Books

  • O. Bodenreider, J.L Oliveira, and F. Rinaldi (Eds.)
    Proceedings of the 6th International Symposium on Semantic Mining in Biomedicine (SMBM 2014), University of Aveiro, 2014
  • M. Santos (Ed.)
    XVth National Congress of Biochemistry, 2006
    ISBN 978-972-789-214-3
  • M. Santos (Ed.)
    IIIrd National Meeting on RNA Biology, 2006
    ISBN 978-972-789-215-0
  • J. L. Oliveira, V. Maojo, F. Martin-Sanchez, and A. S. Pereira (Eds.),
    Biological and Medical Data Analysis, Springer, 2005,
    ISBN 978-972-789-215-0, http://www.springerlink.com/content/k15u6315h070/

Book chapters

  • C. V. Ferreira and C. Costa
    “Challenges of Using Cloud Computing in Medical Imaging”
    in Advances in Cloud Computing Research, M. Ramachandran, 2014.
  •  J. Melo, J. P. Arrais, E.Coelho, P. Lopes, N. Rosa, M. J. Correia, M.Barros and J. L. Oliveira
    “Data Integration Solution for Organ-Specific Studies: An Application for Oral Biology”
    in Biomedical Engineering Systems and Technologies, J. Gabriel, J. Schier, S. Huffel et al, Eds., Springer Berlin Heidelberg, 2013.
  • A. Freitas, W. Ayadi, M. Elloumi, J. L. Oliveira, and J.-K. Hao
    “A Survey on Biclustering of Gene Expression Data”
    in Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data, M. Elloumi & A. Zomaya, Eds., Wiley, 2013.
  • D. Campos, S. Matos, and J. L. Oliveira
    “Current methodologies for biomedical Named Entity Recognition”
    in Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data, M. Elloumi & A. Zomaya, Eds., Wiley, 2013.
  • M. Santos, L. Bastião, C. Costa, A. Silva, N. Rocha
    “Clinical Data Mining in Small Hospital PACS: Contributions for Radiology Department Improvement”
    in Information Systems and Technologies for Enhancing Health and Social Care, IGI Global, 2013.
  • F. Valente, C. Costa, and A. Silva
    “Content Based Retrieval Systems in a Clinical Context”
    in Medical Imaging in Clinical Practice, Okechukwu F. Erondu, Ed., InTech, February 2013.
  • D. Campos, S. Matos, and J. L. Oliveira
    “Biomedical Named Entity Recognition: a Survey of Machine-Learning Tools”
    in Theory and Applications for Advanced Text Mining, S. Sakurai, Ed., InTech, 2012.
  • P. Lopes and J. L. Oliveira
    “Collecting and Enriching Human Variome Datasets”
    in Tecnologías NBIC en Salud: El papel protagonista de la Nanociencia, J. Aguiló, A. Freire, D. Iglesia, V López, A Pazos, Eds., CYTED, 2012, pp. 9-19.
  • L. S. Ribeiro, C. Costa and J. L. Oliveira
    “Current Trends in Archiving and Transmission of Medical Images”
    in Medical Imaging, Okechukwu F. Erondu, Ed., InTech, December 2011.
  • J. Arrais, S. Matos, and J. L. Oliveira
    “Integração de Dados Biomédicos”
    in Nano, Bio, Info y Cogno (Convergencia de Tecnologías NBIC) Conceptos y Aplicaciones, J Aguiló, A Freire, D Iglesia, F Martin, A Pazos, Eds., 2011, pp. 185-226.
  • G. Moura, M. Pinheiro, A. Freitas, J. L. Oliveira, and M. A. Santos
    “Computational and Statistical Methodologies for ORFeome Primary Structure Analysis”
    in Comparative Genomics, Methods in Molecular Biology series, N. Bergman, Ed.: Humana Press, USA, 2007, pp. 449-462.
  • C. Costa, A. Silva, and J. L. Oliveira
    “Current Perspectives on PACS and a Cardiology Case Study”
    in Advanced Computational Intelligence Paradigms in Healthcare 2, vol. 65, S. Vaidya, L. C. Jain, and H. Yoshida, Eds.: Springer-Verlag, 2007, pp. 79-108.
  • C. Costa, A. Silva, J. L. Oliveira, V. Ribeiro, and J. Ribeiro
    “A demanding Web-based PACS supported by Web Services technology”
    in Medical Imaging 2006: PACS and Imaging Informatics, vol. 6145, O. R. Steven C.Horii, Ed., 2006.
  • C. Costa, J. L. Oliveira, A. Silva, V. Ribeiro, and J. Ribeiro
    “Himage: Um Web-PACS inovador para Imagem Cardíaca”
    in TIC em Biomedicina, vol. 6145, M. G. J. R. Rabunal, N. Pedreira, J. Pereira, Ed. Santiago de Compostela 2005.
  • S. Kim, R. I. Doğan, A. Chatr-Aryamontri, C. S. Chang, R. Oughtred, J. Rust, R. Batista-Navarro, J. Carter, S. Ananiadou, S. Matos, A. Santos, D. Campos, J. L. Oliveira, O. Singh, J. Jonnagaddala, H.-J. Dai, E. C.-Y. Su, Y.-C. Chang, Y.-C. Su, C.-H. Chu, C. C. Chen, W.-L. Hsu, Y. Peng, C. Arighi, C. H. Wu, K. Vijay-Shanker, F. Aydın, Z. M. Hüsünbeyi, A. Özgür, S.-Y. Shin, D. Kwon, K. Dolinski, M. Tyers, W. J. Wilbur, D. C. Comeau
    “BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID”
    Database (Oxford), vol. 2016, September 2016, pdf
  • Q. Wang, S. S. Abdul, L. Almeida, S. Ananiadou, Y. I. Balderas-Martínez, R. Batista-Navarro, D. Campos, L. Chilton, H.-J. Chou, G. Contreras, L. Cooper, H.-J. Dai, B. Ferrell, J. Fluck, S. Gama-Castro, N. George, G. Gkoutos, A. K. Irin, L. J. Jensen, S. Jimenez, T. R. Jue, I. Keseler, S. Madan, S. Matos, P. McQuilton, M. Milacic, M. Mort, J. Natarajan, E. Pafilis, E. Pereira, S. Rao, F. Rinaldi, K. Rothfels, D. Salgado, R. Silva, O. Singh, R. Stefancsik, C.-H. Su, S. Subramani, H. D. Tadepally, L. Tsaprouni, N. Vasilevsky, X. Wang, A. Chatr-Aryamontri, S. J. F. Laulederkind, S. Matis-Mitchell, J. McEntyre, S. Orchard, S. Pundir, R. Rodriguez-Esteban, K. Van Auken, Z. Lu, M. Schaeffer, C. H. Wu, L. Hirschman, C. N. Arighi
    “Overview of the interactive task in BioCreative V”
    Database (Oxford), vol. 2016, September 2016, pdf
  • S. Matos, D. Campos, R. Pinho, R. M. Silva, M. Mort, D. N. Cooper, J. L. Oliveira
    “Mining clinical attributes of genomic variants through assisted literature curation in Egas”
    Database (Oxford), vol. 2016, June 2016, pdf
  • J. Arevalo, F. A. González, R. Ramos-Póllan, J. L. Oliveira, M. Guevara
    “Representation learning for mammography mass lesion classification with convolutional neural networks”
    Computer Methods and Programs in Biomedicine, p. 248–257, April 2016, pdf
  • E. Monteiro, C. Costa, and J. L. Oliveira
    “A Cloud Architecture for Teleradiology-as-a-Service”
    Methods of Information in Medicine, March 2016, pdf
  • P. Sernadela, P. Lopes, J. L. Oliveira
    “A knowledge federation architecture for rare disease patient registries and biobanks”
    Journal of Information Systems Engineering & Management, vol.2, March 2016, pdf
  • C. Viana-Ferreira, L. Ribeiro, S. Matos, C. Costa
    “Pattern Recognition for Cache Management in Distributed Medical Imaging Environments”
    International Journal of Computer Assisted Radiology and Surgery, vol. 11, no. 2, p. 327-336, February 2016. pdf
  • V. Afreixo, S. J. M. O. Rodrigues, C. C. A. Bastos, and M. R. Silva
    “The exceptional genomic word symmetry along DNA sequences”
    BMC Bioinformatics, vol. 17, pp. 1-10, February 2016. pdf
  • S. Duarte-Pereira, I. Pereira-Castro, S. S. Silva, M. G. Correia, C. Neto, L. T. da Costa, et al.
    “Extensive regulation of nicotinate phosphoribosyltransferase (NAPRT) expression in human tissues and tumors”
    Oncotarget, December 2015. pdf
  • A. R. Soares, N. Fernandes, M. Reverendo, H. R. Araújo, J. L. Oliveira, G. M. R. Moura, et al.
    “Conserved and highly expressed tRNA derived fragments in zebrafish”
    BMC Molecular Biology, vol. 16, pp. 1-16, December 2015. pdf
  • J. Branco, A. P. Silva, R. M. Silva, A. Silva-Dias, C. Pina-Vaz, G. Butler, et al.
    “Fluconazole and Voriconazole Resistance in Candida parapsilosis Is Conferred by Gain-of-Function Mutations in MRR1 Transcription Factor Gene”
    Antimicrob Agents Chemother, vol. 59, pp. 6629-33, October 2015. pdf
  • F. Valente, L. B. Silva, T. Godinho, C. Costa
    “Anatomy of an Extensible Open Source PACS”
    Journal of Digital Imaging, pp. 1-13, Ocotober 2015, pdf
  • P. Lopes and J. L. Oliveira
    “An automated real-time integration and interoperability framework for bioinformatics”
    BMC Bioinformatics, October 2015, pdf
  • P. Lopes, L. Bastiao Silva, and J. L. Oliveira
    “Challenges and Opportunities for Exploring Patient-Level Data”
    BioMed Research International, August 2015, pdf 
  • R. M. Silva, D. Pratas, L. Castro, A. J. Pinho, and P. J. S. G. Ferreira, “Three minimal sequences found in Ebola virus genomes and absent from human DNA”
    Bioinformatics, vol. 31, pp. 2421-2425, August 2015, pdf
  • E. D. Coelho, A. M. Santiago, J. P. Arrais, and J. L. Oliveira
    “Computational methodology for predicting the landscape of the human-microbial interactome region level influence”
    J Bioinform Comput Biol, August 2015, pdf
  • J. A. Vanegas, S. Matos, F. A. Gonzalez, J. L. Oliveira
    “An Overview of Biomolecular Event Extraction from Scientific Documents”
    Comp. and Mathematical Methods in Medicine, August 2015. pdf
  • D. Pratas, R. M. Silva, A. J. Pinho, and P. J. S. G. Ferreira
    “An alignment-free method to find and visualise rearrangements between pairs of DNA sequences”
    Scientific Reports, vol. 5, May 2015. pdf
  • R. M. Silva, D. Pratas, L. Castro, A. J. Pinho, P. J. Ferreira
    “Three minimal sequences found in Ebola virus genomes and absent from human DNA”
    Bioinformatics, April 2015. pdf
  • J. P. Arrais and J. L. Oliveira
    “RecRWR: A Recursive Random Walk Method for Improved Identification of Diseases”
    BioMed Research International, March 2015. pdf
  • D. Campos, S. Matos, and J. L. Oliveira
    “A document processing pipeline for annotating chemical entities in scientific documents”
    Journal of Cheminformatics, 7(Suppl 1):S7, January 2015. pdf
  • M. Krallinger, O. Rabal, F. Leitner, M. Vazquez, D. Salgado, Z. Lu, R. Leaman, Y. Lu, D. Ji, D. M. Lowe, R. A. Sayle, R. T. Batista-Navarro, R. Rak, T. Huber, T. Rocktäschel, S. Matos, D. Campos, B. Tang, H. Xu, T. Munkhdalai, K. H. Ryu, S. V.Ramanan, S. Nathan, S. Žitnik, M. Bajec, L. Weber, M. Irmer, S. A. Akhondi, J. A. Kors, S. Xu, X. An, U. K. Sikdar, A. Ekbal, M. Yoshioka, T. M. Dieb, M. Choi, K. Verspoor, M. Khabsa, C. L. Giles, H. Liu, K. E. Ravikumar, A. Lamurias, F. M. Couto, H. Dai, R. T.-H. Tsai, C. Ata, T. Can, A. Usié, R. Alves, I. Segura-Bedmar, P. Martínez, J. Oyarzabal, A. Valencia
    “The CHEMDNER corpus of chemicals and drugs and its annotation principles”
    Journal of Cheminformatics, vol. 7, Suppl. 1, p. S2, January 2015. pdf
  • L. Ragionieri, R. Vitorino, J. Frommlet, J. L. Oliveira, P. Gaspar, L. R. de Pouplana, et al
    “Improving the accuracy of recombinant protein production through integration of bioinformatics, statistical and mass spectrometry methodologies”
    FEBS Journal, December 2014. pdf
  • T. M. Godinho, C. Viana-Ferreira, L. B. Silva, and C. Costa
    “A Routing Mechanism for Cloud Outsourcing of Medical Imaging Repositories”
    IEEE Journal of Biomedical and Health Informatics, October 2014. pdf
  • S. Brás, A. Georgakis, L. Ribeiro, D. A. Ferreira, A. Silva, L. Antunes, and C. S. Nunes
    “Electroencephalogram-based indices applied to dogs’ depth of anaesthesia monitoringe”
    Research in Veterinary Science, October 2014. pdf
  • S. Duarte-Pereira, S. S. Silva, L. Azevedo, L. Castro, A. Amorim, and  R. M. Silva
    “Nampt and Naprt1: Novel Polymorphisms and Distribution of Variants between Normal Tissues and Tumor Samples”
    Scientific Reports, Vol. 4,:6311, September 2014. pdf
  • R. Sebastião, J. Gama, and T. Mendonça
    “Constructing fading histograms from data streams”
    Progress in Artificial Intelligence, August 2014. pdf
  • L. B. Silva, S. Campos, C. Costa,  and J. L. Oliveira
    “Sensor-Based Architecture for Medical Imaging Workflow Analysis”
    Journal of Medical Systems, August 2014. pdf
  • D. Campos, J. Lourenco, S. Matos, and J. L. Oliveira
    “Egas: a collaborative and interactive document curation platform”
    Database, June 2014. pdf
  •  N. Rosa,  M. J. Correia, J. P. Arrais, N. Costa, J. L. Oliveira, and M. Barros
    “The Landscape of Protein Biomarkers Proposed for Periodontal Disease: Markers with Functional Meaning”
    BioMed Research International, June 2014. pdf
  • E. Coelho, J. P. Arrais, S. Matos, C. Pereira, N. Rosa, M. J. Correia, M. Barros, and J. L. Oliveira
    “Computational prediction of the human-microbial oral interactome”
    BMC Systems Biology, February 2014. pdf
  • J. C. Santos and S. Matos
    “Analysing Twitter and web queries for flu trend prediction”
    Theoretical Biology and Medical Modelling, vol. 11 (Suppl 1):S6, May 2014, pdf
  • V. M. Prieto, S. Matos, M. Álvarez, F. Cacheda, and J. L. Oliveira
    “Twitter: A Good Place to Detect Health Conditions”
    PLoS ONE, January 2014. pdf
  • M. Reboiro-Jato, J. P. Arrais, J. L. Oliveira, and F. Fdez-Riverola
    “geneCommittee: a web-based tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification”
    BMC Bioinformatics, January 2014. pdf (highly accessed)
  • D. Campos, Q. C. Bui, S. Matos, and J. L. Oliveira
    “TrigNER: automatically optimized biomedical event trigger recognition on scientific documents”
    Source Code for Biology and Medicine, vol. 9:1, January 2014. pdf
  • P. Lopes, T. Nunes, D. Campos, L. Furlong, A. Bauer-Mehren, F. Sanz, M. C. Carrascosa, J. Mestres, J. Kors, B. Singh, E. van Mulligen, J. Van der Lei, G. Diallo, P. Avillach, E. Ahlberg, S. Boyer, C. Diaz, and  J. L. Oliveira
    “ Gathering and Exploring Scientific Knowledge in Pharmacovigilance”
    PLoS ONE, 2013. pdf
  • L. Ribeiro, C. Viana-Ferreira, J. L. Oliveira, and C. Costa
    “ XDS-I outsourcing proxy: ensuring confidentiality while preserving interoperability”
    IEEE Journal of Biomedical and Health Informatics, 2013. pdf
  • P. Gaspar, P. Lopes, J. Oliveira, R. Santos, R. Dalgleish, and J. L. Oliveira
    “Variobox: Automatic Detection and Annotation of Human Genetic Variants”
    Human Mutation , 2013. pdf
  • L. B. Silva, R. Pinho, L. Ribeiro, C. Costa, and J. L. Oliveira
    “A Centralized Platform for Geo-Distributed PACS Management”
    Journal of Digital Imaging , 2013. pdf
  • S. Matos, H. Araújo, and J. L. Oliveira
    “Biomedical literature exploration through latent semantics”
    Advances in Distributed Computing and Artificial Intelligence Journal, Vol. 1(5):65-74, August 2013. pdf
  • L. A. Campos, V. L. Pereira Jr., A. Muralikrishna, S. Albarwani, S. Brás, and S. Gouveia
    “Mathematical Biomarkers for the Autonomic Regulation of Cardiovascular System”
    Frontiers in Integrative Physiology, 2013. pdf
  • D. Campos, S. Matos, and J. L. Oliveira
    “A modular framework for biomedical concept recognition”
    BMC Bioinformatics, 14:281, 2013. pdf (highly accessed)
  • P. M. Coloma, M. J. Schuemie, G. Trifirò, L. Furlong, E.van Mulligen, A. Bauer-Mehren, P. Avillach, J. Kors, F. Sanz, J. Mestres, J. L. Oliveira, S. Boyer, E. A. Helgee, M. Molokhia, J. Matthews, D. Prieto-Merino, R. Gini, R. Herings, G. Mazzaglia, G. Picelli, L. Scotti, L. Pedersen, J. van der Lei, M. Sturkenboom
    “Drug-Induced Acute Myocardial Infarction: Identifying ‘Prime Suspects’ from Electronic Healthcare Records-Based Surveillance System”
    PLoS ONE , 2013. pdf
  • P . Lopes. and J. L. Oliveira
    “An innovative portal for rare genetic diseases research: The semantic Diseasecard”
    Journal of Biomedical Informatics, 2013. pdf
  • M. Cases, L. I. Furlong, J. Albanell, R. B. Altman, R. Bellazzi, S. Boyer, A. Brand, A. J. Brookes, S. Brunak, T. W. Clark, J. Gea, P. Ghazal, N. Graf, R. Guigó, T. E. Klein, N. López-Bigas, V. Maojo, B. Mons, M. Musen, J. L. Oliveira, A. Rowe, P. Ruch, A. Shavo, E. H. Shortliffe, A. Valencia, J. v. d. Lei, M. A. Mayer, and F. Sanz
    “How to improve data and knowledge management to better integrate healthcare and research”
    Journal of Internal Medicine, 2013. pdf
  • T. Nunes, D. Campos, S. Matos, and J. L. Oliveira
    “BeCAS: biomedical concept recognition services and visualization”
    Bioinformatics, Vol. 29(15):1915-6, August 2013. pdf
  • F. Valente, C. Costa, and A. Silva
    “Dicoogle, a PACS featuring Profiled Content Based Image Retrieval”
    PLoS ONE, 2013. pdf
  • K. K. Lee, S. Matos, D. H. Evans, P. White, I. D. Pavord, S. S. Birring
    “A Longitudinal Assessment of Acute Cough”
    American Journal of Respiratory and Critical Care Medicine, vol. 187, no. 9, p. 991-997, May 2013. pdf
  • J. P. Arrais, N. Rosa, J. Melo, E. Coelho, D. Amaral, M. J. Correia, M. Barros, and J. L. Oliveira
    “OralCard: a bioinformatic tool for the study of Oral Proteome”
    Archives of Oral Biology, February 2013. pdf
  • D. Campos, S. Matos, and J. L. Oliveira
    “Gimli: open source and high-performance biomedical name recognition”
    BMC Bioinformatics, 14:54, February 2013. pdf (highly accessed)
  • P. Gaspar, G. Moura, M. A. S. Santos, and J. L. Oliveira
    “mRNA secondary structure optimization using a correlated stem-loop prediction”
    Nucleic Acids Research, January 2013. pdf
  • N. Yousaf, W. Monteiro, S. Matos, S. Birring, and I. D. Pavord
    “Cough frequency in health and disease”
    European Respiratory Journal, vol. 41, no. 1, p. 241-243, January 2013. pdf
  • P. Lopes and J. L. Oliveira
    “COEUS: “semantic web in a box” for biomedical applications”
    Journal of Biomedical Semantics, vol. 3, December 2012. pdf (highly accessed)
  • J. L. Oliveira, P. Lopes, T. Nunes, D. Campos, S. Boyer, E. Ahlberg, E. van Mullingen, J. Kors, B. Singh, L. I. Furlong, F. Sanz, A. Bauer-Mehren, M. D. C. Carrascosa, J. Mestres, P. Avillach, C. Díaz Acedo, and J. van der Lei
    “The EU-ADR Web Platform: delivering advanced pharmacovigilance tools”
    Pharmacoepidemiology and Drug Safety, December 2012. pdf
  • J. P. Lousado, J. L. Oliveira, G. Moura, and M. A. S. Santos
    “An integrative approach for codon repeats evolutionary analyses”
    International Journal of Data Mining and Bioinformatics, vol. 6: 369-381, September 2012. pdf
  • C. Costa and J. L. Oliveira
    “Telecardiology through ubiquitous Internet services”
    International Journal of Medical Informatics, vol. 81: 612-21, September 2012. pdf
  • L. B. Silva, C. Costa, and J. L. Oliveira
    “DICOM Relay over the Cloud”
    International Journal of Computer Assisted Radiology and Surgery, August 2012. pdf
  • P. Gaspar, J. L. Oliveira, J. Frommlet, M. A. S. Santos, and G. Moura
    “EuGene: Maximizing synthetic gene design for heterologous expression”
    Bioinformatics, vol. 28, July 2012. pdf
  • K. K. Lee, A. Savani, S. Matos, D. H. Evans, I. D. Pavord, S. Birring
    “4-hour cough frequency monitoring in chronic cough”
    Chest, July 2012. pdf
  • L. Ribeiro, C. Costa, and J. L. Oliveira
    “Clustering of distinct PACS archives using a cooperative peer-to-peer network”
    Computer Methods and Programs in Biomedicine, June 2012. pdf
  • F. Valente, C. Viana-Ferreira, C. Costa, and J. L. Oliveira
    “A RESTful Image Gateway for Multiple Medical Image Repositories”
    IEEE Transactions on Information Technology in BioMedicine, vol. 16, no. 3: 356-36, 2012. pdf
  • D. Campos, S. Matos, I. Lewin, J. L. Oliveira, and D. Rebholz-Schuhmann
    “Harmonisation of gene/protein annotations: towards a gold standard MEDLINE”
    Bioinformatics, Vol. 28(9):1253-61, May 2012. pdf
  • A. Bauer-Mehren, E. van Mullingen, P. Avillach, M. D. C. Carrascosa, R. García-Serna, J. Pinero, B. Singh, P. Lopes, J. L. Oliveira, G. Diallo, A. E. Helgee, B. Scott, J. Mestres, F. Sanz, J. Kors, and L. I. Furlong
    “Automatic filtering and substantiation of drug safety signals”
    PLoS Computational Biology, 2012. pdf
  • P. Gaspar and J. L. Oliveira
    “Advantages of a Pareto-based genetic algorithm to solve the gene synthetic design problem”
    Current Bioinformatics, vol. 7, no. 4, 2012.
  • S.C. Novais, T. Vandenbrouck, P. Lopes, J. P. Arrais, W. De Coen, A. Soares and M. Amorim
    “Enchytraeus albidus microarray: enrichment, design, annotation and database (EnchyBASE)”
    PLoS ONE, 2012. pdf
  • N. Rosa, M. J. Correia, J. P. Arrais, P. Lopes, J. Melo, J. L. Oliveira, and M. Barros
    “From the salivary proteome to the OralOme: Comprehensive molecular oral biology”
    Archives of Oral Biology, 2012. pdf
  • P. Grynberg, T. Abeel, P. Lopes, G. Macintyre, and L. P. Rubiño
    “Highlights from the Student Council Symposium 2011 at the International Conference on Intelligent Systems for Molecular Biology and European Conference on Computational Biology”
    BMC Bioinformatics, 12 (Suppl 11):A1, November 2011. pdf
  • G. Moura, M. Pinheiro, A. Freitas, J. L. Oliveira, J. Frommlet, L. Carreto, A. R. Soares, A. R. Bezerra, and M. A. S. Santos
    “Species-Specific Codon Context Rules Unveil Non-Neutrality Effects of Synonymous Mutations”
    PLoS ONE, vol. 6, 2011. pdf
  • J. P. Arrais and J. L. Oliveira
    “Using biomedical networks to prioritize gene–disease associations”
    Open Access Bioinformatics, vol. 3, 2011. pdf
  • Z. Lu, H.-Y. Kao, C.-H. Wei, M. Huang, J. Liu, C.-J. Kuo, C.-N. Hsu, R.T.-H. Tsai, H.-J. Dai, N. Okazaki, H.-C. Cho, M. Gerner, I. Solt, S. Agarwal, F. Liu, D. Vishnyakova, P. Ruch, M. Romacker, F. Rinaldi, S. Bhattacharya, P. Srinivasan, H. Liu, M. Torii, S. Matos, D. Campos, K. Verspoor, K.M. Livingston, and W.J. Wilbur
    “The Gene Normalization Task in BioCreative III”
    BMC Bioinformatics, vol. 12 (Suppl 8): S9, September 2011. pdf
  • M. Krallinger, M. Vazquez, F. Leitner, D. Salgado, A. Chatraryamontri, A. Winter, L. Perfetto, L. Briganti, L. Licata, M. Iannuccelli, L. Castagnoli, G. Cesareni, M. Tyers, G. Schneider, F. Rinaldi, R. Leaman, G. Gonzalez, S. Matos, S. Kim, W.J. Wilbur, L. Rocha, A.V. Tendulkar, A. Rangrej, V. Raut, S. Agarwal, F. Liu, X. Wang, R. Rak, K. Noto, C. Elkan, Z. Lu, R. I. Dogan, Jean-F. Fontaine, M.A. Andrade-Navarro, and A. Valencia
    “The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text”
    BMC Bioinformatics, vol. 12 (Suppl 8):S9, September 2011. pdf
  • S. Matos and J. L. Oliveira
    “Classification methods for finding articles describing protein-protein interactions in PubMed”
    Journal of Integrative Bioinformatics, vol. 8: 178, 2011. pdf
  • M. Brochhausen, A. Burgun, W. Ceusters, A. Hasman, T. Y. Leong, M. Musen, J. L. Oliveira, M. Peleg, A. Rector, and S. Schulz
    “Discussion of Biomedical Ontologies: Toward Scientific Debate”
    Methods of Information in Medicine, vol. 50: 217-236, 2011. pdf
  • L. Bastião, C. Costa, and J. L. Oliveira
    “A PACS archive architecture supported on Cloud services”
    International Journal of Computer Assisted Radiology and Surgery, 2011. pdf
  • P. Lopes, R. Dalgleish, and J. L. Oliveira
    “WAVe: web analysis of the variome”
    Human Mutation, 2011. pdf
  • A. Freitas, V. Afreixo, M. Pinheiro, J. L. Oliveira, G. Moura, and M. A. S. Santos
    “Improving the Performance of the Iterative Signature Algorithm for the Identification of Relevant Patterns”
    Statistical Analysis and Data Mining, vol. 4, pp. 71-83, 2011. pdf
  • C. Costa, C. Ferreira, L. Bastião, L. Ribeiro, A. Silva, and J. L. Oliveira
    “Dicoogle – an Open Source Peer-to-Peer PACS”
    Journal of Digital Imaging, October 2010. pdf
  • J. P. Arrais, J. Fernandes, J. Pereira, and J.L. Oliveira
    “GeneBrowser 2: an application to explore and identify common biological traits in a set of genes”
    BMC Bioinformatics,  11:389, July 2010. pdf (highly accessed)
  • S. Matos, J. P. Arrais, J. Maia-Rodrigues, and J. L. Oliveira
    “Concept-based query expansion for retrieving gene related publications from MEDLINE”
    BMC Bioinformatics, 11:212,  April 2010. pdf (highly accessed)
  • N. Yousaf, W. Monteiro, D. Parker, S. Matos, S Birring, and I. D. Pavord
    “Long-term low-dose erythromycin in patients with unexplained chronic cough: a double-blind placebo controlled trial”
    Thorax, vol. 65, no. 12, p. 1107-1110, December 2010 pdf
  • A. R. Soares, P. M. Pereira, B. Santos, C. Egas, A. C. Gomes, J. P. Arrais, J. L. Oliveira, G. Moura, and M. A. S. Santos
    “Parallel DNA pyrosequencing unveils new zebrafish microRNAs”
    BMC Genomics, vol. 10, 2009. pdf (highly accessed)
  • C. Costa, J. L. Oliveira, A. Silva, V. Ribeiro, and J. Ribeiro
    “Design, development, exploitation and assessment of a Cardiology Web PACS”
    Computer Methods and Programs in Biomedicine, vol. 93, pp. 273-282, 2009. pdf
  • C. Costa, F. Freitas, M. Pereira, A. Silva, and J. L. Oliveira
    “Indexing and retrieving DICOM data in disperse and unstructured archives”
    International Journal of Computer Assisted Radiology and Surgery, vol. 4, pp. 71-77, 2009. pdf
  • G. Moura, J. P. Lousado, M. Pinheiro, L. Carreto, R. Silva, J. L. Oliveira, and M. A. Santos
    “Codon-triplet context unveils unique features of the Candida albicans protein coding genome”
    BMC Genomics, vol. 8, no. 444, 2007. pdf
  • J. P. Arrais, B. Santos, J. Fernandes, L. Carreto, M. A. Santos, and J. L. Oliveira
    “GeneBrowser: an approach for integration and functional classification of genomic data”
    Journal of Integrative Bioinformatics, vol. 4, no. 3, 2007. pdf
  • G. Moura, M. Pinheiro, J. P. Arrais, A. C. Gomes, L. Carreto, A. Freitas, J. L. Oliveira, and M. A. 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, e847, doi:10.1371/journal.pone.0000847, 2007. pdf
  • D. Polónia, C. Costa, A. Silva, and J. L. Oliveira
    “PACS procurement planning and negotiation strategies for regional health institutions in the National Health Service of an EU country”
    International Journal of Computer Assisted Radiology and Surgery, Vol 2, Sup 1, 2007.
  • C. Costa, J. L. Oliveira, A. Silva, V. Gama, and J. Ribeiro
    “Enhanced PACS to support Demanding Telemedicine and Telework Scenarios”
    International Journal of Computer Assisted Radiology and Surgery, Vol 2, Sup 1, 2007.
  • M. Pinheiro, V. Afreixo, G. Moura, A. Freitas, M. A. Santos, and J. L. Oliveira
    “Statistical, computational and visualization methodologies to unveil gene primary structure features
    Methods of Information in Medicine, vol. 45, no. 2, pp. 163-168, 2006.
  • I. Oliveira, J. L. Oliveira, J. P. Sanchez, V. López-Alonso, F. Martin-Sanchez, V. Maojo, and A. S. Pereira
    “Grid requirements for the integration of biomedical information resources for health applications”
    Methods of Information in Medicine, vol. 44, no. 2, pp. 161-67, 2005.
  • G. Moura, M. Pinheiro, R. Silva, I. Miranda, V. Afreixo, G. Dias, A. Freitas, J. L. Oliveira, and M. A. Santos
    “Comparative context analysis of codon pairs on an ORFeome scale”
    Genome Biology, vol. 6, no. 3, pp. R28, 2005.

International Magazines

  • L. Bastião and  C. Costa
    “Migrating PACS to the cloud – advantages and drawbacks”
    International Hospital and Equipment, March/April 2012, vol 38, p16-18
  • L. Bastião, C. Costa, and J. L. Oliveira
    “Strengths and Weaknesses of Using Cloud Computing”
    Imaging Management, vol. 11, 2012 pdf
  • C. Costa, L. Bastião, C. Ferreira, S. Campos, A. Silva, and J. L. Oliveira
    “Dicoogle – a paradigm change in medical imaging networks”
    Diagnostic Imaging Europe, pp. 22-23, November 2011 pdf
  • A. Santos, S. Matos, D. Campos and J. L. Oliveira
    “A Curation Pipeline and Web-Services for PDF Documents”
    In Proceedings of the 7th International Symposium on Semantic Mining in Biomedicine (SMBM 2016), Potsdam, Germany, August 2016
  • E. Monteiro, P. Sernadela, S. Matos, C. Costa and J. L. Oliveira
    “Semantic Knowledge Base Construction from Radiology Reports”
    In Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies, Rome, Italy, February 2016
  • P. Sernadela, S. Matos, J. L. Oliveira
    “Ann2RDF: moving annotations to semantic web”
    In 17th International Conference on Information Integration and Web-based Applications & Services (iiWAS 2015), Brussels, Belgium, December 2015
  • P. Lopes, L. Bastião and J. L. Oliveira
    “i2x: an Automated Real-time Integration and Interoperability Platform”
    In Proceedings of the 8th IEEE International Conference on Service Oriented Computing & Applications (SOCA2015), Rome, Italy, October 2015
  • D. Pratas, RM. Silva, AJ. Pinho, PJSG. Ferreira
    “Detection and visualisation of regions of human DNA not present in other primates”
    In Proceedings of the 21st Portuguese Conference on Pattern Recognition, RecPad 2015, Faro, Portugal, October 2015
  • S. Matos, D. Campos, R. Pinho, R. Silva, M. Mort, D. Cooper, J. L. Oliveira
    “Assisted Mining and Curation of Genomic Variants using Egas”
    In Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Sevilla, Spain, September 2015
  • S. Matos, J. Sequeira, D. Campos, J. L. Oliveira
    “Identification of chemical and gene mentions in patent texts using feature-rich conditional random fields”
    In Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Sevilla, Spain, September 2015
  • S. Matos, A. Santos, D. Campos, J. L. Oliveira
    “Neji: a BioC compatible framework for biomedical concept recognition”
    In Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Sevilla, Spain, September 2015
  • L. A. Bastiao Silva, C. Días, J. van der Lei, and J. L. Oliveira
    “Architecture to Summarize Patient-Level Data Across Borders and Countries”
    In Proceedings of MEDINFO 2015, Brasil, August 2015
  • E. Coelho, J. P. Arrais, and J. L. Oliveira
    “Uncovering Microbial Duality within Human Microbiomes: A Novel Algorithm for the Analysis of Host-Pathogen Interactions”
    In Proceedings of the 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC2015), Milan, Italy, August 2015
  • J. Arevalo, F. A. Gonzalez Osorio, R. Ramos-Pollan, J. L. Oliveira, and M. A. Guevara López
    “Convolutional Neural Networks for Mammography Mass Lesion Classification”
    In Proceedings of the 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC2015), Milan, Italy, August 2015
  • E. Monteiro, C. Costa, J. L. Oliveira
    “A Machine Learning Methodology for Medical Imaging Anonymization”
    In Proceedings of the 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC2015), Milan, Italy, August 2015
  • E. Pinho, C. V. Ferreira, and Carlos Costa
    “Simulation of DICOM traffic in PACS networks using behavior profiles”
    In Proceedings of Computer Assisted Radiology and Surgery (CARS 2015), Barcelona, Spain, June 2015
  • S. Matos, J. Sequeira, and J.L. Oliveira
    “BioinformaticsUA: Machine Learning and Rule-Based Recognition of Disorders and Clinical Attributes from Patient Notes”
    In Proceedings of the 9th International Workshop on Semantic Evaluation (SemEval 2015), Denver, Colorado, USA, June 2015
  • T. T. Godinho, L. M. Silva, and C. Costa
    “An automation framework for PACS workflows optimization in shared environments”
    In Proceedings of the 10th Iberian Conference onInformation Systems and Technologies (CISTI 2015), Aveiro, Portugal, June 2015
  • P. Lopes and J. L. Oliveira
    “Integration-as-a-service for bioinformatics”
    In Proceedings of the 10th Iberian Conference on Information Systems and Technologies (CISTI 2015), Aveiro, Portugal, June 2015
  • P. Lopes, P. Sernadela, and J. L. Oliveira
    “Towards a knowledge federation of linked patient registries”
    In Proceedings of the 10th Iberian Conference on Information Systems and Technologies (CISTI 2015), Aveiro, Portugal, June 2015
  • P. Lopes, L. Bastiao, and J. L. Oliveira,
    “Challenges and opportunities for exploring patient-level data: Preliminary results”
    In Proceedings of the 10th Iberian Conference on Information Systems and Technologies (CISTI 2015), Aveiro, Portugal, June 2015
  • P. Sernadela, A. Pereira, and R. Rossetti
    “DISim: Ontology-driven simulation of biomedical data integration tasks”
    In Proceedings of the 10th Iberian Conference on Information Systems and Technologies (CISTI 2015), Aveiro, Portugal, June 2015
  • C. Viana-Ferreira, S. Matos, C. Costa
    ” Long-Term Prefetching for Cloud Medical Imaging Repositories”
    In Proceedings of the 26th Medical Informatics Europe Conference (MIE2015), Madrid, Spain, May 2015
  • E. Monteiro, F. Valente, J. L. Oliveira, C. Costa
    “A Recommender System for Medical Imaging Diagnostic”
    In Proceedings of the 26th Medical Informatics Europe Conference (MIE2015), Madrid, Spain, May 2015
  • P. Sernadela, P. Lopes, D. Campos, S. Matos, J. L. Oliveira
    “A Semantic Layer for Unifying and Exploring Biomedical Document Curation Results”
    In Third International Conference (IWBBIO 2015), Bioinformatics and Biomedical, Granada, Spain, April 2015
  • S. Brás, A. Silva, J. Ribeiro, and J. Oliveira
    “New Insights in Echocardiography Based Left-Ventricle Dynamics Assessment”
    In Third International Conference (IWBBIO 2015), Bioinformatics and Biomedical, Granada, Spain, April 2015
  • P. Lopes and J. Oliveira
    “An Event-Driven Architecture for Biomedical Data Integration and Interoperability”
    In Third International Conference (IWBBIO 2015), Bioinformatics and Biomedical Engineering, Granada, Spain, April 2015
  • C. V. Ferreira, S. Matos, and Carlos Costa
    “Incremental Learning Versus Batch Learning for Classification of User’s Behaviour in Medical Imaging”
    In Proceedings of the 8th International Conference on health informatics (HealthInf 2015), Lisbon, Portugal, January 2015
  • L. Bastião, C. Costa, and J. L. Oliveira
    “Semantic search over DICOM repositories”
    In IEEE International Conference on Healthcare Informatics 2014 (ICHI 2014) Verona, Italy. September 2014
  • F. Valente, A. Silva, C. Costa, J. M. F. Valiente, C. Suárez-Ortega, M. Guevara
    “A dataflow-based appraoch to the design and distribution of medical image analytics”
    In Proceedings of 8th Iberian Grid Infrastructure Conference (IBERGRID 2014)”, p. 201-212, Aveiro, Portugal, September 2014
  • S. Matos, T. Nunes, and J.L. Oliveira
    “BioinformaticsUA: Concept Recognition in Clinical Narratives Using a Modular and Highly Efficient Text Processing Framework”
    In Proceedings of the 8th International Workshop on Semantic Evaluation (SemEval 2014), p. 135–139, Dublin, Ireland, August 2014
  • T. Godinho, L. Bastião, C. Costa, and J. L. Oliveira
    “Multi-provider Architecture for Cloud Outsourcing of Medical Imaging Repositories”
    In 25th European Medical Informatics Conference (MIE2014) Istanbul, Turkey, August 2014
  • L. Bastião, M. Santos, L. Ribeiro, C. Costa, and J. L. Oliveira
    “Screening Radiation Exposure for Quality Assurance”
    In 25th European Medical Informatics Conference (MIE2014). Istanbul, Turkey, August 2014
  • E. Pinho, L. Bastiao Silva, and C. Costa
    “A cloud service integration platform for web applications”
    In Proccedings of the International Conference on High Performance Computing & Simulation (HPCS 2014), Bologna, Italy, July 2014
  • C. V. Ferreira, and C. Costa
    “DICOM traffic generator based on behavior profiles”
    In IEEE International Conference on Biomedical and Health Informatics (BHI 2014), p. 93-96, Valencia, Spain, June 2014
  • T. Nunes, S. Matos, and J.L. Oliveira
    “Extracting sentences describing biomolecular events from the biomedical literature”
    In Proccedings of the 11th International Symposium on Distributed Computing and Artificial Intelligence (DCAI 2014), Salamanca, Spain, June 2014
  •  L. Bastião, L. Bernoud, C. Costa, and J. L. Oliveira
    “NoSQL medical imaging archive: comparison between different implementations”
    In IEEE International Conference on Biomedical and Health Informatics (BHI 2014) Valencia, Spain, June 2014
  • L. Bastião, M. Santos, C. Costa, and J. L. Oliveira
    “Normalizing medical imaging archives for dose quality assurance and productivity auditing”
    In IEEE International Symposium on Medical Measurement and Applications (MeMeA 2014) Lisbon, Portugal, June 2014
  •  S. Brás, L. Ribeiro, D. A. Ferreira, L. Antunes, and C. Nunes
    “Controlling the Hypnotic Drug (propofol) to maintain a stable depth of Anesthesia, in Dogs”
    In Proccedings of IEEE International Symposium on Medical Measurements and Applications (MeMeA 2014), Lisbon, Portugal, June 2014
  • R.Correia, S. Brás, A. Silva, J. Mendes, D. A. Ferreira
    “Development of new research software for real-time raw electroencephalogram analysis”
    In Proccedings of IEEE International Symposium on Medical Measurements and Applications (MeMeA 2014), Lisbon, Portugal, June 2014
  • L. Castro, J. L. Oliveira, and R. M. Silva
    “Mutation Analysis in Park2 Gene Uncovers Patterns of Associated Genetic Variants”,  Advances in Intelligent Systems and Computing,
    In Proceedings of the 8th Internation Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2014), Salamanca, Spain, June 2014
  • P. Sernadela, E. van der Horst, M. Thompson, P. Lopes, M. Roos, and J. L. Oliveira
    “A Nanopublishing Architecture for Biomedical Data”
    In Proceedings of the 8th International Conference on Practical Applications of Computational Biology & Bioinformatics(PACBB 2014), Salamanca, Spain, June 2014
  •  F. Barbosa, J. Arrais and J.L. Oliveira
    “Weighted Gene Co-expression Network Analysis Applied to Head and Neck Squamous Cell Carcinoma Data”
    In Proceedings of the International Conference on Health Informatics (ICHI 2013), Vilamoura, Portugal, November 2013
  • E. Monteiro, C. Costa, and J. L. Oliveira
    “A DICOM viewer based on web technology”
    In Proceedings of IEEE 15th International Conference on e-Health Networking, Applications & Services (Healthcom 2013), Lisboa, Portugal, October 2013
  • C. V. Ferreira, and C. Costa
    “A cloud based architecture for medical imaging services”
    In Proceedings of IEEE 15th International Conference on e-Health Networking, Applications & Services (Healthcom 2013), Lisboa, Portugal, October 2013
  • L. Ribeiro, F. Honório, J. L. Oliveira, C. Costa
    “Leveraging XDS-I and PIX workflows for validating cross-enterprise patient identity linkage”
    In Proceedings of IEEE 15th International Conference on e-Health Networking, Applications & Services (Healthcom 2013), Lisboa, Portugal, October 2013
  • D. Campos, S. Matos, and J. L. Oliveira
    “Chemical name recognition with harmonized feature-rich conditional random fields”
    In Proceedings of Fourth BioCreative Challenge Evaluation Workshop, vol. 2, p. 82-87, October 2013
  • D. Campos, J. Lourenço, T. Nunes, R. Vitorino, P. Domingues, S. Matos, and J. L. Oliveira
    “Egas – Collaborative Biomedical Annotation as a Service”
    In Proceedings of Fourth BioCreative Challenge Evaluation Workshop, vol. 1, p. 254-259, October 2013
  • L. Bastião, C. Costa, and J. L. Oliveira
    “An agile framework to support distributed medical imaging scenarios”
    In IEEE International Conference on Healthcare Informatics 2013 (ICHI 2013) Philadelphia, PA, USA. September 2013
  • F. Marques, P. Azevedo, J. P. Cunha, M. B. Cunha, S. Brás, and J. M. Fernandes
    “IREMAN: FIRefighter team brEathing Management system using ANdroid”
    In 17th International Symposium on Wearable Computers (ISWC 2013), Zurich, Switzerland, September 2013
  • L. Ribeiro, R. Rodrigues, C. Costa and J.L. Oliveira,
    “Enabling Outsourcing XDS for Imaging on the Public Cloud”
    In  Proceedings of the 14th World Congress on Medical and Health Informatics (MEDINFO 2013), Copenhagen, Denmark, August 2013
  • D. Campos, S. Matos, and J. L. Oliveira
    “Neji: a tool for heterogeneous biomedical concept identification”
    In Proceedings of the BioLINK SIG, ISMB/ECCB, Berlin, Germany, July 2013
  • L. Bastiao, S. Campos, C. Costa, and J. L.Oliveira
    “Integrating echocardiogram reports with medical imaging”
    In 26th IEEE International Symposium on Computer-Based Medical Systems (CBMS 2013), Porto, Portugal, June 2013
  • S. Brás, J. M. Fernandes, and J. P.S. Cunha,
    “ECG Delineation and Morphological Analysis for Firefighters Tasks Differentiation”
    In Proceedings of the 26th International Symposium on Computer-Based Medical Systems (CBMS 2013), Porto, Portugal, June 2013
  • M. Santos, L. Bastião, C. Costa, A. Silva, and N. Rocha,
    “Multi Vendor DICOM Metadata Access: A Multi Site Hospital Approach Using Dicoogle”
    In 8th Iberian Conference on Information Systems and Technologies (CISTI 2013), Lisboa, Portugal, June 2013
  • T. Godinho, L. B. Silva, C. Viana-Ferreira, C. Costa and J. L. Oliveira
    “Enhanced regional network for medical imaging repositories”
    In 8th Iberian Conference on Information Systems and Technologies (CISTI 2013), Lisboa, Portugal, June 2013
  • V M. Prieto, S. Matos, M. Álvarez, F.Cacheda, and J. L. Oliveira
    “Analysing Relevant Diseases From Iberian Tweets”
    In Proceedings of the 7th Int. Conf. on Practical Applications of Computational Biology and Bioinformatics (PACBB 2013), Salamanca, Spain, May 2013
  • S. Matos, H. Araújo, and J. L. Oliveira
    “Structuring and Exploring the Biomedical Literature Using Latent Semantics”
    In Proceedings of the 10th International Symposium on Distributed Computing and Artificial Intelligence (DCAI 2013), Salamanca, Spain, May 2013
  • J. C. Santos and S. Matos
    “Predicting Flu Incidence from Portuguese Tweets”
    In Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, Granada, Spain, March 2013
  • J. C. Santos, T. Pedrosa, C. Costa, and J. L. Oliveira
    “Concepts for a Personal Health Record”
    In 24th European Medical Informatics Conference (MIE 2012), Pisa, Italy, 2012.
  • C. Viana-Ferreira, D. Ferreira, F. Valente, E. Monteiro, C. Costa, and J. L. Oliveira
    “Dicoogle Mobile: a medical imaging platform for Android”
    In 24th European Medical Informatics Conference (MIE 2012), Pisa, Italy, 2012
  • L. Ribeiro, C. Costa, and J. L. Oliveira
    “Enhancing the many-to-many relations across IHE Document Sharing Communities”
    In 24th European Medical Informatics Conference (MIE 2012), Pisa, Italy, 2012
  • E. J. M. Monteiro, L. A. B. Silva, and C. Costa
    “CloudMed: Promoting telemedicine processes over the cloud”
    In Proceedings of the 7th Iberian Conference onInformation Systems and Technologies (CISTI 2012) 2012
  • L. Bastião Silva, C. Costa, and J. L. Oliveira
    “A DICOM relay service supported on cloud resources”
    In 5th International Conference on Health Informatics (HEALTHINF 2012), Vilamoura, Portugal, 2012
  • T. Pedrosa, R. P. Lopes, J. C. Santos, C. Costa, and J. L. Oliveira
    “A secury personal health record repository”
    In 5th International Conference on Health Informatics (HEALTHINF 2012), Vilamoura, Portugal, 2012
  • L. Velte, T. Pedrosa, C. Costa, and J. L. Oliveira
    “An OPENEHR repository based on a native XML database”
    In 5th International Conference on Health Informatics (HEALTHINF 2012), Vilamoura, Portugal, 2012
  • R. Mendonça, P. Lopes, H. Rocha, J. Oliveira, L. Vilarinho, R. Santos, and J. L. Oliveira
    “Gathering and managing genotype and phenotype information about rare diseases patients”
    In 5th International Conference on Health Informatics (HEALTHINF 2012), Vilamoura, Portugal, 2012
  • J. Melo, J.P. Arrais, P. Lopes, N. Rosa, M. J. Correia, M. Barros, and J. L. Oliveira
    “OralCard – web information system for oral health”
    In 5th International Conference on Health Informatics (HEALTHINF 2012), Vilamoura, Portugal, 2012
  • C. Viana-Ferreira, C. Costa, and J. L. Oliveira
    “Dicoogle Relay – a Cloud Communications Bridge for Medical Imaging”
    In 25th IEEE International Symposium on Computer-Based Medical Systems (CBMS 2012), Rome, Italy, 2012
  • R. Mendonça, A. F. Rosa, J. L. Oliveira, and A. Teixeira
    “Towards ontology based health information search in Portuguese – A case study in neurologic diseases”
    In 7th Iberian Conference on Information Systems and Technologies (CISTI 2012), Madrid, Spain, 2012
  • P. Gaspar, J. Carbonell, and J. L. Oliveira
    “Parameter influence in genetic algorithm optimization of support vector machines”
    In 7th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2012), Salamanca, Spain, 2012
  • P. Lopes, R. Mendonça, H. Rocha, J. Oliveira, L. Vilarinho, R. Santos, and J. L. Oliveira
    “A Rare Disease Patient Manager”
    In 7th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2012), Salamanca, Spain, 2012
  • P. Lopes and J. L. Oliveira
    “COEUS: A Semantic Web Application Framework”
    In Semantic Web Applications and Tools for Life Sciences (SWAT4LS 2011), London, UK, 2011
  • S. Matos and J. L. Oliveira
    “Prioritizing Literature Search Results Using a Training Set of Classified Documents”
    In 5th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2011), vol. 93, pp. 381-388, 2011.
  • P. Lopes and J. L. Oliveira
    “Towards Knowledge Federation in Biomedical Applications”
    In Proceedings of the 7th International Conference on Semantic Systems (I-Semantics 2011), Graz, Austria, 2011
  • P. Lopes and J. L. Oliveira
    “A Semantic Web Application Framework for Health Systems Interoperability”
    In Proceedings of the first international workshop on Managing interoperability and complexity in health systems (MIXHS 2011), Graz, Austria, 2011
  • C. Santos, T. Pedros, C. Costa, and J. L. Oliveira
    “On the Use of Openehr in a Portable Phr”, Healthinf 2011: Proceedings of the International Conference on Health Informatics (Healthinf 2011), pp. 351-356, 2011.
  • T. Pedrosa, R. P. Lopes, J. C. Santos, C. Costa, and J. L. Oliveira
    “Hybrid Electronic Health Records”, Healthinf 2011: Proceedings of the International Conference on Health Informatics (Healthinf 2011), pp. 571-574, 2011.
  • D. Campos, D. Rebholz-Schuhmann, S. Matos, and J. L. Oliveira
    “A CRF-based approach to harmonize heterogeneous gene/protein annotations”
    In Second CALBC Workshop, Hinxton, UK, 2011.
  • D. Campos, S. Matos, and J. L. Oliveira
    “Annotating the CALBC corpus with a machine learning harmonization approach”
    In Second CALBC Workshop, Hinxton, UK, 2011.
  • L. Bastião, C. Costa, A. Silva, and J. L. Oliveira
    “A PACS Gateway to the Cloud”
    In 6th Iberian Conference on Information Systems and Technologies (CISTI 2011), Chaves, Portugal, 2011, pp. 519-524.
  • J. Arrais and J. L. Oliveira
    “Gene-disease prioritization through biomedical networks,” in 10th IEEE International Conference on Information Technology and Applications in Biomedicine (ITAB 2010), Corfu, Greece, 2010.
  • P. Lopes, D. Campos, and J. L. Oliveira
    “A tagging system for bioinformatics resources,” in 10th IEEE International Conference on Information Technology and Applications in Biomedicine (ITAB 2010), Corfu, Greece, 2010.
  • J. Arrais and J. L. Oliveira
    “On the exploitation of cloud computing in Bioinformatics,” in 10th IEEE International Conference on Information Technology and Applications in Biomedicine (ITAB 2010), Corfu, Greece, 2010.
  • P. Lopes and J. L. Oliveira
    “An extensible platform for variome data integration,” in 10th IEEE International Conference on Information Technology and Applications in Biomedicine (ITAB 2010), Corfu, Greece, 2010.
  • L. S. Ribeiro, C. Costa, and J. L. Oliveira
    “A Distributed and Reliable DICOM Storage Facility”
    In 28th International EuroPACS Meeting (CARS 2010), Geneva, Switzerland, 2010.
  • F. Martin-Sanchez, V. Lopez-Alonso, L. Salamanca, J. L. Oliveira, and E. Andres
    “Managing Knowledge Related to the Clinical Relevance of Biomarkers: An Example in Parkinson’s Disease”
    In 2010 AMIA Summit on Translational Bioinformatics, San Francisco, CA, USA, 2010.
  • S. Matos, D. Campos, and J. L. Oliveira
    “Vector-space models and terminologies in gene normalization and document classification”
    In Proceedings of BioCreative III Workshop, Bethesda, Maryland, USA, September 2010
  • S. Matos, J. Arrais, and J. L. Oliveira
    “Expanding Gene-based PubMed Queries”
    In 4th International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2010), Guimarães, Portugal, 2010.
  • J. Arrais, J. Pereira, P. Lopes, S. Matos, and J. L. Oliveira
    “Improving cross mapping in biomedical databases”
    In 4th International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2010), Guimarães, Portugal, 2010.
  • J. P. Lousado, J. L. Oliveira, G. Moura, and M. A. S. Santos
    “An application for study tandem repeats in ortologous genes”
    In 4th International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2010), Guimarães, Portugal, 2010.
  • P. Lopes and J. L. Oliveira
    “A Holistic Approach for Integrating Genomic Variation Information”
    In Xth Spanish Symposium on Bioinformatics (JBI2010), Malaga, Spain, 2010.
  • J. P. Lousado, J. L. Oliveira, G. Moura, and M. A. S. Santos
    “Análise da evolução de repetições de codões e de aminoácidos em dados biológicos”
    In 5th Iberian Conference on Information Systems and Technologies (CISTI 2010), Santiago de Compostela, Spain, 2010.
  • D. Campos, S. Matos, and J. L. Oliveira
    “Recognition of gene/protein names using Conditional Random Fields”
    In International Joint Conference on Knowledge Discovery and Information Retrieval (KDIR 2010), Valencia, Spain, 2010.
  • L. S. Ribeiro, L. Bastião, C. Costa, and J. L. Oliveira
    “Email-P2P Gateway to Distributed Medical Imaging Repositories”
    In HEALTHINF 2010, Valencia, Spain, 2010.
  • J. C. Santos, T. Pedrosa, C. Costa, and J. L. Oliveira
    “Modelling a Portable Personal Health Record”
    In HEALTHINF 2010, Valencia, Spain, 2010.
  • T. Pedrosa, R. P. Lopes, J. C. Santos, C. Costa, and J. L. Oliveira
    “Towards an EHR architecture for mobilde citizens”
    In HEALTHINF 2010, Valencia, Spain, 2010.
  • J. C. Santos, T. Pedrosa, C. Ferreira, C. Costa, and J. L. Oliveira
    “Gathering and Managing Complementary Diagnostic Tests,” in 5th Iberian Conference on Information Systems and Technologies (CISTI 2010), Santiago de Compostela, Spain, 2010.
  • L. S. Ribeiro, C. Costa, and J. L. Oliveira
    “A Proxy of DICOM services”
    In SPIE Medical Imaging 2010, S. Diego, CA, USA, 2010.
  • J. Arrais, J. Pereira, J. Fernandes, and J. L. Oliveira
    “GeNS: A Biological Data Integration Platform”
    In World Academy of Science, Engineering and Technology (WASET 2009), Venice, Italy, 2009, pp. 416 – 421.
  • P. Lopes and J. L. Oliveira
    “Cloud Computing and Digital Libraries : First Perspectives on a Future Technological Alliance ”
    In 9ª Conferência da Associação Portuguesa de Sistemas de Informação (CAPSI 2009), Viseu, Portugal, 2009.
  • M. Pinheiro, M. J. Simões, C. Egas, and J. L. Oliveira
    “Identifying SNPs candidates using 454 sequencing technology”
    In Jornadas de Bioinformática (JB 2009), Lisbon, Portugal, 2009.
  • P. Lopes, J. Arrais, and J. L. Oliveira
    “Link Integrator: A Link-based Data Integration Architecture”
    In International Conference on Knowledge Discovery and Information Retrieval (KDIR 2009), Madeira, Portugal, 2009.
  • P. Lopes, D. Pinto, D. Campos, and J. L. Oliveira
    “Arabella: A Directed Web Crawler”
    In International Conference on Knowledge Discovery and Information Retrieval (KDIR 2009), Madeira, Portugal, 2009.
  • T. Pedrosa, C. Costa, R. P. Lopes, and J. L. Oliveira
    “Virtual Health Card System”
    In Inforum 2009, Lisbon, Portugal, 2009.
  • D. Polónia, C. Costa, J. L. Oliveira, and A. M. O. Duarte
    “Inequality problems in the distribution of radiologists in Portugal: Requirements for the creation of an imaging marketplace”
    In eChallenges 2009, Ankara, Turkey, 2009.
  • P. Lopes, J. Arrais, and J. L. Oliveira
    “A Client-side Workflow Management System”
    In 3rd International Workshop on Practical Applications of Computational Biology and Bioinformatics(IWPACBB 2009), Salamanca, Spain, 2009.
  • J. P. Lousado, G. Moura, M. A. S. Santos, and J. L. Oliveira
    “Analysing the evolution of repetitive strands in genomes”
    In 3rd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2009), Salamanca, Spain, 2009.
  • S. Matos, A. Barreiro, J.L. Oliveira
    “Syntactic Parsing for Bio-Molecular Event Detection from Scientific Literature”, 14th Portuguese Conference on Artificial Intelligence, EPIA 2009, Aveiro, Portugal, Oct. 2009.
  • P. Lopes, J. Arrais and J. L. Oliveira
    “Dynamic Service Integration using Web-based Workflows”
    In 10th International Conference on Information Integration and Web Applications & Services“, Linz, Austria, Nov. 2008, pp. 622-625.
  • D. Santos, C. Costa, J. L. Oliveira, and A. Neves
    “Alternative lossless compression algorithms in X-ray cardiac images” in Computational Vision and Medical Image Processing, N. J. João Tavares, Ed. London: Taylor & Francis Group, 2008, pp. 143-146.
  • D. Polónia, C. Costa, and J. L. Oliveira
    “A Model to Optimize the Use of Imaging Equipment and Human Skills Scattered in Very Large Geographical Areas”
    In 9th International Conference on Enterprise Information Systems (ICEIS 2004), Madeira, Portugal, 2007.
  • V. Afreixo, A. Freitas, M. Pinheiro, J. L. Oliveira, G. Moura, and M. A. S. Santos
    “Exploiting a Biclustering algorithm in ORFeome analysis”
    In Proceedings of the 2007 VLDB Workshop on Data Mining in Bioinformatics, Vienna, Austria, 2007.
  • A. Freitas, J. Duarte, M. Pinheiro, J. L. Oliveira, G. Moura, and M. A. S. Santos
    “Homo sapiens versus Pan troglodytes: quão diferentes são?” in Actas do XIV Congresso Nacional da Sociedade Portuguesa de Estatística, Covilhã, Portugal, 2007.
  • J. Duarte, A. Freitas, M. Pinheiro, J. L. Oliveira, G. Moura, and M. A. S. Santos
    “ISA: um algoritmo de bi-classificação?” in Actas do XIV Congresso Nacional da Sociedade Portuguesa de Estatística, Covilhã, Portugal, 2007.
  • A. Freitas, M. Pinheiro, V. Afreixo, J. Duarte, J. L. Oliveira, G. Moura, and M. A. Santos
    “A median-based Iterative Signature Algorithm”
    In IASC 07 – Statistics for Data Mining, Learning and Knowledge Extraction, Aveiro, Portugal, 2007.
  • A. Freitas, M. Pinheiro, J. L. Oliveira, G. Moura, and M. A. Santos
    “A new limiting distribution for a statistical test for the homogeneity of two multinomial populations”
    In Workshop in Statistic on Genomics and Proteomic, CIM, 2006.
  • J. Arrais, D. Polónia, and J. L. Oliveira
    “A prospective study on the integration of microarrays data in HIS/ERP”
    In Biological and Medical Data Analysis (ISBMDA’ 2006), Lecture Notes in Computer Science, Vol. 4345, Thessaloniki, Greece, 2006.
  • D. Polónia, C. Costa, and J. L. Oliveira
    “Optimizing PACS and imaging resources”
    In The XX International Congress of the European Federation for Medical Informatics (MIE 2006), Maastricht, Netherlands, 2006.
  • G. Dias, J. L. Oliveira, F. Vicente, and F. Martín-Sanchez
    “Integrating Medical and Genomic Data: a Sucessful Example for Rare Diseases”
    In The XX International Congress of the European Federation for Medical Informatics (MIE 2006), Maastricht, Netherlands, 2006.
  • J. Arrais, J. L. Oliveira, G. Grimes, S. Moodie, K. Robertson, and P. Ghazal
    “Microarray data sharing in BioMedicine”
    In The XX International Congress of the European Federation for Medical Informatics (MIE 2006), Maastricht, Netherlands, 2006.
  • D. Polónia, C. Costa, and J. L. Oliveira
    “A PACS based GRID of resources”
    In 4th International EuroPACS Conference (EuroPACS 2006), Trondheim, Norway, 2006.
  • G. Dias, J. L. Oliveira, F. Vicente, and F. Martin-Sanchez
    “Integration of Genetic and Medical Information Through a Web Crawler System”
    In Biological and Medical Data Analysis (ISBMDA’ 2005), Lecture Notes in Computer Science, Vol. 3745, Aveiro, Portugal, 2005.
  • C. Costa, J. L. Oliveira, A. Silva, V. Ribeiro, and J. Ribeiro
    “Data Management and Visualization Issues in a Fully Digital Echocardiography Laboratory”
    In Biological and Medical Data Analysis (ISBMDA’ 2005), Lecture Notes in Computer Science, Vol. 3745, Aveiro, Portugal, 2005.
  • C. Costa, J. L. Oliveira, A. Silva, V. Ribeiro, and J. Ribeiro
    “A Telemedicine Platform for Cardiovascular Ultrasound”
    In The XIX International Congress of the European Federation for Medical Informatics (MIE 2005), Geneve, Switzerland, 2005.
  • D. Polónia, C. Costa, and J. L. Oliveira
    “Architecture evaluation for the implementation of a Regional Integrated Electronic Health Record”
    In The XIX International Congress of the European Federation for Medical Informatics (MIE 2005), Geneve, Switzerland, 2005.
  • M. Pinheiro, J. L. Oliveira, M. A. S. Santos, H. Rocha, M. L. Cardoso, and L. Vilarinho
    “Results of a Biomedical Application in Newborn Screening Programs”
    In The 3rd European Medical and Biological Engineering Conference (EMBEC 2005), Prague, Czech Republic, 2005.
  • J. Arrais, L. Silva, M. Rodrigues, L. Carreto, J. L. Oliveira, and M. A. S. Santos
    “Why Another Microarrays LIMS”
    In The 3rd European Medical and Biological Engineering Conference (EMBEC 2005), Prague, Czech Republic, 2005.
  • D. Polónia, J. L. Oliveira, and N. P. Rocha
    “Overview of information systems training in Portuguese medicine courses”
    In Health and Medical Informatics Applications – Educational Aspects (EFMI-STC 2005), Athens, Greece, 2005.
  • D. Polónia and J. L. Oliveira
    “Health Information Systems and Telematics: A best of breed evaluation framework for the Portuguese case”
    In European Health Management Association Annual Conference 2005 (EHMA 2005), Barcelona, Spain, 2005.
  • F. Vicente, I. Hermosilla, M. García-Remesal, D. Pérez del Rey, B. Romero, I. Oliveira, J. L. Oliveira, A. S. Pereira, and F. Martin-Sanchez
    “Infogenmed: Un Laboratorio Virtual para la Integración de Información Clínica y Genética en Aplicaciones Médicas”
    In VII Congreso Nacional de Informático de la Salud (Inforsalud 2004), Madrid, Spain, 2004.
  • Oliveira, J. L. Oliveira, F. Martin-Sanchez, V. Maojo, and A. S. Pereira
    “Biomedical information integration for health applications with Grid: a requirements perspective”
    In Healthgrid 2004, Clermont-Ferrand, France, 2004.
  • D. Polónia, J. L. Oliveira, and M. O. Duarte
    “Information Systems (IS) in the Third and Fourth Generation Mobile Operator”
    In 5ª Conferência da Associação Portuguesa de Sistemas de Informação (CAPSI 2004), Lisbon, 2004.
  • C. Costa, A. Silva, J. L. Oliveira, V. Ribeiro, and J. Ribeiro
    “Himage PACS: A new approach to storage, integration and distribution of cardiologic images”
    In Progress in Biomedical Optics and Imaging, vol. 5, H. H. Ratib OM, Ed., SPIE, 2004, pp. 277-287.
  • M. Pinheiro, J. L. Oliveira, M. A. S. Santos, H. Rocha, M. L. Cardoso, and L. Vilarinho
    “NeoScreen: A software application for MS/MS newborn screening analysis”
    In International Symposium on Biological and Medical Data Analysis (ISBMDA 2004), Lecture Notes in Computer Science, Vol. 3337, Barcelona, Spain, 2004.
  • J. L. Oliveira, G. Dias, I. Oliveira, P. Rocha, I. Hermosilla, F. Vicente, I. Spiteri, F. Martin-Sanchez, and A. S. Pereira
    “DiseaseCard: a web-based tool for the collaborative integration of genetic and medical information”
    In Biological and Medical Data Analysis (ISBMDA 2004), Lecture Notes in Computer Science, Vol. 3337, Barcelona, Spain, 2004.
  • D. Polónia, I. Oliveira, and J. L. Oliveira
    “A Business Process Model for Public Health Information Systems: A Governmental Perspective”
    In 6th International Conference on Enterprise Information Systems (ICEIS 2004), Porto, Portugal, 2004.
  • C. Costa, J. L. Oliveira, and A. Silva
    “E-Services in Mission-Critical Organizations: Identification Enforcement”
    In 6th International Conference on Enterprise Information Systems (ICEIS 2004), Porto, Portugal, 2004.
  • M. García-Remesal, V. Maojo, H. Billhardt, J. Crespo, R. Alonso-Calvo, D. Pérez, F. Martín, V. López, J. Sánchez, F. Vicente, M. García-Rojo, A. Gómez de la Cámara, A. Sousa, J. L. Oliveira, I. Oliveira, M. Santos, and A. Babic
    “Designing New Methodologies for Integrating Biomedical Information in Clinical Trials”
    In EuroMISE 2004, Prague, Czech Republic, 2004.
  • C. Costa, A. Silva, J. L. Oliveira, A. S. Pereira, and V. Ribeiro
    “A New Concept for an Integrated Healthcare Access Model”
    In Medical Informatics Europe (MIE 2003), Saint Malo, France, 2003.
  • C. Costa, J. L. Oliveira, and A. Silva
    “Authentication Model to Enforce Network Entities Identification”
    In 4rd Conference on Telecommunications (ConfTele 2003), Aveiro, Portugal, 2003.
  • C. Costa, J. L. Oliveira, A. Silva, and V. Gama
    “An Integrated Access Interface to Multimedia EPR”
    In 21st International EuroPACS Meeting (EuroPACS 2003), London, United Kingdom, 2003.
  • Oliveira, J. L. Oliveira, M. Santos, F. Martin-Sanchez, and A. S. Pereira
    “On the requirements of biomedical information tools for health applications: the INFOGENMED case study”
    In 7th Portuguese Conference on Biomedical Engineering (BioEng 2003), Lisbon, Portugal, 2003.
  • C. Costa, J. L. Oliveira, and A. Silva
    “Electronic Patient Record Virtually Unique based on a Crypto Smart Card”
    In International Conference on Web Engineering (ICWE 2003), Lecture Notes in Computer Science, Vol. 2722, Oviedo, Spain, 2003.
  • C. Costa, J. L. Oliveira, and A. Silva
    “Critical Information Systems Authentication based on PKC and Biometrics”
    In International Conference on Web Engineering (ICWE 2003), Lecture Notes in Computer Science, Vol. 2722, Oviedo, Spain, 2003.
  • C. Costa, J. L. Oliveira, and A. Silva
    “A User-Oriented Model to Manage Multiple Digital Credentials”
    In IEEE 5th International Conference on Enterprise Information Systems (ICEIS 2003), Angers, France, 2003.
  • J. C. Santos, J. L. Oliveira, and C. Costa
    “A User-oriented Multi-service Access Control System”
    In 5ª Conferência sobre Redes de Computadores (CRC 2002), Faro, Portugal, 2002.
  • C. Costa, J. L. Oliveira, and A. Silva
    “A Trusted Brokering Service for PKI Interoperability and Thin-Clients Integration”
    In IEEE Third International Conference on Enterprise Information Systems (ICEIS 2001), Setúbal, Portugal, 2001.
  • C. Costa, J. L. Oliveira, and A. Silva
    “Um Novo Mecanismo de Autenticação para Sistemas de Informação Clínica” (in portuguese)
    In 4ª Conferência sobre Redes de Computadores (CRC 2001), Covilhã, Portugal, 2001.
  • P. M. Coloma, M. J. Schuemie, G. Trifirò, L. Furlong, E. V. Mulligen, A. Bauer-Mehren, P. Avillach, J. Kors, F. Sanz, J. Mestres, J. L. Oliveira, S. Boyer, E. A. Helgee, M. Molokhia, J. Matthews, D. Prieto-Merino, R. Gini, R. M. C. Herings, G. Mazzaglia, G. Picelli, L. Scotti, L. Pedersen, J. V. d. Lei, and M. C. J. M. Sturkenboom, “Triage and Evaluation of Potential Safety Signals Identified from Electronic Healthcare Record Databases,” in 12th Annual Meeting of the International Society of Pharmacovigilance (ISoP 2012), Cancun, Mexico, 2012.
  • P. Lopes and J. L. Oliveira, “COEUS: “Semantic Web in a box” for biomedical applications,” in 11th European Conference on Computational Biology (ECCB 2012), Basel, Switzerland, 2012.
  • P. Lopes, D. Campos, T. Nunes, and J. L. Oliveira, “Delivering advanced pharmacovigilance with the EU-ADR Web Platform,” in 11th European Conference on Computational Biology (ECCB 2012), Basel, Switzerland, 2012.
  • M. J. Correira, N. Rosa, I. Silveira, J. Arrais, J. L. Oliveira, and M. Barros, “Oral microbial proteome: clues of OralCard”, in 22nd IUBMB & 37th FEBS Congress, Seville, Spain, 2012.
  • N. Rosa, J. Arrais, J. Melo, E. Coelho, M. J. Correira, J. L. Oliveira, and M. Barros, “OralCard: a bioinformatic tool dedicated to the oral cavity system”, in 22nd IUBMB & 37th FEBS Congress, Seville, Spain, 2012.
  • E. Molero, C. Diaz, F. Sanz, J. L. Oliveira, G. Trifirò, A. Fourrier, M. Molokhia, L. Pedersen, S. Boyer, L. Scotti, R. Gini, R. Herings, C. Giaquinto, M. I. Loza, G. Mazzaglia, J. v. d. Lei, and M. Sturkenboom, “The EU-ADR Alliance: A Federated Collabora- tive Framework for Drug Safety Studies,” in 12th Annual Meeting of the International Society of Pharmacovigilance (ISoP 2012), Barcelona, Spain, 2012.
  • P. Lopes, J. Arrais, and J. L. Oliveira, “A Knowledge Interoperability Framework for Integrating Genotype-to-Phenotype Data”, in III Xornadas Galegas de Bioinformatics (XGB 2012), Vigo, Spain, 2011.
  • D. Campos, S. Matos, and J. L. Oliveira, “A machine learning-based tool for biomedical entity recognition (Best Poster)”, in III Xornadas Galegas de Bioinformatics (XGB 2012), Vigo, Spain, 2011.
  • J. Arrais and J. L. Oliveira, “Using biomedical networks to gene-disease indentification”, in III Xornadas Galegas de Bioinformatics (XGB 2012), Vigo, Spain, 2011.
  • P. Lopes and J. L. Oliveira, “An Integrated View for Human Variome Information,” in 14th International Conference on Research in Computational Molecular Biology (RECOMB 2010), Lisbon, Portugal, 2010.
  • P. Gaspar, J. L. Oliveira, J. Frommlet, G. Moura, and M. A. S. Santos, “A gene multi-optimization tool as novel approach to heterologous expression,” in 14th International Conference on Research in Computational Molecular Biology (RECOMB 2010), Lisbon, Portugal, 2010.
  • J. Frommet, P. Gaspar, M. Pinheiro, J. L. Oliveira, A. C. Gomes, G. Moura, and M. A. S. Santos, “Integrating tRNA abundance, codon-usage, codon-context and functional rare codon data in de novo synthesis of Plasmodium falciparum genes for optimal expression in Escherichia coli,” in 23rd tRNA Workshop (tRNA 2010), Aveiro, Portugal, 2010.
  • S. Matos, J. Arrais, J. Maia-Rodrigues, and J. L. Oliveira, “QuExT: a concept-based query expansion approach for literature retrieval from MEDLINE”, in Jornadas de Bioinformática (JB 2009), Lisbon, Portugal, 2009.
  • P. Lopes and J. L. Oliveira, “Integration of Variome Data Through a Link Discovery Strategy”, in Jornadas de Bioinformática (JB 2009), Lisbon, Portugal, 2009.
  • A. Freitas, V. Afreixo, M. Pinheiro, J. L. Oliveira, and M. A. S. Santos, “Uma avaliação da performance do algoritmo de bi-classificação ISA-mediana”, in XVI Jornadas de Classificação e Análise de Dados (JOCLAD 2009), Faro, Portugal, 2009.
  • S. Matos, A. Barreiro, “Syntactic-semantic analysis for information extraction in biomedicine”, NooJ Conference 2009, Jozeur, Tunisia, Jun 2009.
  • Maria dos Santos, Miguel Pinheiro, Manuel A. S. Santos (2008). Candida albicans as a model system to study genetic code alterations at genome level. 9th ASM Conference on Candida and Candidiasis, Jersey City, USA (Mar 24-28)
  • M. Santos, M. Pinheiro, J. L. Oliveira and M. A. S. Santos, “Comparative tRNomics of a genetic code alteration”, ESF-EMBO Symposium on Comparative Genomics of Eukaryotic Microorganisms: Eukaryotic Genome Evolution, Sant Feliu de Guixols, Spain, 2007.
  • M. Pinheiro, G. Moura, A. Freitas, M. A. S. Santos, and J. L. Oliveira, “A bioinformatics system to analyze sequences at a genomic scale”, in XVth National Congress of Biochemistry (NBC 2006) Aveiro, Portugal, 2006.
  • G. Moura, M. Pinheiro, C. Gomes, A. Freitas, J. L. Oliveira, and M. A. S. Santos, “Large Scale Comparative Codon Context Analysis Unveils Novel Rules Governing Gene Evolution”, in XVth National Congress of Biochemistry (NBC 2006) Aveiro, Portugal, 2006.
  • J. P. Lousado, G. Moura, M. Pinheiro, J. L. Oliveira, and M. A. S. Santos, “Large Scale Comparative Genomics of Codon Context”, in XVth National Congress of Biochemistry (NBC 2006) Aveiro, Portugal, 2006.
  • S. Lima, E. Fonseca, J. L. Oliveira, and C. Egas, “Computational Methodologies for Metagenomics Projects”, in XVth National Congress of Biochemistry (NBC 2006) Aveiro, Portugal, 2006.
  • C. Gomes, G. Moura, A. C. Gomes, J. L. Oliveira, M. Pinheiro, A. Freitas, and M. A. S. Santos, “The role of codon context on mRNA decoding error in vivo in yeast”, in XVth National Congress of Biochemistry (NBC 2006) Aveiro, Portugal, 2006.
  • A. Freitas, L. Ferreira, J. Duarte, M. Pinheiro, J. L. Oliveira, G. Moura, and M. A. S. Santos, “Homo Sapiens Vs Pan Troglodytes: How Diferent Are They?” in XVth National Congress of Biochemistry (NBC 2006) Aveiro, Portugal, 2006.
  • C. Egas, J. L. Oliveira, M. A. S. Santos, M. S. Costa, and C. Faro, “Whole Genome shotgun mapping of Rubrobacter radiotolerans”, in XVth National Congress of Biochemistry (NBC 2006) (Invited talk), Aveiro, Portugal, 2006.
  • L. Carreto, P. Pereira, J. Arrais, J. L. Oliveira, and M. A. S. Santos, “National Facility For DNA Microarrays”, in XVth National Congress of Biochemistry (NBC 2006) (Invited talk), Aveiro, Portugal, 2006.
  • J. Arrais, J. L. Oliveira, G. Campos, L. Carreto, and M. A. S. Santos, “Microarray data: from the hybridisation to the analysis”, in European Summer School in Biomedical Informatics, Balatonfüred, Hungary, 2006.
  • J. Arrais, L. Carreto, M. A. S. Santos, and J. L. Oliveira, “Collaborative work on microarrays using MAGE-ML”, in 9th International Meeting of the Microarray Gene Expression Data Society (MGED9), Seattle, Washington, USA, 2006.
  • J. Arrais, L. Carreto, H. Pais, F. Lopes, M. A. S. Santos, and J. L. Oliveira, “A Laboratory Information Management System for Microarray Data Storage, Sharing and Analysis”, in XVth National Congress of Biochemistry (NBC 2006) Aveiro, Portugal, 2006.
  • P. R. Almeida, L. Carreto, J. L. Oliveira, and M. A. S. Santos, “Software-Assisted Design of Probes for SNPs Detection using Oligonucleotide Microarrays: Applications in a Case Study”, in XVth National Congress of Biochemistry (NBC 2006) Aveiro, Portugal, 2006.
  • J. Arrais, J. L. Oliveira, G. Campos, L. Carreto, and M. A. S. Santos, “Microarray data: from the hybridisation to the analysis”, in European Summer School in Biomedical Informatics, Balatonfüred, Hungary, 2006.
  • J. Arrais, L. Carreto, M. A. S. Santos, and J. L. Oliveira, “Collaborative work on microarrays using MAGE-ML”, in 9th International Meeting of the Microarray Gene Expression Data Society (MGED9), Seattle, Washington, USA, 2006.
  • L. Carreto, M. C. Santos, J. Arrais, M. Rodrigues, L. Silva, J. L. Oliveira, and M. A. S. Santos, “Implementation of a National Facility for DNA Microarrays in Portugal”, in 8th International Meeting of the Microarray Gene Expression Data Society (MGED8), Bergen, Norway, 2005.
  • J. L. Oliveira, M. Pinheiro, M. A. S. Santos, H. Rocha, M. L. Cardoso, and L. Vilarinho, “On the Processing of MS/MS Data: an Application for Metabolic Diseases Screening”, in XIV Congresso Nacional de Bioquímica, Vilamoura, Portugal, 2004.
  • M. Pinheiro, V. Afreixo, G. Moura, A. Freitas, M. A. S. Santos, and J. L. Oliveira, “Bioinformation System for Unveil General Rules of Codon Context”, in XIV Congresso Nacional de Bioquímica, Vilamoura, Portugal, 2004.
  • G. Moura, M. Pinheiro, V. Afreixo, A. Freitas, J. L. Oliveira, and M. A. S. Santos, “Comparative codon context analysis in complete genomes unveils new decoding rules in yeast”, in XIV Congresso Nacional de Bioquímica, Vilamoura, Portugal, 2004.
  • G. Moura, M. Pinheiro, V. Afreixo, A. Valente, J. L. Oliveira, and M. A. S. Santos, “Comparative codon context analysis at a genomic scale defines new mRNA decoding rules”, in Translational Control Meeting, Cold Spring Harbor, New York, 2004.
  • L. Carreto, J. Pereira, J. L. Oliveira, A. S. Pereira, V. Afreixo, A. Valente, and M. A. S. Santos, “Implementation of a DNA-microarray platform for yeast expression, genome diversity and evolution and molecular diagnostics research.” in XII Jornadas de Biologia de Leveduras (Leveduras’2004), Aveiro, Portugal, 2004.
  • G. Moura, M. Pinheiro, V. Afreixo, A. Valente, J. L. Oliveira, and M. A. S. Santos, “Genome scale codon context analysis for Saccharomyces cerevisiae and Candida albicans.” in XII Jornadas de Biologia de Leveduras (Leveduras’2004), Aveiro, Portugal, 2004.
  • M. Pinheiro, V. Afreixo, G. Moura, G. Dias, A. S. Pereira, A. Valente, M. A. S. Santos, and J. L. Oliveira, “Bioinformation system and statistical methodologies for gene primary structure analysis”, in EuroMISE 2004, Prague, Czech Republic, 2004.
  • J. L. Oliveira, M. Pinheiro, G. Dias, G. Moura, V. Afreixo, A. Valente, A. S. Pereira, and M. A. S. Santos, “New software tools for gene analysis”, in ESF Programme in Functional Genomics: 1st European Conference (ESFFG’2003), Prague, Czech Republic, 2003.
  • Oliveira, A. Furtado, J. L. Oliveira, A. S. Pereira, V. Maojo, F. Martin-Sanchez, A. Babic, and M. Santos, “Integration of Genetic and Clinical Information Sources for Health Applications”, in ESF Programme in Functional Genomics: 1st European Conference (ESFFG’2003), Prague, Czech Republic, 2003.
  • J. L. Oliveira, G. Dias, R. Silva, and M. A. S. Santos, “An open environment for management of proteomics data and projects”, in ESF Programme in Functional Genomics: 1st European Conference (ESFFG’2003), Prague, Czech Republic, 2003.
  • Paulo Gaspar
    Title: Computational methods for gene characterization and genome knowledge extraction
    Supervisor: José Luis Oliveira, Sérgio Matos
    Date: 2015
  • Luis Ribeiro
    Title: Distributed Medical Imaging Repositories
    Supervisor: Carlos Costa
    Date: 2014
  • David Campos
    Title: Term expansion methodologies in biomedical information retrieval
    Supervisor: José Luis Oliveira, Sérgio Matos
    Date: 2014
  • Tiago Pedrosa
    Title: Electronic Health Records for Mobile Citizens
    Supervisor: José Luis Oliveira, Rui Pedro Lopes
    Date: 2013
  • Pedro Lopes
    Title: Service Composition in Biomedical Applications
    Supervisor: José Luis Oliveira
    Date: 2012
  • Nuno Rosa
    Title: From the oral cavity proteome to the proteome
    Supervisor: Marlene Barros, José Luis Oliveira
    Date: 2012
  • Daniel Ferreira Polónia
    Title: An electronic market for teleradiology services
    Supervisor: José Luis Oliveira, Manuel Oliveira Duarte
    Date: 2011
  • José Paulo Lousado
    Title: Analysis of tandem repeats in DNA primary structures
    Supervisor: José Luis Oliveira
    Date: 2011
  • Miguel Monsanto Pinheiro
    Title: Computational systems for the study of the primary structure and redesign of genes
    Supervisor: José Luis Oliveira, Manuel Santos
    Date: 2010
  • Joel Perdiz Arrais
    Title: Microarrays information systems and healthcare information systems
    Supervisor: José Luis Oliveira
    Date: 2010
  • Carlos Manuel Azevedo Costa
    Title: A security dynamic model for healthcare information systems
    Supervisor: José Luis Oliveira, Augusto Silva
    Date: 2004