José Luís Oliveira

Position	Associate professor
Group	Information Systems and Telematics Laboratory
Transverse activity	Transverse Activity on Innovative Biomedical Technologies
Status	Integrated member
Country	Portugal
Students	David Campos, Fernanda Barbosa, João Cândido Santos, Luís Bastião Silva, Nuno Rosa, Paulo Gaspar, Pedro Lopes, Tiago Pedrosa
Former PhD students	Joel Arrais, Carlos Costa, Pedro Gonçalves, Rui Pedro Sanches de Castro Lopes, José Paulo Lousado, Miguel Pinheiro, Daniel Polónia
Former masters students	Show list
Courses	Programação 2
Projects	DECODING, DICOM P2P, EU-ADR, GEN2PHEN, GlobalClimate, IBERO-NBIC, QueryTermExp, Smartphones for Smart Seniors, World Search
Past projects	NF DNAmicroarrays, mRNATools
Events
Proposals
Personal page	http://www.ieeta.pt/~jlo

Publications

Books

• 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, Carlos Costa, José Luís Oliveira. A PACS archive architecture supported on Cloud services. International Journal of Computer Assisted Radiology and Surgery, vol. 7, no. 3, p. 349-358, May 2012
• Anna Bauer-Mehren, Erik M. van Mullingen, Paul Avillach, María del Carmen Carrascosa, Ricard Garcia-Serna, Janet Piñero, Bharat Singh, Pedro Lopes, José Luís Oliveira, Gayo Diallo, Ernst Ahlberg Helgee, Scott Boyer, Jordi Mestres, Ferran Sanz, Jan A. Kors, Laura I. Furlong. Automatic Filtering and Substantiation of Drug Safety Signals. PLoS Computational Biology, vol. 8, no. 4, April 2012 (IF 2010: 5.515)
• David Campos, Sérgio Matos, Ian Lewin, José Luís Oliveira, Dietrich Rebholz-Schuhmann. Harmonisation of gene/protein annotations: towards a gold standard MEDLINE. Bioinformatics, vol. Online first, March 2012 (IF 2010: 4.877)
• Pedro Gonçalves, José Luís Oliveira, Rui Aguiar. A study of encoding overhead in network management protocols. International Journal of Network Management, vol. Online first, February 2012 (IF 2010: 0,323)
• Nuno Rosa, Maria João Correira, Joel Arrais, Pedro Lopes, José Melo, José Luís Oliveira, Marlene Barros. From the salivary proteome to the OralOme: Comprehensive molecular oral biology. Archives of Oral Biology, January 2012 (IF 2010: 1.463)
• Frederico Valente, Carlos Viana Ferreira, Carlos Costa, José Luís Oliveira. A RESTful Image Gateway for Multiple Medical Image Repositories. IEEE Transactions on Information Technology in Biomedicine, vol. PP, no. 99, November 2011 (IF 2010: 1.707)
• Gabriela Moura, Miguel Pinheiro, Adelaide Freitas, José Luís Oliveira, Jorg Frommlet, Ana R Soares, Ana R Bezerra, Manuel A.S. Santos. Species-specific codon context rules unveil non-neutrality effects of synonymous mutations. PLoS ONE, vol. 6, no. 10, October 2011 (IF 2010: 4.411)
• Pedro Lopes, Raymond Dalgleish, José Luís Oliveira. WAVe: web analysis of the variome. Human Mutation, vol. 32, no. 7, p. 729–734, July 2011 (IF 2010: 5.956)
• Mathias Brochhausen, Anita Burgun, Werner Ceusters, Arie Hasman, Tze Yun Leong, Mark Musen, José Luís Oliveira, Mor Peleg, Alan Rector, Stefan Schulz. Discussion of "Biomedical Ontologies: Toward Scientific Debate". Methods of Information in Medicine, vol. 50, no. 3, p. 217-236, May 2011 (IF 2010: 1.472)
• Carlos Costa, Carlos Viana Ferreira, Luís Bastião Silva, Luis Ribeiro, Augusto Silva, José Luís Oliveira. Dicoogle - an Open Source Peer-to-Peer PACS. Journal of Digital Imaging, vol. online first, October 2010 (IF 2010: 1.421)
• Joel Arrais, João Fernandes, João Pereira, José Luís Oliveira. GeneBrowser 2: an application to explore and identify common biological traits in a set of genes. BMC Bioinformatics, vol. 11, no. 389, July 2010 (IF 2010: 3.028)
• Sérgio Matos, Joel Arrais, João Maia-Rodrigues, José Luís Oliveira. Concept-based query expansion for retrieving gene related publications from MEDLINE. BMC Bioinformatics, vol. 11, no. 212, April 2010 (IF 2010: 3.028)
• Ana R. Soares, Patricia M. Pereira, Bruno Santos, Conceição Egas, Ana C. Gomes, Joel Arrais, José Luís Oliveira, Gabriela Moura, Manuel A. S. Santos. Parallel DNA pyrosequencing unveils new zebrafish microRNAs. BMC Genomics, vol. 10, April 2009 (IF 2009: 3.759) (IF 2010: 4.206)
• Carlos Costa, José Luís Oliveira, Augusto Silva, Vasco Gama Ribeiro, José Ribeiro. Design, development, exploitation and assessment of a Cardiology Web PACS. Computer Methods and Programs in Biomedicine, vol. 93, no. 3, p. 273-282, March 2009 (IF 2009: 1.144) (IF 2010: 1.238)
• Carlos Costa, Filipe Freitas, Marco Pereira, Augusto Silva, José Luís Oliveira. Indexing and retrieving DICOM data in disperse and unstructured archives. International Journal of Computer Assisted Radiology and Surgery, vol. 4, no. 1, p. 71-77, January 2009
• Gabriela Moura, José Paulo Lousado, Miguel Pinheiro, Laura Carreto, Raquel M. Silva, José Luís Oliveira, Manuel A. S. Santos. Codon-triplet context unveils unique features of the Candida albicans protein coding genome. BMC Genomics, vol. 8, November 2007 (IF 2007: 4.180) (IF 2010: 4.206)
• Gabriela Moura, Miguel Pinheiro, Joel Arrais, Ana Cristina Gomes, Laura Carreto, Adelaide Freitas, José Luís Oliveira, Manuel A. S. Santos. Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure. PLoS ONE, vol. 2, no. 9, September 2007 (IF 2010: 4.411)
• Miguel Pinheiro, Vera Afreixo, Gabriela Moura, Adelaide Freitas, Manuel A. S. Santos, José Luís Oliveira. Statistical, computational and visualization methodologies to unveil gene primary structure features. Methods of Information in Medicine, vol. 45, no. 2, p. 163–168, 2006 (IF 2006: 1.684) (IF 2010: 1.472)
• Gabriela Moura, Miguel Pinheiro, R. Silva, I. Miranda, Vera Afreixo, G. Dias, Adelaide Freitas, José Luís Oliveira, Manuel A. S. Santos. Comparative context analysis of codon pairs on an ORFeome scale. Genome Biology, vol. 6, no. 3, 2005 (IF 2005: 9.712) (IF 2010: 6.885)
• Ilídio Oliveira, José Luís Oliveira, J. P. Sanchez, V. Lopez-Alonso, F. Martin-Sanchez, V. Maojo, António Sousa Pereira. Grid requirements for the integration of biomedical information resources for health applications. Methods of Information in Medicine, vol. 44, no. 2, p. 161-167, 2005 (IF 2005: 0.970) (IF 2010: 1.472)

Other articles in journals

• 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
• Adelaide Freitas, Vera Afreixo, Miguel Pinheiro, José Luís Oliveira, Gabriela Moura, Manuel A.S. Santos. Improving the Performance of the Iterative Signature Algorithm for the Identification of Relevant Patterns. Statistical Analysis and Data Mining, vol. 4, no. 1, p. 71-83, February 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

• 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 proceedings of international conferences

• Rafael Mendonça, Ana Filipa Rosa, José Luís Oliveira, António J. S. Teixeira. Towards Ontology Based Health Information Search in Portuguese - A case study in Neurologic Diseases. CISTI'2012 ((7th Iberian Conference on Information Systems and Technologies), Madrid, June 2012
• Paulo Gaspar, Jaime Carbonell, José Luís Oliveira. Parameter Influence in Genetic Algorithm Optimization of Support Vector Machines. Advances in Intelligent and Soft Computing, Proc. of the 6th Int. Conf. on Practical Applications of Computational Biology & Bioinformatics, PACBB 2012, vol. 154, p. 43-51, April 2012
• Pedro Lopes, Rafael Mendonça, Hugo Rocha, Jorge Oliveira, Laura Vilarinho, Rosário Santos, José Luís Oliveira. A Rare Disease Patient Manager. 6th International Conference on Practical Application of Computational Biology & Bioinformatics, Salamanca, Spain, March 2012
• Luís Bastião Silva, Carlos Costa, José Luís Oliveira. A DICOM RELAY SERVICE SUPPORTED ON CLOUD RESOURCES. Healthinf, February 2012
• Pedro Lopes, José Luís Oliveira. COEUS: A Semantic Web Application Framework. 4th International Semantic Web Applications & Tools for Life Sciences Workshop, London, United Kingdom, p. 66-73, December 2011
• Pedro Lopes, José Luís Oliveira. A semantic web application framework for health systems interoperability. Proceedings of the first international workshop on Managing interoperability and complexity in health systems, p. 87-90, November 2011
• Joel Arrais, Pedro Lopes, José Luís Oliveira. Challenges Storing and Representing Biomedical Data. Information Quality in e-Health: 7th Conference of the Workgroup Human-Computer Interaction and Usability Engineering of the Austrian Computer Society, USAB 2011, Graz, Austria, vol. LNCS 7058, p. 53-62, November 2011
• Pedro Lopes, José Luís Oliveira. Towards knowledge federation in biomedical applications. Proceedings of the 7th International Conference on Semantic Systems, p. 87-94, September 2011
• Luís Bastião Silva, Carlos Costa, José Luís Oliveira. A Pacs Gateway To The Cloud. CISTI2011 - 6ª Conferência Ibérica de Sistemas e Tecnologias de Informação Chaves, June 2011
• Luís Bastião Silva, Carlos Costa, José Luís Oliveira. A Secure PACS Cloud Archive. CARS, June 2011
• Luis Ribeiro, Carlos Costa, Ignacio Blanquer, José Luís Oliveira. On Demand IHE XDS Document Registries on the Cloud. 29th International EuroPACS Meeting (CARS 2010), Berlin, Germany, vol. 6, p. S297-S298, June 2011
• Sérgio Matos, José Luís Oliveira. Prioritizing Literature Search Results Using a Training Set of Classified Documents. Proc. of the 5th Int. Conf. on Practical Applications of Computational Biology and Bioinformatics, PACBB 2011, April 2011
• David Campos, D. Rebholz-Schuhman, Sérgio Matos, José Luís Oliveira. A CRF-based approach to harmonize heterogeneous gene/protein annotations. Proceedings of the Second CALBC workshop, p. 17-18, March 2011
• David Campos, Sérgio Matos, José Luís Oliveira. Annotating the CALBC corpus with a machine learning harmonization approach. Proceedings of the Second CALBC workshop, p. 43-45, March 2011
• Pedro Lopes, David Campos, José Luís Oliveira. A tagging system for bioinformatics resources. 10th IEEE International Conference on Information Technology and Applications in Biomedicine (ITAB 2010), Corfu, Greece, November 2010
• Pedro Lopes, José Luís Oliveira. An extensible platform for variome data integration. 10th IEEE International Conference on Information Technology and Applications in Biomedicine (ITAB 2010), Corfu, Greece, November 2010
• Joel Arrais, José Luís Oliveira. Gene-disease prioritization through biomedical networks. 10th IEEE International Conference on Information Technology and Applications in Biomedicine (ITAB 2010), November 2010
• Joel Arrais, José Luís Oliveira. On the exploitation of cloud computing in Bioinformatics. 10th IEEE International Conference on Information Technology and Applications in Biomedicine (ITAB 2010), November 2010
• Pedro Lopes, José Luís Oliveira. A Holistic Approach for Integrating Genomic Variation Information. Xth Spanish Symposium on Bioinformatics (JBI2010), Malaga, Spain, October 2010
• David Campos, Sérgio Matos, José Luís Oliveira. Recognition of Gene/Protein names using Conditional Random Fields. Proceedings of the International Conference on Knowledge Discovery and Information Retrieval 2010 (KDIR2010), Valencia, Spain, October 2010
• ...further results

PhD thesis

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