Joel Arrais

Position	Aux. professor
Affiliation	Univ. Coimbra
Group	Biomedical Informatics and Technologies
Status	Researcher with PhD
Country	Portugal
Students
Former PhD students	Edgar Coelho, Fernanda Brito Correia
Former masters students	Show list
Courses
Projects
Past projects	GEN2PHEN, QueryTermExp
Events
Proposals
ORCID	0000-0003-4937-2334
Personal page	http://joelarrais.info

Publications

Articles in international journals listed in the ISI

• Edgar Coelho, Joel Arrais, José Luís Oliveira. Computational Discovery of Putative Leads for Drug Repositioning through Drug-Target Interaction Prediction. PLoS Computational Biology, vol. 12, no. 11, p. e1005219, November 2016 [IF 2016: 4.542 (Q1, 4/57)] [IF 2018: 4.428 (Q1, 5/59)]
• Edgar Coelho, André M. Santiago, Joel Arrais, José Luís Oliveira. Computational methodology for predicting the landscape of the human–microbial interactome region level influence. Journal of Bioinformatics and Computational Biology, vol. 13, no. 5, October 2015 [IF 2015: 0.785 (Q4, 48/56)]
• Joel Arrais, José Luís Oliveira. RecRWR: A Recursive Random Walk Method for Improved Identification of Diseases. BioMed Research International, vol. 2015, no. 747156, March 2015 [IF 2015: 2.134 (Q3, 82/161)]
• Nuno Rosa, Maria José Correia, Joel Arrais, Nuno Costa, José Luís Oliveira, Marlene Barros. The Landscape of Protein Biomarkers Proposed for Periodontal Disease: Markers with Functional Meaning. BioMed Research International, vol. 2014, no. 569632, June 2014 [IF 2014: 1.579 (Q3, 107/163)]
• Edgar Coelho, Joel Arrais, Sérgio Matos, Carlos Pereira, Nuno Rosa, Maria José Correia, Marlene Barros, José Luís Oliveira. Computational prediction of the human-microbial oral interactome. BMC Systems Biology, vol. 8, p. 24, February 2014 [IF 2014: 2.435 (Q1, 13/57)]
• Miguel Reboiro-Jato, Joel Arrais, José Luís Oliveira, Florentino Fdez-Riverola. geneCommittee: a web-based tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification. BMC Bioinformatics, vol. 15, no. 31, January 2014 [IF 2014: 2.576 (Q1, 11/57)]
• Joel Arrais, Nuno Rosa, José Melo, Edgar Coelho, Diana Amaral, Maria José Correira, Marlene Barros, José Luís Oliveira. OralCard: a bioinformatic tool for the study of Oral Proteome. Archives of Oral Biology, vol. 58, no. 7, p. 762-772, July 2013 [IF 2013: 1.880, 1.880 (Q2, 23/83)]
• Edgar Coelho, Joel Arrais, José Luís Oliveira. From Protein-Protein Interactions to Rational Drug Design: Are Computational Methods Up to the Challenge?. Current Topics in Medicinal Chemistry, vol. 13, p. 602-618 (17), March 2013 [IF 2013: 3.453 (Q1, 11/58)]
• Nuno Rosa, Maria José Correia, Joel Arrais, Pedro Lopes, José Melo, José Luís Oliveira, Marlene Barros. From the salivary proteome to the OralOme: Comprehensive molecular oral biology. Archives of Oral Biology, vol. 57, no. 7, p. 853-864, July 2012 [IF 2012: 1.549, 1.549 (Q2, 31/83)]
• Sara C. Novais, Joel Arrais, Pedro Lopes, Tine Vandenbrouck, Wim De Coen, Dick Roelofs, Amadeu M. V. M. Soares, Mónica J. B. Amorim. Enchytraeus albidus Microarray: Enrichment, Design, Annotation and Database (EnchyBASE). PLoS ONE, vol. 7, no. 4, April 2012 [IF 2012: 3.730 (Q1, 7/56)] [IF 2018: 2.776 (Q2, 24/69)]
• Joel Arrais, João Fernandes, João Pereira, José Luís Oliveira. GeneBrowser 2: an application to explore and identify common biological traits in a set of genes. BMC Bioinformatics, vol. 11, no. 389, July 2010 [IF 2010: 3.028 (Q1, 4/37)]
• Sérgio Matos, Joel Arrais, João Maia-Rodrigues, José Luís Oliveira. Concept-based query expansion for retrieving gene related publications from MEDLINE. BMC Bioinformatics, vol. 11, no. 212, April 2010 [IF 2010: 3.028 (Q1, 4/37)]
• Ana R. Soares, Patricia M. Pereira, Bruno Santos, Conceição Egas, Ana C. Gomes, Joel Arrais, José Luís Oliveira, Gabriela Moura, Manuel A. S. Santos. Parallel DNA pyrosequencing unveils new zebrafish microRNAs. BMC Genomics, vol. 10, April 2009 [IF 2009: 3.759, 3.759]
• Gabriela Moura, Miguel Pinheiro, Joel Arrais, Ana Cristina Gomes, Laura Carreto, Adelaide Freitas, José Luís Oliveira, Manuel A. S. Santos. Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure. PLoS ONE, vol. 2, no. 9, September 2007 [IF 2018: 2.776 (Q2, 24/69)]

Other articles in journals

• Joel Arrais, José Luís Oliveira. Using biomedical networks to prioritize gene–disease associations. Open Access Bioinformatics, vol. 2011:3, p. 123-130, August 2011
• Joel Arrais, Bruno Santos, João Fernandes, Laura Carreto, Manuel A. S. Santos, José Luís Oliveira. GeneBrowser: an approach for integration and functional classification of genomics data. Journal of Integrative Bioinformatics, vol. 4, no. 3, October 2007

Chapters in books

• José Melo, Joel Arrais, Edgar Coelho, Pedro Lopes, Nuno Rosa, Maria José Correia, Marlene Barros, José Luís Oliveira. Data Integration Solution for Organ-Specific Studies: An Application for Oral Biology. Biomedical Engineering Systems and Technologies, Joaquim Gabriel, Jan Schier, Sabine Huffel, Emmanuel Conchon, Carlos Correia, Ana Fred, Hugo Gamboa (Ed.), Springer Berlin Heidelberg, vol. 357, p. 401-412, January 2013
• Joel Arrais, Sérgio Matos, José Luís Oliveira. Integração de dados biomédicos. Nano, Bio, Info y Cogno (Convergencia de tecnologias NBIC), Conceptos y aplicaciones, J. Aguiló, A. Figueras, A. Freire, D. de la Iglesia, F. Martín, A. Pazos (Ed.), CYTED, p. 185-224, 2011
• Joel Arrais, Sérgio Matos, José Luís Oliveira. Expansão de termos de pesquisa usando redes de conceitos associadas a genes. Nuevas Fronteras Tecnológicas, Alejandre Pazos (Ed.), CYTED, 2010

Articles in conference proceedings

• Edgar Coelho, Joel Arrais, José Luís Oliveira. Ensemble-Based Methodology for the Prediction of Drug-Target Interactions. IEEE 29th International Symposium on Computer-Based Medical Systems (CBMS 2016), June 2016
• Fernanda Brito Correia, Joel Arrais, José Luís Oliveira. Prediction of Cancer using Network Topological Features. 7th International Conference on Bioinformatics Models, Methods and Algorithms, February 2016
• Edgar Coelho, Joel Arrais, José Luís Oliveira. Uncovering Microbial Duality within Human Microbiomes: A Novel Algorithm for the Analysis of Host-Pathogen Interactions. 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC2015), Milan, Italy, August 2015
• Fernanda Brito Correia, Joel Arrais, José Luís Oliveira. Weighted Gene Co-expression Network Analysis Applied to Head and Neck Squamous Cell Carcinoma Data. International Conference on Health Informatics (ICHI), Vilamoura, Portugal, November 2013
• Fernanda Brito Correia, Joel Arrais, José Luís Oliveira. Quantitative Characterization of Protein Networks of the Oral Cavity. 7th International Conference on Practical Applications of Computational Biology & Bioinformatics, Spain, June 2013
• José Melo, Joel Arrais, Pedro Lopes, Nuno Rosa, Maria José Correia, Marlene Barros, José Luís Oliveira. WEB INFORMATION SYSTEM FOR THE STUDY OF ORAL HEALTH. Healthinf 2012 - International Conference of Health Informatics, Vilamoura - Portugal, February 2012
• Joel Arrais, Pedro Lopes, José Luís Oliveira. Challenges Storing and Representing Biomedical Data. Information Quality in e-Health: 7th Conference of the Workgroup Human-Computer Interaction and Usability Engineering of the Austrian Computer Society, USAB 2011, Graz, Austria, vol. LNCS 7058, p. 53-62, November 2011
• Joel Arrais, José Luís Oliveira. Gene-disease prioritization through biomedical networks. 10th IEEE International Conference on Information Technology and Applications in Biomedicine (ITAB 2010), November 2010
• Joel Arrais, José Luís Oliveira. On the exploitation of cloud computing in Bioinformatics. 10th IEEE International Conference on Information Technology and Applications in Biomedicine (ITAB 2010), November 2010
• Sérgio Matos, Joel Arrais, José Luís Oliveira. Expanding Gene-based PubMed Queries. Proceedings of the 4th International Workshop on Practical Applications of Computational Biology and Bioinformatics 2010 (IWPACBB 2010), Guimarães, Portugal, vol. 74, p. 61-68, June 2010
• Joel Arrais, João Pereira, Pedro Lopes, Sérgio Matos, José Luís Oliveira. Improving cross mapping in biomedical databases. 4th International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2010), June 2010
• Joel Arrais, João Pereira, João Fernandes, José Luís Oliveira. GeNS: A Biological Data Integration Platform. World Academy of Science, Engineering and Technology (WASET 2009), Venice, Italy, p. 416 - 421, 2009
• Pedro Lopes, Joel Arrais, José Luís Oliveira. Link Integrator: A Link-based Data Integration Architecture. International Conference on Knowledge Discovery and Information Retrieval (KDIR 2009), Madeira, Portugal, 2009
• Sérgio Matos, Joel Arrais, João Maia-Rodrigues, José Luís Oliveira. QuExT: a concept-based query expansion approach for literature retrieval from MEDLINE. Jornadas de Bioinformática (JB 2009), Lisbon, Portugal, 2009
• Pedro Lopes, Joel Arrais, José Luís Oliveira. DynamicFlow: A Client-Side Workflow Management System. 10th International Work-Conference on Artificial Neural Networks (IWANN 2009), Salamanca, Spain, vol. 5518, p. 1101-1108, June 2009
• Joel Arrais, Laura Carreto, Manuel A. S. Santos, José Luís Oliveira. A Microarray Information Database. International Conference on Biocomputation, Bioinformatics, and Biomedical Technologies (BIOTECHNO'2008), Bucharest, Romania, 2008
• Pedro Lopes, Joel Arrais, José Luís Oliveira. Dynamic Service Integration using Web-based Workflows. 10th International Conference on Information Integration and Web Applications & Services, Linz, Austria, November 2008
• Joel Arrais, João G. L. M. Rodrigues, José Luís Oliveira. Improving Literature Searches in Gene Expression Studies. 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 08), Salamanca, Spain, vol. 49, p. 74-82, October 2008
• Valery Sklyarov, Iouliia Skliarova, Bruno Pimentel, Joel Arrais. Hardware/Software Implementation of FPGA-targeted Matrix-Oriented SAT Solvers. Proceedings of the 14th International Conference on Field-Programmable Logic and Applications - FPL'2004, Belgium, p. 922-926, September 2004

PhD thesis

• Joel Arrais. Sistemas de informação para DNA microarrays. PhD Thesis, Universidade de Aveiro, March 2010