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Aluno de doutoramento e investigador na Universidade do Minho (UMinho), noemadamente no Centro de Engenharia Biológica (CEB). O ramo de especialização consiste na área das Ciências da Computação e da Informação com ênfase na Bioinformática e Biologia de Sistemas.
Identification

Personal identification

Full name
Fernando João Pereira Cruz

Citation names

  • Cruz, Fernando

Author identifiers

Ciência ID
3514-F068-6B2D
ORCID iD
0000-0003-2468-7364

Email addresses

  • fernandocruz184@gmail.com (Professional)

Addresses

  • Rua das Azedas, 121, 4905-644, Vila de Punhe, Viana do Castelo, Portugal (Personal)

Websites

  • https://cruz-f.github.io/ (Personal)

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics

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
2018/10/01 - 2022/10/01
Ongoing
 Programa Doutoral em Engenharia Biomédica (Doutoramento)
Universidade do Minho Centro de Engenharia Biológica, Portugal
"Blueprint: Documenting the Complexity of Metabolic Regulation by Reconstruction of Integrated Metabolic-Regulatory Models" (THESIS/DISSERTATION)
2017
Concluded
 Bioinformática (Mestrado)
Major in Área de especialização: Tecnologias da Informação
Universidade do Minho, Portugal
"reconstrução da rede metalica à escala genómica de streptococus thermophilus " (THESIS/DISSERTATION)
 17 valores
2012/09/15 - 2015/07/15
Concluded
 Biologia Aplicada (Licenciatura)
Universidade do Minho, Portugal
 16
Affiliation

Science

Category
Host institution 		Employer
2018/10/01 - 2022/10/31 Researcher (Research) Universidade do Minho Centro de Engenharia Biológica, Portugal
2018/02/01 - 2018/09/30 Research Assistant (Research) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Teaching in Higher Education

Category
Host institution 		Employer
2022/10/03 - 2023/03/19 Invited Assistant (University Teacher) Universidade do Minho Departamento de Informática, Portugal
Universidade do Minho Departamento de Informática, Portugal
Projects

Grant

Designation Funders
2018/10/01 - 2022/10/01 Blueprint: Documenting the Complexity of Metabolic Regulation by Reconstruction of Integrated Metabolic-Regulatory Models
SFRH/BD/139198/2018
PhD Student Fellow
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
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
  2. Cruz, Fernando. "Towards the Reconstruction of Integrated Genome-Scale Models of Metabolism and Gene Expression". 2020.
    10.1007/978-3-030-23873-5_21
Conference paper
  1. "Reconciliation of Regulatory Data: The Regulatory Networks of Escherichia coli and Bacillus subtilis". 2021.
    10.1007/978-3-030-54568-0_16
Journal article
  1. 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
  2. Cruz, Fernando. "MEWpy: A Computational Strain Optimization Workbench in Python.". Bioinformatics (Oxford, England) (2021): https://doi.org/10.1093/bioinformatics/btab013.
    10.1093/bioinformatics/btab013
  3. "merlin v4.0: an updated platform for the reconstruction of high-quality genome-scale metabolic models". bioRxiv (2021): https://www.biorxiv.org/content/early/2021/02/25/2021.02.24.432752.
    10.1101/2021.02.24.432752
  4. Fernando Cruz; José P. Faria; Miguel Rocha; Isabel Rocha; Oscar Dias. "A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation". Biochemical Society Transactions (2020): https://doi.org/10.1042/BST20190840.
    10.1042/BST20190840
  5. Cruz, Fernando. "SamPler – a novel method for selecting parameters for gene functional annotation routines". BMC Bioinformatics (2019): http://dx.doi.org/10.1186/s12859-019-3038-4.
    10.1186/s12859-019-3038-4
  6. Cruz, Fernando. "A LysM Domain Intervenes in Sequential Protein-Protein and Protein-Peptidoglycan Interactions Important for Spore Coat Assembly in Bacillus subtilis". Journal of Bacteriology (2018): http://dx.doi.org/10.1128/jb.00642-18.
    10.1128/jb.00642-18

Other

Other output
  1. BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic models. 2021. Fernando Cruz; João Capela; Eugénio C. Ferreira; Miguel Rocha; Oscar Dias. https://doi.org/10.1101/2021.03.07.434259.
    10.1101/2021.03.07.434259
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2019/06/26 Towards the Reconstruction of Integrated Genome-Scale Models of Metabolism and Gene Expression Practical Applications of Computational Biology and Bioinformatics, 13th International Conference
(Ávila, Spain)
Distinctions

Award

2020 Bolsa de Estudo por Mérito Escolar
Universidade do Minho, Portugal