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My name is João Capela, I am 26 years old and holder of a Master's degree in Bioinformatics, since 2021, from the School of Engineering of the University of Minho (EEUM), and a Bachelor's degree in Biology with complementary formation in Informatics, since 2018, from the Faculty of Sciences of the University of Porto (FCUP). I have skills in software development and chemoinformatics as well as on subjects such as biosynthesis of natural compounds, general biochemistry, and metabolic modelling. I am currently the main developer of merlin (https://merlin-sysbio.org/team/), a large-scale software to assist in the reconstruction of GSMMs and genome annotation. I joined the DeepBio project, where I am developing tools using machine and deep learning towards the production of biotechnologically relevant compounds. Right now, I am a PhD student at the Centre of Biological Engineering developing the project: "AI2SM: Artificial Intelligence to Expose Plant Secondary Metabolism".
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Identification

Personal identification

Full name
João Capela

Citation names

  • Capela, João

Author identifiers

Ciência ID
0510-DBB6-7904
ORCID iD
0000-0002-1235-2922

Email addresses

  • joao.capela@ceb.uminho.pt (Professional)

Websites

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Natural sciences - Biological Sciences - Plant sciences
  • Exact Sciences - Computer and Information Sciences

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Proficiency (C2) Proficiency (C2) Advanced (C1) Advanced (C1) Proficiency (C2)
German Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1)
Education
Degree Classification
2022/03/01 - 2026/03/01
Ongoing
 Doutoramento em Informática (Doutoramento)
Universidade do Minho, Portugal

Universidade do Minho Centro de Engenharia Biológica, Portugal
"AI2SM: Artificial Intelligence to expose plant secondary metabolism" (THESIS/DISSERTATION)
2018/09/15 - 2021/03/01
Concluded
 Bioinformática (Mestrado)
Universidade do Minho, Portugal
"Biochemical Complex data Generation and Integration in Genome-Scale Metabolic Models" (THESIS/DISSERTATION)
 18
2020/07/26 - 2020/09/26
Concluded
 Summer School in Constraint Based Reconstruction and Analysis of metabolic models (Outros)
Major in Bioinformatics and Industrial biotechnology
Universidade do Minho, Portugal
2015/09/15 - 2018/07/15
Concluded
 Biologia (Licenciatura)
Major in Minor em Informática
Universidade do Porto, Portugal
 16
Affiliation

Science

Category
Host institution 		Employer
2022/03/01 - 2026/03/01 Researcher (Research) Fundação para a Ciência e a Tecnologia, Portugal
Universidade do Minho, Portugal
(...)
2020/11/15 - 2022/03/01 Contracted Researcher (Research) Fundação para a Ciência e a Tecnologia, Portugal
Universidade do Minho, Portugal
(...)
2017/10/15 - 2018/06/15 Researcher (Research) Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2017/02/01 - 2017/06/01 Research Trainee (Research) Universidade do Porto Faculdade de Ciências, Portugal
Plant Stress Lab, Portugal

Others

Category
Host institution 		Employer
2022 - 2026 PhD Student Universidade do Minho Centro de Engenharia Biológica, Portugal
2020/02/01 - 2022 Repository mantainer - BOIMMG (https://boimmg.bio.di.uminho.pt/) Universidade do Minho Centro de Engenharia Biológica, Portugal
2019/02/15 - 2022 Software mantainer - merlin (https://merlin-sysbio.org/team/) Universidade do Minho, Portugal
2019/07/01 - 2019/07/31 Monitor de Fisiologia Vegetal no projeto Universidade Júnior Universidade Júnior, Portugal
Universidade do Porto Faculdade de Ciências, Portugal
2018/07/01 - 2019/07/31 Monitor de Fisiologia Vegetal no projeto Universidade Júnior Universidade Júnior, Portugal
Universidade do Porto Faculdade de Ciências, Portugal
2018/08/01 - 2018/09/30 Monitor de sensibilização ambiental na campanha Comércio a Reciclar BioRumo - Consultoria em ambiente e sustentabilidade LA, Portugal
Projects

Contract

Designation Funders
2020/11/15 - 2021/08/15 DeepBio - Abordagens de aprendizagem máquina e deep learning para aplicações de biotecnologia industrial
NORTE-01-0247-FEDER-039831
Research Fellow
SilicoLife, Portugal

Universidade do Minho, Portugal
Ongoing
Outputs

Publications

Book chapter
  1. "Towards a Multivariate Analysis of Genome-Scale Metabolic Models Derived from the BiGG Models Database". 136-144. Springer International Publishing, 2022.
    10.1007/978-3-030-86258-9_14
Conference abstract
  1. Capela, João; Filipe Liu; Oscar Dias. "Revising lipid chemical structures in genome-wide metabolic models with BOIMMG". Paper presented in BOD 2021 - X Bioinformatics Open Days, Braga, 2021.
    Accepted
  2. "Revising lipid chemical structures in genome-wide metabolic models with BOIMMG". Braga, 2021.
  3. Diogo Lima; Davide Lagoa; Fernando Cruz; José Bastos; Capela, João; Eugénio C. Ferreira; Miguel Rocha; Oscar Dias. "merlin v4: an updated platform for reconstructing genome-scale metabolic models". Paper presented in BOD 2020 - IX Bioinformatics Open Days, Braga, 2020.
    Published
Conference paper
  1. Capela, Joao; Correia, Joao; Pereira, Vitor; Rocha, Miguel. "Development of Deep Learning approaches to predict relationships between chemical structures and sweetness". Paper presented in International Joint Conference on Neural Networks (IJCNN), 2022.
    10.1109/ijcnn55064.2022.9891992
Journal article
  1. Correia, João; Capela, João; Rocha, Miguel. "Deepmol: an automated machine and deep learning framework for computational chemistry". Journal of Cheminformatics 16 1 (2024): https://doi.org/10.1186/s13321-024-00937-7.
    10.1186/s13321-024-00937-7
  2. João Capela; Davide Lagoa; Ruben Rodrigues; Emanuel Cunha; Fernando Cruz; Ana Barbosa; José Bastos; et al. "merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models". Nucleic Acids Research (2022): https://doi.org/10.1093/nar/gkac459.
    10.1093/nar/gkac459
  3. Capela, João; Davide Lagoa; Ruben Rodrigues; Emanuel Cunha; Fernando Cruz; Ana Barbosa; José Bastos; et al. "merlin v4.0: an updated platform for the reconstruction of high-quality genome-scale metabolic models". Nucleic Acid Research (2021): https://www.biorxiv.org/content/10.1101/2021.02.24.432752v1.
    Submitted • https://doi.org/10.1101/2021.02.24.432752
  4. Fernando Cruz; Capela, João; Eugénio C. Ferreira; Miguel Rocha; Oscar Dias. "BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic models". BMC Bioinformatics (2021):
    Submitted • https://doi.org/10.1101/2021.03.07.434259
Activities

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2020/02/19 - 2020/02/21 Bioinformatics Open Days IX - BOD, University of Minho, Braga, Portugal (2020/02/19 - 2020/02/21)
Conference (Member of the Organising Committee)
 Universidade do Minho, Portugal

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2019/02/20 - 2019/02/22 Short communication about the output of my work on the "Bioinformatics Laboratories" discipline - VIII Bioinformatics Open Days , Braga, Portugal
Conference
 VIII Bioinformatics Open Days , Braga, Portugal
Universidade do Minho, Portugal

Association member

Society Organization name Role
2019/11/21 - Current NEBiUM - Núcleo de Estudos de Bioinformática da Universidade do Minho Direction Member

Committee member

Activity description
Role 		Institution / Organization
2018/09/15 - 2020/10/31 Students' representative of the 2018 class of the Master's course in Bioinformatics
Coordinator
 Universidade do Minho, Portugal

Mentoring / Tutoring

Topic Student name
2020/02/17 - 2020/07/22 Implementation of two plugins in merlin software to improve validation and visualization of metabolic models. Ana Carolina Costa Barbosa