Personal identification

Full name

José Vítor de Castro Vieira

Citation names

• Vieira, Vítor

Author identifiers

Ciência ID

7A1C-47B6-BD61

ORCID iD

0000-0001-9604-9586

Email addresses

• vvieira@ceb.uminho.pt (Professional)

Knowledge fields

• Natural sciences - Biological Sciences
• Engineering and Technology - Industrial Biotechnology

Languages

Language	Speaking	Reading	Writing	Listening	Peer-review
Portuguese (Mother tongue)	Advanced (C1)	Advanced (C1)	Advanced (C1)	Advanced (C1)
English	Advanced (C1)	Advanced (C1)	Advanced (C1)	Advanced (C1)
Spanish; Castilian	Intermediate (B1)	Intermediate (B1)	Beginner (A1)	Intermediate (B1)

	Degree	Classification
2017/02/01 - 2022/04/28 Concluded	Engenharia Biomédica (Doutoramento) Universidade do Minho Escola de Engenharia, Portugal "Integrative pathway analysis approaches for cancer research and drug development" (THESIS/DISSERTATION)
2013 - 2015 Concluded	Bioinformática (Mestrado) Universidade do Minho, Portugal "Desenvolvimento de algorítmos para otimização de estirpes baseados em análise de vias metabólicas" (THESIS/DISSERTATION)	18
2010 - 2013 Concluded	Ciências Biomédicas (Licenciatura) Universidade de Aveiro, Portugal	15

Science

	Category Host institution	Employer
2014/12/16 - 2017/02/28	Researcher (Research)	Universidade do Minho, Portugal
	Universidade do Minho Centro de Engenharia Biológica, Portugal
2014/05 - 2014/07	Research Assistant (Research)	Universidade do Minho, Portugal

Teaching in Higher Education

	Category Host institution	Employer
2018/02/01 - 2019/02/01	Invited Assistant (University Teacher)	Universidade do Minho, Portugal
	Universidade do Minho, Portugal

Other

	Designation	Funders
2014/12 - 2017/02	DeYeastLibrary ERA-IB-2/0003/2013 Master Student Fellow Universidade do Minho, Portugal	Concluded
2011 - 2014	ToMEGIM: Ferramentas Computacionais para Engenharia Metabólica usando Modelos Integrados de Escala Genómica PTDC/EIA-EIA/115176/2009 Universidade do Minho, Portugal	Concluded

Publications

Book chapter	Jorge Ferreira; Vítor Vieira; Jorge Gomes; Sara Correia; Miguel Rocha. "Troppo - A Python Framework for the Reconstruction of Context-Specific Metabolic Models". 2020. 10.1007/978-3-030-23873-5_18 Vieira, Vítor. "Genome-Scale Metabolic Models". 2019. 10.1016/b978-0-12-801238-3.11514-4 Vieira, Vítor; Maia, Paulo; Rocha, Isabel; Rocha, Miguel. "Development of an Integrated Framework for Minimal Cut Set Enumeration in Constraint-Based Models". In 10th International Conference on Practical Applications of Computational Biology & Bioinformatics, 193-201. Cham: Springer International Publishing, 2016. Published • 10.1007/978-3-319-40126-3_20
Conference abstract	Vieira, Vítor; Maia, Paulo; Rocha, Miguel; Rocha, Isabel. "Development of pathway analysis based algorithms for strain optimization". Paper presented in Bioinformatics Open Days, Braga, 2016. Published Vieira, Vítor; Maia, Paulo; Rocha, Miguel; Rocha, Isabel. "Comparing knockout strategies from in silico rational strain design tools". Paper presented in 4th Conference on Constraint-Based Reconstruction and Analysis (COBRA), Heidelberg, Alemanha, 2015. Published
Conference paper	Vieira, Vítor. "Development of an Integrated Framework for Minimal Cut Set Enumeration in Constraint-Based Models". Paper presented in 10th International Conference on Practical Applications of Computational Biology & Bioinformatics, Sevilla, Espanha, 2016. Published
Journal article	Vítor Vieira; Christoph Kaleta; Jorge Ferreira; Miguel Rocha. "A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale". PLOS Computational Biology (2022): https://doi.org/10.1371/journal.pcbi.1009294. 10.1371/journal.pcbi.1009294 Vítor Vieira; Miguel Rocha; Alfonso Valencia. "CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models". Bioinformatics (2019): https://doi.org/10.1093/bioinformatics/btz598. 10.1093/bioinformatics/btz598 Vieira, Vítor. "Comparison of pathway analysis and constraint-based methods for cell factory design". BMC Bioinformatics (2019): http://dx.doi.org/10.1186/s12859-019-2934-y. 10.1186/s12859-019-2934-y Vítor Vieira; Jorge Ferreira; Rúben Rodrigues; Filipe Liu; Miguel Rocha. "A Model Integration Pipeline for the Improvement of Human Genome-Scale Metabolic Reconstructions". Journal of Integrative Bioinformatics 16 1 (2019): https://doi.org/10.1515/jib-2018-0068. 10.1515/jib-2018-0068 Vieira, Vítor. "Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data". The Lancet Oncology (2017): http://dx.doi.org/10.1016/s1470-2045(16)30560-5. 10.1016/s1470-2045(16)30560-5 Vieira, Vítor; Maia, Paulo; Rocha, Isabel; Rocha, Miguel. "Development of a Framework for Metabolic Pathway Analysis-Driven Strain Optimization Methods". Interdisciplinary Sciences: Computational Life Sciences 9 1 (2017): 46-55. Published • 10.1007/s12539-017-0218-7

Other

Other output

A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale. 2021. Vítor Vieira; Jorge Ferreira; Miguel Rocha. https://doi.org/10.1101/2021.07.22.453372. 10.1101/2021.07.22.453372 HABIT – a webserver for interactive T cell neoepitope discovery. 2019. Vieira, Vítor. http://dx.doi.org/10.1101/535716. 10.1101/535716 Minimal cut set enumeration plugin for OptFlux. Software. 2016. Vieira, Vítor; Maia, Paulo; Rocha, Miguel; Rocha, Isabel. https://sourceforge.net/p/optflux/optflux-mcs/.