes, J. Teixeira, A. Pinheiro
F. Couto
M. Barros
Conference papers
2016
Extraction of regulatory events using kernel-based classifiers and distant supervision (2016)
A. Lamurias, M. Rodrigues, L. Clarke
F. Couto
Conference papers
2016
A pipeline for producing a scientifically accurate visualisation of the Milky Way (2016)
M. Barros et al., with 7 authors including:
F. Couto
A. Krone-Martins
Conference papers
2016
A flexible recommendation system for cable TV (2016)
D. Goncalves, M. Costa
F. Couto
Conference papers
2016
A large-scale characterization of user behaviour in cable TV (2016)
D. Goncalves, M. Costa
F. Couto
Conference papers
2016
OAEI 2016 results of AML (2016)
D. Faria
C. Pesquita
B. Balasubramani, C. Martins, J. Cardoso, H. Curado
F. Couto
I. Cruz
Conference papers
2016
Anthropometric data analytics: Portuguese case-study (2016)
A. Barata
F. Couto
L. Carvalho
Conference papers
2016
Extraction of temporal expressions and clinical events from clinical notes (2016)
M. Barros, A. Lamúrias, M. Antunes, J. Teixeira, G. Figueiró, A. Pinheiro
F. Couto
Conference papers
2016
Exploring machine learning algorithms to predict subcellular localizations (2016)
P. Martins, L. Clarke, M. Amaral
F. Couto
Conference papers
2016
Identifying human phenotype terms in text using a machine learning approach (2016)
M. Lobo, A. Lamurias
F. Couto
Conference papers
2016
A proposal for allele validation tool (AVT) for whole genome multilocus sequence typing (wgMLST) schemas (2016)
H. Curado, M. Cândido, M. Silva, J. Carriço
F. Couto
Conference papers
2016
Maternal copy number variants (CNV) transmission to their Autism Spectrum Disorder (ASD) sons correlates with phenotypic traits (2016)
M. Asif, I. Conceição, K. Kwiatkowska, C. Rasga
F. Couto
A. Vicente
Conference papers
2016
WS4A: a biomedical question and answering system based on public web services and ontologies (2016)
M. Rodriques, M. Fale
F. Couto
Conference papers
2016
Knowledge ratings in MetaboLights (2016)
C. Ramos, M. Louro, M. Santos
F. Couto
Other
2015
GRYFUN: A web application for GO term annotation visualization and analysis in protein sets (2015)
Hugo Bastos
L. Sousa
L. Clarke
Francisco Couto
Journal articles
2015
Improving chemical entity recognition through h-index based semantic similarity (2015)
Andre Lamurias
João D Ferreira
Francisco M Couto
Journal articles
2015
Improving chemical entity recognition through h-index based semantic similarity (2015)
André Lamúrias
João Ferreira
Francisco Couto
Journal articles
2015
The semantic web in translational medicine: current applications and future directions (2015)
Cátia Machado
Dietrich Rebholz-Schuhmann
Ana Freitas
Francisco Couto
Journal articles
2015
IICE: Web Tool for Automatic Identification of Chemical Entities and Interactions (2015)
Andre Lamurias
Luka A. Clarke
Francisco M. Couto
Conference papers
2015
Ontology alignment repair through modularization and confidence-based heuristics (2015)
Emanuel Santos
Daniel Faria
Cátia Pesquita
Francisco Couto
Journal articles
2015
The CHEMDNER corpus of chemicals and drugs and its annotation principles (2015)
Martin Krallinger et al., with 53 authors including:
Francisco M. Couto
Journal articles
2015
IICE: Web Tool for Automatic Identification of Chemical Entities and Interactions (2015)
Andre Lamurias
Luka A. Clarke
Francisco M. Couto
Conference papers
2015
Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora (2015)
Tudor Groza et al., with 10 authors including:
Francisco M. Couto
Journal articles
2015
ULisboa: Recognition and normalization of medical concepts (2015)
André Leal
Bruno Martins
Francisco Couto
Conference papers
2015
Identifying chemical entities in patents using brown clustering and semantic similarity (2015)
André Lamúrias
Manuel Lobo
M. Antunes
L. Clarke
Francisco Couto
Conference papers
2015
Annotating biomedical terms in electronic health records using crowd-sourcing (2015)
André Lamurias
V. Pedro
L. Clarke
Francisco Couto
Conference papers
2015
A high-throughput method to detect privacy-sensitive human genomic data (2015)
Vinicius Vielmo Cogo
Alysson Bessani
Francisco M. Couto
Paulo Veríssimo
Conference papers
2015
Metarate - incentivize data integration and sharing by rating and rewarding metadata annotation (2015)
Francisco Couto
Conference papers
2015
Recognition and normalization of biomedical entities based on ontologies (2015)
André Leal
Bruno Martins
Francisco Couto
Conference papers
2015
Social impact - identifying quotes of literary works in social networks (2015)
Carlos Barata et al., with 6 authors including:
Francisco Couto
Conference papers
2015
Proocedings of the International Conference on Biomedical Ontologies (ICBO) (2015)
Alastair Francisco Couto
Janna Hastings
Books
2015
AML results for OAEI 2015 (2015)
Daniel Faria et al., with 9 authors including:
Francisco Couto
Other
2015
Functional coherence and annotation agreement metrics for enzyme families (2015)
Hugo Bastos
Francisco José Moreira Couto
Luka Alexander Clarke
Academic documents
2015
Development of a scalable, precise, and high-coverage genomics mapping tool for NGS (2015)
Natacha Leitão
Francisco José Moreira Couto
João Carlos Antunes Leitão
Academic documents
2015
3D Visualization of Very Large Databases - Integrating and expanding the state of the art in Bioinformatics and Astroinformatics (2015)
Miguel Gomes
André Maria da Silva Dias Moitinho de Almeida
Francisco José Moreira Couto
Academic documents
2015
Assessing pseudogene expression during neural differentiation by RNA-Seq (2015)
Luis Simões
Ana Rita Fialho Grosso
Francisco José Moreira Couto
Academic documents
2015
Anti and Pro-longevity Genes Differentiation and Overlap with Age-related Diseases (2015)
Maria Fernandes
João Pedro de Magalhães
Francisco M. Couto
Academic documents
2015
Desenvolvimento de Aplicação Web de Pesquisa, Gestão e Partilha de Eventos (2015)
Luís Oliveira
António Emanuel Magalhães Duarte Pereira dos Santos
Francisco José Moreira Couto
Academic documents
2015
Recognition and normalization of biomedical entities within clinical notes (2015)
André Leal
Francisco José Moreira Couto
Bruno Emanuel da Graça Martins
Academic documents
2015
Towards an engaging social TV on a second screen (2015)
Vítor Martins
Francisco José Moreira Couto
Paulo Ricardo Pacheco Rodrigues Trezentos
Academic documents
2015
Recommendation system for modern television (2015)
Diogo Gonçalves
Francisco José Moreira Couto
Paulo Ricardo Pacheco Rodrigues Trezentos
Academic documents
2015
Análise de corpora jornalístico através das ocorrências de N-gramas (2015)
João Oliveira
Francisco José Moreira Couto
Bruno Emanuel da Graça Martins
Academic documents
2014
Towards an intelligent biographical cognitive prosthesis (2014)
Carilho, José Alberto Barreto Duarte
Guerreiro, Tiago
Couto, Francisco José Moreira
Academic documents
2014
Impacto de obras literárias nas redes sociais (2014)
Barata, Carlos André Freitas
Couto, Francisco José Moreira
Guerreiro, Tiago
Academic documents
2014
Identifying interactions between chemical entities in text (2014)
Lamúrias, André Francisco Martins
Couto, Francisco José Moreira
Academic documents
2014
NGSOnto - Proposta de uma ontologia para descrever o processo de Sequenciação de Alto Desempenho (2014)
Silva, Mickael Santos da
Carriço, João André Nogueira Custódio
Couto, Francisco José Moreira
Academic documents
2014
Knowledge representation for data integration and exploration in translational medicine (2014)
Machado, Cátia Maria
Couto, Francisco José Moreira
Freitas, Ana Teresa
Academic documents
2014
Information Search in Web Archives (2014)
Costa, Miguel Ângelo Leal da
Silva, Mário J. Gaspar da
Couto, Francisco José Moreira
Academic documents
2014
Towards Annotating Potential Incoherences in BioPortal Mappings (2014)
Daniel Faria
Ernesto Jiménez-Ruiz
Catia Pesquita
Emanuel Santos
Francisco M. Couto
Conference papers
2014
Friendsourcing the unmet needs of people with dementia (2014)
João Martins et al., with 7 authors including:
Carlos Duarte
Francisco M. Couto
Luís Carriço
Tiago Guerreiro
Conference papers
2014
Towards annotating potential incoherences in BioPortal mappings (2014)
Daniel Faria
E. Jiménez-Ruiz
Cátia Pesquita
Emanuel Santos
Francisco Couto
Conference papers
2014
AgreementMakerLight: A Scalable Automated Ontology Matching System (2014)
Daniel Faria
Cátia Pesquita
Emanuel Santos
Isabel Cruz
Francisco Couto
Conference papers
2014
Veja - visual exploration just anywhere (2014)
Andre Moitinho et al., with 6 authors including:
Alberto Krone-Martins
Francisco M. Couto
Conference papers
2014
Ulisboa: Identification and classification of medical concepts (2014)
Andre Leal Diogo Gonçalves
Bruno Martins
Francisco Couto
Conference papers
2014
Exploração visual online de bases de dados astronómicas (2014)
Tiago Mendes et al., with 7 authors including:
Francisco Couto
Tiago Guerreiro
Alberto Krone-Martins
Conference papers
2014
AgreementMakerLight 2.0: Towards efficient large-scale ontology matching (2014)
Daniel Faria
Cátia Pesquita
Emanuel Santos
Isabel Cruz
Francisco Couto
Conference papers
2014
Building reference alignments for compound matching of multiple ontologies using obo cross-products (2014)
Catia Pesquita et al., with 6 authors including:
Catia Pesquita
Daniel Faria
Francisco M. Couto
Conference papers
2014
Automatic Background Knowledge Selection for Matching Biomedical Ontologies (2014)
Daniel Faria
Cátia Pesquita
Emanuel Santos
Isabel Cruz
Francisco Couto
Journal articles
2014
Using Google Scholar to predict self-citation: A case study in health economics (2014)
Richard Norman
Francisco M Couto
Other
2014
Predicting Relevant Events in the Life of a Person with Alzheime (2014)
José Carilho et al., with 7 authors including:
Luís Carriço
Carlos Duarte
Francisco M Couto
Conference papers
2013
Annotation extension through protein family annotation coherence metrics (2013)
Hugo P. Bastos
Luka A. Clarke
Francisco M. Couto
Journal articles
2013
REACTION: A naive machine learning approach for sentiment classification (2013)
S. Moreira
J. Filgueiras
Bruno Martins
Francisco Couto
Mário Silva
Conference papers
2013
LASIGE: using conditional random fields and chebi ontology (2013)
Tiago Grego
F. Pinto
Francisco Couto
Conference papers
2013
Comparative genomics of bacillus spp.: can core genome be the key for new therapeutics? assessment of the core genome of bacillus spp. and its stability (2013)
C. Alonso
Francisco Couto
R. Dias
Conference papers
2013
Semantic similarity in the biomedical domain (2013)
João Ferreira
Francisco Couto
Conference papers
2013
NGSOnto - keeping track of the ngs pipeline process using an ontological approach and its application on molecular epidemiology (2013)
Mário Silva et al., with 6 authors including:
Francisco Couto
Conference papers
2013
Ontology alignment repair through modularization and confidence-based heuristics (2013)
Emanuel Santos
Daniel Faria
Cátia Pesquita
Francisco Couto
Other
2013
Benchmarking some portuguese S&T system research units: 2nd edition (2013)
Francisco Couto
Daniel Faria
Bruno Tavares
Pedro Gonçalves
Paulo Verissimo
Other
2013
Identifying Chemical Entities on Literature: a Machine Learning Approach using Dictionaries as Domain Knowledge (2013)
Tiago Daniel Pereira Grego
Couto, Francisco José Moreira
Academic documents
2013
A tool for ontology instance matching (2013)
André Filipe Agostinho Lopes
Couto, Francisco José Moreira
Silva, Mário J. Gaspar da
Academic documents
2013
Implementação de uma Base de Dados Geográficos para a Gestão das Matérias-Primas do grupo Cimpor (2013)
Tiago Filipe Francisco Santos
Catita, Cristina Maria Sousa
Couto, Francisco José Moreira
Academic documents
2013
Metagenomic analysis of Mariana Trench sediment samples (2013)
Vera Maria Leal Carvalho
Couto, Francisco José Moreira
Hansen, Martin Asser
Academic documents
2013
Enrichment analysis applied to disease prognosis (2013)
Cátia Machado
A. Freitas
Francisco Couto
Journal articles
2013
The next generation of similarity measures that fully explore the semantics in biomedical ontologies (2013)
Francisco Couto
H. Pinto
Journal articles
2013
Annotation extension through protein family annotation coherence metrics (2013)
Hugo Bastos
L. Clarke
Francisco Couto
Other
2013
Exploiting disjointness axioms to improve semantic similarity measures (2013)
João Ferreira
J. Hastings
Francisco Couto
Journal articles
2013
Tracking politics with POWER (2013)
Silvio Moreira
David Batista
Paula Carvalho
Francisco Couto
Mário Silva
Journal articles
2013
Enhancement of chemical entity identification in text using semantic similarity validation (2013)
Tiago Grego
Francisco Couto
Journal articles
2013
Chemical compound and drug name recognition using crfs and semantic similarity based on chebi (2013)
André Lamurias
Tiago Grego
Francisco Couto
Conference papers
2013
Exploring ontological knowledge for translational medicine (2013)
Cátia Machado
Francisco Couto
A. Freitas
Conference papers
2013
What's in a `nym'? synonyms in biomedical ontology matching (2013)
Cátia Pesquita et al., with 6 authors including:
Cátia Pesquita
Daniel Faria
Francisco Couto
Conference papers
2013
To repair or not to repair: reconciling correctness and coherence in ontology reference alignments (2013)
Cátia Pesquita
Daniel Faria
Emanuel Santos
Francisco Couto
Conference papers
2013
Semi-automated annotation of epidemiological resources (2013)
Cátia Pesquita
João Ferreira
Francisco Couto
Mário Silva
Conference papers
2013
The AgreementMakerLight ontology matching system (2013)
Daniel Faria et al., with 6 authors including:
Daniel Faria
Cátia Pesquita
Francisco Couto
Conference papers
2013
Digital preservation of epidemic resources: coupling metadata and ontologies (2013)
João Ferreira
Cátia Pesquita
Francisco Couto
Mário Silva
Conference papers
2013
A survey of web archive search architectures (2013)
Miguel Costa
Daniel Gomes
Francisco Couto
Mário Silva
Conference papers
2012
The Epidemic Marketplace Platform: towards semantic characterization of epidemiological resources using biomedical ontologies (2012)
Francisco M Couto et al., with 8 authors including:
Francisco M Couto
João D Ferreira
Conference papers
2012
Semantic Similarity in Biomedical Ontologies: measurement, assessment and applications (2012)
F. Couto
Conference papers
2012
Testing the AgreementMaker system in the anatomy task of OAEI 2012 (2012)
Daniel Faria et al., with 6 authors including:
Francisco Couto
Other
2012
Chemical Entity Recognition and Resolution to ChEBI (2012)
Tiago Grego
 Catia Pesquita
 Hugo Bastos
 Francisco M. Couto
Other
2012
Bringing epidemiology into the Semantic Web (2012)
João D. Ferreira
Catia Pesquita
Francisco M. Couto
Mário J. Silva
Conference papers
2012
Predicting the Extension of Biomedical Ontologies (2012)
Catia Pesquita
Francisco M. Couto
Journal articles
2012
Automated Extension of Biomedical Ontologies (2012)
Pesquita, Cátia Luísa Santana Calisto
Couto, Francisco José Moreira
Academic documents
2012
Citation Impact Discerning Self-Citation: Improving User Interaction (2012)
Sousa, Tiago Alberto Paiva de
Couto, Francisco José Moreira
Veríssimo, Paulo
Academic documents
2011
Generic semantic relatedness measure for biomedical ontologies (2011)
J. Ferreira
F. Couto
Conference papers
2011
Where GO is going and what it means for ontology extension (2011)
C. Pesquita
F. Couto
Conference papers
2011
Biomedical ontology matching using the AgreementMaker system (2011)
I. Cruz
C. Stroe
C. Pesquita
F. Couto
V. Cross
Conference papers
2011
POWER: Politics ontology for web entity retrieval (2011)
S. Moreira
D. Batista
P. Carvalho
F. Couto
M. Silva
Conference papers
2011
Exploring gene ontology relationships in enzyme families: An application to polysaccharide lyases (2011)
H. Bastos
F. Couto
P. Coutinho
Conference papers
2011
Medidas de semelhança semântica aplicadas às ontologias geográficas (2011)
Amoedo, Daniel António Correia
Couto, Francisco José Moreira
Academic documents
2011
Aplicações com base em ontologias biomédicas: uma abordagem web semântica (2011)
Tavares, Bruno Filipe Gomes Feteira da Costa
Couto, Francisco José Moreira
Academic documents
2010
Semantic similarity for automatic classification of chemical compounds (2010)
João D. Ferreira
Francisco Couto
Journal articles
2010
Rescue of F508del-CFTR by RXR motif inactivation triggers proteome modulation associated with the unfolded protein response (2010)
Patricia Gomes-Alves
Francisco Couto
Cátia Pesquita
AV Coelho
Deborah Penque
Journal articles
2010
Semantic Characterization of Hypertrophic Cardiomyopathy Disease (2010)
Cátia M. Machado et al., with 6 authors including:
Francisco Couto
Conference papers
2010
BLOOMS on AgreementMaker: results for OAEI 2010 (2010)
Cátia Pesquita
Cosmin Stroe
Isabel F. Cruz
Francisco Couto
Conference papers
2010
Geographic Signatures for Semantic Retrieval (2010)
David Batista
Mário J. Silva
Francisco Couto
Bibek Behera
Conference papers
2010
MEDCollector: Multisource Epidemic Data Collector (2010)
João Zamite
Fabrício Silva
Francisco Couto
Mário J. Silva
Conference papers
2010
Epidemic Marketplace: An Information Management System for Epidemiological Data (2010)
Luis Filipe Lopes et al., with 7 authors including:
Francisco Couto
Conference papers
2010
Building a Digital Library for Epidemic Modelling (2010)
Mário J. Silva
Fabrício A.B. Silva
Luís Filipe Lopes
Francisco Couto
Conference papers
2010
Epidemic Marketplace: an e-Science Platform for Epidemic Modelling and Analysis (2010)
Fabrício A.B. Silva
Mário J. Silva
Francisco Couto
Other
2010
Chemical and Metabolic Pathway SemanticSimilarity (2010)
Tiago Grego et al., with 7 authors including:
João D. Ferreira
Francisco Couto
Other
2010
The Geo-Net- PT/Yahoo! GeoPlanet (TM) concordance (2010)
João Ferreira
David Batista
Francisco Couto
Mário J. Silva
Other
2009
GREAT: Gene Regulation EvAluation Tool (2009)
Catia Machado
Hugo Bastos
Francisco Couto
Conference papers
2009
Measuring coherence between electronic and manual annotations in biological databases (2009)
Catia Pesquita
Daniel Faria
Rui Lopes
Francisco M. Couto
Conference papers
2009
Collaborative Evaluation of GO-based Similarity Measures (2009)
Catia Pesquita
Delphine Pessoa
Daniel Faria
Francisco Couto
Conference papers
2009
GO where we need it to go: focused automated enrichment of the Gene Ontology.Student Council Symposium (2009)
Catia Pesquita
Francisco Couto
Conference papers
2009
Identifying Gene Ontology Areas for Automated Enrichment (2009)
Catia Pesquita
Tiago Grego
Francisco M. Couto
Conference papers
2009
GOclasses: molecular function as viewed by proteins (2009)
Daniel Faria
Catia Pesquita
Francisco Couto
André Falcão
Conference papers
2009
Identification of Chemical Entities in Patent Documents (2009)
Tiago Grego
Piotr Pezik
Francisco Couto
Dietrich Rebholz-Schuhmann
Conference papers
2009
ThermInfo: Collecting and Presenting Thermochemical Properties (2009)
Ana Teixeira
Rui C Santos
Francisco Couto
Conference papers
2009
Enzyme family coherence assessment: validation and prediction (2009)
Hugo Bastos
Tiago Grego
Francisco Couto
Pedro M. Coutinho
Conference papers
2009
Automated Social Network Epidemic Data Collector (2009)
Luis Filipe Lopes et al., with 6 authors including:
Francisco Couto
Conference papers
2009
Carbohydrate-Active Enzymes Database: Principles and Classification of Glycosyltransferases (2009)
P.M. Coutinho et al., with 7 authors including:
Francisco Couto
Book chapters
2009
Semantic Similarity in Biomedical Ontologies (2009)
Cátia Pesquita
Daniel Faria
André O. Falcão
P. Lord
Francisco M. Couto
Journal articles
2008
Untangling BioOntologies for Mining Biomedical Information (2008)
Catia Pesquita
Daniel Faria
Tiago Grego
Francisco Couto
Mário J. Silva
Book chapters
2008
Metrics for GO based protein semantic similarity: a systematic evaluation (2008)
Catia Pesquita et al., with 6 authors including:
Francisco Couto
Journal articles
2008
Identifying Bioentity Recognition Errors of Rule-Based Text-Mining Systems (2008)
Francisco Couto et al., with 8 authors including:
Francisco Couto
Conference papers
2008
Biomedical research line of LASIGE (2008)
Francisco M. Couto
Mário J. Silva
Other
2007
Measuring semantic similarity between gene ontology terms (2007)
Francisco Couto
Mário J. Silva
Pedro M. Coutinho
Journal articles
2007
Evaluating GO-based Semantic Similarity Measures (2007)
Cátia Pesquita
Daniel Faria
Hugo Bastos
André O. Falcão
Francisco M. Couto
Conference papers
2007
Filtering Bioentity Recognition Errors in Bioliterature using a Casebased Approach (2007)
Francisco M. Couto et al., with 6 authors including:
Francisco M. Couto
Conference papers
2005
Facts from text: Is Text Mining ready to deliver? (2005)
D. Rebholz-Schuhmann
H. Kirsch
Francisco Couto
Journal articles
2005
Finding Genomic Ontology Terms in Text using Evidence Content (2005)
Francisco Couto
Mário J. Silva
Pedro Coutinho
Journal articles
2005
Semantic Similarity over the Gene Ontology: Family Correlation and Selecting Disjunctive Ancestors (2005)
Francisco Couto
Mário J. Silva
Pedro Coutinho
Conference papers
2005
Literature Based Functional Annotation of Genes (2005)
Pooja Jain
Francisco Couto
Mário J. Silva
Jorg D. Becker
Conference papers
2005
Bioinformatics: Knowledge Discovery in Biology (2005)
Francisco Couto
Mário J. Silva
Pedro Fernandes
Books
2005
Validation of Automated Protein Annotation (2005)
Francisco Couto
Mário J. Silva
Pedro M. Coutinho
Other
2005
GOAnnotator: linking electronic protein GO annotation to evidence text (2005)
Francisco Couto et al., with 8 authors including:
Francisco Couto
Other
2005
Mining the BioLiterature: towards automatic annotation of genes and proteins (2005)
Francisco Couto
Mário J. Silva
Book chapters
2004
FiGO: Finding GO terms in unstructured text (2004)
Francisco Couto
Mário J. Silva
Pedro Coutinho
Conference papers
2004
Classifying Biomedical Articles using Web Resources (2004)
Francisco Couto
Bruno Martins
Mário J. Silva
Pedro Coutinho
Conference papers
2003
ReBIL: Relating Biological Information through Literature (2003)
Francisco Couto
Pooja Jain
Mário J. Silva
Pedro Coutinho
Conference papers
2003
ProFAL: PROtein Functional Annotation through Literature (2003)
Francisco Couto
Mário J. Silva
Pedro Coutinho
Conference papers
2003
Curating Extracted Information through the Correlation between Structure and Function (2003)
Francisco Couto
Mário J. Silva
Pedro Coutinho
Conference papers
2003
ReBIL: Relating Biological Information through Literature (2003)
Francisco Couto
Mário J. Silva
Pedro Coutinho
Conference papers
2003
Improving Information Extraction through Biological Correlation (2003)
Francisco Couto
Mário J. Silva
Pedro Coutinho
Conference papers
2003
Bioinformática - Exploração da Informação (2003)
Francisco Couto
Mário J. Silva
Other
2003
Implementation of a Functional Semantic Similarity Measure between Gene-Products (2003)
Francisco Couto
Mário J. Silva
Pedro Coutinho
Other
2003
Classifying Biomedical Articles using Web Resources: application to KDD Cup 02 (2003)
Francisco Couto
Bruno Martins
Mário J. Silva
Pedro Coutinho
Other