Journal Articles 2020(2 publications) [publication]Lucas, P. and Silva, J. and Araujo, F. and Silva, C. and P. Gil and Arrais, J.P. and Coutinho, D. and Salgueiro, P. and Rato, L. and Saias, J. and Nogueira, V. and Alberto Cardoso and Ribeiro, B. , "NanoSen-AQM: From Sensors to Users", International Journal of Online and Biomedical Engineering (iJOE), vol. 16, 2020 [publication]Nelson R. C. Monteiro and Ribeiro, B. and Arrais, J.P. , "Drug-Target Interaction Prediction: End-to-End Deep Learning Approach", IEEE/ACM Transactions on Computational Biology and Bioinformatics, pp. 1-1, 2020 2019(2 publications) [publication]Correia, F.B. and Oliveira, J.L. and Arrais, J.P. , "Handling noise in protein interaction networks", BioMed Research International, vol. 2019, 2019 [publication]Cruz, A. and Penousal Machado and Arrais, J.P. , "CroP—Coordinated Panel visualization for biological networks analysis", Bioinformatics, 2019 2018(3 publications) [publication]Cruz, I. and Correia, M. and Barros, M. and rosa, n. and Arrais, J.P. , "SalivaPRINT Toolkit--Protein profile evaluation and phenotype stratification", Journal of proteomics, vol. 171, pp. 81-86, 2018 [publication]Cruz, A. and Arrais, J.P. and Penousal Machado , "Interactive and coordinated visualization approaches for biological data analysis", Briefings in bioinformatics, 2018 [publication]Cruz, A. and Arrais, J.P. and Penousal Machado , "Interactive and coordinated visualization approaches for biological data analysis", Briefings in Bioinformatics, 2018 2017(2 publications) [publication]Ribeiro, B. and Oliveira, G. and Laranjeira, A.F.F. and Arrais, J.P. , "Deep Learning in Digital Marketing: Brand Detection and Emotion Recognition", Machine Intelligence and Sensory Signal Processing, InderScience Publishers, vol. 2, pp. 32-50, 2017 [publication]Arrais, J.P. and Correia, M. and Barros, M. and rosa, n. , "New Targets for Zika Virus Determined by Human-Viral Interactomic: A Bioinformatics Approach", BioMed Research International, vol. 2017, 2017 2016(3 publications) [publication]Coelho, E.D. and Arrais, J.P. and Oliveira, J.L. , "Computational Discovery of Putative Leads for Drug Repositioning through Drug-Target Interaction Prediction", PLOS Computational Biology, 2016 [publication]Arrais, J.P. , "Reconstructing the temporal progression of HIV-1 immune response pathways", Bioinformatics, vol. 32, pp. 253-253, 2016 [publication]Correia, M. and rosa, n. and Arrais, J.P. and Barros, M. , "CanisOme—The protein signatures of Canis lupus familiaris diseases", Journal of proteomics, vol. 136, pp. 193-201, 2016 [citation][year=2016]I Katsafadou, Angeliki, et al. "Applied Proteomics in Companion Animal Medicine." Current Proteomics 13.3 (2016): 165-171. [citation][year=2016]Myers, Michael J., Emily R. Smith, and Phillip G. Turfle. "Biomarkers in Veterinary Medicine." Annual Review of Animal Biosciences 0 (2016). [citation][year=2016]Ceciliani, F., et al. "Application of post-genomic techniques in dog cancer research." Molecular BioSystems 12.9 (2016): 2665-2679. 2015(2 publications) [publication]Coelho, E.D. and Oliveira, J.L. and Santiago, A. and Arrais, J.P. , "Computational methodology for predicting the landscape of the human–microbial interactome region level influence", Journal of bioinformatics and computational biology, vol. 13, pp. 1550023, 2015 [citation][year=2016]Gomes, Francisco Isaac Fernandes, et al. "Inflammatory Cytokines Interleukin-1? and Tumour Necrosis Factor-?-Novel Biomarkers for the Detection of Periodontal Diseases: a Literature Review." Journal of Oral & Maxillofacial Research 7.2 (2016). [citation][year=2016]Sousa, Luzia Hermínia, et al. "Effects of atorvastatin on periodontitis of rats subjected to glucocorticoid-induced osteoporosis." Journal of periodontology 87.10 (2016): 1206-1216. [citation][year=2015]Marques, Jéssica Raquel Cortez. In search of the molecular profile characteristic of attention deficit hyperactivity disorder and of dyslexia. MS thesis. Universidade de Aveiro, 2015. [citation][year=2015]Serra, Beatriz Patrício. Identificação de biomarcadores salivares de doença periodontal em pacientes com gengivite. Diss. 2015. [citation][year=2015]Hortênsio, Andreia Soraia Pinto. Identificação de biomarcadores salivares de doença periodontal em pacientes com diabetes mellitus tipo 2. Diss. 2015. [publication]Arrais, J.P. and Oliveira, J.L. , "RecRWR: A Recursive Random Walk Method for Improved Identification of Diseases", BioMed research international, 2015 [citation][year=2015]Yuan, Jie, et al. "Predicting disease genes based on normalized protein modules and phenotype ontology." Bioinformatics and Biomedicine (BIBM), 2015 IEEE International Conference on. IEEE, 2015. 2014(3 publications) [publication]Coelho, E.D. and Arrais, J.P. and Oliveira, J.L. and rosa, n. and Correia, M. and Matos, S. and Pereira, C. , "Computational prediction of the human-microbial oral interactome", BMC Systems Biology, 2014 [citation][year=2016]Leite, Diogo Manuel Carvalho. Modélisation prédictive des interactions entre bactéries et virus bactériophages. Diss. 2016. [citation][year=2016]Campo Nieves, Livia. Aplicación de técnicas bioinformáticas en la predicción de fracasos endodónticos por fracturas radiculares verticales. Diss. Universidad Complutense de Madrid, 2016. [citation][year=2016]Vala, Helena, and Marlene Barros. "CanisOme—The protein signatures of Canis lupus familiaris diseases." (2016). [citation][year=2016]Fernandes, Mónica, et al. "CanisOme—The protein signatures of Canis lupus familiaris diseases." Journal of proteomics 136 (2016): 193-201. [citation][year=2016]Coelho, Edgar D., Joel P. Arrais, and José Luís Oliveira. "Ensemble-Based Methodology for the Prediction of Drug-Target Interactions." Computer-Based Medical Systems (CBMS), 2016 IEEE 29th International Symposium on. IEEE, 2016. [citation][year=2015]Nourani, Esmaeil, Farshad Khunjush, and Saliha Durmu?. "Computational approaches for prediction of pathogen-host protein-protein interactions." Frontiers in microbiology 6 (2015): 94. [citation][year=2015]Perdiz Arrais, Joel, and José Luís Oliveira. "RecRWR: a recursive random walk method for improved identification of diseases." BioMed research international 2015 (2015). [citation][year=2015]Coelho, Edgar D., et al. "Computational methodology for predicting the landscape of the human–microbial interactome region level influence." Journal of bioinformatics and computational biology 13.05 (2015): 1550023. [citation][year=2015]Kaur, Navneet, et al. "Screening the Drug Resistance Property Among Aerobic Pathogenic Microorganisms of Dental Caries in North-Western Indian Population: A Preliminary Study." Journal of clinical and diagnostic research: JCDR 9.7 (2015): ZC05. [citation][year=2015]Rizzetto, Lisa, Carlotta De Filippo, and Duccio Cavalieri. "Mycobiota: Micro-Eukaryotes Inhabiting Our Body as Commensals or Opportunistic Pathogens." Fungal Genomics & Biology 5.1 (2015): 1. [citation][year=2015]Luiz Folador, Edson, et al. "In Silico Protein-Protein Interactions: Avoiding Data and Method Biases Over Sensitivity and Specificity." Current Protein and Peptide Science 16.8 (2015): 689-700. [citation][year=2015]Lopes, Sara Filipa Nunes. Interatómica da cavidade oral-oralint V2. 0. Diss. 2015. [citation][year=2015]Lourenço, Ana Carolina Fernandes. Identificação na saliva de biomarcadores de suscetibilidade à cárie dentária. Diss. 2015. [citation][year=2014]Soares, André do Nascimento Gonçalves. Interatómica da cavidade oral. Diss. Universidade Católica Portuguesa, 2014. [citation][year=2014]Fernandes, Mónica Figueiredo. Biomarkers in Canis lupus familiaris. MS thesis. Universidade de Aveiro, 2014. [citation][year=2014]Folador, Edson Luiz, et al. "An improved interolog mapping-based computational prediction of protein–protein interactions with increased network coverage." Integrative Biology 6.11 (2014): 1080-1087. [publication]Oliveira, J.L. and Arrais, J.P. , "geneCommittee: a web-based tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification", BMC bioinformatics, 2014 [citation][year=2016]Nguyen, Thanh, and Saeid Nahavandi. "Modified AHP for gene selection and cancer classification using type-2 fuzzy logic." IEEE Transactions on Fuzzy Systems 24.2 (2016): 273-287. [citation][year=2016]Jin, Cong, and Shu-Wei Jin. "Gene selection approach based on improved swarm intelligent optimisation algorithm for tumour classification." IET systems biology 10.3 (2016): 107-115. [citation][year=2016]Chowdhury, Linkon, et al. "MetaG: a graph-based metagenomic gene analysis for big DNA data." Network Modeling Analysis in Health Informatics and Bioinformatics 5.1 (2016): 1-16. [citation][year=2015]Nguyen, Thanh, et al. "Hierarchical gene selection and genetic fuzzy system for cancer microarray data classification." PloS one 10.3 (2015): e0120364. [publication]Arrais, J.P. and Oliveira, J.L. , "RecRWR: A Recursive Random Walk Method for Improved Identification of Diseases", BioMed Research International, 2014 2013(2 publications) [publication]Arrais, J.P. and Coelho, E.D. and Oliveira, J.L. , "From Protein-Protein Interactions to Rational Drug Design: Are Computational Methods Up to the Challenge?", Current Topics in Medicinal Chemistry, vol. 13, pp. 602-618, 2013 [citation][year=2017]Leney, Aneika C., and Albert JR Heck. "Native Mass Spectrometry: What is in the Name?." Journal of The American Society for Mass Spectrometry 28.1 (2017): 5-13. [citation][year=2016]Roukos, Dimitrios H. "Crossroad between linear and nonlinear transcription concepts in the discovery of next-generation sequencing systems-based anticancer therapies." Drug discovery today 21.4 (2016): 663-673. [citation][year=2015]Sable, Rushikesh, and Seetharama Jois. "Surfing the protein-protein interaction surface using docking methods: application to the design of PPI inhibitors." Molecules 20.6 (2015): 11569-11603.\ [citation][year=2015]Coelho, Edgar D., et al. "Computational methodology for predicting the landscape of the human–microbial interactome region level influence." Journal of bioinformatics and computational biology 13.05 (2015): 1550023. [citation][year=2015]Coelho, Edgar D., Joel P. Arrais, and José Luís Oliveira. "Uncovering microbial duality within human microbiomes: A novel algorithm for the analysis of host-pathogen interactions." Engineering in Medicine and Biology Society (EMBC), 2015 37th Annual International Conference of the IEEE. IEEE, 2015. [citation][year=2015]Zhu, Fei, et al. "Protein-protein interaction network constructing based on text mining and reinforcement learning with application to prostate cancer." Trustcom/BigDataSE/ISPA, 2015 IEEE. Vol. 1. IEEE, 2015. [citation][year=2014]Soares, André do Nascimento Gonçalves. Interatómica da cavidade oral. Diss. Universidade Católica Portuguesa, 2014. [citation][year=2013]Baaden, Marc, and Siewert J. Marrink. "Coarse-grain modelling of protein–protein interactions." Current opinion in structural biology 23.6 (2013): 878-886. [citation][year=2013]Huang, Sui, and Stuart Kauffman. "How to escape the cancer attractor: rationale and limitations of multi-target drugs." Seminars in cancer biology. Vol. 23. No. 4. Academic Press, 2013. [publication]Arrais, J.P. and Coelho, E.D. and Oliveira, J.L. and rosa, n. and Correia, M. , "OralCard: A bioinformatic tool for the study of oral proteome", Archives of Oral Biology, vol. 58, pp. 762-772, 2013 [citation][year=2016]Fernandes, Mónica, et al. "CanisOme—The protein signatures of Canis lupus familiaris diseases." Journal of proteomics 136 (2016): 193-201. [citation][year=2016]Rosa, Nuno, et al. "Protein Quality Assessment on Saliva Samples for Biobanking Purposes." Biopreservation and biobanking 14.4 (2016): 289-297. [citation][year=2016]Schweigel, Hardy, Michael Wicht, and Falk Schwendicke. "Salivary and pellicle proteome: A datamining analysis." Scientific Reports 6 (2016). [citation][year=2016]Vala, Helena, and Marlene Barros. "CanisOme—The protein signatures of Canis lupus familiaris diseases." (2016). [citation][year=2015]Bragazzi, Nicola Luigi, and Claudio Nicolini. "Lichen planus." Genomics, Personalized Medicine and Oral Disease. Springer International Publishing, 2015. 185-217. [citation][year=2015]Glurich, Ingrid, et al. "The Oral Microbiome and Its Relationship to Genomics and Oral Disease." Genomics, Personalized Medicine and Oral Disease. Springer International Publishing, 2015. 35-65. [citation][year=2015]Marques, Jéssica Raquel Cortez. In search of the molecular profile characteristic of attention deficit hyperactivity disorder and of dyslexia. MS thesis. Universidade de Aveiro, 2015. [citation][year=2015]Glurich, Ingrid, et al. "Progress in oral personalized medicine: contribution of ‘omics’." Journal of oral microbiology 7 (2015). [citation][year=2015]Lopes, Sara Filipa Nunes. Interatómica da cavidade oral-oralint V2. 0. Diss. 2015. [citation][year=2015]Lourenço, Ana Carolina Fernandes. Identificação na saliva de biomarcadores de suscetibilidade à cárie dentária. Diss. 2015. [citation][year=2015]Hortênsio, Andreia Soraia Pinto. Identificação de biomarcadores salivares de doença periodontal em pacientes com diabetes mellitus tipo 2. Diss. 2015. [citation][year=2014]Coelho, Edgar D., et al. "Computational prediction of the human-microbial oral interactome." BMC systems biology 8.1 (2014): 24. [citation][year=2014]Bragazzi, Nicola Luigi, Eugenia Pechkova, and Claudio Nicolini. "Proteomics and proteogenomics approaches for oral diseases." Adv Protein Chem Struct Biol 95 (2014): 125-162. [citation][year=2014]Rosa, Nuno, et al. "The landscape of protein biomarkers proposed for periodontal disease: markers with functional meaning." BioMed research international 2014 (2014). [citation][year=2014]Bragazzi, Nicola Luigi. "Nanogenomics and Nanoproteomics Enabling Personalized, Predictive and Preventive Medicine." (2014). [citation][year=2014]Lopes, Ricardo Jorge Nogueira. Interactoma da cavidade oral em diabetes. Diss. 2014. [citation][year=2014]Sá, Carlos Eduardo Nogueira. Criação da base de dados oralm associada à base oralome. Diss. 2014. [citation][year=2014]Fernandes, Mónica Figueiredo. Biomarkers in Canis lupus familiaris. MS thesis. Universidade de Aveiro, 2014. [citation][year=2014]Moreira, Patrícia Maria Iria. Os microorganismos orais e o oraloma da diabetes tipo 2. Diss. 2013. [citation][year=2014]Fonseca, Jorge Filipe Raposo. Biomarcadores na saliva-presente e futuro. Diss. 2014. [citation][year=2014]Santos, Jenifer Amorim dos. O proteoma do microbioma oral humano-que funções exercem as proteínas microbianas?. Diss. 2014. [citation][year=2014]Soares, André do Nascimento Gonçalves. Interatómica da cavidade oral. Diss. Universidade Católica Portuguesa, 2014. [citation][year=2013]Marques, Ana Margarida. Fatores associados a cancro: proposta de ontologia. Diss. 2013. [citation][year=2013]Brás, Vítor Daniel Moreira. O oraloma da diabetes melitos tipo 1 vs diabetes melitos tipo 2-um estudo comparativo. Diss. 2013. [citation][year=2013]Moreira, Patrícia Maria Iria. Os microorganismos orais e o oraloma da diabetes tipo 2. Diss. 2013. [citation][year=2013]Barbosa, Fernanda Correia, Joel P. Arrais, and José Luís Oliveira. "Quantitative Characterization of Protein Networks of the Oral Cavity." 7th International Conference on Practical Applications of Computational Biology & Bioinformatics. Springer International Publishing, 2013. Conference Articles 2020(2 publications) [publication]Pereira, T. and Maryam Abbasi and Ribeiro, B. and Arrais, J.P. , "Deep Reinforcement Learning for Optimized Drug Design", in Bioinformatics Open Days, 2020 [publication]Torres, L.H.M. and Nelson R. C. Monteiro and Ribeiro, B. and Arrais, J.P. , "Siamese Neural Networks for One-Shot Drug Discovery", in Bioinformatics Open Days (BOD) 2020, 2020 2019(7 publications) [publication]Silva, J. and Lucas, P. and Araujo, F. and Silva, C. and P. Gil and Alberto Cardoso and Arrais, J.P. and Ribeiro, B. and Coutinho, D. and Salgueiro, P. and Rato, L. and Saias, J. and Nogueira, V. , "A Hybrid Application for Real-Time Air Quality Monitoring", in 2019 5th Experiment International Conference (exp.at'19), 2019 [publication]Silva, J. and Lucas, P. and Araujo, F. and Silva, C. and P. Gil and Alberto Cardoso and Arrais, J.P. and Ribeiro, B. and Coutinho, D. and Salgueiro, P. and Rato, L. and Saias, J. and Nogueira, V. , "An Online Platform For Real-Time Air Quality Monitoring", in 2019 5th Experiment International Conference (exp.at'19), 2019 [publication]Nelson R. C. Monteiro and Ribeiro, B. and Arrais, J.P. , "Deep Neural Network Architecture for Drug-Target Interaction Prediction", in Artificial Neural Networks and Machine Learning – ICANN 2019, 2019 [publication]Coutinho, D. and Salgueiro, P. and Saias, J. and Rato, L. and Nogueira, V. and Silva, J. and Lucas, P. and Araujo, F. and Silva, C. and P. Gil and Alberto Cardoso and Arrais, J.P. and Ribeiro, B. , "Considerations for a cloud-based system for IoT data acquisition from heterogeneous sensors", in III CONGRESSO LUSO-EXTREMADURENSE, 2019 [publication]Maryam Abbasi and Ribeiro, B. and Arrais, J.P. , "Deep Recurrent Networks for Molecular Drug Design", in RECPAD2019, 2019 [publication]Nelson R. C. Monteiro and Ribeiro, B. and Arrais, J.P. , "Drug-Target Interaction Prediction: End-to-End Deep Learn-ing Approach", in Bioinformatics Open Days (BOD) 2019, 2019 [publication]Nelson R. C. Monteiro and Ribeiro, B. and Arrais, J.P. , "End-to-End Deep Learning Approach for Drug-Target Interaction Prediction", in Ciência2019, 2019 2018(5 publications) [publication]Arrais, J.P. and Coelho, E.D. and Oliveira, J.L. , "Fighting Fire with Fire: Computational Prediction of Microbial Targets for Bacteriocins", in International Conference on Bioinformatics and Biomedical Engineering, 2018 [publication]Pedro Henriques Abreu and Martins, P. and Penousal Machado and Arrais, J.P. and Gomes, A. , "The Relationship Between Learning Styles and Creativity Students: An Information Visualization Class Case Study", in EdMedia: World Conference on Educational Media and Technology, pp.1246-1255, 2018 [publication]Cruz, A. and Arrais, J.P. and Penousal Machado , "Interactive Network Visualization of Gene Expression Time-Series Data", in iV2018 – 22nd International Conference Information Visualisation, 2018 [publication]Albuquerque, J. and Pereira, C. and Arrais, J.P. , "Analysis of Auto-encoders for Feature Representation of Protein Sequences", in 24th Portuguese Conference on Pattern Recognition, 2018 [publication]Nelson R. C. Monteiro and Ribeiro, B. and Arrais, J.P. , "Drug-Target Interaction Prediction: End-to-End Deep Learning Approach", in EJIBCE2018, 2018 2017(2 publications) [publication]Polisciuc, E. and Cruz, A. and Penousal Machado and Arrais, J.P. , "On the Role of Aesthetics in Genetic Algorithms Applied to Graph Drawing", in Proceedings of the Genetic and Evolutionary Computation Conference Companion, 2017 [publication]Arrais, J.P. and António Dourado and Santiago, A. and Rocha, M. , "Mixed-Integer Programming Model for Profiling Disease Biomarkers from Gene Expression Studies", in IWBBIO 2017: Bioinformatics and Biomedical Engineering, 2017 2016(2 publications) [publication]Arrais, J.P. and Oliveira, J.L. and Coelho, E.D. , "Ensemble-Based Methodology for the Prediction of Drug-Target Interactions", in Computer-Based Medical Systems (CBMS), 2016 IEEE 29th International Symposium on, 2016 [publication]Correia, F.B. and Arrais, J.P. and Oliveira, J.L. , "Prediction of Cancer using Network Topological Features", in Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies, 2016 2015(1 publication) [publication]Arrais, J.P. and Coelho, E.D. and Oliveira, J.L. , "Uncovering microbial duality within human microbiomes: A novel algorithm for the analysis of host-pathogen interactions", in Engineering in Medicine and Biology Society (EMBC), 2015 37th Annual International Conference of the IEEE, 2015 2014(3 publications) [publication]Arrais, J.P. , "Metagenomic Analysis of the Saliva Microbiome with Merlin", in 8th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2014), 2014 [publication]Arrais, J.P. and Oliveira, J.L. , "A Cytoscape-Based Web Tool for Representing Protein Networks", in The International Conference on Health Informatics, 2014 [publication]Arrais, J.P. and Oliveira, J.L. and Barbosa, F. , "Weighted Gene Co-expression Network Analysis Applied to Head and Neck Squamous Cell Carcinoma Data", in The International Conference on Health Informatics, 2014 2013(1 publication) [publication]Arrais, J.P. and Oliveira, J.L. and Barbosa, F. , "Quantitative Characterization of Protein Networks of the Oral Cavity", in 7th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2013