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Nelson Rodrigo Carvalho Monteiro. Concluiu o(a) Mestrado integrado em Engenharia Biomédica em 2019/07/15 pelo(a) Universidade de Coimbra Faculdade de Ciencias e Tecnologia. Frequenta o(a) Doutoramento em Engenharia Informática pelo(a) Universidade de Coimbra Departamento de Engenharia Informática desde 2019/10/01. Publicou 6 artigos em revistas especializadas. Possui 1 capítulo(s) de livros. Organizou 1 evento(s). Participou em 3 evento(s). Coorientou 2 dissertação(ões) de mestrado. Participa e/ou participou como Bolseiro de Doutoramento em 1 projeto(s), Bolseiro de Investigação em 1 projeto(s) e Bolseiro de Mestrado em 1 projeto(s). Atua na(s) área(s) de Ciências Exatas com ênfase em Ciências da Computação e da Informação com ênfase em Bioinformática, Ciências Exatas com ênfase em Ciências da Computação e da Informação com ênfase em Ciências da Computação e Ciências da Engenharia e Tecnologias com ênfase em Engenharia Médica.
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Identification

Personal identification

Full name
Nelson Rodrigo Carvalho Monteiro

Citation names

  • Nelson R. C. Monteiro

Author identifiers

Ciência ID
FD1C-01C1-1F5D
ORCID iD
0000-0002-2147-7321

Email addresses

  • nelsonrcm@dei.uc.pt (Professional)
  • nelsonrcmonteiro@gmail.com (Personal)

Telephones

Mobile phone
  • 925908743 (Personal)

Websites

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Exact Sciences - Computer and Information Sciences - Computer Sciences
  • Engineering and Technology - Medical Engineering

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Education
Degree Classification
2019/10/01 - 2024/07/02
Concluded
 Engenharia Informática (Doutoramento)
Major in Sistemas Inteligentes - Ciência de Dados
Universidade de Coimbra Departamento de Engenharia Informática, Portugal
"Toward the Explainability of Drug--Target Interactions: End-to-End Deep Learning Architectures for Binding Affinity Prediction" (THESIS/DISSERTATION)
 Aprovado com Distinção e Louvor
2014/09/11 - 2019/07/15
Concluded
 Engenharia Biomédica (Mestrado integrado)
Major in Clinical Informatics and Bioinformatics
Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal
"End-to-End Deep Learning Approach for Drug-Target Interaction Prediction" (THESIS/DISSERTATION)
 15 (M. Sc. 18, M.Sc. Thesis 20)
Affiliation

Science

Category
Host institution 		Employer
2019/09 - 2023/11 Researcher (Research) Universidade de Coimbra Centro de Informatica e Sistemas, Portugal
Universidade de Coimbra Centro de Informatica e Sistemas, Portugal
2019/09/01 - 2020/08/31 Researcher (Research) Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal
Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal

Others

Category
Host institution 		Employer
2019/01 - 2019/08 Head of Technology and Innovation Department Junior Enterprise for Science and Technology (JEST), Portugal
Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal
2018/04 - 2019/08 Data Scientist Junior Enterprise for Science and Technology (JEST), Portugal
Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal
Projects

Grant

Designation Funders
2020/11 - 2023/10 Toward the Explainability of Drug-Target Interactions: End-to-End Deep Learning Architectures for Binding Affinity Prediction
2020.04741
PhD Student Fellow
Universidade de Coimbra Centro de Informatica e Sistemas, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2019/09/01 - 2020/08/31 D4: Deep Drug Discovery and Deployment
CENTRO-01-0145-FEDER-29266
Research Fellow
Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2019/02 - 2019/04 D4: Deep Drug Discovery and Deployment (MSc)
CENTRO-01-0145-FEDER-29266
Master Student Fellow
Universidade de Coimbra Centro de Informatica e Sistemas, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Book chapter
  1. Nelson R. C. Monteiro; Ribeiro, Bernardete; Arrais, Joel. "Deep Neural Network Architecture for Drug-Target Interaction Prediction". 804-809. Springer International Publishing, 2019.
    Published • 10.1007/978-3-030-30493-5_76
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. Torres, Luis H. M.; Nelson R. C. Monteiro; Oliveira, José Luis; Arrais, Joel; Ribeiro, Bernardete. "Exploring a Siamese Neural Network Architecture for One-Shot Drug Discovery". Paper presented in 2020 IEEE 20th International Conference on Bioinformatics and Bioengineering (BIBE), Cincinnati, OH, USA, 2020.
    Published • 10.1109/bibe50027.2020.00035
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.; Nelson R. C. Monteiro; Ribeiro, Bernardete; Oliveira, José Luis; Arrais, Joel. "Siamese Neural Networks for One-Shot Drug Discovery". Paper presented in BOD2020, Bioinformatics Open Days 2020, 2020.
  3. Nelson R. C. Monteiro; Ribeiro, Bernardete; Arrais, Joel. "Drug-Target Interaction Prediction: End-to-End Deep Learn-ing Approach". Paper presented in BOD2019, Bioinformatics Open Days 2019, 2019.
  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. Nelson R. C. Monteiro; Ribeiro, Bernardete; Arrais, Joel. "Drug-Target Interaction Prediction: End-to-End Deep Learning Approach". Paper presented in EJIBCE2018, Structural Computational Biology Meeting of Junior Researchers, 2018.
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. Abbasi, Maryam; Beatriz P. Santos; Tiago C. Pereira; Raul Sofia; Nelson R. C. Monteiro; Simões, Carlos J. V. ; Rui M. M. Brito; et al. "Designing optimized drug candidates with Generative Adversarial Network". Journal of Cheminformatics 14 1 (2022): http://dx.doi.org/10.1186/s13321-022-00623-6.
    Published • 10.1186/s13321-022-00623-6
  4. Monteiro, Nelson; Simões, Carlos J. V. ; Henrique V. Ávila; Oliveira, José Luis; Joel P. Arrais. Corresponding author: Monteiro, Nelson. "Explainable deep drug-target representations for binding affinity prediction". BMC Bioinformatics 23 1 (2022): http://dx.doi.org/10.1186/s12859-022-04767-y.
    Published • 10.1186/s12859-022-04767-y
  5. Nelson R. C. Monteiro; Oliveira, José Luis; Joel P. Arrais. Corresponding author: Nelson R. C. Monteiro. "DTITR: End-to-end drug-target binding affinity prediction with transformers". Computers in Biology and Medicine (2022): https://doi.org/10.1016/j.compbiomed.2022.105772.
    Published • 10.1016/j.compbiomed.2022.105772
  6. Monteiro, Nelson; Ribeiro, Bernardete; Arrais, Joel. "Drug-Target Interaction Prediction: End-to-End Deep Learning Approach". IEEE/ACM Transactions on Computational Biology and Bioinformatics (2020): http://dx.doi.org/10.1109/tcbb.2020.2977335.
    Published • 10.1109/tcbb.2020.2977335
Activities

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2022/09 - 2023/09 Deep Generative Models for Protein Repositioning
Co-supervisor
 Mestrado em Engenharia e Ciência de Dados (Master)
Universidade de Coimbra Centro de Informatica e Sistemas, Portugal
2021/09 - 2022/09 End-to-End Transformer-based Approach for Optimized De Novo Drug Design
Co-supervisor
 Mestrado em Engenharia Biomédica - Bioinformática e Informática Clinica (Master)
Universidade de Coimbra Centro de Informatica e Sistemas, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2018 - 2019/02/10 (Mind Your Data: Data Science Conference) Involved in the speaker's selection and recruitment processes and in the organization of the workshops. (2019/02/09 - 2019/02/10)
Conference (Member of the Organising Committee)
 Junior Enterprise for Science and Technology (JEST), Portugal

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2023/03 - 2023/03 Invited speaker on the topic "Alumni: Career Path and Academic Journey"
Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal
2020/03/01 - 2020/03/01 Invited speaker on the topic "Artificial Intelligence in Portugal"
Conference
 Mind Your Data
Junior Enterprise for Science and Technology (JEST), Portugal
2019/04/20 - 2019/04/20 Python Programming and Statistics Workshop Instructor
Conference
 Bioengineering Week
Universidade de Lisboa Instituto Superior Técnico, Portugal