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International Journal Articles

  • Maria Raimundo and Susana Santos and Joana Mendonça and Ana T. Freitas, Are You Eating Right? Ask Your Genes: Developing a Value Proposition in Nutrigenetics, Annals of Nutrition and Metabolism, 71(), pp. 38, Jul. 2017, . [DOI link]
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  • Jorge dos Santos Oliveira and Wydemberg J. Araújo and Ricardo M. Figueiredo and Rita C. B. Silva-Portela and Alaine de Brito Guerra and Sinara Carla da Silva Araújo and Carolina Minnicelli and Aline Cardoso Carlos and Ana Tereza Ribeiro de Vasconcelos and Ana T. Freitas and Lucymara F. Agnez-Lima, Biogeographical distribution analysis of hydrocarbon degrading and biosurfactant producing genes suggests that near equatorial biomes have higher abundance of genes with potential for bioremediation, BMC Microbiology, 17(), pp. 168, Jul. 2017, Biomed Central. [DOI link]
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  • André Menolli and H. Sofia Pinto and Sheila Reinehr and Andreia Malucelli, SECOL: a semantic environment based on social media to support organisational learning, Behaviour & Information Technology, 36(4), pp. 364-389, Jun. 2017, Taylor&Francis. [DOI link]
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  • Rui Miguel Carrasqueiro Henriques and Francisco Luis Sarreira Lourenço Ferreira and Sara C. Madeira, BicPAMS: software for biological data analysis with pattern-based biclustering, BMC Bioinformatics, 18(82), pp. , Feb. 2017, . [DOI link]
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  • Thiago Elias and Icaro Pinto and Luciano Costa and Paulo Carvalho and Daniel Omote and Ihosvany Camps and Tati Ishikawa and Helen Arcuri and Susana Vinga and Arlindo L. Oliveira and Walter Junior and Nelson Silveira, Computational Approach to the Discovery of Phytochemical Molecules with Therapeutic Potential Targets to the PKCZ protein, Letters in Drug Design & Discovery, 14(), pp. 1-12, Jan. 2017, Bentham Science. [DOI link]
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  • Rui Miguel Carrasqueiro Henriques and Francisco Luis Sarreira Lourenço Ferreira and Sara Alexandra Aires da Encarnação, BicPAMS: Software for Biological Data Analysis with Pattern-based Biclustering, BMC Bioinformatics, to appear. Biomed Central
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  • Andreia Teixeira and Francisco Fernandes and A. P. Francisco, SpliceTAPyR – An Efficient Method For Transcriptome Alignment, International Journal of Foundations of Computer Science, to appear. Blackwell Publishing Inc.
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  • André Veríssimo and Arlindo L. Oliveira and Marie-France Sagot and Susana Vinga, DegreeCox–a network-based regularization method for survival analysis, BMC Bioinformatics, 17(16), pp. 109-121, Dec. 2016, Biomed Center. [DOI link]
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  • Miguel bastos Alves and Paulo Jorge Fernandes Carreira and António A. Costa, BIMSL: A Generic Approach to the Integration of Building Information Models with Real-time Sensor Data, Automation in Construction, to appear. Elsevier
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  • Henrique Ramalho Monteiro Latourrette Pombeiro and Rodolfo André Henriques dos Santos and Paulo Jorge Fernandes Carreira and Carlos Silva and João M. C. Sousa, Comparative assessment of low-complexity models to predict electricity consumption in an institutional building: Linear regression vs. fuzzy modeling vs. neural networks , Energy and Buildings, to appear. Elsevier [DOI link]
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  • Paulo Jorge Fernandes Carreira and Alfredo Ferreira and Cláudia RIbeiro and Cristina C. Gomes and António A. Costa, Virtual Reality as Integration Environments for Facilities Management: Application and Users Perception, Engineering, Construction and Architectural Management Journal, to appear.
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  • Rui Miguel Carrasqueiro Henriques and Sara C. Madeira, BiC2PAM: constraint-guided biclustering for biological data analysis with domain knowledge, Algorithms for Molecular Biology, 11(23), pp. 1-23, Sep. 2016, . [DOI link]
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  • Marta Alexandra Fragoso Nascimento and A. Sousa and M. Ramirez and A. P. Francisco and João Carriço and Cátia Vaz, PHYLOViZ 2.0: Providing scalable data integration and visualization for multiple phylogenetic inference methods, Bioinformatics, (), pp. , Sep. 2016, . [DOI link]
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  • Rui Miguel Carrasqueiro Henriques and Sara C. Madeira, BicNET: Flexible Module Discovery in Large-Scale Biological Networks using Biclustering, Algorithms for Molecular Biology, 11(14), pp. 1-30, May. 2016, BioMed Central. [DOI link]
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  • Luís M. S. Russo and A. P. Francisco, Extending quick hypervolume, Journal of Heuristics, (), pp. 1-27, Mar. 2016, Springer. Article [DOI link]
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  • Luis de Sousa and Alberto Rodrigues da Silva, A Domain Specific Language for Spatial Simulation Scenarios, GeoInformatica, 20(1), pp. 117-149, Jan. 2016, Springer. Article
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  • Paulo Jorge Fernandes Carreira and José Cavalheiro, A multidimensional data model design for building energy management, Advanced Engineering Informatics, to appear. Elsevier [DOI link]
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  • Miguel Costa and Daniel Gomes and Mário J. Silva, The Evolution of Web Archiving International Journal on Digital Libraries, International Journal on Digital Libraries, (), pp. , May. 2016, Springer. Article [DOI link]
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  • Pedro Rijo and A. P. Francisco and Mário J. Silva, Evaluating the impact of k-anonymization on the inference of interaction networks, Transactions on Data Privacy , 9(1), pp. 49-72, Apr. 2016, U. of Skövde,. Article
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  • B. Ribeiro-Gonçalves and A. P. Francisco and Cátia Vaz and M. Ramirez and João Carriço, PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees, Nucleic Acids Research, (), pp. , Jan. 2016, . [DOI link]
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  • Paulo Jorge Fernandes Carreira and Pedro Lima and Pedro Fazenda, Context-based thermodynamic modeling of buildings spaces, Energy and Buildings, to appear. Elsevier [DOI link]
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  • Rui Miguel Carrasqueiro Henriques and Claudia Antunes and Sara C. Madeira, A Structured View on Patern Mining-based Biclustering, Pattern Recognition, 48(12), pp. 3941-3958, Dec. 2015, Elsevier . [DOI link]
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  • André Filipe Oliveira Pinto Ribeiro and Afonso Silva and Alberto Rodrigues da Silva, Data Modeling and Data Analytics: A Survey from a Big Data Perspective, Journal of Software Engineering and Applications, 8(12), pp. 617-634, Dec. 2015, Scientific Research Publishing. Article
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  • Naercio David Pedro Magaia and A. P. Francisco and Paulo Rogério Pereira and Miguel Correia, Betweenness centrality in Delay Tolerant Networks: A survey, Ad Hoc Networks, 33(), pp. 284-305, Oct. 2015, Elsevier. [DOI link]
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  • André Carreiro and Pedro Miguel Torpes de Amaral and Susana Pinto and Pedro Tomás and Mamede de Carvalho and Sara C. Madeira, Prognostic Models based on Patient Snapshots and Time Windows: Predicting Disease Progression to Assisted Ventilation in Amyotrophic Lateral Sclerosis, Journal of Biomedical Informatics, 58(), pp. 133-144, Nov. 2015, Elsevier . Article [DOI link]
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  • André Carreiro and Alexandre de Mendonça and Mamede de Carvalho and Sara C. Madeira, Integrative biomarker discovery in neurodegenerative diseases, WIREs Systems Biology and Medicine, 7(6), pp. 357–379, Oct. 2015, Willey. Article [DOI link]
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  • Alberto Rodrigues da Silva, Model-Driven Engineering: A Survey Supported by a Unified Conceptual Model, Computer Languages, Systems & Structures, 43(), pp. 139-155, Oct. 2015, Elsevier. Article [DOI link]
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  • Dušan Savić, Siniša Vlajić, Saša Lazarević, Vojislav Stanojevi&#2 and Alberto Rodrigues da Silva, Use Case Specification Using the SILABREQ Domain Specific Language, Computing and Informatics Journal, 34(4), pp. 877–910, Oct. 2015, . Article
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  • Jorge dos Santos Oliveira, BioSurfDB : Knowledge and algorithms to support biosurfactants and biodegradation studies, , to appear.
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  • Rui Miguel Carrasqueiro Henriques and Sara C. Madeira, Biclustering with Flexible Plaid Models to Unravel Interactions between Biological Processes, IEEE/ACM Transactions on Computacional Biology and Bioinformatics, 12(4), pp. 738-752, Aug. 2015, . Article [DOI link]
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  • Rui Miguel Carrasqueiro Henriques and Sara C. Madeira and Claudia Antunes, Multi-period Classification: Learning Sequent Classes from Temporal Domains, Data Mining and Knowledge Discovery (DAMI), 29(3), pp. 792-819, May. 2015, Springer US. [DOI link]
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  • João Ferreira and José Almeida and Alberto Rodrigues da Silva, The Impact of Driving Styles on Fuel Consumption: A Data Warehouse and Data Mining based Discovery Process, IEEE Transactions on Intelligent Transportation Systems, 16(5), pp. 2653-2662, May. 2015, IEEE. Article
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  • Carolina Maruta and Telma Filipa Lucas de Mira Pereira and Sara C. Madeira and Alexandre de Mendonça and Manuela Guerreiro, Classification of primary progressive aphasia: Do unsupervised data mining methods support a logopenic variant?, Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration, (), pp. 1-13, Apr. 2015, . [DOI link]
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  • Rudolf Mayer and Gonçalo Antunes and Artur Caetano and Marzieh Bakhshandeh and Andreas Rauber and José Borbinha, Using ontologies to capture the semantics of a (business) process for digital preservation, Int. J. Digit. Libr, (15), pp. 2-4, Apr. 2015, . [DOI link]
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  • Jorge dos Santos Oliveira and Wydemberg Araújo and Ana Sales and Alaine Guerra and Sinara Araújo and Ana T Vasconcelos and Lucymara Agnez-Lima and Ana T. Freitas, BioSurfDB : Knowledge and algorithms to support biosurfactants and biodegradation studies, Database, 2015(2015), pp. 1-8, Mar. 2015, Oxford University Press. [DOI link]
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  • João Santos and Ivo Anastácio and Bruno Martins, Named Entity Disambiguation over Texts Written in the Portuguese or Spanish Languages, IEEE Latin America Transactions, 13(3), pp. , Mar. 2015, IEEE Region 9. Article
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  • Andreia Teixeira and Pedro T. Monteiro and Mário Ramirez and João Carriço and A. P. Francisco, Not seeing the forest for the trees: Size of the minimum spanning trees (MSTs) forest and branch significance in MST-based phylogenetic analysis, PLoS One, 10(3), pp. , Mar. 2015, . [DOI link]
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  • Marco R Oggioni and Joana Coelho and Leonardo Furi and Daniel R Knight and Carlo Viti and Graziella Orefici and Jose-Luis Martinez and Ana T. Freitas and Teresa M Coque and Ian Morrissey, Significant Differences Characterise the Correlation Coefficients between Biocide and Antibiotic Susceptibility Profiles in Staphylococcus aureus., Current pharmaceutical design , 21(), pp. , Mar. 2015, .
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  • Cátia M. Machado and Dietrich Rebholz-Schuhmann and Ana T. Freitas and Francisco M. Couto, The semantic web in translational medicine: current applications and future directions, Briefings in Bioinformatics, 16(1), pp. 89-103, Jan. 2015, Oxford Journals. [DOI link]
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  • João Pombinho and David Sardinha Andrade de Aveiro and José Manuel Nunes Salvador Tribolet, Value-Oriented Specification of Service Systems: Modeling the Contribution Perspective of Enterprise Networks, International Journal of Information Systems in the Service Sector (IJISSS), 7(1), pp. 60-81, Jan. 2015, IGI Global. Article [DOI link]
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  • Daniel H. Dalip and Marcos André Gonçalves and Marco Cristo and Pável Calado, A General Multiview Framework for Assessing the Quality of Collaboratively Created Content on Web 2.0, JOURNAL OF THE ASSOCIATION FOR INFORMATION SCIENCE AND TECHNOLOGY, to appear. [DOI link]
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  • Paulo Jorge Fernandes Carreira and Renato Filipe Gonçalves Vieira and Pedro Domingues, Building Automation: Concepts and Technology Review, Computer Standards and Interfaces Journal, to appear. Elsevier [DOI link]
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  • Rui Miguel Carrasqueiro Henriques and Sara C. Madeira, BicPAM: Pattern-based Biclustering for Biomedical Data Analysis, Algorithms for Molecular Biology, 9(27), pp. , Dec. 2014, Pubmed Central. [DOI link]
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  • J Zamite and D Domingos and Mário J. Silva and C Santos, Group-Based Discretionary Access Control in Health Related Repositories, Journal of Information Technology Research (JITR) , 7(1), pp. 78-94, Nov. 2014, IGI Global. [DOI link]
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  • João André Lopes Ferreira and Alberto Rodrigues da Silva, Mobile Cloud Computing, Open Journal of Mobile Computing and Cloud Computing, 1(2), pp. 59-77, Nov. 2014, Scientific Online Publishing. Article
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  • Rui Miguel Carrasqueiro Henriques and Sara C. Madeira, BicSPAM: Flexible Biclustering using Sequential Patterns, BMC Bioinformatics, 15(130), pp. , May. 2014, . [DOI link]
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  • Miguel Antunes Mendes Ferreira and Nuno Roma and Luís M. S. Russo, Cache-Oblivious Parallel SIMD Viterbi Decoding for Sequence Search in HMMER, BMC Bioinformatics, 15(165), pp. 1-13, May. 2014, BioMed Central. [DOI link]
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  • Cláudia RIbeiro and Carla Farinha and João António Madeiras Pereira and Miguel Mira da Silva, Gamifying requirement elicitation: Practical implications and outcomes in improving stakeholders collaboration, Entertainment Computing Journal, 5(4), pp. 335-345, Dec. 2014, Elsevier. [DOI link]
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  • Rui Miguel Carrasqueiro Henriques and Cláudia Antunes and Sara C. Madeira, Generative Modeling of Repositories of Health Records for Predictive Tasks, Data Mining and Knowledge Discovery (DAMI), 29(4), pp. 999-1032, Nov. 2014, Springer. Article [DOI link]
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  • Rui Camacho and Paulo Jorge Fernandes Carreira and Inês Lynce and Sílvia Resendes, An ontology-based approach to conflict resolution in Home and Building Automation Systems, Expert Systems with Applications, 41(14), pp. 6161-6173, Oct. 2014, Elsevier. [DOI link]
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  • André Filipe Oliveira Pinto Ribeiro and Alberto Rodrigues da Silva, Evaluation of XIS-Mobile, a Domain Specific Language for Mobile Application Developmen, Journal of Software Engineering and Applications, 7(11), pp. 906-919, Oct. 2014, Scientific Research Publishing. Article [DOI link]
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  • Cátia Vaz and A. P. Francisco and Mickael Silva and Keith A Jolley and James E Bray and Hannes Pouseele and Joerg Rothganger and Mário Ramirez and João Carriço, TypOn: The Microbial Typing Ontology, Journal of Biomedical Semantics, 5(43), pp. 1-11, Oct. 2014, BioMed Central Ltd. . Article [DOI link]
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  • Joana P. Gonçalves and Sara C. Madeira, LateBiclustering: Efficient Heuristic Algorithm for Time-Lagged Bicluster Identification, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11(5), pp. 801–813, Sep. 2014, . [DOI link]
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  • José Manuel Nunes Salvador Tribolet and Pedro Manuel Moreira Vaz Antunes de Sousa and Artur Caetano, The Role of Enterprise Governance and Cartography in Enterprise Engineering, Enterprise Modelling and Information Systems Architectures – An International Journal. ISSN: 1866-3621, 9(1), pp. 38-49, Jun. 2014, German Informatics Society (GI). Article [DOI link]
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  • Mauro Castelli and Sara Silva and Leonardo Vanneschi, A C++ framework for geometric semantic genetic programming, Genetic Programming and Evolvable Machines, (), pp. , Apr. 2014, . [DOI link]
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  • Mauro Castelli and Leonardo Vanneschi and Sara Silva, Semantic Search-Based Genetic Programming and the Effect of Intron Deletion, IEEE Transactions on Cybernetics, 44(1), pp. 103-113, Jan. 2014, IEEE Press.
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  • Francisco Fernandes and Ana T. Freitas, slaMEM: Efficient retrieval of Maximal Exact Matches using a Sampled LCP Array, Bioinformatics , 30(4), pp. 464 – 471 , Jan. 2014, . [DOI link]
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  • A. P. Francisco and Luís M. S. Russo, Quick Hypervolume, IEEE Trans. Evolutionary Computation, to appear. [DOI link]
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  • Paulo Jorge Fernandes Carreira and Miguel Mira da Silva and Pedro Antunes, Towards an Energy Management Maturity Model, Energy Policy Journal, to appear. Article [DOI link]
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  • Filipe Manuel Lemos Ferreira and Miguel Carvalho Valente Esaguy Coimbra and Raquel Bairrão and Renato Filipe Gonçalves Vieira and Ana T. Freitas and José Borbinha and Luís M. S. Russo, Data Management in Metagenomics: A Risk Management Approach, International Journal of Digital Curation, 9(1), pp. 41-56, May. 2014, University of Edinburgh. Article [DOI link]
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  • Cátia Pesquita and João D Ferreira and Francisco M Couto and Mário J. Silva, The Epidemiology Ontology: an ontology for the semantic annotation of epidemiology resources, Journal of Biomedical Semantics, 5(4), pp. , May. 2014, BioMed Central. Article [DOI link]
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  • Eduardo Cunha and Bruno Martins, Using One-Class Classifiers and Multiple Kernel Learning For Defining Imprecise Geographic Regions, International Journal of Geographical Information Science, 28(11), pp. , May. 2014, Taylor & Francis. Article [DOI link]
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  • João Santos and Ivo Anastácio and Bruno Martins, Using Machine Learning Methods for Disambiguating Place References in Textual Documents, GeoJournal, (), pp. , Apr. 2014, Springer. Article [DOI link]
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  • Mauro Castelli and Leonardo Vanneschi and Sara Silva, Prediction of the Unified Parkinson’s Disease Rating Scale assessment using a genetic programming system with geometric semantic genetic operators, Expert Systems with Applications, 41(), pp. 4608–4616, Mar. 2014, .
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  • Gonçalo José Branquinho Antunes and Marzieh Bakhshandeh and Rudolf Mayer and José Borbinha and Artur Caetano, Using Ontologies for Enterprise Architecture Integration and Analysis, Complex Systems Informatics and Modeling Quarterly, 1(1), pp. 1-23, Mar. 2014, RTU Press. [DOI link]
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  • Miguel Teixeira and Pedro T. Monteiro and Joana Guerreiro and Joana Gonçalves and Nuno Mira and Sandra dos Santos and Tânia Cabrito and Margarida Palma and Catarina Costa and A. P. Francisco and Sara C. Madeira and Arlindo L. Oliveira and Ana T. Freitas and Isabel Sá-Correia, The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae, Nucleic Acids Research , 42(1), pp. D1-D6, Jan. 2014, . [DOI link]
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  • Andras Hartmann and J. M. Lemos and Rafael Costa and Susana Vinga, Identifying IIR Filter Coefficients using Particle Swarm Optimization with Application to Reconstruction of Missing Cardiovascular Signals, Engineering Applications of Artificial Intelligence, to appear. Elsevier
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  • Nuno Castela and Paulo DIas and Marielba Zacarias and José Manuel Nunes Salvador Tribolet, Atualização Colaborativa do Modelo de Processos de Negócio, Iberian Journal of Information Systems and Technologies, 12(), pp. 33-47, Dec. 2013, ACADEMY PUBLISHER. [DOI link]
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  • Gabriel César Ferreira Pestana and Sebastian Heuschler and Augusto Casaca and Pedro Reis and Joachim Metter, Complex Event Processing for Decision Support in na Airport Environment, International Journal on Advances in Software, 6(4), pp. 246-260, Dec. 2013, .
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  • Cátia M. Machado and Ana T. Freitas and Francisco M. Couto, Enrichment analysis applied to disease prognosis, Journal of Biomedical Semantics, 4(21), pp. , Oct. 2013, . [DOI link]
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  • Alberto Moraglio and Julian Togelius and Sara Silva, Geometric Differential Evolution for Combinatorial and Programs Spaces, Evolutionary Computation, 21(4), pp. 591-624, Oct. 2013, .
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  • Gonzalo Navarro and Luís M. S. Russo and Yakov Nekrich, Space-Efficient Data-Analysis Queries on Grids, Theoretical Computer Science, 482(), pp. 60-72, Oct. 2013, Elsevier. [DOI link]
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  • Luís M. S. Russo and A. P. Francisco, Quick HyperVolume, IEEE Transactions on Evolutionary Computation , 1(99), pp. 1, Sep. 2013, IEEE. Article [DOI link]
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  • Mauro Castelli and Leonardo Vanneschi and Sara Silva, Prediction of High Performance Concrete Strength Using Genetic Programming with Geometric Semantic Genetic Operators, Expert Systems with Applications, 40(17), pp. 6856-6862, Dec. 2013, .
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  • Orlando Anunciação and Susana Vinga and Arlindo L. Oliveira, Using Information Interaction to Discover Epistatic Effects in Complex Diseases, PLoS ONE, 8(10), pp. , Oct. 2013, . Article [DOI link]
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  • Carlos Nuno da Cruz Ribeiro and Ivo Miguel da Quinta Anastácio and Márcia Lourenço Baptista and André Loureiro da Costa, A Framework for Robust Address Assignment in WSNs Whispering to Avoid Intruders, International Journal of Distributed Sensor Networks, 2013(), pp. 16, Sep. 2013, Hindawi Publishing Corporation. [DOI link]
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  • Carlos Páscoa and Nelson Ferreira and José Manuel Nunes Salvador Tribolet, Strategy essentials: organizational simulators, The LEarning Organziation, 20(6), pp. 358-376, Sep. 2013, Emerald Group Publishing Limited. [DOI link]
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  • Gonçalo Fernandes Simões and Helena Galhardas and Luis Gravano, When speed has a price: Fast information extraction using approximate algorithms, Proceedings of the VLDB Endowment (PVLDB), 6(13), pp. , Aug. 2013, .
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  • Luis Leitão and Pável Calado, An automatic blocking strategy for XML duplicate detection, ACM SIGAPP Applied Computing Review, 13(2), pp. 42–53, Jun. 2013, . [DOI link]
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  • José Manuel Nunes Salvador Tribolet, Educating the educators to innovate: the need to reinvent academia´ s mission and to reengineer their basic tool: the Educator., Journal of Innovation Management, 1(1), pp. 7-10, Aug. 2013, University of Oporto.
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  • L. Furi and M.L. Ciusa and D. Knight and V. Di Lourenzo and N. Tocci and D. Cirasola and L. Aragones and Joana Coelho and Ana T. Freitas and E. Marchi and L. Moce and P. Visa and J. B. Northwood and C. Viti and G. Orefici and the BIOHYPO Consortium and I. Morrissey and M. R. Oggioni, Evaluation of Reduced Susceptibility to Quaternary Ammonium Compounds and Bisbiguanides in Clinical Isolates and Laboratory-Generated Mutants of Staphylococcus aureus, Antimicrobial agents and chemotherapy, 57(8), pp. , Aug. 2013, .
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  • Francisco Couto and H. Sofia Pinto, The Next Generation of Similarity Measures that fully explore the Semantics in Biomedical Ontologies, Journal of Bioinformatics and Computational Biology, 11(5), pp. , Jun. 2013, World Scienti c Publishing Company. [DOI link]
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  • Paulo Jorge Fernandes Carreira and Alfredo Ferreira, New Interaction Paradigms in Energy Management, ERCIM News, 93(), pp. 49-50, Apr. 2013, ERCIM.
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  • Jorge dos Santos Oliveira and Nuno D. Mendes and Vitor Carocha and Clara Graça and Jorge A. P. Paiva and Ana T. Freitas, A computational approach for microRNA identification in plants: combining genome-based predictions with RNA-Seq data, , (), pp. , May. 2013, .
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  • Paulo Jorge Fernandes Carreira and André Guilherme Nogueira Coelho dos Santos and Silvia Resendes, Conflict Detection and Resoltion in Home and Building Automation Systems: A literature review, Springer Journal of Ambient Intelligence and Humanized Computing, (), pp. 1-17, May. 2013, .
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  • Luis Leitão and Pável Calado and Melanie Herschel, Efficient and Effective Duplicate Detection in Hierarchical Data, IEEE Transactions on Knowledge and Data Engineering, 25(5), pp. 1028–1041, Mar. 2013, IEEE. [DOI link]
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  • Sílvio Moreira and David Batista and Paula Carvalho and Francisco Couto and Mário J. Silva, Tracking politics with POWER, Program: electronic library and information systems, 47(2), pp. 120-135, Feb. 2013, Emerald . Article [DOI link]
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  • Paulo G. S. da Fonseca and Jorge A. P. Paiva and Luiz G. P. Almeida and Ana Tereza Vasconcelos and Ana T. Freitas, Empirical assessment of sequencing errors for high through-put pyrosequencing data, BMC Research Notes, 6(25), pp. , Jan. 2013, .
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  • Catarina Moreira and Pável Calado and Bruno Martins, Learning to Rank Academic Experts in the DBLP dataset, Journal of Expert Systems, to appear. Wiley Article [DOI link]
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  • André Guilherme Nogueira Coelho dos Santos and Silvia Resendes and Paulo Jorge Fernandes Carreira, Towards automatic conflict detection in home and building automation systems, Pervasive and Mobile Computing, 12(), pp. , May. 2013, . [DOI link]
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  • Joana Coelho and João Carriço and Daniel Knight and Jose Luis Martinez and Ian Morrissey and Marco R. Oggioni and Ana T. Freitas, The use of Machine Learning methodologies to analyse Antibiotic and Biocide susceptibility in Staphylococcus aureus, PLOS ONE, (), pp. , Feb. 2013, . [DOI link]
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  • Jan LG Dietz and Jan AP Hoogervorst and Antonia Albani and David Aveiro and Eduard Babkin and Artur Caetano and Philip Huysmans and Junichi Iijima and Steven JH Van Kervel and Hans Mulder and Martin Op’t Land and Henderik A Proper and Jorge Sanz and Linda Terlouw and José Manuel Nunes Salvador Tribolet and Jan Verelst and Robert Winte, The discipline of enterprise engineering, International Journal of Organisational Design and Engineering, ISSN online: 1758-9800 ISSN print: 1758-9797, 3(1), pp. 86-114, Jan. 2013, Inderscience Publishers. Article [DOI link]
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  • Sílvio Moreira and David Batista and Paula Carvalho and Francisco M. Couto and Mário J. Silva, Tracking Politics with POWER, Program: electronic library and information systems, to appear. Emerald
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  • A. P. Francisco and R. Baeza-Yates and Arlindo L. Oliveira, Mining query log graphs towards a query folksonomy, Concurrency and Computation: Practice and Experience, (1), pp. , Dec. 2012, Wiley. Article [DOI link]
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  • Artur Caetano and António Rito Silva and José Manuel Nunes Salvador Tribolet, Applying the principle of separation of concerns to business process design, International Journal of Organisational Design and Engineering, Special Issue on Enterprise Engineering, 2(3), pp. 250-270, Nov. 2012, Inderscience. [DOI link]
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  • Sara Silva and Leonardo Vanneschi, Bloat Free Genetic Programming: Application to Human Oral Bioavailability Prediction, International Journal of Data Mining and Bioinformatics, 6(6), pp. 585-601, Nov. 2012, Inderscience.
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  • Jonas S. Almeida and Alexander Gruneberg and Wolfgang Maass and Susana Vinga, Fractal MapReduce decomposition of sequence alignment, Algorithms for Molecular Biology, 7(), pp. 12, May. 2012, . [DOI link]
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  • Joana P. Gonçalves and A. P. Francisco and Yves Moreau and Sara C. Madeira, Interactogeneous: disease gene prioritization using heterogeneous networks and full topology scores, PLoS ONE, 7(11), pp. e49634, Nov. 2012, . [DOI link]
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  • João D Ferreira and Daniela Paolotti and Francisco M Couto and Mário J. Silva, On the usefulness of ontologies in epidemiology research and practice, The Journal of Epidemiology and Community Health, (), pp. , Nov. 2012, BMJ Publishing Group. [DOI link]
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  • Jucimar Souza and André Carvalho and Marco Cristo and Edleno Moura and Pável Calado and Paul-Alexandru Chirita and Wolfgang Nejdl, Using Site-Level Connections to Estimate Link Confidence, Journal of the American Society for Information Science and Technology, (), pp. , Oct. 2012, . Article
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  • M.L. Ciusa and L. Furi and Daniel Knight and F. Decorosi and Marco Fondi and Carla Raggi and Joana Coelho and Luis Aragones and Laura Moce and Pilar Visa and Ana T. Freitas and L. Baldassarri and Renato Fani and Carlo Viti and G. Orefici and Jose Luis Martinez and the BIOHYPO Consortium and Ian Morrissey and Marco R. Oggioni, A novel resistance mechanism to triclosan that suggests horizontal gene transfer and demonstrates a potential selective pressure for reduced biocide susceptibility in clinical strains of Staphylococcus aureus, International Journal of Antimicrobial Agents, 40(3), pp. 210-220, Sep. 2012, .
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  • Nuno D. Mendes and Ana T. Freitas and Steffen Heyne and Marie-France Sagot and Rolf Backofen, Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches, Bioinformatics, 28(23), pp. 3034-3041, Sep. 2012, . [DOI link]
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  • André Carreiro and Artur J. Ferreira and Mário A. T. Figueiredo and Sara C. Madeira, Towards a Classification Approach using Meta-Biclustering: Impact of Discretization in the Analysis of Expression Time Series, Journal of Integrative Bioinformatics, 9(3), pp. 207, Jul. 2012, . Article [DOI link]
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  • Joana P. Gonçalves and Yves Moreau and Sara C. Madeira, AliBiMotif: Integrating Alignment and Biclustering to Unravel Transcription Factor Binding Sites in DNA Sequences , International Journal of Data Mining and Bioinformatics (IJDMB), 6(2), pp. 196-215, Jun. 2012, Inderscience Publishers. [DOI link]
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  • Bruno Félix and André Ferreira Ferrão Couto e Vasconcelos and José Manuel Nunes Salvador Tribolet, SimplexIS: Evaluating the impact of eGov Simplification measures in the Information System Architecure, International Journal of Computer and Communication Engineering (IJCCE), 6(), pp. 238-243, Jun. 2012, World Academy of Science, Engineering and Technology (p-ISSN.
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  • Carlos Pascoa and Nuno Belo and José Manuel Nunes Salvador Tribolet, Business Objectives and Business Processes: Alignment and Verification, Information Resources Management Journal (IRMJ), 25(2), pp. 52-68, May. 2012, IGI Global. [DOI link]
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  • Susana Vinga and Alexandra M. Carvalho and A. P. Francisco and Luís M. S. Russo and Jonas S. Almeida, Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis, Algorithms for Molecular Biology, 7(), pp. 10, May. 2012, . [DOI link]
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  • A. P. Francisco and Cátia Vaz and Pedro T. Monteiro and J. Melo-Cristino and M. Ramirez and João Carriço, PHYLOViZ: Phylogenetic inference and data visualization for sequence based typing methods, BMC Bioinformatics, 13(87), pp. , May. 2012, . [DOI link]
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  • Sara Silva and Stephen Dignum and Leonardo Vanneschi, Operator equalisation for bloat free genetic programming and a survey of bloat control methods, Genetic Programming and Evolvable Machines, 13(2), pp. 197-238, Apr. 2012, Springer.
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  • Nuno Castela and Marielba Silva Zacarias and José Manuel Nunes Salvador Tribolet, Collaborative Maintenance of Business Process Models, International Journal of Organisational Design and Engineering, 2(1), pp. 61-84, Mar. 2012, . [DOI link]
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  • Ricardo Vieira and José Borbinha and David Ferreira, A Requirements Engineering analysis of MoReq, Records Management Journal, to appear. Emerald
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  • Isadora Rosa and Paulo Fidalgo and José Soares and Susana Vinga and Carla Oliveira and João P Silva and Susana M Ferro and Paula Chaves and António G Oliveira and Carlos N Leitão, Adenoma incidence decreases under the effect of polypectomy, World journal of gastroenterology, 18(11), pp. 1243-8, Mar. 2012, . [DOI link]
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  • Daniel Hasan Dalip and Marcos André Gonçalves and Thiago Cardoso and Marco Cristo and Pável Calado, A Multi-view Approach for the Quality Assessment of Wiki Articles, Journal of Information and Data Management, 3(1), pp. 73–82, Feb. 2012, . Article
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  • João Fernandes and Diogo Duarte and Cláudia RIbeiro and Carla Farinha and João António Madeiras Pereira and Miguel Mira da Silva, iThink: A Game-Based Approach Towards Improving Collaboration and Participation in Requirement Elicitation, Procedia Computer Science, 15(), pp. 66-77, Jan. 2012, Elsevier; ISSN: 1877-0509. [DOI link]
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  • Hugo Miguel Álvaro Manguinhas and Nuno Miguel Antunes Freire and Jorge Miguel Calha Rainho Machado and José Borbinha, Supporting multilingual bibliographic resource discovery with functional requirements for bibliographic records, Semantic Web, (), pp. 3-21, Jan. 2012, .
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  • João Leitão and José Pereira and Luis Rodrigues and João Marques, X-BOT: A Protocol for Resilient Optimization of Unstructured Overlay Networks, IEEE Transactions on Parallel and Distributed Systems, (), pp. , Jan. 2012, . [DOI link]
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  • Hugo Miguel Álvaro Manguinhas and José Borbinha and Nuno Miguel Antunes Freire and Jorge Miguel Calha Rainho Machado, Supporting multilingual bibliographic resource discovery with Functional Requirements for Bibliographic Records, Semantic Web, to appear. IOS Press Article [DOI link]
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  • Daniel Hasan Dalip and Marcos André Gonçalves and Marco Cristo and Pável Calado, Automatic Assessment of Document Quality in Web Collaborative Digital Libraries, Journal of Data and Information Quality, 2(3), pp. , Dec. 2011, . [DOI link]
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  • Luís M. S. Russo, Monge properties of sequence alignment, Theoretical Computer Science, 423(0), pp. 30 – 49, Dec. 2011, ELSEVIER. Article [DOI link]
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  • Alberto Rodrigues da Silva, Padrões de Interfaces Sociais no Desenho do BOA (Social Interface Patterns for the Design of BOA System), Informática na Educação: Teoria & Prática, UFRGS, (), pp. , Oct. 2011, .
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  • Sara Silva, Reassembling Operator Equalisation – A Secret Revealed, SIGEVOlution, 5(3), pp. 10-22, Sep. 2011, ACM Press. Article
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  • Nelson Gama and Raul Nunes da Silva and Miguel Mira da Silva, Using People-CMM for Diminishing Resistance to ITIL, International Journal of Human Capital and Information Technology Professionals, 2(3), pp. 29-43, Sep. 2011, IGI. Article
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  • Francisco M Couto and Mário J. Silva, Disjunctive Shared Information between Ontology Concepts: application to Gene Ontology, Journal of Biomedical Semantics, 2(5), pp. , Aug. 2011, . [DOI link]
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  • Joana P. Gonçalves and A. P. Francisco and Nuno P. Mira and Miguel C. Teixeira and Isabel Sá-Correia and Arlindo L. Oliveira and Sara C. Madeira, TFRank: network-based prioritization of regulatory associations underlying transcriptional responses, Bioinformatics, 27(22), pp. 3149–3157, Nov. 2011, Oxford University Press. Article [DOI link]
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  • Dulce Calçada and Susana Vinga and Ana T. Freitas and Arlindo L. Oliveira, Quantitative modeling of the Saccharomyces cerevisiae FLR1 Regulatory Network using an S-System Formalism, Journal of Bioinformatics and Computational BIology, 9(5), pp. , Oct. 2011, World Scientific. Article [DOI link]
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  • Pedro T. Monteiro and Paulo J. Dias and Delphine Ropers and Arlindo L. Oliveira and Isabel Sá-Correia and Miguel C. Teixeira and Ana T. Freitas, Qualitative modelling and formal verification of the FLR1 gene mancozeb response in Saccharomyces cerevisiae, IET Systems Biology, 5(5), pp. 308-316, Sep. 2011, IET. Article [DOI link]
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  • André Carreiro and Orlando Anunciação and João Carriço and Sara C. Madeira, Prognostic Prediction through Biclustering-Based Classiffication of Clinical Gene Expression Time Series, Journal of Integrative Bionformatics, 8(3), pp. , Aug. 2011, . [DOI link]
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  • Nuno Tenazinha and Susana Vinga, A Survey on Methods for Modeling and Analyzing Integrated Biological Networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 8(4), pp. 943-958, Jul. 2011, . [DOI link]
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  • Alexandra M. Carvalho and Teemu Roos and Arlindo L. Oliveira and Petri Myllymäki, Discriminative learning of Bayesian networks via factorized conditional log-likelihood, Journal of Machine Learning Research, 12(7), pp. 2181-2210, Jul. 2011, . Article
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  • Daniela Nitsch and Léon-Charles Tranchevent and Joana P. Gonçalves and Josef Korbinian Vogt and Sara C. Madeira and Yves Moreau, PINTA: a web server for network-based gene prioritization from expression data, Nucleic Acids Research, 39(), pp. W334-W338, Jul. 2011, Oxford University Press. Article [DOI link]
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  • Francisco Fernandes and Paulo G. S. da Fonseca and Luís M. S. Russo and Arlindo L. Oliveira and Ana T. Freitas, Efficient alignment of pyrosequencing reads for resequencing applications, BMC Bioinformatics, 12(163), pp. , Jun. 2011, BioMed Central. [DOI link]
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  • José Barateiro and Gonçalo Antunes and José Borbinha, Designing Digital Preservation Solutions: A Risk Management-Based Approach, In International Journal of Digital Curation, 5(1), pp. 4-17, Dec. 2010, .
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  • Gabriel César Ferreira Pestana and Andrea Kurz and Antero Kuvonen and Augusto Casaca, Location-based services to improve aircraft ground handling and safety procedures, European Journal of Navigation, 8(3), pp. 16-21, Dec. 2010, Druck Center Meckenheim GmbH.
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  • André Luiz da Costa Carvalho and Edleno Silva de Moura and Pável Calado, Using Statistical Features to Find Phrasal Terms in Text Collections, Journal of Information and Data Management, 1(3), pp. 583–597, Oct. 2010, .
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  • Alexandra M. Carvalho and Arlindo L. Oliveira, GRISOTTO: A greedy approach to improve combinatorial algorithms for motif discovery with prior knowledge, Algorithms for Molecular Biology, 6(13), pp. , Apr. 2011, . Article [DOI link]
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  • Fernando Sequeira Sousa and Fábio O. Teixeira and Alex E. Falcão and Anderson D. Hummel and Thiago M. Costa and Pável Calado and Luciano V. Araújo and Ivan T. Pisa and Filipe Mancini, Use of Medical Subject Headings (MeSH) in Portuguese for Categorizing Web-based Healthcare Content, Journal of Biomedical Informatics, 44(2), pp. 299–309, Apr. 2011, . Article
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  • Jorge A P Paiva and Elisa Prat and Sonia Vautrin and Mauro D Santos and Hélène San-Clement and Sérgio Brommonschenkel and Paulo G. S. da Fonseca and Dário Grattapaglia and Xiang Song and Jetty S S Ammiraju and David Kudrna and Rod A Wing and Ana T. Freitas and Hélène Bèrges and Jacqueline Grima-Pettenati, Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries, BMC Genomics, 12(137), pp. , Mar. 2011, . [DOI link]
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  • David Sardinha Andrade de Aveiro and António Rito Silva and José Manuel Nunes Salvador Tribolet, GOD-theory for organizational engineering: continuously modeling the continuous (re)Generation, Operation and Deletion of the enterprise, International Journal of Internet and Enterprise Management: Special Issue on Enterprise Systems Modeling and Simulation, 7(1), pp. 64-83, Jan. 2011, Inderscience Publishers.
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  • Ana Sofia Graça and Joao Marques Silva and Inês Lynce and Arlindo L. Oliveira, Haplotype inference with pseudo-Boolean optimization, Annals of Operations Research, 184(1), pp. 137-162, Jan. 2011, Springer. Article [DOI link]
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  • Dario Abdulrehman and Pedro T. Monteiro and Miguel C. Teixeira and Nuno P. Mira and Artur B. Lourenço and Sónia C. dos Santos and Tânia R. Cabrito and A. P. Francisco and Sara C. Madeira and Ricardo Rubén dos Santos Aires and Arlindo L. Oliveira and Isabel Sá-Correia and Ana T. Freitas, YEASTRACT: Providing a programmatic access to curated transcriptional regulatory associations in Saccharomyces cerevisiae through a web services interface, Nucleic Acids Research, 39(1), pp. D136-D140, Jan. 2011, . [DOI link]
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  • João Zamite and Fabrício A. B. Silva and Francisco Couto and Mário J. Silva, MEDCollector: Multisource epidemic data collector, Transactions on Large-scale Data-and Knowledge-centered Systems IV: Special Issue on Database Systems for Biomedical App, to appear. Springer-Verlag New York, Inc. Article [DOI link]
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  • Miguel C. Teixeira and Paulo J. Dias and Pedro T. Monteiro and Arlindo L. Oliveira and Ana T. Freitas and Isabel Sá-Correia, Refining current knowledge on the yeast FLR1 regulatory network by combined experimental and computational approaches, Molecular BioSystems, 6(12), pp. 2471-2481, Nov. 2010, RCS Publishing. [DOI link]
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  • Susana Vinga and Ana Rute Neves and Helena Santos and B. W. Brandt and S. A. L. M. Kooijman, Subcellular metabolic organization in the context of Dynamic Energy Budget and Biochemical Systems theories, Philosophical Transactions of the Royal Society B, 365(1557), pp. 3429-42, Nov. 2010, . [DOI link]
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  • Andreas Wichert and Pedro Teixeira and Pedro Santos and Helena Galhardas, Subspace tree: High dimensional multimedia indexing with logarithmic temporal complexity, Journal of Intelligent Information Systems, 35(3), pp. 495-516, Nov. 2010, Springer. [DOI link]
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  • Nuno D. Mendes and Ana T. Freitas and Ana T. Vasconcelos and Marie-France Sagot, Combination of measures distinguishes pre-miRNAs from other stem-loops in the genome of the newly sequenced Anopheles darlingi, BMC Genomics, (), pp. 11:529, Oct. 2010, . [DOI link]
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  • Ana Sofia Graça and Inês Lynce and Joao Marques Silva and Arlindo L. Oliveira, Haplotype Inference by Pure Parsimony: a Survey, Journal of Computational Biology, 17(8), pp. 969–992, Aug. 2010, Mary Ann Liebert, Inc.. [DOI link]
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  • Alexandre Domingues and Susana Vinga and J. M. Lemos, Optimization strategies for metabolic networks, BMC Systems Biology, 4(), pp. 113, Aug. 2010, . [DOI link]
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  • Marielba Silva Zacarias and Rodrigo Magalhães and H. Sofia Pinto and José Manuel Nunes Salvador Tribolet, Defining an Architectural View for Human Resources, IJBIS – International Journal of Business Information Systems, Special Issue on the Design and Engineering of Human Reso, 5(2), pp. 121-133, Jun. 2010, .
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  • Cátia M. Machado and Francisco Couto and Alexandra R. Fernandes and Susana Santos and Nuno Cardim and Ana T. Freitas, Unraveling Hypertrophic Cardiomyopathy Variability, ERCIM NEWS, 82(), pp. 48-49, Jun. 2010, ERCIM.
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  • José Borbinha, SHAMAN – Sustaining Heritage Access through Multivalent Archiving, ERCIM News, to appear.
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  • Daniela Nitsch and Joana P. Gonçalves and Fabian Ojeda and Bart De Moor and Yves Moreau, Candidate gene prioritization by network analysis of differential expression using machine learning approaches, BMC Bioinformatics, 11(460), pp. , Sep. 2010, BioMed Central. Article [DOI link]
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  • Thierson Couto and Nivio Ziviani and Pável Calado and Marco Cristo and Marcos André Gonçalves and Edleno S. de Moura and Wladimir Brandão, Classifying documents with link-based bibliometric measures, Information Retrieval, 13(4), pp. 315–345, Aug. 2010, . Article [DOI link]
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  • Ignacio Medina and Jose Carbonell and Luis Pulido and Sara C. Madeira and Stefan Goetz and Ana Conesa and Joaquin Tarraga and Alberto Pascual-Montano and Ruben Nogales-Cadenas and Javier Santoyo and Francisco Garcia and Martina Marba and David Montaner and Joaquin Dopazo, Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling, Nucleic Acids Research, 38(), pp. W210-W213, Jul. 2010, Oxford Journals. Article [DOI link]
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  • Artur Caetano and António Rito Silva and José Manuel Nunes Salvador Tribolet, Business Process Decomposition – An Approach Based on the Principle of Separation of Concerns, Enterprise Modelling and Information Systems Architecture Journal – An International Journal, Special Issue on Methodo, 5(1), pp. , Jul. 2010, SIG MOBIS (Special Interest Group on Modelling Business Info.
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  • Marielba Zacarias and H. Sofia Pinto and Rodrigo Magalhães and José Manuel Nunes Salvador Tribolet, A “context aware” and agent-centric perspective for the alignment between individuals and organizations, Information Systems Journal – Vocabularies, Ontologies and Rules for Enterprise and Business Process Modeling and Manag, 35(4), pp. 441-466, Jun. 2010, Elsevier Science Publisher. [DOI link]
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  • João Saraiva and Alberto Rodrigues da Silva, A Reference Model for the Analysis and Comparison of MDE Approaches for Web-Application Development, Journal of Software Engineering and Applications, 3(), pp. 419-425, May. 2010, Scientific Research Publishing. [DOI link] Supplementary Material
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  • Sara C. Madeira and Miguel C. Teixeira and Isabel Sá Correia and Arlindo L. Oliveira, Identification of Regulatory Modules in Time Series Gene Expression Data using a Linear Time Biclustering Algorithm, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7(1), pp. 153-165, Jan. 2010, IEEE/ACM. [DOI link]
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  • José Barateiro and Gonçalo José Branquinho Antunes and Filipe Bastos de Freitas and José Borbinha, Designing Digital Preservation Solutions: A Risk Management-Based Approach, International Journal of Digital Curation, to appear. UKOLN Article
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  • Luís M. S. Russo and Gonzalo Navarro and Arlindo L. Oliveira and Pedro Morales, Approximate String Matching with Compressed Indexes, Algorithms, 2(3), pp. 1105-1136, Sep. 2009, . Article [DOI link]
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  • Luis Lapão and Álvaro Rebuge and Miguel Mira da Silva and Rui Gomes, ITIL Assessment in a Healthcare Environment, Studies in Health Technology and Informatics, 150(1), pp. 76-80, Aug. 2009, IOS Press.
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  • Patricia Silva and Alberto Rodrigues da Silva, Application Scenarios for the Learning Objects Pool, Journal of Universal Computer Science, 15(7), pp. pp. 1455-147, Jul. 2009, .
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  • Francisco Fernandes and Luisa Pereira and Ana T. Freitas, CSA: An efficient algorithm to improve circular DNA multiple alignment, BMC Bioinformatics, 10(), pp. 230, Jul. 2009, BioMed Central. [DOI link]
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  • Andreas Wichert and Pedro Santos and Helena Galhardas, Panoramix: a content-based health record system, Internal Journal of Computer Assisted Radiology and Surgery, 4(), pp. 152, Jun. 2009, Springer. [DOI link]
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  • Francisco Fernandes and Ana T. Freitas and Jonas S. Almeida and Susana Vinga, Entropic Profiler – Detection of conservation in genomes using Information Theory, BMC Research Notes, 2(72), pp. , May. 2009, . Article
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  • Pedro T. Monteiro and Estelle Dumas and Bruno Besson and Radu Mateescu and Michel Page and Ana T. Freitas and Hidde de Jong, A service-oriented architecture for integrating the modeling and verification of genetic regulatory networks, BMC Bioinformatics, 10(450), pp. , Dec. 2009, BioMed Central. [DOI link]
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  • Joana P. Gonçalves and Mário Grãos and André X. C. N. Valente, Polar Mapper: a computational tool for integrated visualization of protein interaction networks and mRNA expression data, Journal of the Royal Society Interface, 6(39), pp. 881-896, Oct. 2009, Royal Society Publishing. Article [DOI link] Supplementary Material
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  • Joana P. Gonçalves and Sara C. Madeira and Arlindo L. Oliveira, BiGGEsTS: integrated environment for biclustering analysis of time series gene expression data, BMC Research Notes, 2(124), pp. , Jul. 2009, BioMed Central. Article [DOI link]
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  • Sara C. Madeira and Arlindo L. Oliveira, A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series, Algorithms for Molecular Biology, 4(8), pp. , Jun. 2009, BioMed Central. Article [DOI link]
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  • Nuno D. Mendes and Ana T. Freitas and Marie-France Sagot, Current tools for the identification of miRNA genes and their targets, Nucleic Acids Research, 8(37), pp. 2419-2433, May. 2009, . Article [DOI link] Supplementary Material
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  • A. P. Francisco and Miguel Bugalho and Mário Ramirez and João Carriço, Global optimal eburst analysis of multilocus typing data using a graphic matroid approach, BMC Bioinformatics, 10(1), pp. 152, May. 2009, BioMed Central Ltd. Article [DOI link]
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  • Marco Vilela and Susana Vinga and Marco A Grivet Mattoso Maia and Eberhard O Voit and Jonas S. Almeida, Identification of neutral biochemical network models from time series data, BMC Systems Biology, 3(), pp. 47, May. 2009, . Article [DOI link]
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  • Jonas S. Almeida and Susana Vinga, Biological sequences as pictures – a generic two dimensional solution for iterated maps, BMC Bioinformatics, 10(), pp. 100, Mar. 2009, . [DOI link]
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  • Paula Cristina Negrão Ventura Martins and Alberto Rodrigues da Silva, ProPAM: discussion for a new SPI approach, Software Quality Professional Journal, 11(), pp. , Feb. 2009, American Society for Quality.
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  • Marielba Zacarias and H. Sofia Pinto and Patricio Serendero and José Manuel Nunes Salvador Tribolet, Capturing and Modelling Work Practice, Revue de Intelligence Artificielle, 22(5), pp. 669, Oct. 2008, .
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  • João Saraiva and Alberto Rodrigues da Silva, Evaluation of MDE tools from a Metamodeling Perspective, Journal of Database Management, 19(4), pp. 50-75, Oct. 2008, IGI Publishing.
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  • Luís M. S. Russo and Arlindo L. Oliveira, A Compressed Self-Index using a Ziv-Lempel Dictionary, Information Retrieval, 11(4), pp. 359-388, Aug. 2008, Springer. [DOI link]
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  • Andreas Wichert and João Carlos Serrenho Dias Pereira and Paulo Jorge Fernandes Carreira, Visual search light model for mental problem solving, Neurocomputing, 71(13), pp. 2806-2822, Jun. 2008, . [DOI link]
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  • Marco Vilela and I-Chun Chou and Susana Vinga and Ana Tereza R. Vasconcelos and Eberhard O. Voit and Jonas S. Almeida, Parameter optimization in S-system models, BMC Systems Biology, 2(), pp. 35, Apr. 2008, BiomedCentral. [DOI link]
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  • Edleno S. de Moura and Célia F. dos Santos and Bruno S. de Araújo and Altigran S. da Silva and Pável Calado and Mário A. Nascimento, Locality based pruning methods for web search, ACM Transactions on Information Systems, 26(2), pp. , Mar. 2008, ACM. Article
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  • Daniel Gomes and Mário J. Silva, The Viúva Negra crawler: an experience report, Software: Practice and Experience (SPE) , 38(2), pp. 161-168, Feb. 2008, Wiley. [DOI link]
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  • Miguel Bugalho and Arlindo L. Oliveira, Constant Time Clash Detection in Protein Folding, Journal of Bioinformatics and Computational Biology, 7(1), pp. 55-74, Feb. 2009, World Scientific. Article [DOI link]
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  • Carlos Alberto Lourenço dos Santos and Pedro Manuel Moreira Vaz Antunes de Sousa and C. Ferreira and José Manuel Nunes Salvador Tribolet, Conceptual Model for Continuous Organizational Auditing with Real Time Analysis and Modern Control Theory, JOURNAL OF EMERGING TECHNOLOGIES IN ACCOUNTING, 5(), pp. 37-63, Dec. 2008, .
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  • André Ferreira Ferrão Couto e Vasconcelos and Pedro Manuel Moreira Vaz Antunes de Sousa and José Manuel Nunes Salvador Tribolet, Enterprise Architecture Analysis – An Information System Evaluation Approach, Enterprise Modelling and Information Systems Architectures – EMISA Special Issue 2008, (), pp. , Dec. 2008, .
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  • Pedro T. Monteiro and Delphine Ropers and Radu Mateescu and Ana T. Freitas and Hidde de Jong, Temporal Logic Patterns for Querying Dynamic Models of Cellular Interaction Networks, Bioinformatics, 24(16), pp. i227-i233, Aug. 2008, . Article [DOI link]
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  • Duarte Oliveira and Mauro Santos and Catarina Milheiriço and João Carriço and Susana Vinga and Arlindo L. Oliveira and Hermínia de Lencastre, ccrB Typing Tool: An online resource for staphylococci ccrB sequence, Journal of Antimicrobial Chemotherapy, 58(1), pp. 959-960, Apr. 2008, . [DOI link]
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  • Christoph Tempich and Elena Simperl and Markus Luczak and Rudi Studer and H. Sofia Pinto, Argumentation-based Ontology Engineering, IEEE Intelligent Systems, 22(6), pp. 52-59, Dec. 2007, IEEE. [DOI link]
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  • Alberto Rodrigues da Silva and João Saraiva and David Ferreira and Rui Silva and Carlos Videira, Integration of RE and MDE Paradigms: The ProjectIT Approach and Tools, IET Software Journal, (), pp. 21, Dec. 2007, IET.
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  • Rodrigo Magalhães and Marielba Silva Zacarias and José Manuel Nunes Salvador Tribolet, Making Sense of Entreprise Architectures as Tools of Organizational Self- Awareness, Journal of Entreprise Architecture, 3(4), pp. 64-72, Nov. 2007, Association of Entreprise Architects.
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  • Ana Casimiro and Susana Vinga and Ana T. Freitas and Arlindo L. Oliveira, An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance, BMC Bioinformatics, 9(), pp. 89, Feb. 2008, BiomedCentral. Article [DOI link]
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  • Nuno A. Faria and João Carriço and Duarte C. Oliveira and Mário Ramirez and Hermínia de Lencastre, Analysis of typing methods for epidemiological surveillance of both methicillin-resistant and susceptible Staphylococcus aureus, Journal of Clinical Microbiology, 46(1), pp. 136-44, Jan. 2008, American Society for Microbiology.
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  • Maria Miragaia and João Carriço and J.C. Thomas and Isabel Couto and M.C. Enright and Hermínia de Lencastre, Comparison of molecular typing methods for characterization of Staphylococcus epidermidis: a proposal for clone definition, Journal of Clinical Microbiology, 46(1), pp. 118-29, Jan. 2008, American Society for Microbiology.
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  • Raquel Sá-Leão and Sónia Nunes and António Brito-Avô and Carla R. Alves and João Carriço and Joana Saldanha and Jonas S. Almeida and Ilda Santos-Sanches and Hermína de Lencastre, High dynamics of transmission and colonization by Streptococcus pneumoniae and Haemophilus influenzae within a day-care center revealed in a longitudinal study, Journal of Clinical Microbiology, 46(1), pp. 1225-34, Jan. 2008, American Society for Microbiology.
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  • André Martins and H. Sofia Pinto and Arlindo L. Oliveira, Using Grammatical Inference Techniques to Learn Ontologies that Describe the Structure of Domain Instances, Applied Artificial Intelligence, 22(1), pp. 139-167, Jan. 2008, Taylor & Francis. [DOI link]
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  • José Borbinha and Hugo Miguel Álvaro Manguinhas and Nuno Miguel Antunes Freire, UNIMARC Registry, International Cataloguing and Bibliographic Control, 36(4), pp. 74-77, Nov. 2007, IFLA – International Federation of Libraries Associations.
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  • Susana Vinga and Jonas S Almeida, Local Renyi entropic profiles of DNA sequences, BMC Bioinformatics, 8(), pp. 393, Oct. 2007, . [DOI link]
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  • Luís M. S. Russo and Arlindo L. Oliveira, Efficient generation of super condensed neighborhoods, Journal of Discrete Algorithms, 5(3), pp. 501-513, Sep. 2007, Elsevier. [DOI link]
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  • Pedro T. Monteiro and Nuno D. Mendes and Miguel C. Teixeira and Sofia Orey and Sandra Tenreiro and Nuno Mira and Hélio Pais and A. P. Francisco and Alexandra M. Carvalho and Artur Lourenço and Isabel Sá-Correia and Arlindo L. Oliveira and Ana T. Freitas, YEASTRACT-DISCOVERER: new tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae, Nucleic Acids Research, 36(), pp. D132-D136, Jan. 2008, Oxford University Press. Article [DOI link]
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  • Paulo Jorge Fernandes Carreira and Helena Galhardas and Antónia Lopes and João Carlos Serrenho Dias Pereira, One-to-many data transformations through data mappers, Data & Knowledge Engineering, 62(3), pp. 483-503, Sep. 2007, Elsevier. Article [DOI link]
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  • Paula Cristina Negrão Ventura Martins and Alberto Rodrigues da Silva, A case study applying Process and Project Alignment Methodology, JBCS – Journal of the Brazilian Computer Society, 12(3), pp. 65-82, Dec. 2006, SBC – Brazilian Computer Society.
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  • Marco Vilela and Carlos C.H Borges and Susana Vinga and Ana Tereza R Vanconcelos and Helena Santos and Eberhard O Voit and Jonas S Almeida, Automated smoother for the numerical decoupling of dynamics models, BMC Bioinformatics, 8(), pp. 305, Aug. 2007, . [DOI link]
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  • Filipe Mesquita and Altigran S. da Silva and Edleno S. de Moura and Pável Calado and Alberto H. F. Laender, LABRADOR: Efficiently publishing relational databases on the Web by using keyword-based query interfaces, Information Processing & Management, 43(4), pp. 983–1004, Jul. 2007, Elsevier.
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  • André Ferreira Ferrão Couto e Vasconcelos and Pedro Manuel Moreira Vaz Antunes de Sousa and José Manuel Nunes Salvador Tribolet, Information System Architecture Metrics: An Enterprise Engineering Evaluation Approach, The Electronic Journal Information Systems Evaluation, 10(1), pp. 91-122, Jun. 2007, .
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  • Francisco R Pinto and João Carriço and Mário Ramirez and Jonas S. Almeida, Ranked Adjusted Rand: integrating distance and partition information in a measure of clustering agreement, BMC Bioinformatics, 8(44), pp. , Feb. 2007, Biomed Central. Article Supplementary Material
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  • Jonas S Almeida and Susana Vinga, Computing distribution of scale independent motifs in biological sequences., Algorithms Mol Biol., 1(), pp. 18, Oct. 2006, .
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  • Pável Calado and Marco Cristo and Marcos André Gonçalves and Edleno S. de Moura and Berthier Ribeiro-Neto and Nivio Ziviani, Link-based similarity measures for the classification of web documents, Journal of the American Society for Information Science and Technology, 57(2), pp. 208-221, Jan. 2006, .
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  • Denny Vrandecic and H. Sofia Pinto and York Sure and Christoph Tempich, The DILIGENT Knowledge Processes, Journal of Knowledge Management, 9(5), pp. 85-96, Oct. 2005, EmeraldInsight.
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  • Nuno D. Mendes and Ana Casimiro and Pedro M. Santos and Isabel Sá-Correia and Arlindo L. Oliveira and Ana T. Freitas, MUSA: a parameter free algorithm for the identification of biologically significant motifs, Bioinformatics, 22(24), pp. 2996-3002, Dec. 2006, Oxford Journals. Article [DOI link]
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  • Jorge Pena and Arlindo L. Oliveira, A new algorithm for exact reduction of incompletely specified finite state machines, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems , 18(11), pp. 1619-1632, Nov. 2006, IEEE. Article [DOI link]
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  • Duarte C. Oliveira and Catarina Milheiriço and Susana Vinga and Herminia de Lencastre, Assessment of allelic variation in the ccrAB locus in methicillin-resistant Staphylococcus aureus clones, Journal of Antimicrobial Chemotherapy, 58(1), pp. 23-30, Jul. 2006, .
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  • Alexandra M. Carvalho and Ana T. Freitas and Arlindo L. Oliveira and Marie-France Sagot, An Efficient Algorithm for the Identification of Structured Motifs in DNA Promoter Sequences, IEEE Transactions on Computational Biology and Bioinformatics, 3(2), pp. 126-140, Apr. 2006, IEEE. Article [DOI link]
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  • Miguel C. Teixeira and Pedro T. Monteiro and Pooja Jain and Sandra Tenreiro and Alexandra R. Fernandes and Nuno P. Mira and Marta Alenquer and Ana T. Freitas and Arlindo L. Oliveira and Isabel Sá-Correia, The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae, Nucleic Acids Research, 34(), pp. D446-D451, Jan. 2006, Oxford Journals. Article [DOI link]
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  • José Eduardo Barateiro and Helena Galhardas, A survey of data quality tools, Datenbank-Spektrum, (14), pp. 15-21, Aug. 2005, dpunkt.verlag.
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  • José Borbinha and John Kunze and Angela Spinazzè and Peter Mutschke and Hans-Jörg Lieder and Michael Mabe and Larry Dixson and Howard Besser and Becky Dean and Warwick Cathro, Reference models for digital libraries: actors and roles, International Journal on Digital Libraries, 5(4), pp. 325-330, Aug. 2005, Springer-Verlaag.
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  • Susana Vinga and Jonas S Almeida, Renyi continuous entropy of DNA sequences, Journal of Theoretical Biology, 231(3), pp. 377-88, Dec. 2004, .
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  • José Borbinha, An approach to creating a national digital library, International Journal on Digital Libraries, 4(1), pp. 19-22, Aug. 2004, Springer-Verlaag.
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  • Miguel Bugalho and Arlindo L. Oliveira, Inference of regular languages using state merging algorithms with search, Pattern Recognition, 38(9), pp. 1457-1467, Sep. 2005, Elsevier. Article [DOI link]
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  • Ana Rocheta Gomes and Susana Vinga and Mihaela Zavolan and Herminia de Lencastre, Analysis of the genetic variability of virulence-related loci in epidemic clones of methicillin-resistant Staphylococcus aureus, Antimicrob Agents Chemother, 49(1), pp. 366-79, Jan. 2005, .
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  • José Borbinha, Authority Control in the World of Metadata, Cataloguing & Classification Quarterly, 38(3), pp. 105-116, Jul. 2004, Haworth Information Press.
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  • H. Sofia Pinto and João P. Martins, Ontologies: How Can They Be Built?, Knowledge and Information Systems, 6(4), pp. 441-464, Jul. 2004, Springer Verlag.
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  • Pável Calado and Altigran Silva and Rodrigo Vieira and Alberto Laender and Berthier Ribeiro-Neto, A bayesian network approach to searching databases through keyword-based queries, Information Processing & Management, 40(5), pp. 773-790, Apr. 2004, .
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  • Tatiana Coelho and Pável Calado and Lamarque Souza and Berthier Ribeiro-Neto, Image retrieval using multiple evidence ranking, IEEE Transactions on Knowledge and Data Engineering, 16(4), pp. 408-417, Apr. 2004, .
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  • Sara C. Madeira and Arlindo L. Oliveira, Biclustering algorithms for biological data analysis: a survey, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1(1), pp. 24-45, Jan. 2004, IEEE/ACM. Article [DOI link]
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  • Susana Vinga and Rodrigo Gouveia-Oliveira and Jonas S Almeida, Comparative evaluation of word composition distances for the recognition of SCOP relationships, Bioinformatics, 20(2), pp. 206-15, Jan. 2004, .
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  • Marco Cristo and Pável Calado and Ilmério Silva and Maria de Lourdes da Silveira and Richard Muntz and Berthier Ribeiro-Neto, Bayesian belief networks for IR, International Journal Of Approximate Reasoning, 34(2), pp. 163-179, Nov. 2003, .
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  • Elsa Alexandra Cabral da Rocha Cardoso and Helena Galhardas and Maria José Trigueiros and António Rito Silva, A Decision Support System for IST Academic Information, Informatica – Int. Journal of Computing and Informatics, Special issue, 27(3), pp. , Oct. 2003, Slovene Society Informatika.
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  • Arlindo L. Oliveira and Rajeev Murgai, On the Problem of Gate Assignment Under Different Rise and Fall Delays, IEEE Transactions on Computer Aided Design, 22(11), pp. 807–814, Jun. 2003, IEEE. Article [DOI link]
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  • Susana Vinga and Jonas Almeida, Alignment-free sequence comparison-a review, Bioinformatics, 19(4), pp. 513-23, Mar. 2003, .
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  • Pável Calado and Berthier Ribeiro-Neto, An information retrieval approach for approximate queries, IEEE Transactions on Knowledge and Data Engineering, 15(1), pp. 236-239, Jan. 2003, .
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  • Pável Calado and Berthier Ribeiro-Neto and Nivio Ziviani and Edleno Moura and Ilmério Silva, Local versus global link information in the Web, ACM Transactions On Information Systems, 21(1), pp. 42-63, Jan. 2003, .
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  • J. Monteiro and Arlindo L. Oliveira, Implicit FSM Decomposition Applied To Low Power Design, IEEE Transactions on Very Large Scale Integration Systems, 10(5), pp. 560-565, Oct. 2002, IEEE Press. Article [DOI link]
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  • Jonas S Almeida and Susana Vinga, Universal sequence map (USM) of arbitrary discrete sequences, BMC Bioinformatics, 3(), pp. 6, Feb. 2002, .
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  • Arlindo L. Oliveira, Techniques For The Creation Of Digital Watermarks In Sequential Circuit Designs, IEEE Transactions on Computer Aided Design, 20(9), pp. 1101-1117, Sep. 2001, IEEE. Article [DOI link]
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  • Alberto Rodrigues da Silva and Artur Manuel Pereira Romão and Dwight Deugo and Miguel Mira da Silva, Towards a Reference Model for Surveying Mobile Agent Systems, Autonomous Agents and Multi-Agent Systems Journal, 4(3), pp. 187-231, Sep. 2001, Kluwer Academic Publishers.
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  • Arpírez Vega Júlio César and Assunción Gómez-Pérez and Adolfo Lozano Tello and H. Sofia Pinto, Reference Ontology and (ONTO)2Agent: The Ontology Yellow Pages, Knowledge and Information Systems, 2(4), pp. 387-412, Nov. 2000, Springer Verlag.
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  • Artur Manuel Pereira Romão and Miguel Mira da Silva and Alberto Rodrigues da Silva, Secure Electronic Payments Based on Mobile Agents, Journal of Distributed and Parallel Databases, 8(4), pp. 447-470, Oct. 2000, Kluwer Academic Publishers.
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  • Arlindo L. Oliveira and Joao Marques Silva, Efficient Algorithms For The Inference Of Minimum Size DFAs, Machine Learning, 44(1), pp. 93-119, Jul. 2001, Kluwer Academic Publishers. Article [DOI link]
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  • J. G. Pena and Arlindo L. Oliveira, A new algorithm for exact reduction of incompletely specified finite state machines, IEEE Transactions on Computer Aided Design, 18(11), pp. 1619–1632, Nov. 1999, IEEE. Article [DOI link]
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  • Arlindo L. Oliveira and Luca Carloni and Tiziano Villa and Alberto Sangiovanni-Vincentelli, Exact Minimization of Binary Decision Diagrams Using Implicit Techniques, IEEE Transactions on Computers, 47(11), pp. 1282-1296, Nov. 1998, IEEE Press. Article [DOI link]
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  • José Borbinha and José Carlos Martins Delgado, Networked Digital Libraries, Microcomputers for Information Management, to appear. Ablex Publishing, USA
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  • Arlindo L. Oliveira and A. Sangiovanni-Vincentelli, Using the minimum description length principle to infer reduced ordered decision graphs, Machine Learning, 25(1), pp. 23–50, Jan. 1996, Kluwer. Article [DOI link]
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  • Peter ten Berge and Thomas S. Plaskett and Hans J. Boeve and G. Albuquerque and João Ferreira and Anabela R. Morais and José L. Leal and Nuno J. Oliveira and Ana T. Freitas and Luís M. Rodrigues and Paulo P. Freitas, Spin-valve MR heads for tape and disk Applications, IEEE Transactions on Magnetics, 30(6), pp. 2603-2608, Nov. 1995, IEEE.
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  • José L. Leal and Luís M. Rodrigues and Ana T. Freitas and Paulo P. Freitas, Narrow trackwidth TbCo-biased magnetoresistive spin-valve sensors, Journal of Magnetism and Magnetic Materials, 140(3), pp. 2215-2216, Aug. 1995, Elsevier.
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  • José L. Leal and Nuno J. Oliveira and Luís M. Rodrigues and Ana T. Freitas and Paulo P. Freitas, Unshielded spin-valve sensors exchange-biased by thin TbCo layers, IEEE Transactions on Magnetics,, 30(6), pp. 3831-3833, Nov. 1994, IEEE.
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  • Paulo P. Freitas and José L. Leal and Nuno J. Oliveira and Luís V. Melo and Luís M. Rodrigues and Ana T. Freitas, Spin-valve sensors exchange-biased by ultra-thin TbCo films, Application Physics Letters, 65(4), pp. 493-495, Jul. 1994, American Institute of Physics.
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  • Pedro Manuel Moreira Vaz Antunes de Sousa and André Ventura da Cruz Marnôto Zúquete and Nuno Neves and José Alves Marques, Orthogonal Persistence in a Heterogeneous Distributed Object-Oriented Environment, The Computer Journal, to appear. Oxford University Press
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  • Pedro Manuel Moreira Vaz Antunes de Sousa and Manuel Sequeira and André Ventura da Cruz Marnôto Zúquete and Paulo Ferreira and Cristina Lopes and Paulo Jorge Tavares Guedes and José Alves Marques, Distribution and Persistence in the IK Platform: Overview and Evaluation, Usenix Computing Systems, 6(4), pp. 391-424, Nov. 1993, .
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