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Joel P. Arrais is an Associate Professor at the Department of Informatics Engineering, University of Coimbra. He has received his MSc and PhD in Computer Science from University of Aveiro in 2004 and 2010 respectively. His research interest are on developing algorithms to model biological problems. He is particularly interested in using pattern recognition and machine learning methods. On the recent past He has been involved on several studies that focused on the analysis and knowledge extraction from gene-expression data.
Identification

Personal identification

Full name
Joel Arrais

Citation names

  • Arrais, Joel
  • Joel P. Arrais

Author identifiers

Ciência ID
B919-5159-C962
ORCID iD
0000-0003-4937-2334
Google Scholar ID
0pEkBdwAAAAJ

Email addresses

  • jpa@dei.uc.pt (Professional)

Addresses

  • FCTUC - Universidade de Coimbra. Pólo II - Pinhal de Marrocos, 3030-290, Coimbra, Coimbra, Portugal (Professional)

Websites

  • joelarrais.github.io (Professional)

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Exact Sciences - Computer and Information Sciences - Computer Sciences
Education
Degree Classification
2005 - 2010
Concluded
 Engenharia Informática (Doutoramento)
Major in Sem especialidade
Universidade de Aveiro, Portugal
"Sistemas de Informação para Dna Microarrays" (THESIS/DISSERTATION)
1999/09 - 2004/07
Concluded
 Licenciatura em Engenharia de Computadores e Telemática (Licenciatura)
Universidade de Aveiro Departamento de Electrónica Telecomunicações e Informática, Portugal
 16
Affiliation

Science

Category
Host institution 		Employer
2010 - 2012 Researcher (Research) Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal
Universidade de Aveiro, Portugal
2006 - 2010 Researcher (Research) Fundação para a Ciência e a Tecnologia, Portugal
Universidade de Aveiro, Portugal
2004/11 - 2005/12 Researcher (Research) Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal
Universidade de Aveiro, Portugal

Teaching in Higher Education

Category
Host institution 		Employer
2024/01 - Current Associate Professor (University Teacher) Universidade de Coimbra, Portugal
Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal
2018/09 - 2023/12 Assistant Professor (University Teacher) Universidade de Coimbra Departamento de Engenharia Informática, Portugal
2012/09 - 2018/08 Invited Assistant Professor (University Teacher) Universidade de Coimbra Departamento de Engenharia Informática, Portugal
2010 - 2012 Invited Adjunct Teacher (Polytechnic Teacher) Universidade de Aveiro Escola Superior de Tecnologia e Gestão de Águeda, Portugal
Universidade de Aveiro, Portugal
Projects

Grant

Designation Funders
2018 - 2022 Real-time Condition-based Maintenance for Adaptive Aircraft Maintenance Planning
769288-2
 European Commission
2018/05 - 2021/05 D4-FCT: Deep Drug Discovery and Deployment
FCT-SAICT-2017-029266
Principal investigator
Fundação para a Ciência e a Tecnologia
2018/04 - 2021/03 NanoSen-AQM - Development and field validation of a low-cost nano-sensor system for real-time monitoring of ambient air quality
SOE2/P1/E0569 (EU-INTERREG-SUDOE)
 European Commission
2016/05 - 2019/05 SASSI - Sistema de Apoio à Decisão de Segurança em Sistemas Informáticos
017775
 Agência Nacional de Inovação SA
2016/01 - 2018/12 Linking excellence in biomedical knowledge and computational intelligence research for personalized management of CVD within PHC
692023
 European Commission
2010/05 - 2013/10 Query term expansion methodologies for improved biomedical literature retrieval
grant.Provided by PTCRIS: 100541
 Fundação para a Ciência e a Tecnologia
Outputs

Publications

Book
  1. Antunes, D.; Martins, D.; Correia, F.; Rocha, M.; Arrais, J.P.. Computational Methods for the Identification of Genetic Variants in Complex Diseases. 2022.
    10.1007/978-3-030-86258-9_1
  2. Santiago, A.M.; Rocha, M.; Dourado, A.; Arrais, J.P.. Mixed-integer programming model for profiling disease biomarkers from gene expression studies. 2017.
    10.1007/978-3-319-56154-7_6
  3. Barbosa, P.; Dias, O.; Arrais, J.P.; Rocha, M.. Metagenomic analysis of the saliva microbiome with merlin. 2014.
    10.1007/978-3-319-07581-5_23
  4. Melo, J.; Arrais, J.P.; Coelho, E.; Lopes, P.; Rosa, N.; Correia, M.J.; Barros, M.; Oliveira, J.L.. Data Integration Solution for Organ-Specific Studies: An Application for Oral Biology. 2013.
    10.1007/978-3-642-38256-7_27
  5. Barbosa, F.C.; Arrais, J.P.; Oliveira, J.L.. Quantitative Characterization of Protein Networks of the Oral Cavity. 2013.
    10.1007/978-3-319-00578-2_9
  6. Arrais, J.P.; Lopes, P.; Oliveira, J.L.. Challenges storing and representing biomedical data. 2011.
    10.1007/978-3-642-25364-5_6
  7. Lopes, P.; Arrais, J.; Oliveira, J.L.. DynamicFlow: A client-side workflow management system. 2009.
    10.1007/978-3-642-02481-8_167
  8. Arrais, J.P.; Rodrigues, J.G.L.M.; Oliveira, J.L.. Improving literature searches in gene expression studies. 2009.
    10.1007/978-3-540-85861-4_10
Book chapter
  1. Daniel Martins; Conceição Egas; Joel P. Arrais. "The Impact of Schizophrenia Misdiagnosis Rates on Machine Learning Models Performance". 2023.
    10.1007/978-3-031-38079-2_1
  2. Nelson R. C. Monteiro; Bernardete Ribeiro; Joel P. Arrais. "Deep Neural Network Architecture for Drug-Target Interaction Prediction". 2019.
    10.1007/978-3-030-30493-5_76
  3. Arrais, Joel. "Expanding Gene-Based PubMed Queries". 61-68. Springer, Berlin, Heidelberg, 2010.
    10.1007/978-3-642-13214-8_8
  4. Arrais, Joel; Pereira, Joao E.; Lopes, Pedro; Matos, Sergio; Oliveira, Jose Luis. "Improving Cross Mapping in Biomedical Databases". edited by Rocha, M. P. Riverola F. F. Shatkay H. Corchado J. M., 69-76. 2010.
    10.1007/978-3-642-13214-8_9
Conference paper
  1. Nelson R. C. Monteiro; Abbasi, Maryam; Ana Catarina Machado; Joel P. Arrais. Corresponding author: Nelson R. C. Monteiro. "Multi-Optimized Drug Design using Transformers". Paper presented in 28th Portuguese Conference on Pattern Recognition (RECPAD2022), leiria, 2022.
  2. Santos, R.; Arrais, J.P.; Silva, P.A.. "Analysing games for health through users' opinion mining". 2021.
    10.1109/CBMS52027.2021.00035
  3. Santos, B.P.; Abbasi, M.; Pereira, T.; Ribeiro, B.; Arrais, J.P.. "Optimizing recurrent neural network architectures for de novo drug design". 2021.
    10.1109/CBMS52027.2021.00067
  4. Santos, B.P.; Abbasi, M.; Pereira, T.; Ribeiro, B.; Arrais, J.P.. "Improvement on Generative Adversarial Network for Targeted Drug Design". 2021.
    10.14428/esann/2021.ES2021-96
  5. Fernandes, M.; Silva, C.; Arrais, J.P.; Cardoso, A.; Ribeiro, B.. "Decay Momentum for Improving Federated Learning". 2021.
    10.14428/esann/2021.ES2021-106
  6. Abbasi, M.; Pereira, T.; Santos, B.P.; Ribeiro, B.; Arrais, J.P.. "Multiobjective Reinforcement Learning in Optimized Drug Design". 2021.
    10.14428/esann/2021.ES2021-87
  7. Torres, L.; Monteiro, N.; Oliveira, J.; Arrais, J.; Ribeiro, B.. "Exploring a Siamese Neural Network Architecture for One-Shot Drug Discovery". 2020.
    10.1109/BIBE50027.2020.00035
  8. Silva, L.; Pereira, C.; Arrais, J.P.. "Using a Novel Unbiased Dataset and Deep Learning Architectures to Predict Protein-Protein Interactions". 2020.
    10.1109/BIBM49941.2020.9313393
  9. Cruz, A.; Arrais, J.P.; MacHado, P.. "Exploring Time-Series through Force-Directed Timelines". 2020.
    10.1109/IV51561.2020.00061
  10. Silva, J.; Lucas, P.; Araujo, F.; Silva, C.; Gil, P.; Cardoso, A.; Arrais, J.; et al. "A hybrid application for real-time air quality monitoring". 2019.
    10.1109/EXPAT.2019.8876498
  11. Silva, J.; Lucas, P.; Araujo, F.; Silva, C.; Gil, P.; Cardoso, A.; Arrais, J.; et al. "An online platform for real-time air quality monitoring". 2019.
    10.1109/EXPAT.2019.8876486
  12. Cruz, A.; Arrais, J.P.; Machado, P.. "Interactive network visualization of gene expression time-series data". 2018.
    10.1109/iV.2018.00105
  13. Henriques Abreu, Pedro; Pedro Jorge Martins; Penousal Machado; Joel P. Arrais; Anabela Gomes. "The Relationship Between Learning Styles and Creativity Students: An Information Visualization Class Case Study". Paper presented in EdMedia: World Conference on Educational Media and Technology, 2018.
  14. Coelho, E.D.; Arrais, J.P.; Oliveira, J.L.. "Ensemble-based methodology for the prediction of drug-target interactions". 2016.
    10.1109/CBMS.2016.67
  15. Correia, F.B.; Arrais, J.P.; Oliveira, J.L.. "Prediction of cancer using network topological features". 2016.
  16. Coelho, E.D.; Arrais, J.P.; Oliveira, J.L.. "Uncovering microbial duality within human microbiomes: A novel algorithm for the analysis of host-pathogen interactions". 2015.
    10.1109/EMBC.2015.7319086
  17. Barbosa, F.C.; Arrais, J.P.; Oliveira, J.L.. "Weighted gene co-expression network analysis applied to head and neck squamous cell carcinoma data". 2014.
    10.1007/978-3-319-03005-0_76
  18. Rodrigues, R.P.; Arrais, J.P.; Coelho, E.D.; Oliveira, J.L.. "A cytoscape-based web tool for representing protein networks". 2014.
    10.1007/978-3-319-03005-0_79
  19. Arrais, Joel. "Computational Approach to Predict Inter-Species Oral Protein-Protein Interactions.". 2013.
  20. Arrais, Joel. "Representation of Semantic Networks of Biomedical Terms.". 2013.
  21. Melo, J.; Arrais, J.P.; Lopes, P.; Rosa, N.; Correia, M.J.; Barros, M.; Oliveira, J.L.. "Web information system for the study of oral health". 2012.
  22. Arrais, J.P.; Oliveira, J.L.. "Gene-disease prioritization through biomedical networks". 2010.
    10.1109/ITAB.2010.5687629
  23. Arrais, J.P.; Oliveira, J.L.. "On the exploitation of cloud computing in bioinformatics". 2010.
    10.1109/ITAB.2010.5687653
  24. Lopes, P.; Arrais, J.; Oliveira, J.L.. "Link integrator: A link-based data integration architecture". 2009.
  25. Lopes, P.; Arrais, J.; Oliveira, J.L.. "Dynamic Service integration using web-based workflows". 2008.
    10.1145/1497308.1497426
  26. Arrais, J.P.; Carreto, L.; Santos, M.A.; Oliveira, J.L.. "A microarray information database". 2008.
    10.1109/BIOTECHNO.2008.22
  27. Polónia, D.F.; Arrais, J.; Oliveira, J.L.. "A prospective study on the integration of microarray data in HIS/EPR". 2006.
Conference poster
  1. Nelson R. C. Monteiro; Oliveira, José Luis; Joel P. Arrais. Corresponding author: Nelson R. C. Monteiro. "Intrinsic Explainability and Multi-Domain Inter-Dependency: End-to-End Drug-Target Binding Affinity Prediction with Transformers". Paper presented in Science and Technology Summit, 2013 (Ciência 2023), 2023.
  2. Torres, Luis H. M.; Ribeiro, Bernardete; Arrais, Joel. "Exploring a Siamese Neural Network Architecture for Drug Discovery". Paper presented in RECPAD2020, 26th Portuguese Conference on Pattern Recognition, 2020.
  3. Torres, Luis H. M.; Nelson R. C. Monteiro; Ribeiro, Bernardete; José L. Oliveira; Arrais, Joel. "Siamese Neural Networks for One-Shot Drug Discovery". Paper presented in Bioinformatics Open Days (BOD) 2020, 2020.
  4. Nelson R. C. Monteiro; Ribeiro, Bernardete; Arrais, Joel. "End-to-End Deep Learning Approach for Drug-Target Interaction Prediction". Paper presented in Ciência2019, Science and Technology Summit, 2019.
  5. S Rei; Luís Filipe de Sepúlveda Silva Santos; Joel P. Arrais; Nuno Ricardo das Neves Rosa; Marlene Maria Tourais de Barros; Maria José Serol de Brito Correia. "miRNAs como biomarcadores: actualização da base de dados OralOme". Paper presented in I Jornadas Científicas da Primavera, 2015.
Journal article
  1. Nelson R. C. Monteiro; Oliveira, José Luis; Joel P. Arrais. Corresponding author: Nelson R. C. Monteiro. "TAG-DTA: Binding-region-guided strategy to predict drug-target affinity using transformers". Expert Systems with Applications (2024): https://doi.org/10.1016/j.eswa.2023.122334.
    Published • 10.1016/j.eswa.2023.122334
  2. Nelson R. C. Monteiro; Tiago O. Pereira; Ana Catarina D. Machado; Oliveira, José Luis; Abbasi, Maryam; Joel P. Arrais. Corresponding author: Nelson R. C. Monteiro. "FSM-DDTR: End-to-end feedback strategy for multi-objective De Novo drug design using transformers". Computers in Biology and Medicine (2023): https://doi.org/10.1016/j.compbiomed.2023.107285.
    Published • 10.1016/j.compbiomed.2023.107285
  3. Luis H.M. Torres; Bernardete Ribeiro; Joel P. Arrais. "Few-shot learning with transformers via graph embeddings for molecular property prediction". Expert Systems with Applications (2023): https://doi.org/10.1016/j.eswa.2023.120005.
    10.1016/j.eswa.2023.120005
  4. Luis Torres; Joel P. Arrais; Bernardete Ribeiro. "Few-shot learning via graph embeddings with convolutional networks for low-data molecular property prediction". Neural Computing and Applications 35 (2023): 13167-13185.
    10.1007/s00521-023-08403-5
  5. António Cruz; Joel P. Arrais; Penousal Machado. "Force-Directed Timelines: Visualizing & Exploring Temporal Patterns". Big Data Research 27 (2022): 100291-100291. https://doi.org/10.1016/j.bdr.2021.100291.
    10.1016/j.bdr.2021.100291
  6. Anuschka Silva-Spínola; Inês Baldeiras; Joel P. Arrais; Isabel Santana. "The Road to Personalized Medicine in Alzheimer’s Disease: The Use of Artificial Intelligence". Biomedicines 10 2 (2022): 315-315. https://doi.org/10.3390/biomedicines10020315.
    10.3390/biomedicines10020315
  7. Abbasi, M.; Santos, B.P.; Pereira, T.C.; Sofia, R.; Monteiro, N.R.C.; Simões, C.J.V.; Brito, R.; et al. "Designing optimized drug candidates with Generative Adversarial Network". Journal of Cheminformatics 14 1 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85133030061&partnerID=MN8TOARS.
    10.1186/s13321-022-00623-6
  8. Papaiz, F.; Dourado, M.E.T.; Valentim, R.A.D.M.; de Morais, A.H.F.; Arrais, J.P.. "Machine Learning Solutions Applied to Amyotrophic Lateral Sclerosis Prognosis: A Review". Frontiers in Computer Science 4 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85130128050&partnerID=MN8TOARS.
    10.3389/fcomp.2022.869140
  9. Monteiro, N.R.C.; Simões, C.J.V.; Ávila, H.V.; Abbasi, M.; Oliveira, J.L.; Arrais, J.P.. "Explainable deep drug–target representations for binding affinity prediction". BMC Bioinformatics 23 1 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85132117723&partnerID=MN8TOARS.
    10.1186/s12859-022-04767-y
  10. Monteiro, N.R.C.; Oliveira, J.L.; Arrais, J.P.. "DTITR: End-to-end drug–target binding affinity prediction with transformers". Computers in Biology and Medicine 147 (2022): http://www.scopus.com/inward/record.url?eid=2-s2.0-85132857403&partnerID=MN8TOARS.
    10.1016/j.compbiomed.2022.105772
  11. Antonio Cruz; Joel P. Arrais; Penousal Machado. "Multivariate Data Exploration Through Coordinated Views". IEEE Access (2022): https://doi.org/10.1109/ACCESS.2022.3194072.
    10.1109/ACCESS.2022.3194072
  12. Pereira, T.; Abbasi, M.; Oliveira, J.L.; Ribeiro, B.; Arrais, J.. "Optimizing blood-brain barrier permeation through deep reinforcement learning for de novo drug design". Bioinformatics 37 (2021): I84-I92. http://www.scopus.com/inward/record.url?eid=2-s2.0-85111954864&partnerID=MN8TOARS.
    10.1093/bioinformatics/btab301
  13. Pereira, T.; Abbasi, M.; Ribeiro, B.; Arrais, J.P.. "Diversity oriented Deep Reinforcement Learning for targeted molecule generation". Journal of Cheminformatics 13 1 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85102299240&partnerID=MN8TOARS.
    10.1186/s13321-021-00498-z
  14. Monteiro NRC; Ribeiro B; Arrais J. "Drug-Target Interaction Prediction: End-to-End Deep Learning Approach.". IEEE/ACM transactions on computational biology and bioinformatics (2020): http://europepmc.org/abstract/med/32142454.
    10.1109/tcbb.2020.2977335
  15. Lucas, P.; Silva, J.; Araujo, F.; Silva, C.; Gil, P.; Arrais, J.P.; Coutinho, D.; et al. "NanoSen-AQM: From sensors to users". International journal of online and biomedical engineering 16 4 (2020): 51-62. http://www.scopus.com/inward/record.url?eid=2-s2.0-85085898487&partnerID=MN8TOARS.
    10.3991/ijoe.v16i04.11871
  16. Cruz, A.; MacHado, P.; Arrais, J.P.. "CroP-Coordinated Panel visualization for biological networks analysis". Bioinformatics 36 4 (2020): 1298-1299. http://www.scopus.com/inward/record.url?eid=2-s2.0-85080842178&partnerID=MN8TOARS.
    10.1093/bioinformatics/btz688
  17. Fernanda B. Correia; Edgar D. Coelho; José L. Oliveira; Joel P. Arrais; Brito Correia F; Coelho ED; Oliveira JL; Arrais JP. "Handling Noise in Protein Interaction Networks". BioMed Research International (2019): https://doi.org/10.1155/2019/8984248.
    10.1155/2019/8984248
  18. Arrais, Joel; Cruz, A.; Arrais, J.P.; Machado, P.. "Interactive and coordinated visualization approaches for biological data analysis". Briefings in bioinformatics 20 4 (2018): 1513-1523. https://doi.org/10.1093/bib/bby019.
    https://doi.org/10.1093/bib/bby019
  19. Cruz, I.; Esteves, E.; Fernandes, M.; Rosa, N.; Correia, M.J.; Arrais, J.P.; Barros, M.; Arrais, Joel. "SalivaPRINT Toolkit – Protein profile evaluation and phenotype stratification". Journal of Proteomics 171 (2018): 81-86. http://www.scopus.com/inward/record.url?eid=2-s2.0-85028633099&partnerID=MN8TOARS.
    10.1016/j.jprot.2017.08.011
  20. Eduardo Esteves; Nuno Rosa; Maria José Correia; Joel P. Arrais; Marlene Barros. "New Targets for Zika Virus Determined by Human-Viral Interactomic: A Bioinformatics Approach". BioMed Research International (2017): https://doi.org/10.1155/2017/1734151.
    10.1155/2017/1734151
  21. Joel P. Arrais; Ana Laranjeira; Gonçalo Oliveira; Bernardete Ribeiro. "Deep learning in digital marketing: brand detection and emotion recognition". International Journal of Machine Intelligence and Sensory Signal Processing 2 1 (2017): 32-32. https://doi.org/10.1504%2Fijmissp.2017.10009120.
    10.1504/ijmissp.2017.10009120
  22. Edgar D. Coelho; James M. Briggs; Joel P. Arrais; José Luís Oliveira. "Computational Discovery of Putative Leads for Drug Repositioning through Drug-Target Interaction Prediction". PLOS Computational Biology 12 11 (2016): e1005219-e1005219. https://doi.org/10.1371%2Fjournal.pcbi.1005219.
    10.1371/journal.pcbi.1005219
  23. Fernandes, M.; Rosa, N.; Esteves, E.; Correia, M.J.; Arrais, J.; Ribeiro, P.; Vala, H.; Barros, M.. "CanisOme - The protein signatures of Canis lupus familiaris diseases". Journal of Proteomics 136 (2016): 193-201. http://www.scopus.com/inward/record.url?eid=2-s2.0-84959339632&partnerID=MN8TOARS.
    10.1016/j.jprot.2016.01.005
  24. Jain, S.; Arrais, J.; Venkatachari, N.J.; Ayyavoo, V.; Bar-Joseph, Z.. "Reconstructing the temporal progression of HIV-1 immune response pathways". Bioinformatics 32 12 (2016): i253-i261. http://www.scopus.com/inward/record.url?eid=2-s2.0-84976491685&partnerID=MN8TOARS.
    10.1093/bioinformatics/btw254
  25. Coelho, E.D.; Santiago, A.M.; Arrais, J.P.; Oliveira, J.L.. "Computational methodology for predicting the landscape of the human-microbial interactome region level influence". Journal of Bioinformatics and Computational Biology 13 5 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84947041842&partnerID=MN8TOARS.
    10.1142/S0219720015500237
  26. Perdiz Arrais, J.; Oliveira, J.L.. "RecRWR: A recursive random walk method for improved identification of diseases". BioMed Research International 2015 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84927144569&partnerID=MN8TOARS.
    10.1155/2015/747156
  27. Reboiro-Jato, M.; Arrais, J.P.; Oliveira, J.L.; Fdez-Riverola, F.. "GeneCommittee: A web-based tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification". BMC Bioinformatics 15 1 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84893179202&partnerID=MN8TOARS.
    10.1186/1471-2105-15-31
  28. Rosa, N.; Correia, M.J.; Arrais, J.P.; Costa, N.; Oliveira, J.L.; Barros, M.. "The landscape of protein biomarkers proposed for periodontal disease: Markers with functional meaning". BioMed Research International 2014 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84904108852&partnerID=MN8TOARS.
    10.1155/2014/569632
  29. Coelho, E.D.; Arrais, J.P.; Matos, S.; Pereira, C.; Rosa, N.; Correia, M.J.; Barros, M.; Oliveira, J.L.. "Computational prediction of the human-microbial oral interactome". BMC Systems Biology 8 1 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84897570043&partnerID=MN8TOARS.
    10.1186/1752-0509-8-24
  30. Coelho, E.D.; Arrais, J.P.; Oliveira, J.L.. "From protein-protein interactions to rational drug design: Are computational methods up to the challenge?". Current Topics in Medicinal Chemistry 13 5 (2013): 602-618. http://www.scopus.com/inward/record.url?eid=2-s2.0-84878589163&partnerID=MN8TOARS.
    10.2174/1568026611313050005
  31. Arrais, J.P.; Rosa, N.; Melo, J.; Coelho, E.D.; Amaral, D.; Correia, M.J.; Barros, M.; Oliveira, J.L.. "OralCard: A bioinformatic tool for the study of oral proteome". Archives of Oral Biology 58 7 (2013): 762-772. http://www.scopus.com/inward/record.url?eid=2-s2.0-84878216035&partnerID=MN8TOARS.
    10.1016/j.archoralbio.2012.12.012
  32. Rosa, N.; Correia, M.J.; Arrais, J.P.; Lopes, P.; Melo, J.; Oliveira, J.L.; Barros, M.. "From the salivary proteome to the OralOme: Comprehensive molecular oral biology". Archives of Oral Biology 57 7 (2012): 853-864. http://www.scopus.com/inward/record.url?eid=2-s2.0-84862872419&partnerID=MN8TOARS.
    10.1016/j.archoralbio.2011.12.010
  33. Novais, S.C.; Arrais, J.; Lopes, P.; Vandenbrouck, T.; de Coen, W.; Roelofs, D.; Soares, A.M.V.M.; Amorim, M.J.B.. "Enchytraeus albidus microarray: Enrichment, design, annotation and database (enchyBASE)". PLoS ONE 7 4 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84860441378&partnerID=MN8TOARS.
    10.1371/journal.pone.0034266
  34. Arrais, Joel. "Using biomedical networks to prioritize gene-disease associations". Open Access Bioinformatics 2011 3 (2011): 123-130.
  35. Matos, S.; Arrais, J.P.; Maia-Rodrigues, J.; Oliveira, J.L.. "Concept-based query expansion for retrieving gene related publications from MEDLINE". BMC Bioinformatics 11 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-77951569837&partnerID=MN8TOARS.
    10.1186/1471-2105-11-212
  36. Arrais, J.P.; Fernandes, J.; Pereira, J.; Oliveira, J.L.. "GeneBrowser 2: An application to explore and identify common biological traits in a set of genes". BMC Bioinformatics 11 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-77954675055&partnerID=MN8TOARS.
    10.1186/1471-2105-11-389
  37. Arrais, J.; Pereira, J.E.; Fernandes, J.; Oliveira, J.L.. "GeNS: A biological data integration platform". World Academy of Science, Engineering and Technology 58 (2009): 850-855. http://www.scopus.com/inward/record.url?eid=2-s2.0-79954504232&partnerID=MN8TOARS.
  38. Soares, A.R.; Pereira, P.M.; Santos, B.; Egas, C.; Gomes, A.C.; Arrais, J.; Oliveira, J.L.; Moura, G.R.; Santos, M.A.S.. "Parallel DNA pyrosequencing unveils new zebrafish microRNAs". BMC Genomics 10 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-65949098165&partnerID=MN8TOARS.
    10.1186/1471-2164-10-195
  39. Moura, G.; Pinheiro, M.; Arrais, J.; Gomes, A.C.; Carreto, L.; Freitas, A.; Oliveira, J.L.; Santos, M.A.S.. "Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure". PLoS ONE 2 9 (2007): http://www.scopus.com/inward/record.url?eid=2-s2.0-39449087192&partnerID=MN8TOARS.
    10.1371/journal.pone.0000847
  40. Arrais, Joel. "GeneBrowser: an approach for integration and functional classification of genomic data". Journal of Integrative Bioinformatics 4 3 (2007): 264-273.
    10.1515/jib-2007-82
  41. Arrais, Joel. "Implementação de Algoritmo de Compressão e Descompressão de Dados para Modelo de Co-processamento baseado em FPGA’s". Electrónica e Telecomunicações 4 2 (2004): 215-220.

Other

Other output
  1. Enhancing Reinforcement Learning for de novo Molecular Design Applying Self Attention Mechanisms. 2023. Tiago Pereira; Maryam Abbasi; Joel P. Arrais. https://doi.org/10.1093/bib/bbad368.
    10.1093/bib/bbad368
  2. Diversity Oriented Deep Reinforcement Learning for Targeted Molecule Generation. 2020. Tiago Pereira; Maryam Abbasi; Bernardete Ribeiro; Joel P. Arrais. https://doi.org/10.21203/rs.3.rs-110570/v1.
    10.21203/rs.3.rs-110570/v1
  3. Interactive Network Visualization of Gene Expression Time-Series Data. 2018. Antonio Cruz; Joel P. Arrais; Penousal Machado. https://doi.org/10.1109%2Fiv.2018.00105.
    10.1109/iv.2018.00105
  4. Fighting Fire with Fire: Computational Prediction of Microbial Targets for Bacteriocins. 2018. Edgar D. Coelho; Joel P. Arrais; José Luís Oliveira. https://doi.org/10.1007%2F978-3-319-78723-7_19.
    10.1007/978-3-319-78723-7_19
  5. On the role of aesthetics in genetic algorithms applied to graph drawing. 2017. Evgheni Polisciuc; António Cruz; Penousal Machado; Joel P. Arrais. https://doi.org/10.1145%2F3067695.3082552.
    10.1145/3067695.3082552
  6. A sequence-based mesh classifier for the prediction of protein-protein interactions. 2017. Coelho, E.D.; Cruz, I.N.; Santiago, A.; Oliveira, J.L.; Dourado, A.; Arrais, J.P.. http://www.scopus.com/inward/record.url?eid=2-s2.0-85094478095&partnerID=MN8TOARS.
  7. CanisOme Database. Software. 2016. Fernandes, Mónica; Rosa, Nuno; Esteves, Eduardo; Correia, M.J.; Arrais, Joel; Vala, Helena; Barros, Marlene. http://salivatec.viseu.ucp.pt/canisome/.
  8. Hardware/Software Implementation of FPGA-Targeted Matrix-Oriented SAT Solvers. Lecture Notes in Computer Science. 2004. Sklyarov, Valery; Skliarova, Iouliia; Pimentel, Bruno; Arrais, Joel. http://dx.doi.org/10.1007/978-3-540-30117-2_100.
    10.1007/978-3-540-30117-2_100
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2021/03 Deep Learning techniques for drug discovery Biomedical students meeting
(Coimbra)
2020 Joel P. Arrais, "Exploring Deep Learning for improved Drug Discovery", Bioinformatics Open Days, Braga, Portugal, 2020
2019 Joel P. Arrais, "The impact of Bioinformatics and Machine Learning in Drug Discovery", 53rd Annual Scientific Meeting of the European Society for Clinical Investigation, Coimbra, Portugal, 2019
2019 Joel P. Arrais, "Deep Learning potential to fill the gene-disease gap", Biotech-UC, Cantanhede, Portugal, 2019
2018 Joel P. Arrais, "Using gene expression data to reconstruct gene regulatory networks", 2nd Portuguese Meeting in Biomathematics, Aveiro, Portugal, 2018
2017 Joel P. Arrais, “The role of intelligent algorithms on phealth”, Center for Research & Development in Mathematics and Applications (CIDMA), Aveiro, Portugal, 2017
2016 Joel P. Arrais, "From time series data to gene regulatory networks", CECAD, Cologne, Germany, 2016
2015 Joel P. Arrais, "Using time series data to reconstruct gene signalling networks", Laboratório de Armindo Salvador, Centro de Neurociências e Biologia Celular, Coimbra, Portugal, 2015
2014 Joel P. Arrais, "Computational Prediction and analysis of Biological Networks", Ziv Bar-Zoseph Group, Carnegie Mellon, USA, 2014
2013 Joel P. Arrais, "Computational Prediction of the Human-Bacteria Interactome", Bioinformatics Open Days, Braga, Portugal, 2013
2008 Joel P. Arrais, “Improving data management in a [small] gene expression laboratory”, European Bioinformatics Institute, Cambridge, UK, 2008
2006 Joel P. Arrais, “Microarray data: from the hybridisation to the analysis”, sessão “Best of results”, European Summer School on Biomedical Informatics, Balatonfüred, Hungria, 2006

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2019 - Current Deep Learning architectures for optimal analysis of Type 2 diabetes heritability
Supervisor
Universidade de Coimbra Centro de Informatica e Sistemas, Portugal
2019 - Current Deep Learning Approach for Drug-Target Interaction Prediction
Supervisor
 Computer Science (PhD)
Universidade de Coimbra Centro de Informatica e Sistemas, Portugal
2019 - Current Machine learning for aircraft maintenance adaptive real-timeplanning and scheduling based on constraints
Co-supervisor
 Computer Science (PhD)
Universidade de Coimbra Centro de Informatica e Sistemas, Portugal
2017 - Current Interactive Visualization Models for Complex Biological Networks
Co-supervisor of Anto´nio Malta Lopes da Cruz
Universidade de Coimbra Centro de Informatica e Sistemas, Portugal
2012 - 2019 Prediction and analysis of biological networks structure and dynamics
Co-supervisor
Universidade de Aveiro, Portugal
2012 - 2017 Computational prediction of inter-species protein-protein interactions
Co-supervisor of Edgar Duarte de Jesus Valente Marques Coelho
 Doutoramento em Ciências da Computação (PhD)
Universidade de Aveiro, Portugal

Association member

Society Organization name Role
2017 - Current Membro da Associação Portuguesa de Reconhecimento de Padrões (APRP), que visa a promoção de avanços, quer na teoria quer nas aplicações práticas, da disciplina científica do reconhecimento de padrões. http://www.aprp.pt
2017 - Current Membro da rede HCI-KDD que visa explorar soluções que combinem técnicas de Human-Computer Interaction (HCI) com Knowledge Discovery/Data Mining (KDD). http://hci-kdd.org/international-expert-network

Conference scientific committee

Conference name Conference host
2019 - Current 15th Mediterranean Conference on Medical and Biological Engineering and Computing (MEDICON2019))
2012 - Current APCA International Conference on Control and Soft Computing (CONTROLO)
2012 - Current International Conference on Intelligent Systems for Molecular Biology (ISMB/ECCB)
2012 - Current International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB)
2012 - Current International Work-Conference on Bioinformatics and Biomedical Engineering (IWIBBIO)
2012 - Current International Joint Conference on Biomedical Engineering Systems and Technologies (BIOINFORMATICS)
2012 - Current Simpósio de Informática (INFORUM)
2012 - Current Iberian Conference on Information Systems and Technologies (CISTI)
2012 - Current World Congress on Medical and Health Informatics (MedInfo)
2012 - Current The International Conference on Health Informatics (ICHI)

Evaluation committee

Activity description
Role 		Institution / Organization Funding entity
2020/10 - Current Project evaluator for the ANI (national innovation agency) for the call 17/SI/2019.
2019/10 - Current Project evaluator for the cal for proposals "Innovative eScience Technologies for ‘Big Science’" promoted by the Netherlands eScience center.
Evaluator

Journal scientific committee

Journal title (ISSN) Publisher
2012 - Current Applied Computational Intelligence and Soft Computing (1687-9732) Hindawi Limited
2012 - Current Bioinformatics (1460-2059) Oxford University Press
2012 - Current BMC Bioinformatics (1471-2105) Springer (Biomed Central Ltd.)
2012 - Current Briefings in Bioinformatics (1477-4054) Oxford University Press
2012 - Current IEEE/ACM Transactions on Computational Biology and Bioinformatics (1557-9964) Institute of Electrical and Electronics Engineers
2012 - Current Journal of Integrative Bioinformatics (1613-4516) Walter de Gruyter GmbH
2012 - Current Computational and Structural Biotechnology Journal (2001-0370) Elsevier