José Luís Oliveira

Position	Full professor
Affiliation	DETI / University of Aveiro
Group	Biomedical Informatics and Technologies
Status	Researcher with PhD
Country	Portugal
Students	Arnaldo Pereira, João Almeida, Sara Pereira
Former PhD students	Joel Arrais, Luís Bastião Silva, David Campos, Edgar Coelho, Fernanda Brito Correia, Carlos Costa, Eriksson Monteiro, Paulo Gaspar, Pedro Gonçalves, Rui Pedro Lopes, Pedro Lopes, José Paulo Lousado, Miguel Pinheiro, Daniel Polónia, Nuno Rosa, Pedro Sernadela, Tiago Pedrosa
Former masters students	Show list
Courses	Complementos de Bases de Dados, Padrões e Desenho de Software, Programacao3, Programação Orientada a Objetos
Projects	EHDEN
Past projects	Cloud Thinking, D4, DECODING, DICOM P2P, EMIF, EU-ADR, GEN2PHEN, GlobalClimate, IBERO-NBIC, MMIR, NETDIAMOND, NF DNAmicroarrays, NeuroPath, QueryTermExp, RD-Connect, SOCA - Smart Open Campus, Smartphones for Smart Seniors, World Search, mRNATools
Events	ECTB'2017, INForum 2017, SMBM2014
Proposals
ORCID	0000-0002-6672-6176
Personal page	http://www.ieeta.pt/~jlo

Publications

Books

• João Almeida, Alejandro Rodríguez González, Linlin Shen, Bridget Kane, Agma Traina, Paolo Soda, José Luís Oliveira. 2021 IEEE 34th International Symposium on Computer-Based Medical Systems. IEEE Computer Society Conference Publishing Services, Aveiro, June 2021
• Olivier Bodenreider, José Luís Oliveira, Fabio Rinaldi. SMBM 2014 - Proceedings of the 6th International Symposium on Semantic Mining in Biomedicine. Universidade de Aveiro, Aveiro, September 2014
• José Luís Oliveira, Victor Maojo, Fernando Martin-Sanchez, António Sousa Pereira. Biological and Medical Data Analysis. Springer, 2005

Articles in international journals listed in the ISI

• João 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. Journal of Biomedical Informatics, vol. 120, p. 103849, August 2021 [IF 2018: 2.950 (Q2, 33/106)]
• João Almeida, Diogo Pratas, José Luís Oliveira. A semi-automatic methodology for analysing distributed and private biobanks. Computers in Biology and Medicine, vol. 130, p. 104180, January 2021 [IF 2018: 2.895]
• Arnaldo Pereira, Rui Pedro Lopes, José Luís Oliveira. SCALEUS-FD: A FAIR Data Tool for Biomedical Applications. BioMed Research International, August 2020
• João Almeida, Armando J. Pinho, José Luís Oliveira, Olga Fajarda, Diogo Pratas. GTO: A toolkit to unify pipelines in genomic and proteomic research. SoftwareX, vol. 12, p. 100535, July 2020
• Olga Fajarda, Sara Pereira, Raquel Silva, José Luís Oliveira. Merging microarray studies to identify a common gene expression signature to several structural heart diseases. BioData Mining, vol. 13, no. 8, p. 1-20, July 2020
• Alina Trifan, Maryse Oliveira, José Luís Oliveira. Passive Sensing of Health Outcomes Through Smartphones: Systematic Review of Current Solutions and Possible Limitations. JMIR mHealth and uHealth, vol. 7, no. 8, p. e12649, August 2019 [IF 2018: 4.301 (Q1, 2/26)]
• João Almeida, Rosa Gini, Giuseppe Roberto, Peter Rijnbeek, José Luís Oliveira. TASKA: A modular task management system to support health research studies. BMC Medical Informatics and Decision Making, vol. 19, no. 1, p. 121, July 2019 [IF 2018: 2.067 (Q3, 15/26)]
• José Luís Oliveira, Alina Trifan, Luís Bastião Silva. EMIF Catalogue: A collaborative platform for sharing and reusing biomedical data. International Journal of Medical Informatics, vol. 126, p. 35-45, June 2019 [IF 2018: 2.731 (Q2, 57/155)]
• Alina Trifan, José Luís Oliveira. Patient data discovery platforms as enablers of biomedical and translational research: a systematic review. Journal of Biomedical Informatics, vol. 93, p. 103154, May 2019 [IF 2018: 2.950 (Q2, 33/106)]
• Luís Bastião Silva, Alina Trifan, José Luís Oliveira. MONTRA: An agile architecture for data publishing and discovery. Computer Methods and Programs in Biomedicine, vol. 160, p. 33-42, April 2018 [IF 2018: 3.424 (Q1, 15/105)]
• Pedro Sernadela, Lorena González-Castro, José Luís Oliveira. SCALEUS: Semantic Web Services Integration for Biomedical Applications. Journal of Medical Systems, vol. 41, no. 4, April 2017 [IF 2017: 2.098 (Q2, 46/94)] [IF 2018: 2.415 (Q2, 12/26)]
• Tiago Godinho, Carlos Costa, José Luís Oliveira. Intelligent Generator of Big Data Medical Imaging Repositories. IET Software, vol. 11, no. 3, p. 100, February 2017 [IF 2018: 0.695 (Q4, 95/107)]
• Edgar Coelho, Joel Arrais, José Luís Oliveira. Computational Discovery of Putative Leads for Drug Repositioning through Drug-Target Interaction Prediction. PLoS Computational Biology, vol. 12, no. 11, p. e1005219, November 2016 [IF 2016: 4.542 (Q1, 4/57)] [IF 2018: 4.428 (Q1, 5/59)]
• Sun Kim, Rezarta Islamaj Doğan, Andrew Chatr-Aryamontri, Christie S. Chang, Rose Oughtred, Jennifer Rust, Riza Batista-Navarro, Jacob Carter, Sophia Ananiadou, Sérgio Matos, André Santos, David Campos, José Luís Oliveira, Onkar Singh, Jitendra Jonnagaddala, Hong-Jie Dai, Emily Chia-Yu Su, Yung-Chun Chang, Yu-Chen Su, Chun-Han Chu, Chien Chin Chen, Wen-Lian Hsu, Yifan Peng, Cecilia Arighi, Cathy H. Wu, K. Vijay-Shanker, Ferhat Aydın, Zehra Melce Hüsünbeyi, Arzucan Özgür, Soo-Yong Shin, Dongseop Kwon, Kara Dolinski, Mike Tyers, W. John Wilbur, and Donald C. Comeau. BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database, vol. 2016, no. baw121, September 2016 [IF 2016: 3.290 (Q1, 8/57)] [IF 2018: 3.683 (Q1, 7/59)]
• Sérgio Matos, David Campos, Renato Pinho, Raquel Silva, Matthew Mort, David N. Cooper, José Luís Oliveira. Mining clinical attributes of genomic variants through assisted literature curation in Egas. Database, vol. 2016, June 2016 [IF 2016: 3.290 (Q1, 8/57)] [IF 2018: 3.683 (Q1, 7/59)]
• John Arevalo, Fabio A. González, Raúl Ramos-Póllan, José Luís Oliveira, Miguel Guevara. Representation learning for mammography mass lesion classification with convolutional neural networks. Computer Methods and Programs in Biomedicine, p. 248-257, April 2016 [IF 2016: 2.503 (Q1, 21/104)] [IF 2018: 3.424 (Q1, 15/105)]
• Eriksson Monteiro, Carlos Costa, José Luís Oliveira. A Cloud Architecture for Teleradiology-as-a-Service. Methods of Information in Medicine, vol. 55, no. 3, p. 203-214, March 2016 [IF 2016: 1.772, 1.772 (Q3, Q3, 78/146, 78/146)]
• Ana Raquel Soares, Noémia Fernandes, Marisa Reverendo, Hugo Araújo, José Luís Oliveira, Gabriela M. R. Moura, Manuel A. S. Santos. Conserved and highly expressed tRNA derived fragments in zebrafish. BMC Molecular Biology, vol. 16, no. 22, December 2015 [IF 2015: 2.500 (Q3, 162/289)]
• Pedro Lopes, José Luís Oliveira. An automated real-time integration and interoperability framework for bioinformatics. BMC Bioinformatics, vol. 16, no. 328, October 2015 [IF 2015: 2.435 (Q1, 10/56)]
• Edgar Coelho, André M. Santiago, Joel Arrais, José Luís Oliveira. Computational methodology for predicting the landscape of the human–microbial interactome region level influence. Journal of Bioinformatics and Computational Biology, vol. 13, no. 5, October 2015 [IF 2015: 0.785 (Q4, 48/56)]
• ...further results

Other articles in journals

• Alina Trifan, José Luís Oliveira. A Methodology for fine grained access control in exposing biomedical data. Studies in Health Technologies and Informatics, vol. 247, p. 561-565, May 2018
• Pedro Sernadela, Pedro Lopes, José Luís Oliveira. A knowledge federation architecture for rare disease patient registries and biobanks. Journal of Information Systems Engineering & Management, vol. 1, no. 2, p. 83-90, March 2016
• R. Gini, M. Schuemie, J. Brown, P. Ryan, E. Vacchi, M. Coppola, W. Cazzola, P. Coloma, R. Berni, G. Diallo, José Luís Oliveira, P. Avillach, G. Trifirò, P. Rijnbeek, M. Bellentani, J. van Der Lei, N. Klazinga, M. Sturkenboom. Data Extraction and Management in Networks of Observational Health Care Databases For Scientific Research: A Comparison Among EU-ADR, OMOP, Mini-Sentinel and MATRICE Strategies. eGEMs, vol. 4, February 2016
• David Campos, Quoc-Chinh Bui, Sérgio Matos, José Luís Oliveira. TrigNER: automatically optimized biomedical event trigger recognition on scientific documents. Source Code for Biology and Medicine, vol. 9, no. 1, January 2014
• Sérgio Matos, Hugo Araújo, José Luís Oliveira. Biomedical literature exploration through latent semantics. Advances in Distributed Computing and Artificial Intelligence Journal, vol. 1, no. 5, p. 65-74, August 2013
• Paulo Gaspar, Jaime Carbonell, José Luís Oliveira. On the parameter optimization of Support Vector Machines for binary classification. Journal of Integrative Bioinformatics, vol. 9, no. 3, July 2012
• Sérgio Matos, José Luís Oliveira. Classification methods for finding articles describing protein-protein interactions in PubMed. Journal of Integrative Bioinformatics, vol. 8, no. 3, p. 178, September 2011
• Joel Arrais, José Luís Oliveira. Using biomedical networks to prioritize gene–disease associations. Open Access Bioinformatics, vol. 2011:3, p. 123-130, August 2011
• José Paulo Lousado, José Luís Oliveira. Análise de repetições em dados biológicos. Millenium, vol. 1, no. 38, p. 7-18, June 2010
• Joel Arrais, Bruno Santos, João Fernandes, Laura Carreto, Manuel A. S. Santos, José Luís Oliveira. GeneBrowser: an approach for integration and functional classification of genomics data. Journal of Integrative Bioinformatics, vol. 4, no. 3, October 2007

Chapters in books

• João Almeida, João Figueira Silva, Alejandro Pazos, Sérgio Matos, José Luís Oliveira. Leveraging Clinical Notes for Enhancing Decision-Making Systems with Relevant Patient Information. Biomedical Engineering Systems and Technologies, Xuesong Ye, Filipe Soares, Elisabetta De Maria, Pedro Gómez Vilda, Federico Cabitza, Ana Fred, Hugo Gamboa (Ed.), Springer International Publishing, vol. 1400, p. 521-540, March 2021
• João Almeida, Olga Fajarda, José Luís Oliveira. File Forgery Detection Using a Weighted Rule-Based System. Experimental IR Meets Multilinguality, Multimodality, and Interaction, CLEF 2020. Lecture Notes in Computer Science (Ed.), Springer, Cham, vol. 12260, p. 85-96, September 2020
• Olga Fajarda, Alina Trifan, Michel Van Speybroeck, Peter R Rijnbeek, José Luís Oliveira. Exploring the Value of Electronic Health Records from Multiple Datasets. Biomedical Engineering Systems and Technologies. BIOSTEC 2018. Communications in Computer and Information Science, Cliquet Jr. A. et al. (Ed.), Springer, Cham, vol. 1024, p. 367-383, 2019
• Susana Brás, Augusto Silva, José Ribeiro, José Luís Oliveira. New Insights in Echocardiography Based Left-Ventricle Dynamics Assessment. Bioinformatics and Biomedical Engineering SE - 30, F. Ortuño and I. Rojas (Ed.), Springer International Publishing, vol. 9043, p. 292-302, April 2015
• David Campos, Sérgio Matos, José Luís Oliveira. Current methodologies for biomedical Named Entity Recognition. Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data, Mourad Elloumi and Albert Y. Zomaya (Ed.), Wiley, p. 1390, January 2014
• Luís Bastião Silva, Carlos Costa, José Luís Oliveira. Regional PACS over the Cloud.. Líneas estratégicas de las Tecnologías de la Información y las Comunicaciones en Salud, CYTED, p. 21-32, 2013
• Adelaide V. Freitas, Wassim Ayadi, Mourad Elloumi, José Luís Oliveira, Jin-Kao Hao. Survey on Biclustering of Gene Expression Data. Biological Knowledge Discovery Handbook: Preprocessing, Mining, and Postprocessing of Biological Data, Mourad Elloumi, Albert Y. Zomaya (Ed.), Wiley, USA, p. 591-609, December 2013
• José Melo, Joel Arrais, Edgar Coelho, Pedro Lopes, Nuno Rosa, Maria José Correia, Marlene Barros, José Luís Oliveira. Data Integration Solution for Organ-Specific Studies: An Application for Oral Biology. Biomedical Engineering Systems and Technologies, Joaquim Gabriel, Jan Schier, Sabine Huffel, Emmanuel Conchon, Carlos Correia, Ana Fred, Hugo Gamboa (Ed.), Springer Berlin Heidelberg, vol. 357, p. 401-412, January 2013
• Pedro Lopes, José Luís Oliveira. Collecting and Enriching Human Variome Datasets. Tecnologias NBIC em Salud: El papel protagonista de la Neurociencia, CYTED, p. 9-19, 2012
• David Campos, Sérgio Matos, José Luís Oliveira. Biomedical Named Entity Recognition: A Survey of Machine-Learning Tools. Theory and Applications for Advanced Text Mining, Shigeaki Sakurai (Ed.), InTech, p. 175-195, November 2012
• Joel Arrais, Sérgio Matos, José Luís Oliveira. Integração de dados biomédicos. Nano, Bio, Info y Cogno (Convergencia de tecnologias NBIC), Conceptos y aplicaciones, J. Aguiló, A. Figueras, A. Freire, D. de la Iglesia, F. Martín, A. Pazos (Ed.), CYTED, p. 185-224, 2011
• Luis Ribeiro, Carlos Costa, José Luís Oliveira. Current Trends in Archiving and Transmission of Medical Images. Medical Imaging, Okechukwu Felix Erondu (Ed.), InTech, p. 89-106, December 2011
• Joel Arrais, Sérgio Matos, José Luís Oliveira. Expansão de termos de pesquisa usando redes de conceitos associadas a genes. Nuevas Fronteras Tecnológicas, Alejandre Pazos (Ed.), CYTED, 2010
• Carlos Costa, Augusto Silva, José Luís Oliveira. Current Perspectives on PACS and a Cardiology Case Study. Advanced Computational Intelligence Paradigms in Healthcare-2, S. Vaidya, L. C. Jain, H. Yoshida (Ed.), Springer-Verlag, vol. 65, p. 79-108, 2007
• Joaquim Arnaldo Martins, Nelson Rocha, José Luís Oliveira, Joaquim Sousa Pinto. Learning and Teaching the Data Communication Basic Concepts through the Implementation of a Simulator for HDLC Protocol. Computer Based Experiments, Learning and Teaching, Andrzej Kasprzak, Leszek Koszalka, Iwona Pozniak-Koszalka (Ed.), NK, 1999

Articles in conference proceedings

• Mariana Sequeira, João Almeida, José Luís Oliveira. A Comprehensive Analysis on Retrieval and Visualisation Platforms about Rare Diseases. IEEE 34th International Symposium on Computer-Based Medical Systems (CBMS), Aveiro, Portugal, June 2021
• João Almeida, Eriksson Monteiro, José Luís Oliveira. An Architecture to Define Cohorts over Medical Imaging Datasets. IEEE 34th International Symposium on Computer-Based Medical Systems (CBMS), Aveiro, Portugal, June 2021
• João Almeida, João Figueira Silva, Sérgio Matos, José Luís Oliveira. A Recommender System to Help Refining Clinical Research Studies. 31st Medical Informatics Europe conference, Studies in health technology and informatics, May 2021
• Alina Trifan, Rui Antunes, José Luís Oliveira. Machine learning for depression screening in online communities. 14th International Conference on Practical Applications of Computational Biology & Bioinformatics, PACBB 2020, L'Aquila, Italy, October 2020
• João Almeida, Eriksson Monteiro, Luís Bastião Silva, Alejandro Pazos Sierra, José Luís Oliveira. A Recommender System to Help Discovering Cohorts in Rare Diseases. IEEE 33rd International Symposium on Computer-Based Medical Systems (CBMS), Rochester, MN, USA, p. 25-28, July 2020
• João Almeida, José Luís Oliveira. Multi-language Concept Normalisation of Clinical Cohorts. IEEE 33rd International Symposium on Computer-Based Medical Systems (CBMS), Rochester, MN, USA, p. 261-264, July 2020
• João Almeida, Eriksson Monteiro, Luís Bastião Silva, Alejandro Pazos, José Luís Oliveira. A Recommender System based on Cohorts' Similarity. 30th Medical Informatics Europe conference, MIE 2020, Studies in health technology and informatics, vol. 270, p. 1183-1184, April 2020
• Alina Trifan, Dave Semeraro, Justin Drake, Radek Bukowski, José Luís Oliveira. Social media mining for post-partum depression prediction. MIE2020 - Medical Informatics Europe, Geneva, Switzerland, April 2020
• Alina Trifan, Rui Antunes, Sérgio Matos, José Luís Oliveira. Understanding depression from psycholinguistic patterns in social media texts. 42nd European Conference on Information Retrieval, ECIR 2020, Online event, April 2020
• João Almeida, Pedro Freire, Olga Fajarda, José Luís Oliveira. A Computational Platform for Heart Failure Cases Research. Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 5: HEALTHINF, Malta, vol. 5, p. 601-608, February 2020
• João Almeida, João Figueira Silva, Alejandro Sierra, Sérgio Matos, José Luís Oliveira. Enhancing Decision-making Systems with Relevant Patient Information by Leveraging Clinical Notes. Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 5: HEALTHINF, vol. 5, p. 254-262, February 2020
• João Almeida, Pedro Freire, Olga Fajarda, José Luís Oliveira. A Weighted Rule-Based Model for File Forgery Detection: UA. PT Bioinformatics at ImageCLEF 2019. CLEF 2019 Working Notes, September 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 eRisk Working Lab Notes, Lugano, Switzerland, September 2019
• João Almeida, José Luís Oliveira. GenericCDSS - A Generic Clinical Decision Support System. 2019 IEEE 32st International Symposium on Computer-Based Medical Systems (CBMS), Cordoba, Spain, June 2019
• Alina Trifan, José Luís Oliveira. FAIRness in Biomedical Data Discovery. Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies, Prague, Czech Republic, February 2019
• João Almeida, Olga Fajarda, Arnaldo Pereira, José Luís Oliveira. Strategies to Access Patient Clinical Data from Distributed Databases. Proceedings of the 12th International Joint Conference on Biomedical Engineering Systems and Technologies, Prague, Czech Republic, vol. 5, p. 466-473, February 2019
• Alina Trifan, José Luís Oliveira. A FAIR marketplace for biomedical data custodians and clinical researchers. 2018 IEEE 31st International Symposium on Computer-Based Medical Systems (CBMS)., p. 188-193, 2018
• Vitor Pereira, Sérgio Matos, José Luís Oliveira. Automated ICD-9-CM medical coding of diabetic patient's clinical reports. Proceedings of the First International Conference on Data Science, E-learning and Information Systems, Madrid, October 2018
• João Almeida, Tiago Godinho, Luís Bastião Silva, Carlos Costa, José Luís Oliveira. Services Orchestration and Workflow Management in Distributed Medical Imaging Environments. 2018 IEEE 31st International Symposium on Computer-Based Medical Systems (CBMS), Karlstad, Sweden, p. 170-175, June 2018
• João Almeida, Joana Guimarães, José Luís Oliveira. Simplifying the digitization of clinical protocols for diabetes management. 2018 IEEE 31st International Symposium on Computer-Based Medical Systems (CBMS, Karlstad, Sweden, p. 176-181, June 2018
• ...further results

PhD thesis

• José Luís Oliveira. Arquitectura para desenvolvimento e integração de aplicações de gestão de redes. PhD Thesis, Universidade de Aveiro, 1996