José Luís Oliveira

Position	Associate professor
Affiliation	DETI / University of Aveiro
Group	Biomedical Informatics and Technologies
Status	Researcher with PhD
Country	Portugal
Students	Assel Syzdykova, Fernanda Brito Correia, João Almeida, Sara Pereira
Former PhD students	Joel Arrais, Luís Bastião Silva, David Campos, Edgar Coelho, Carlos Costa, Eriksson Monteiro, Paulo Gaspar, Pedro Gonçalves, Rui Pedro Lopes, Pedro Lopes, José Paulo Lousado, Miguel Pinheiro, Daniel Polónia, Nuno Rosa, Tiago Pedrosa
Former masters students	Show list
Courses	Complementos de Bases de Dados, Padrões e Desenho de Software, Programacao3
Projects	EMIF, MMIR, NETDIAMOND, RD-Connect, SOCA - Smart Open Campus
Past projects	Cloud Thinking, DECODING, DICOM P2P, EU-ADR, GEN2PHEN, GlobalClimate, IBERO-NBIC, NF DNAmicroarrays, NeuroPath, QueryTermExp, 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

• 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

• 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 2016: 2.503 (Q1, 21/104)]
• 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 2016: 2.456 (Q2, 9/23)]
• 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 2016: 0.733 (Q4, 85/106)]
• 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)]
• 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)]
• 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)]
• 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)]
• 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 (Q3, 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)] [IF 2016: 1.939 (Q3, 217/290)]
• 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)] [IF 2016: 2.448 (Q1, 10/57)]
• 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)] [IF 2016: 0.800 (Q4, 46/57)]
• Jorge A. Vanegas, Sérgio Matos, Fabio A. Gonzalez, José Luís Oliveira. An Overview of Biomolecular Event Extraction from Scientific Documents. Computational and Mathematical Methods in Medicine, vol. 2015, no. 571381, August 2015 [IF 2015: 0.887 (Q3, 42/56)]
• Pedro Lopes, Luís Bastião Silva, José Luís Oliveira. Challenges and Opportunities for Exploring Patient-Level Data. BioMed Research International, vol. 2015, no. 150435, p. 11 pages, August 2015 [IF 2015: 2.134 (Q3, 82/161)]
• Joel Arrais, José Luís Oliveira. RecRWR: A Recursive Random Walk Method for Improved Identification of Diseases. BioMed Research International, vol. 2015, no. 747156, March 2015 [IF 2015: 2.134 (Q3, 82/161)]
• Lapo Ragionieri, Rui Miguel Pinheiro Vitorino, Jörg Frommlet, José Luís Oliveira, Paulo Gaspar, Lluís Ribas de Pouplana, Manuel Santos, Gabriela Moura. Improving the accuracy of recombinant protein production through integration of bioinformatics, statistical and mass spectrometry methodologies. FEBS Journal, vol. 282, no. 4, p. 769-787, February 2015 [IF 2015: 4.237 (Q1, 72/289)]
• David Campos, Sérgio Matos, José Luís Oliveira. A document processing pipeline for annotating chemical entities in scientific documents. Journal of Cheminformatics, vol. 7, no. Suppl. 1, p. S7, January 2015 [IF 2015: 3.949 (Q1, 36/163)]
• Luís Bastião Silva, Samuel Campos, Carlos Costa, José Luís Oliveira. Sensor-Based Architecture for Medical Imaging Workflow Analysis. Journal of Medical Systems, vol. 38, p. 1-11, August 2014 [IF 2014: 2.213 (Q2, 7/24)] [IF 2016: 2.456 (Q2, 9/23)]
• Luis Ribeiro, Carlos Viana Ferreira, José Luís Oliveira, Carlos Costa. XDS-I outsourcing proxy: ensuring confidentiality while preserving interoperability. IEEE Journal of Biomedical and Health Informatics, vol. 18, no. 4, p. 1404-1412, July 2014 [IF 2014: 1.440 (Q2, 47/139)] [IF 2016: 3.451 (Q1, 20/146)]
• David Campos, Jóni Lourenço, Sérgio Matos, José Luís Oliveira. Egas: a collaborative and interactive document curation platform. Database, vol. 2014, no. 10.1093, p. 1-12, June 2014 [IF 2014: 3.372 (Q1, 7/57)] [IF 2016: 3.290 (Q1, 8/57)]
• Nuno Rosa, Maria José Correia, Joel Arrais, Nuno Costa, José Luís Oliveira, Marlene Barros. The Landscape of Protein Biomarkers Proposed for Periodontal Disease: Markers with Functional Meaning. BioMed Research International, vol. 2014, no. 569632, June 2014 [IF 2014: 1.579 (Q3, 107/163)]
• ...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

• 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

Articles in conference proceedings

• Eriksson Monteiro, Carlos Costa, José Luís Oliveira. Using Deep Machine Learning for Medical Image De-identification. RecPad 2016, October 2016
• André Santos, Sérgio Matos, David Campos, José Luís Oliveira. A Curation Pipeline and Web-Services for PDF Documents. Proceedings of the 7th International Symposium on Semantic Mining in Biomedicine, Potsdam, Germany, August 2016
• Eriksson Monteiro, Carlos Costa, José Luís Oliveira. Caching and Prefetching Images in a Web-based DICOM Viewer. 29th International Symposium on Computer-Based Medical Systems (CBMS 2016), June 2016
• Edgar Coelho, Joel Arrais, José Luís Oliveira. Ensemble-Based Methodology for the Prediction of Drug-Target Interactions. IEEE 29th International Symposium on Computer-Based Medical Systems (CBMS 2016), June 2016
• Tiago Godinho, Carlos Costa, José Luís Oliveira. Generating Big Data Repositories for Research in Medical Imaging. n 11th Iberian Conference on Information Systems and Technologies (CISTI2016), June 2016
• Fernanda Brito Correia, Joel Arrais, José Luís Oliveira. Prediction of Cancer using Network Topological Features. 7th International Conference on Bioinformatics Models, Methods and Algorithms, February 2016
• Eriksson Monteiro, Pedro Sernadela, Sérgio Matos, Carlos Costa, José Luís Oliveira. Semantic Knowledge Base Construction from Radiology Reports. Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies, Rome, Italy, p. 345-352, February 2016
• Pedro Sernadela, Sérgio Matos, José Luís Oliveira. Ann2RDF: moving annotations to semantic web,. 17th International Conference on Information Integration and Web-based Applications & Services (iiWAS 2015), Brussels, Belgium, December 2015
• Pedro Lopes, Luís Bastião Silva, José Luís Oliveira. i2x: an Automated Real-time Integration and Interoperability Platform. 8th IEEE International Conference on Service Oriented Computing & Applications (SOCA 2015), Rome, Italy, October 2015
• Sérgio Matos, David Campos, Renato Pinho, Raquel Silva, Matthew Mort, David N. Cooper, José Luís Oliveira. Assisted Mining and Curation of Genomic Variants using Egas. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Sevilla, Spain, p. 396-402, September 2015
• Sérgio Matos, José Sequeira, David Campos, José Luís Oliveira. Identification of chemical and gene mentions in patent texts using feature-rich conditional random fields. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Sevilla, Spain, p. 76-81, September 2015
• Sérgio Matos, André Santos, David Campos, José Luís Oliveira. Neji: a BioC compatible framework for biomedical concept recognition. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Sevilla, Spain, p. 17-21, September 2015
• Eriksson Monteiro, Carlos Costa, José Luís Oliveira. A Machine Learning Methodology for Medical Imaging Anonymization. 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC2015), August 2015
• Luís Bastião Silva, Carlos Días, Johan van der Lei, José Luís Oliveira. Architecture to Summarize Patient-Level Data Across Borders and Countries. MEDINFO 2015, Brasil, vol. 216, p. 687-690, August 2015
• John Arevalo, Fabio Osorio, Raul Ramos-Pollan, José Luís Oliveira, Miguel Guevara. Convolutional Neural Networks for Mammography Mass Lesion Classification. 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC2015), Milan, Italy, August 2015
• Edgar Coelho, Joel Arrais, José Luís Oliveira. Uncovering Microbial Duality within Human Microbiomes: A Novel Algorithm for the Analysis of Host-Pathogen Interactions. 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC2015), Milan, Italy, August 2015
• Sérgio Matos, José Sequeira, José Luís Oliveira. BioinformaticsUA: Machine Learning and Rule-Based Recognition of Disorders and Clinical Attributes from Patient Notes. Proceedings of the 9th International Workshop on Semantic Evaluation (SemEval 2015), Denver, Colorado (USA), p. 422-426, June 2015
• Pedro Lopes, Luís Bastião Silva, José Luís Oliveira. Challenges and opportunities for exploring patient-level data: Preliminary results. CISTI 2015 - 10ª Conferencia Ibérica de Sistemas y Tecnologías de Información, Portugal, p. 1-5, June 2015
• Pedro Lopes, José Luís Oliveira. Integration-as-a-service for bioinformatics. CISTI 2015 - 10ª Conferencia Ibérica de Sistemas y Tecnologías de Información, Portugal, p. 1-6, June 2015
• Pedro Lopes, Pedro Sernadela, José Luís Oliveira. Towards a knowledge federation of linked patient registries. 10th Iberian Conference on Information Systems and Technologies (CISTI), 2015, Portugal, June 2015
• ...further results

PhD thesis

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