José Luís Oliveira

ORCID

Publication Activity (10 Years)

Years Active: 1994-2024
Publications (10 Years): 102

Top Venues

Publications

Jorge Miguel Silva, José Luís Oliveira
BIT.UA at iDPP: Predictive Analytics on ALS Disease Progression Using Sensor Data with Machine Learning. CLEF (Working Notes) (2024)
Rodrigo Escobar Díaz Guerrero, José Luís Oliveira, Jürgen Popp, Thomas Bocklitz
MMIR: an open-source software for the registration of multimodal histological images. BMC Medical Informatics Decis. Mak. 24 (1) (2024)
Nelson R. C. Monteiro, José Luís Oliveira, Joel P. Arrais
TAG-DTA: Binding-region-guided strategy to predict drug-target affinity using transformers. Expert Syst. Appl. 238 (Part F) (2024)
João Rafael Almeida, Jorge Miguel Silva, Luís Carlos Afonso, Tiago Melo Almeida, Rui Antunes, Richard A. A. Jonker, João António Reis, Dimitri Silva, Sérgio Matos, José Luís Oliveira
HealthDBFinder: a question-answering task for health database discovery. CBMS (2024)
João Rafael Almeida, Peter R. Rijnbeek, Maxim Moinat, José Luís Oliveira
Assessing the feasibility of observational data sources for multicenter clinical studies. CBMS (2024)
Dinis Barroqueiro Cruz, João Rafael Almeida, José Luís Oliveira
Open Source Solutions for Vulnerability Assessment: A Comparative Analysis. IEEE Access 11 (2023)
Sara Duarte-Pereira, Sérgio Matos, José Luís Oliveira, Raquel M. Silva
Study of NAD-interacting proteins highlights the extent of NAD regulatory roles in the cell and its potential as a therapeutic target. J. Integr. Bioinform. 20 (2) (2023)
Arnaldo Pereira, João Rafael Almeida, Rui Pedro Lopes, José Luís Oliveira
Querying semantic catalogues of biomedical databases. J. Biomed. Informatics 137 (2023)
Olga Fajarda, João Rafael Almeida, Sara Duarte-Pereira, Raquel M. Silva, José Luís Oliveira
Methodology to identify a gene expression signature by merging microarray datasets. Comput. Biol. Medicine 159 (2023)
Nelson R. C. Monteiro, Tiago Pereira, Ana Catarina D. Machado, José Luís Oliveira, Maryam Abbasi, Joel P. Arrais
drug design using transformers. Comput. Biol. Medicine 164 (2023)
João Rafael Almeida, Jorge Miguel Silva, José Luís Oliveira
A FAIR Approach to Real-World Health Data Management and Analysis. CBMS (2023)
Richard Adolph Aires Jonker, Roshan Poudel, Olga Fajarda, José Luís Oliveira, Rui Pedro Lopes, Sérgio Matos
DyPrune: Dynamic Pruning Rates for Neural Networks. EPIA (1) (2023)
Diniz Cruz, João Rafael Almeida, Jorge Miguel Silva, José Luís Oliveira
SecureFASTA: Ensuring privacy and trust when sharing genomic data. CBMS (2023)
Rodrigo Escobar Díaz Guerrero, Yubraj Gupta, Thomas Bocklitz, José Luís Oliveira
A Multimodal Image Registration System for Histology Images. CBMS (2023)
João Rafael Almeida, Alejandro Pazos, José Luís Oliveira
Clinical Data Integration Strategies for Multicenter Studies. DoCEIS (2023)
João Rafael Almeida, José Luís Oliveira
A 20-Year Journey of Tracing the Development of Web Catalogues for Rare Diseases. IWBBIO (2) (2023)
Miguel Pinheiro, Jorge Miguel Silva, José Luís Oliveira
Optimizing Variant Calling for Human Genome Analysis: A Comprehensive Pipeline Approach. IWBBIO (2) (2023)
Dinis. B. Cruz, João R. Almeida, Jorge M. Silva, José Luís Oliveira
A Reliable and Secure Method for Sharing Genomic Data. MIE (2023)
João Rafael Almeida, João Paulo Barraca, José Luís Oliveira
Preserving Privacy when Querying OMOP CDM Databases. EFMI-STC (2022)
Arnaldo Pereira, João Rafael Almeida, Rui Pedro Lopes, Alejandro Pazos, José Luís Oliveira
Discovery of Biomedical Databases Through Semantic Questioning. MIE (2022)
Jorge Miguel Silva, João Rafael Almeida, José Luís Oliveira
Classifying and discovering genomic sequences in metagenomic repositories. CENTERIS/ProjMAN/HCist (2022)
Nelson R. C. Monteiro, Carlos J. V. Simões, Henrique V. Ávila, Maryam Abbasi, José Luís Oliveira, Joel P. Arrais
Explainable deep drug-target representations for binding affinity prediction. BMC Bioinform. 23 (1) (2022)
João Rafael Almeida, Luís Bastião Silva, Alejandro Pazos, José Luís Oliveira
Combining heterogeneous patient-level data into tranSMART to support multicentre studies. CBMS (2022)
Maryam Abbasi, Beatriz P. Santos, Tiago Pereira, Raul Sofia, Nelson R. C. Monteiro, Carlos J. V. Simões, Rui Brito, Bernardete Ribeiro, José Luís Oliveira, Joel P. Arrais
Designing optimized drug candidates with Generative Adversarial Network. J. Cheminformatics 14 (1) (2022)
Edgar Morais, José Luís Oliveira, Alina Trifan, Olga Fajarda
BioInfo@UAVR@SMM4H'22: Classification and Extraction of Adverse Event mentions in Tweets using Transformer Models. SMM4H@COLING (2022)
Arnaldo Pereira, João Rafael Almeida, Rui Pedro Lopes, José Luís Oliveira
Visualising Time-evolving Semantic Biomedical Data. CBMS (2022)
Rodrigo Ferreira, Alina Trifan, José Luís Oliveira
Early risk detection of mental illnesses using various types of textual features. CLEF (Working Notes) (2022)
Nelson R. C. Monteiro, José Luís Oliveira, Joel P. Arrais
DTITR: End-to-end drug-target binding affinity prediction with transformers. Comput. Biol. Medicine 147 (2022)
Arnaldo Pereira, Alina Trifan, Rui Pedro Lopes, José Luís Oliveira
Systematic review of question answering over knowledge bases. IET Softw. 16 (1) (2022)
Alina Yanchuk, Alina Trifan, Olga Fajarda, José Luís Oliveira
Automatic Classification of Stigmatizing Articles of Mental Illness: The Case of Portuguese Online Newspapers. ADBIS (Short Papers) (2022)
Maryam Abbasi, Beatriz P. Santos, Tiago Pereira, Raul Sofa, Nelson R. C. Monteiro, Carlos J. V. Simões, Rui M. M. Brito, Bernardete Ribeiro, José Luís Oliveira, Joel P. Arrais
Correction to: Designing optimized drug candidates with Generative Adversarial Network. J. Cheminformatics 14 (1) (2022)
Richard Adolph Aires Jonker, Roshan Poudel, Olga Fajarda, Sérgio Matos, José Luís Oliveira, Rui Pedro Lopes
Portuguese Twitter Dataset on COVID-19. ASONAM (2022)
João Rafael Almeida, João Paulo Barraca, José Luís Oliveira
A secure architecture for exploring patient-level databases from distributed institutions. CBMS (2022)
Sara Duarte-Pereira, Sérgio Matos, José Luís Oliveira, Raquel M. Silva
The NAD Interactome, Identification of Putative New NAD-Binding Proteins. PACBB (2022)
João Rafael Almeida, Diogo Pratas, José Luís Oliveira
A semi-automatic methodology for analysing distributed and private biobanks. Comput. Biol. Medicine 130 (2021)
Alina Trifan, Sérgio Matos, Pedro Morgado, José Luís Oliveira
Bilingual Emotion Analysis on Social Media throughout the COVID19 Pandemic in Portugal. HEALTHINF (2021)
João Rafael Almeida, João Figueira Silva, Sérgio Matos, Alejandro Pazos, José Luís Oliveira
A Recommender System to Help Refining Clinical Research Studies. MIE (2021)
Arnaldo Pereira, Rui Pedro Lopes, José Luís Oliveira
Easing the Questioning of Semantic Biomedical Data. CBMS (2021)
Alina Trifan, José Luís Oliveira
Cross-evaluation of social mining for classification of depressed online personas. J. Integr. Bioinform. 18 (2) (2021)
João Rafael Almeida, Eriksson J. Melicio Monteiro, José Luís Oliveira
An Architecture to Define Cohorts over Medical Imaging Datasets. CBMS (2021)
Rodrigo Escobar Díaz Guerrero, José Luís Oliveira
Improvements in lymphocytes detection using deep learning with a preprocessing stage. CBMS (2021)
Tiago Pereira, Maryam Abbasi, José Luís Oliveira, Bernardete Ribeiro, Joel Arrais
Optimizing blood-brain barrier permeation through deep reinforcement learning for de novo drug design. Bioinform. 37 (Supplement) (2021)
Mariana Sequeira, João Rafael Almeida, José Luís Oliveira
A Comparative Analysis of Data Platforms for Rare Diseases. CBMS (2021)
João Rafael Almeida, João Figueira Silva, Sérgio Matos, José Luís Oliveira
A two-stage workflow to extract and harmonize drug mentions from clinical notes into observational databases. J. Biomed. Informatics 120 (2021)
João Rafael Almeida, Leonardo Coelho, José Luís Oliveira
BIcenter: A collaborative Web ETL solution based on a reflective software approach. SoftwareX 16 (2021)
Lucas Barros, Alina Trifan, José Luís Oliveira
VADER meets BERT: sentiment analysis for early detection of signs of self-harm through social mining. CLEF (Working Notes) (2021)
Alina Trifan, Rui Antunes, Sérgio Matos, José Luís Oliveira
Understanding Depression from Psycholinguistic Patterns in Social Media Texts. ECIR (2) (2020)
Olga Fajarda, Sara Duarte-Pereira, Raquel M. Silva, José Luís Oliveira
Merging microarray studies to identify a common gene expression signature to several structural heart diseases. BioData Min. 13 (1) (2020)
Alina Trifan, Pedro Salgado, José Luís Oliveira
BioInfo@UAVR at eRisk 2020: on the Use of Psycholinguistics Features and Machine Learning for the Classification and Quantification of Mental Diseases. CLEF (Working Notes) (2020)
João Rafael Almeida, Eriksson J. Melicio Monteiro, Luís A. Bastião Silva, Alejandro Pazos, José Luís Oliveira
A Recommender System Based on Cohorts' Similarity. MIE (2020)
João Rafael Almeida, Armando J. Pinho, José Luís Oliveira, Olga Fajarda, Diogo Pratas
GTO: A toolkit to unify pipelines in genomic and proteomic research. SoftwareX 12 (2020)
João Rafael Almeida, João Figueira Silva, Alejandro Pazos Sierra, Sérgio Matos, José Luís Oliveira
Enhancing Decision-making Systems with Relevant Patient Information by Leveraging Clinical Notes. HEALTHINF (2020)
João Rafael Almeida, José Luís Oliveira
Multi-language Concept Normalisation of Clinical Cohorts. CBMS (2020)
João Rafael Almeida, Olga Fajarda, José Luís Oliveira
File Forgery Detection Using a Weighted Rule-Based System. CLEF (2020)
Luis Torres, Nelson R. C. Monteiro, José Luís Oliveira, Joel Arrais, Bernardete Ribeiro
Exploring a Siamese Neural Network Architecture for One-Shot Drug Discovery. BIBE (2020)
João Rafael Almeida, João Figueira Silva, Alejandro Pazos Sierra, Sérgio Matos, José Luís Oliveira
Leveraging Clinical Notes for Enhancing Decision-Making Systems with Relevant Patient Information. BIOSTEC (Selected Papers) (2020)
Ricardo F. Ribeiro, Júlio Silva, Alina Trifan, José Luís Oliveira, António J. R. Neves
UA.PT Bioinformatics at ImageCLEF 2020: Lifelog Moment Retrieval Web based Tool. CLEF (Working Notes) (2020)
João Rafael Almeida, Pedro Freire, Olga Fajarda, José Luís Oliveira
A Computational Platform for Heart Failure Cases Research. HEALTHINF (2020)
Alina Trifan, Rui Antunes, José Luís Oliveira
Machine Learning for Depression Screening in Online Communities. PACBB (2020)
João Rafael Almeida, Eriksson J. Melicio Monteiro, Luís A. Bastião Silva, Alejandro Pazos Sierra, José Luís Oliveira
A Recommender System to Help Discovering Cohorts in Rare Diseases. CBMS (2020)
Alina Trifan, Dave Semeraro, Justin Drake, Radek Bukowski, José Luís Oliveira
Social Media Mining for Postpartum Depression Prediction. MIE (2020)
Alina Trifan, José Luís Oliveira
Patient data discovery platforms as enablers of biomedical and translational research: A systematic review. J. Biomed. Informatics 93 (2019)
João Rafael Almeida, Pedro Freire, Olga Fajarda, José Luís Oliveira
A Weighted Rule-Based Model for File Forgery Detection: UA.PT Bioinformatics at ImageCLEF 2019. CLEF (Working Notes) (2019)
Ricardo F. Ribeiro, António J. R. Neves, José Luís Oliveira
Image selection based on low level properties for lifelog moment retrieval. ICMV (2019)
Alina Trifan, José Luís Oliveira
BioInfo@UAVR at eRisk 2019: delving into Social Media Texts for the Early Detection of Mental and Food Disorders. CLEF (Working Notes) (2019)
Ricardo F. Ribeiro, António J. R. Neves, José Luís Oliveira
UA.PT Bioinformatics at ImageCLEF 2019: Lifelog Moment Retrieval based on Image Annotation and Natural Language Processing. CLEF (Working Notes) (2019)
João Rafael Almeida, Rosa Gini, Giuseppe Roberto, Peter R. Rijnbeek, José Luís Oliveira
TASKA: A modular task management system to support health research studies. BMC Medical Informatics Decis. Mak. 19 (1) (2019)
João Rafael Duarte de Almeida, José Luís Oliveira
GenericCDSS - A Generic Clinical Decision Support System. CBMS (2019)
João Rafael Almeida, Olga Fajarda, Arnaldo Pereira, José Luís Oliveira
Strategies to Access Patient Clinical Data from Distributed Databases. HEALTHINF (2019)
Alina Trifan, José Luís Oliveira
FAIRness in Biomedical Data Discovery. HEALTHINF (2019)
José Luís Oliveira, Alina Trifan, Luís A. Bastião Silva
EMIF Catalogue: A collaborative platform for sharing and reusing biomedical data. Int. J. Medical Informatics 126 (2019)
Alina Trifan, José Luís Oliveira
Towards a More Reproducible Biomedical Research Environment: Endorsement and Adoption of the FAIR Principles. BIOSTEC (Selected Papers) (2019)
Edgar D. Coelho, Joel P. Arrais, José Luís Oliveira
Fighting Fire with Fire: Computational Prediction of Microbial Targets for Bacteriocins. IWBBIO (1) (2018)
Luís A. Bastião Silva, Alina Trifan, José Luís Oliveira
MONTRA: An agile architecture for data publishing and discovery. Comput. Methods Programs Biomed. 160 (2018)
João Rafael Almeida, Joana Guimaraes, José Luís Oliveira
Simplifying the Digitization of Clinical Protocols for Diabetes Management. CBMS (2018)
Maryse Oliveira, José Luís Oliveira
Smartphone as data collector in health monitoring. DATA (2018)
Pedro Sernadela, José Luís Oliveira
COEUS 2.0: automated platform to integrate and publish biomedical data as nanopublications. IET Softw. 12 (2) (2018)
David Campos, Renato P. Pinho, Ute Neugebauer, Jürgen Popp, José Luís Oliveira
A Computational Pipeline for Sepsis Patients' Stratification and Diagnosis. HEALTHINF (2018)
João Rafael Almeida, Ricardo F. Ribeiro, José Luís Oliveira
A Modular Workflow Management Framework. HEALTHINF (2018)
Andre Malta, José Luís Oliveira
Simplifying biomedical data sharing through a web portal generator. HealthCom (2018)
Fábio Maia, Luís A. Bastião Silva, José Luís Oliveira
Biomedical Informatics - How to Choose the Best Tool for Each Task. MIE (2018)
Olga Fajarda, Alina Trifan, Michel Van Speybroeck, Peter R. Rijnbeek, José Luís Oliveira
Exploring the Value of Electronic Health Records from Multiple Datasets. BIOSTEC (Selected Papers) (2018)
Alina Trifan, Johan van der Lei, Carlos Díaz, José Luís Oliveira
A Methodology for Fine-Grained Access Control in Exposing Biomedical Data. MIE (2018)
Vitor Pereira, Sérgio Matos, José Luís Oliveira
Automated ICD-9-CM medical coding of diabetic patient's clinical reports. DATA (2018)
João Rafael Almeida, Tiago Marques Godinho, Luís A. Bastião Silva, Carlos Costa, José Luís Oliveira
Services Orchestration and Workflow Management in Distributed Medical Imaging Environments. CBMS (2018)
Olga Fajarda, Luís A. Bastião Silva, Peter R. Rijnbeek, Michel Van Speybroeck, José Luís Oliveira
A Methodology to Perform Semi-automatic Distributed EHR Database Queries. HEALTHINF (2018)
Alina Trifan, José Luís Oliveira
A FAIR Marketplace for Biomedical Data Custodians and Clinical Researchers. CBMS (2018)
Pedro Sernadela, Lorena González-Castro, José Luís Oliveira
SCALEUS: Semantic Web Services Integration for Biomedical Applications. J. Medical Syst. 41 (4) (2017)
Pedro Sernadela, José Luís Oliveira
A semantic-based workflow for biomedical literature annotation. Database J. Biol. Databases Curation 2017 (2017)
Luís Bastião Silva, Rafael C. Jiménez, Niklas Blomberg, José Luís Oliveira
General guidelines for biomedical software development. F1000Research 6 (2017)
Eriksson J. Melicio Monteiro, Carlos Costa, José Luís Oliveira
A De-Identification Pipeline for Ultrasound Medical Images in DICOM Format. J. Medical Syst. 41 (5) (2017)
Tiago Marques Godinho, Carlos Costa, José Luís Oliveira
Intelligent generator of big data medical imaging repositories. IET Softw. 11 (3) (2017)
John Edison Arevalo Ovalle, Fabio A. González, Raúl Ramos-Pollán, José Luís Oliveira, Miguel Ángel Guevara-López
Representation learning for mammography mass lesion classification with convolutional neural networks. Comput. Methods Programs Biomed. 127 (2016)
Sérgio Matos, David Campos, Renato P. Pinho, Raquel M. Silva, Matthew E. Mort, David N. Cooper, José Luís Oliveira
Mining clinical attributes of genomic variants through assisted literature curation in Egas. Database J. Biol. Databases Curation 2016 (2016)
Eriksson J. Melicio Monteiro, Carlos Costa, José Luís Oliveira, David Campos, Luís A. Bastião Silva
Caching and Prefetching Images in a Web-Based DICOM Viewer. CBMS (2016)
Edgar D. Coelho, Joel P. Arrais, José Luís Oliveira
Computational Discovery of Putative Leads for Drug Repositioning through Drug-Target Interaction Prediction. PLoS Comput. Biol. 12 (11) (2016)
Fernanda Brito Correia, Joel P. Arrais, José Luís Oliveira
Prediction of Cancer using Network Topological Features. BIOINFORMATICS (2016)
Paulo Gaspar, José Luís Oliveira, Jörg Frommlet, Manuel A. S. Santos, Gabriela R. Moura
EuGene: maximizing synthetic gene design for heterologous expression. Bioinform. 32 (7) (2016)
Edgar D. Coelho, Joel P. Arrais, José Luís Oliveira
Ensemble-Based Methodology for the Prediction of Drug-Target Interactions. CBMS (2016)
Eriksson J. Melicio Monteiro, Pedro Sernadela, Sérgio Matos, Carlos Costa, José Luís Oliveira
Semantic Knowledge Base Construction from Radiology Reports. HEALTHINF (2016)

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Publication Activity (10 Years)

Top Topics

Top Venues

José Luís Oliveira