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Oscar Dias is an accomplished professional with a dynamic role as an Auxiliary Researcher at the University of Minho since 2016. In this capacity, he passionately imparts knowledge in Bioinformatics, Systems Biology, and the Modeling of Biological Processes. Simultaneously, Oscar holds the position of CEO at OMNIUMAI, a forward-thinking company providing cutting-edge solutions in Artificial Intelligence and Data Sciences. As an academic, Oscar brings a wealth of expertise with a background in Biological Engineering, an MSc in Informatics, and a PhD in Chemical and Biological Engineering. Elected to the Scientific Steering Committee of the Center and invited to join the Scientific Steering Committee of the Department, Oscar actively participates in shaping the academic landscape. Currently, he serves on the Steering Committee of the master’s in bioinformatics at the University of Minho, further demonstrating his commitment to advancing education and research. As a proficient investigator, Oscar has led as Principal Investigator in one short project and is actively engaged in four ongoing research projects, contributing to a total of approximately 16 projects throughout his career. His academic output includes over 50 publications in international peer-reviewed journals, conferences, and book chapters. A mentor and guide, Oscar has supervised two PhD theses (1 pending defense) and currently supervises five and co-supervises three, with a remarkable track record of successfully guiding 40 master's dissertations and overseeing the progress of 17 more. Recognizing his outstanding contributions, Oscar has been honored with three prestigious awards. Oscar's research endeavors encompass Bioinformatics, Machine Learning, Systems Biology, and Biotechnology, fostering collaborations across Denmark, Germany, The Netherlands, Spain, the UK, USA, among others.
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Identification

Personal identification

Full name
ÓSCAR MANUEL LIMA DIAS

Citation names

  • Dias, O.

Author identifiers

Ciência ID
B81F-26CB-714A
ORCID iD
0000-0002-1765-7178
Google Scholar ID
e4aWA5UAAAAJ

Email addresses

  • odias@deb.uminho.pt (Professional)
  • odias@deb.uminho.pt (Personal)

Telephones

Telephone
  • (351) 253604421 (Professional)

Addresses

  • Centro de Engenharia Biológica (CEB), Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Braga, Portugal (Professional)

Websites

  • http://ceb.uminho.pt/People/Profile/odias (Scholar)

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Engineering and Technology - Industrial Biotechnology

Languages

Language Speaking Reading Writing Listening Peer-review
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
French Upper intermediate (B2) Upper intermediate (B2) Intermediate (B1) Upper intermediate (B2)
Spanish; Castilian Beginner (A1) Beginner (A1) Intermediate (B1) Advanced (C1)
Education
Degree Classification
2009 - 2013
Concluded
 Engenharia Química e Biológica (Doutoramento)
Major in Sem especialidade
Universidade do Minho, Portugal
"Reconstruction of the Genome-scale Metabolic Network of Kluyveromyces Lactis" (THESIS/DISSERTATION)
 Muito bom
2006 - 2008
Concluded
 Informática (Mestrado)
Universidade do Minho, Portugal
"Bioinformática" (THESIS/DISSERTATION)
 Muito Bom
1999 - 2005
Concluded
 Engenharia Biológica (Licenciatura)
Universidade do Minho, Portugal
 14
Affiliation

Science

Category
Host institution 		Employer
2020/12/31 - Current Auxiliary Researcher (Research) Universidade do Minho, Portugal
Universidade do Minho Centro de Engenharia Biológica, Portugal
2014/06/01 - 2020/12/30 Invited Auxiliary Researcher (Research) Universidade do Minho Centro de Engenharia Biológica, Portugal
2013/07/01 - 2014/08/31 Postdoc (Research) Universidade do Minho Centro de Engenharia Biológica, Portugal
2013/02 - 2013/07 Research Assistant (Research) Universidade do Minho, Portugal
2009/03 - 2013/02 Researcher (Research) Universidade do Minho, Portugal
2008/03 - 2008/12 Research Trainee (Research) Universidade do Minho, Portugal
2006/10 - 2008/03 Research Trainee (Research) Universidade do Minho, Portugal

Teaching in Higher Education

Category
Host institution 		Employer
2016/09/01 - 2020/12/30 Invited Assistant Professor (University Teacher) Universidade do Minho Departamento de Engenharia Biológica, Portugal

Positions / Appointments

Category
Host institution 		Employer
2021/06/01 - Current Chief Executive Officer OMNIUMAI - INTELIGÊNCIA ARTIFICIAL E CIÊNCIAS DE DADOS, LDA, Portugal
OMNIUMAI - INTELIGÊNCIA ARTIFICIAL E CIÊNCIAS DE DADOS, LDA, Portugal
2020 - Current Member of the Steering Committee of the Masters in Bioinformatics Universidade do Minho, Portugal
2019/11 - Current Member of the Scientific Steering Committee of Department, Department of Biological Engineering Universidade do Minho Departamento de Engenharia Biológica, Portugal
Universidade do Minho, Portugal
2018/03/01 - 2021/07 Member of the Scientific Steering Committee of the Research Unit, Centre of Biological Engineering Universidade do Minho Centro de Engenharia Biológica, Portugal

Others

Category
Host institution 		Employer
2009/09/01 - 2012/08/31 Member of the Academic Senate Universidade do Minho, Portugal
Projects

Grant

Designation Funders
2016/03/01 - 2020/02/29 DD-Decaf - Bioinformatics Services for Data-Driven Design of Cell Factories and Communities
H2020-LEIT-BIO-2015-1 686070-1
Science and Technology Management Fellow
Universidade do Minho Centro de Engenharia Biológica, Portugal
 European Commission
Ongoing
2012/07 - 2015/06 PEM - Metabolic Engineering Platform
ADI-QREN- 23060
Researcher
Universidade do Minho, Portugal
Concluded
2009/02/01 - 2013/01/31 RECONSTRUCTION OF THE GENOME-SCALE METABOLIC NETWORK OF KLUYVEROMYCES LACTIS
SFRH/BD/47307/2008
Universidade do Minho, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2005/10 - 2008/03 Monitoring of a Wastewater Treatment Plant by Image Analysis Techniques
57069
Provided by PTCRIS: 57069
Research Fellow
Fundação para a Ciência e a Tecnologia, I.P.
Concluded

Contract

Designation Funders
2020/12/31 - Current iPlants.pt: in silico models of Portuguese flora
CEECIND/03425/2018
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2019/01/01 - Current Centre of Biological Engineering - University of Minho
UID/BIO/04469/2019
Universidade do Minho, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2021/01/01 - 2025/12/31 Laboratório Associado em Biotecnologia, Bioengenharia e Sistemas microELetromecânicos
LA/P/0029/2020
Universidade do Minho, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2021/01/01 - 2025/12/31 Associate Laboratory on Biotechnology, Bioengineering and microELectromechanical Systems
10.54499/LA/P/0029/2020
Universidade do Minho, Portugal

Universidade do Minho Centro de Engenharia Biológica, Portugal

Universidade do Minho Labbels, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2023/03/01 - 2024/08/31 Methane mitigation strategies based on photosynthetic microorganisms
2022.05196.PTDC
Universidade do Minho, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2021/03/01 - 2024/08/31 Activating Dormant Bacteria with phage-derived proteins to enhance antibiotic efficacy
10.54499/PTDC/BIA-MIC/2312/2020
Universidade do Minho, Portugal

Universidade do Minho Centro de Engenharia Biológica, Portugal

Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal

Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2022/01/03 - 2024/01/02 Unveiling genetic REgulatory MOdules acting on the crosstalk between cork Development and EnvironmentaL factors – CorkREMODEL
10.54499/EXPL/ASP-SIL/1190/2021
Universidade NOVA de Lisboa, Portugal

BioResources 4 Sustainability, Portugal

Universidade do Minho, Portugal

Universidade do Minho Centro de Engenharia Biológica, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2016/07/01 - 2020/06/30 BioTecNorte - Underpinning Biotechnology to foster the north of Portugal bioeconomy
NORTE-01-0145-FEDER-000004
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Comissao de Coordenacao e Desenvolvimento Regional do Norte
Concluded
2016/07 - 2020/06 BioTecNorte - Underpinning Biotechnology to foster the north of Portugal bioeconomy
NORTE-01-0145-FEDER-000004
 Comissao de Coordenacao e Desenvolvimento Regional do Norte
2015/04/01 - 2018/12/31 DYNAMICS: Analysis and optimization of industrial microorganisms under dynamic process conditions
ERA-IB-2/0002/2014
Universidade do Minho, Portugal

Universidade do Minho Centro de Engenharia Biológica, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2014/03/01 - 2017/12/31 Designer yeast strain library optimized for metabolic engineering applications
ERA-IB-2/0003/2013
Universidade do Minho, Portugal

Universidade do Minho Centro de Engenharia Biológica, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2012/04/01 - 2015/09/30 Caracterização dos princípios de design de circuitos metabólicos prevalentes
PTDC/QUI-BIQ/119657/2010
Universidade do Minho, Portugal

Universidade de Coimbra, Portugal

Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2011/01/01 - 2014/06/30 In silico reconstruction of Streptococcus pneumoniae cellular networks and their impact on virulence
PTDC/EBB-EBI/113824/2009
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal

Universidade de Lisboa Centro de Química e Bioquímica, Portugal

Instituto de Biotecnologia e Bioengenharia, Portugal

Universidade do Minho, Portugal

Universidade de Lisboa Faculdade de Ciências, Portugal

LASIGE Laboratório de Sistemas Informáticos de Grande Escala, Portugal

Universidade de Lisboa Instituto de Medicina Molecular João Lobo Antunes, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2011/01/01 - 2012/12/31 Projecto Estratégico - LA 23 - 2011-2012
PEst-OE/EQB/LA0023/2011
Universidade do Minho, Portugal

Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal

Universidade de Trás-os-Montes e Alto Douro, Portugal

Universidade do Algarve, Portugal

Instituto de Biotecnologia e Bioengenharia, Portugal

Fundação Gaspar Frutuoso, Portugal

Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal

Universidade dos Açores, Portugal

Universidade de Lisboa Instituto Superior Técnico, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2011/01/01 - 2012/12/31 Strategic Project - LA 23 - 2011-2012
PEst-OE/EQB/LA0023/2011
Instituto de Biotecnologia e Bioengenharia, Portugal

Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal

Universidade de Lisboa Instituto Superior Técnico, Portugal

Fundação Gaspar Frutuoso, Portugal

Universidade do Minho, Portugal

Universidade do Algarve, Portugal

Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal

Universidade de Trás-os-Montes e Alto Douro, Portugal

Universidade dos Açores, Portugal
Fundação para a Ciência e a Tecnologia
Concluded

Other

Designation Funders
2021/03/01 - 2024/02/29 Activating Dormant Bacteria with phage-derived proteins to enhance antibiotic efficacy
PTDC/BIA-MIC/2312/2020
Researcher
Fundação para a Ciência e a Tecnologia
2022/03/01 - 2023/07/02 Unveiling genetic REgulatory MOdules acting on the crosstalk between cork Development and EnvironmentaL factors – CorkREMODEL
EXPL/ASP-SIL/1190/2021
Researcher
2018/10/01 - 2022/09/30 Targeting pathogenesis and engineering cell factories: by developing mixed regulatory-metabolic genomic models in yeasts
PTDC/BII-BIO/28216/2017
Researcher
Universidade do Minho, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2018/10/01 - 2020/12/31 MIXED-UP - Targeting pathogenesis and engineering cell factories: developing mixed regulatory-metabolic genomic models in yeasts
PTDC/BII-BIO/28216/2017
Researcher
Fundação para a Ciência e a Tecnologia
Ongoing
2020/07/27 - 2020/10/26 Summer School in Constraint Based Reconstruction and Analysis of metabolic models
S2CoBRA
Principal investigator
Universidade do Minho, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2017/06/01 - 2020/05/31 Biodata.pt - Portuguese Biological Data Network
22231
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2017/01/01 - 2019/12/31 BBRI - Biomass and Bioenergy Research Infrastructure
PINFRA/22059/2016
Researcher
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2014/03 - 2017/02 DeYeast Library - Designer yeast strain library optimized for metabolic engineering applications
info:eu-repo/grantAgreement/FCT/3599-PPCDT/137211/PT
Researcher
European Commission
Concluded
2012/04 - 2015/03 Metabolic Circuits - Finding the naturally evolved design principles of prevalent metabolic circuits
Provided by PTCRIS: 119657
119657
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2011/01 - 2014/06 PNEUMONIAE - In silico reconstruction of Streptococcus pneumoniae cellular networks and their impact on virulence
Provided by PTCRIS: 113824
113824
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
Concluded
2010/04 - 2013/09 AshByofactory - Ashbya gossypii: a systems metabolic engineered cell factory
Provided by PTCRIS: 101985
101985
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
Concluded
Outputs

Publications

Book chapter
  1. Dias, Oscar; Rocha, Miguel; Ferreira, Eugénio Campos; Rocha, Isabel. "Reconstructing High-Quality Large-Scale Metabolic Models with merlin". In Metabolic Network Reconstruction and Modeling, edited by Marco Fondi, 1-36. New York, United States: Springer New York, 2017.
    Published • 10.1007/978-1-4939-7528-0_1
  2. Dias, Oscar; Rocha, Isabel. "Systems Biology in Fungi". In Molecular Biology of Food and Water Borne Mycotoxigenic and Mycotic Fungi, 1-1. Boca Raton: CRC Press, 2013.
    Published
Conference abstract
  1. Lopes, M. J. ; Rodrigues, J. L.; Dias, O.. "Bioinformatics approaches for engineering L-Tyrosine production in Escherichia coli". Paper presented in Bioinformatics Open Days Edition XI, Online, 2022.
    Published
  2. Couto, M. R.; Dias, O.; Rodrigues, J. L.; Rodrigues, L. R.. "Stoichiometric genome-scale models for the chondroitin production in Escherichia coli". Paper presented in Bioinformatics Open Days Edition X, Online, 2021.
    Published
  3. Dias, Oscar; Rocha, Miguel; Ferreira, Eugénio C.; Rocha, Isabel; Rocha, I.. "MEtabolic models Reconstruction using genome scaLe INformation (merlin) - assessment and validation". Paper presented in Copenhagen Biosciences Conferences - 7th Conference: Cell Factories and Biosustainability, Copenhagen, 2015.
    Published
  4. Dias, Oscar; Rocha, Miguel; Ferreira, Eugénio C.; Rocha, Isabel; Rocha, I.. "Merlin Latest Developments for Pathways Analysis". Paper presented in MPA2015 - Metabolic Pathway Analysis 2015, Braga, 2015.
    Published
  5. Dias, Oscar; Saraiva, João; Ferreira, Eugénio C.; Rocha, Isabel. "Towards a Genome-Scale Metabolic Model of the Streptococcus Pneumoniae R6 Avirulent Strain". Paper presented in COBRA 2015 - 4th Conference on Constraint-Based Reconstruction and Analysis, Heidelberg, 2015.
    Published
  6. Gomes, Daniel; Dias, Oscar; Ferreira, Eugénio C.; Rocha, Isabel. "Reconstruction of a genome-scale metabolic model for the filamentous fungus Ashbya gossypii". Paper presented in PYFF5 - 5th Conference on Physiology of Yeast and Filamentous Fungi, Montpellier, 2014.
    Published
  7. Dias, Oscar; Gombert, Andreas K.; Ferreira, Eugénio C.; Rocha, Isabel. "Towards a genome-scale metabolic model for the Kluyveromyces lactis yeast.". Paper presented in 9th European Congress of Chemical Engineering / 2nd European Congress of Applied Biotechnology, The Hague, 2013.
    Published
  8. Dias, Oscar; Rocha, Miguel; Rocha, Isabel; Ferreira, Eugénio C.. "Metabolic reconstruction of less characterized microorganisms: a new methodology for reaction identification from genome sequencing data.". Paper presented in JORNADAS DE BIOINFORMÁTICA, Lisboa, 2009.
    Published
  9. Mesquita, Daniela P.; Dias, Oscar; Ferreira, Eugénio C.. "Monitoring activated sludge systems from wastewater treatment plants: automated image analysis procedures and their relation with operating parameters". Paper presented in Congresso Micro '07 - Biotec '07 - XXIII JPG, Lisboa, 2007.
    Published
Conference paper
  1. Sampaio, Marta; Rocha, Miguel; Dias, O.. Corresponding author: Sampaio, Marta. "A multi-omics approach for understanding grape metabolism throughout development". Paper presented in 10th IFAC International Conference on Foundations of Systems Biology in Engineering, 2024.
    Under revision
  2. Sampaio, Marta; Rocha, Miguel; Dias, O.. Corresponding author: Sampaio, Marta. "iplants: a repository of plant metabolic data". Paper presented in 18th International Conference on Practical Applications of Computational Biology and Bioinformatics, Salamanca, 2024.
    Under revision
  3. Apolinário, Gonçalo; Gonçalves, Joana Oliveira; Cunha, Emanuel Rodrigues; Madureira, Leandro Filipe Feiteira; Maciel, José Filipe Gonçalves; Geada, Pedro Miguel Macedo; Dias, Oscar. "Exploring methane mitigation strategies in photosynthetic microorganisms through genome-scale metabolic models". 2024.
  4. Oliveira, Hugo Alexandre Mendes; Dias, Oscar. "Machine learning in the service of phage analysis: advancements, applications, and future prospects". 2023.
  5. Alexandre Oliveira; Emanuel Cunha; Miguel Silva; Cristiana Faria; Oscar Dias. Corresponding author: Oscar Dias. "Exploring Xylella fastidiosa's Metabolic Traits Using a GSM Model of the Phytopathogenic Bacterium". Paper presented in 16th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2022.
    Published • 10.1007/978-3-031-17024-9_8
  6. Oliveira, Hugo Alexandre Mendes; Duarte, José; Domingues, Rita; Vieira, Maria; Silva, Sónia Carina; Santos, Sílvio Roberto Branco; Oliveira, Ricardo; et al. "Understanding the complete reservoir of bacteriophage depolymerases against A. baumannii capsules". 2022.
  7. Macedo, Diogo; Santos, Sílvio Roberto Branco; Dias, Oscar. "COAST: A bioinformatic tool to identify the closest proteomes". 2022.
  8. Couceiro, Diogo; Viana, Romeu; Carreiro, Tiago; Dias, Oscar; Rocha, Isabel; Teixeira, Miguel C.. "Drug Target Identification based on the construction of a Genome-scale metabolic model for the human pathogen Candida parapsilosis". 2022.
  9. Lopes, Maria João; Rodrigues, Joana Lúcia Lima Correia; Dias, Oscar. "Bioinformatics approaches for engineering L-Tyrosine production in Escherichia coli". 2022.
  10. Oliveira, Alexandre; Cunha, Emanuel; Cruz, Fernando; Capela, João; Sequeira, João; Sampaio, Marta; Dias, Oscar. Corresponding author: Dias, Oscar. "Towards a Multivariate Analysis of Genome-Scale Metabolic Models Derived from the BiGG Models Database". Paper presented in 15th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2021.
    Published • 10.1007/978-3-030-86258-9_14
  11. Viana, Romeu; Couceiro, Diogo; Carneiro, Tiago; Souza, Caio; Dias, Oscar; Rocha, Isabel; Soares, Cláudio; Teixeira, Miguel C.. "A computational approach to finding new drug targets for pathogenic Candida species". 2021.
  12. Couto, Márcia Regina; Dias, Oscar; Rodrigues, Joana Lúcia Lima Correia; Rodrigues, L. R.. "Stoichiometric genome-scale models for the chondroitin production in Escherichia coli". 2021.
  13. Ribeiro, João Manuel Capela Araújo; Liu, Filipe; Dias, Oscar. "Revising lipid chemical structures in genome-wide metabolic models with BOIMMG". 2021.
  14. Cunha, Emanuel; Zeidan, Ahmad Adel; Dias, O.. Corresponding author: Dias, O.. "Towards the Reconstruction of the Genome-Scale Metabolic Model of Lactobacillus acidophilus La-14". Paper presented in 14th International Conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2020, 2020.
    Published • 10.1007/978-3-030-54568-0_21
  15. Diogo Lima; Fernando Cruz; Miguel Rocha; Oscar Dias. Corresponding author: Oscar Dias. "Reconciliation of regulatory data: the regulatory networks of Escherichia coli and Bacillus subtilis". Paper presented in 14th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2020.
    Published • 10.1007/978-3-030-54568-0_16
  16. Lima, Diogo Batista; Lagoa, Davide Rafael Santos; Cruz, Fernando João Pereira da; Bastos, José; Capela, João; Ferreira, Eugénio C.; Rocha, Miguel; Dias, Oscar. "merlin v4: an updated platform for reconstructing genome-scale metabolic models". 2020.
  17. Cruz, Fernando; Lima, Diogo; Faria, José P.; Rocha, Miguel; Dias, O.. Corresponding author: Dias, O.. "Towards the Reconstruction of Integrated Genome-Scale Models of Metabolism and Gene Expression". Paper presented in Practical Applications of Computational Biology and Bioinformatics, 13th International Conference, Ávila, 2019.
    10.1007/978-3-030-23873-5_21
  18. Sampaio, Marta; Rocha, Miguel; Oliveira, Hugo; Dias, Oscar. "Predicting Promoters in Phage Genomes Using Machine Learning Models". Paper presented in Practical Applications of Computational Biology and Bioinformatics, 13th International Conference, Ávila, 2019.
    Published • 10.1007/978-3-030-23873-5_13
  19. Demirci, H.; Dias, Oscar; Chaves, Inês; Miguel, Célia; Rocha, Miguel; Rocha, I.. "The metabolic model of the Quercus suber (cork oak tree) leaf". 2019.
  20. Lagoa, D.; Liu, Filipe; Ferreira, Eugénio C.; Faria, J.; Henry, C.; Dias, Oscar. "Towards a genome-wide transport systems encoding genes tracker". Paper presented in 4th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2018), 2018.
  21. Dias, Oscar; Castro, Rita; Pereira, M. A.; Rocha, Isabel. "Towards the identification of pathways for lipids biosynthesis in HCB". 2017.
  22. Oliveira, Emanuel; Ferreira, Eugénio C.; Dias, Oscar. "Modelling interspecies interactions of syntrophic communities". 2017.
  23. Fernandes, Bruna S.; Dias, Oscar; Zaiat, Marcelo; Pradella, José G. C.; Rocha, I.. "Eicosapentaenoic acid (EPA) production in silico by Pythium irregulare, as value-added product, using sugarcane vinasse as carbon source". 2017.
  24. Dias, Oscar; Santos, Sophia Torres; Ferreira, Eugénio C.; Rocha, I.. "Towards an improved version of Kluyveromyces lactis genome-scale metabolic model". 2016.
  25. Barbosa, Pedro; Dias, Oscar; Arrais, Joel P.; Rocha, Miguel. "Metagenomic Analysis of the Saliva Microbiome with Merlin". Paper presented in 8th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2014), 2015.
    Published • 10.1007/978-3-319-07581-5_23
  26. Dias, Oscar; Saraiva, João; Ferreira, Eugénio C.; Rocha, I.. "Towards a genome-scale metabolic model of the Streptococcus pneumoniae R6 avirulent strain". 2015.
  27. Dias, Oscar; Liu, Filipe; Rocha, Miguel; Ferreira, Eugénio C.; Rocha, I.; Rocha, Isabel. "Prediction of protein subunits using KEGG BRITE". Paper presented in COBRA 2014 - 3rd Conference on Constraint-Based Reconstruction and Analysis, Charlottesville, 2014.
  28. Gomes, Daniel Gonçalves; Dias, Oscar; Ferreira, Eugénio C.; Domingues, Lucília; Rocha, I.. "Reconstruction of a genome-scale metabolic model for the filamentous fungus Ashbya gossypii". 2013.
  29. Dias, Oscar; Gombert, Andreas Karoly; Ferreira, Eugénio C.; Rocha, I.. "iOD962 - the first genome-scale metabolic model of Kluyveromyces lactis". 2013.
  30. Dias, Oscar; Gombert, Andreas Karoly; Ferreira, Eugénio C.; Rocha, I.. "Towards a genome-scale metabolic model for the Kluyveromyces lactis yeast". 2013.
  31. Dias, Oscar; Gomes, Daniel; Ferreira, Eugénio C.; Rocha, Isabel. "Reconstructing genome-scale metabolic models with merlin : the Ashbya gossypii case study". Paper presented in 3rd Meeting of the Institute for Biotechnology and Bioengineering, Lisboa, 2012.
    Published
  32. Gomes, Daniel; Dias, Oscar; Ferreira, Eugénio C.; Rocha, Isabel. "Reconstruction of a genome-scale metabolic model for the riboflavin producer fungus Ashbya gossypii". Paper presented in EMBO Conference Series - From Functional Genomics to Systems Biology, Heidelberg, 2012.
    Published
  33. Gomes, Daniel Gonçalves; Dias, Oscar; Ferreira, Eugénio C.; Domingues, Lucília; Rocha, I.. "Reconstruction of a genome-scale metabolic model for the riboflavin producer fungus Ashbya gossypii". 2012.
  34. Dias, Oscar; Rocha, Miguel; Ferreira, Eugénio C.; Rocha, I.. "Assembling genome-wide transporter system annotations". 2012.
  35. Gomes, Daniel Gonçalves; Dias, Oscar; Ferreira, Eugénio C.; Domingues, Lucília; Rocha, I.. "Reconstruction of a genome-scale metabolic model for the filamentous fungus Ashbya gossypii". 2012.
  36. Dias, Oscar; Gomes, Daniel Gonçalves; Ferreira, Eugénio C.; Domingues, Lucília; Rocha, I.. "Reconstructing genome-scale metabolic models with merlin: the Ashbya gossypii case study". 2012.
  37. Gomes, Daniel Gonçalves; Dias, Oscar; Domingues, Lucília; Rocha, I.; Gomes, Daniel; Ferreira, Eugénio C.; Rocha, Isabel. "Revealing new biotechnological potentialities of the riboflavin producer fungus Ashbya gossypii by means of the construction and analysis of its metabolic network". Paper presented in MicroBiotec'11, Braga, 2011.
    Published
  38. Dias, Oscar; Ferreira, Eugénio C.; Rocha, I.; Rocha, Isabel. "Towards genome-wide semi-automated transporter system annotations". Paper presented in 12th International Conference on Systems Biology ¿ ICSB 2011, Mannheim, 2011.
  39. Rocha, I.; Dias, Oscar; Rocha, Miguel; Ferreira, Eugénio C.. "Genome-scale metabolic models reconstruction of less characterized organisms with Merlin". 2010.
  40. Dias, Oscar; Ferreira, Eugénio C.; Rocha, I.; Gombert, Andreas Karoly. "Reconstructing genome-scale metabolic models with Merlin". 2010.
  41. Mesquita, Daniela P.; Dias, Oscar; Amaral, António L.; Ferreira, Eugénio C.; Mesquita, D. P.; Amaral, A. L.. "Bright field versus phase contrast microscopy in activated sludge image acquisition methodologies". Paper presented in Chemical and Biological Engineering Conference - CHEMPOR 2008, Braga, 2008.
    Published
  42. Dias, Oscar; Mesquita, Daniela P.; Amaral, António L.; Ferreira, Eugénio C.. "Dilution effects on aggregates and filaments contents in automated image analysis methodologies". Paper presented in International Symposium on Sanitary and Environmental Engineering : SIDISA 08, Florence, 2008.
    Published
  43. Mesquita, Daniela P.; Dias, Oscar; Amaral, António L.; Ferreira, Eugénio C.. "Evaluation of activated sludge systems by image analysis procedures". Paper presented in International Symposium on Sanitary and Environmental Engineering: SIDISA 08, Florence, 2008.
    Published
  44. Mesquita, Daniela P.; Dias, Oscar; Amaral, António L.; Ferreira, Eugénio C.; Mesquita, D. P.; Amaral, A. L.. "Relationship between sludge volume index and biomass structure within activated sludge systems". Paper presented in XVII Congresso Brasileiro de Engenharia Química - COBEQ 2008, Recife, 2008.
    Published
  45. Pinto, José P.; Dias, Oscar; Lourenço, Anália; Carneiro, Sónia; Ferreira, Eugénio C.; Rocha, Isabel; Rocha, Miguel. "Data Integration Issues in the Reconstruction of the Genome-Scale Metabolic Model of Zymomonas Mobillis". Paper presented in 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008), 2008.
    Published • 10.1007/978-3-540-85861-4_12
Conference poster
  1. Couto, M. R.; Dias, O.; Rodrigues, J. L.; Rodrigues, L. R.; Dias, O.. "Metabolic engineering of Escherichia coli for biotechnological chondroitin production". Paper presented in The 2nd International BioDesign Research Conference, 2021.
    10.12236/ibdrc2021-p-0062
Journal article
  1. Márcia R. Couto; Joana L. Rodrigues; Oscar Dias; Lígia R. Rodrigues. "Saccharomyces cerevisiae as a Host for Chondroitin Production". SynBio (2024): https://doi.org/10.3390/synbio2020008.
    10.3390/synbio2020008
  2. Fernando Cruz; João Capela; Eugénio C. Ferreira; Miguel Rocha; Oscar Dias. "BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic models". IEEE/ACM Transactions on Computational Biology and Bioinformatics (2024): https://doi.org/10.1109/TCBB.2023.3339972.
    10.1109/TCBB.2023.3339972
  3. Márcia R. Couto; Joana L. Rodrigues; Adelaide Braga; Oscar Dias; Lígia R. Rodrigues; Couto, M. R.; Rodrigues, J.L.; et al. "Optimization of chondroitin production in E. coli using genome scale models". Molecular Systems Design & Engineering (2024): https://doi.org/10.1039/D3ME00199G.
    Published • 10.1039/D3ME00199G
  4. Sousa, Vítor; Hijo, Ariel A. C. Toledo; Lüdtke, Fernanda Luisa; Vicente, A. A.; Dias, Oscar; Geada, Pedro Miguel Macedo. "Recovery and encapsulation of Dunaliella salina -carotene through a novel sustainable approach: Sequential application of an ionic liquid as naturally-derived solvent and emulsifier". (2024): https://hdl.handle.net/1822/92460.
    10.1016/j.foodchem.2024.140232
  5. Emanuel Cunha; Davide Lagoa; José P Faria; Filipe Liu; Christopher S Henry; Oscar Dias; Janet Kelso. "TranSyT, an innovative framework for identifying transport systems". Bioinformatics (2023): https://doi.org/10.1093/bioinformatics/btad466.
    10.1093/bioinformatics/btad466
  6. Cunha, Emanuel; Sousa, Vítor; Geada, Pedro; Teixeira, José A.; Vicente, António A.; Dias, O.. Corresponding author: Dias, O.. "Systems biology's role in leveraging microalgal biomass potential: Current status and future perspectives". Algal Research 69 (2023): 102963. http://dx.doi.org/10.1016/j.algal.2022.102963.
    Open access • 10.1016/j.algal.2022.102963
  7. Cunha, Emanuel Rodrigues; Silva, Miguel; Chaves, Inês; Demirci, Huseyin; Lagoa, Davide Rafael Santos; Lima, Diogo; Rocha, Miguel; Rocha, Isabel; Dias, Oscar. "The first multi-tissue genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber". (2023): https://hdl.handle.net/1822/86827.
    10.1371/journal.pcbi.1011499
  8. Sousa, Vítor; Pereira, Ricardo Nuno Correia; Vicente, A. A.; Dias, Oscar; Geada, Pedro. "Microalgae biomass as an alternative source of biocompounds: New insights and future perspectives of extraction methodologies". (2023): https://hdl.handle.net/1822/85701.
    10.1016/j.foodres.2023.113282
  9. Viana, Romeu; Carreiro, Tiago; Couceiro, Diogo; Dias, Oscar; Rocha, Isabel; Teixeira, Miguel Cacho; Viana, Romeu; et al. "Metabolic reconstruction of the human pathogen Candida auris". (2023): http://hdl.handle.net/10362/165658.
    https://doi.org/10.1093/femsyr/foad045
  10. Alexandre Oliveira; Emanuel Cunha; Fernando Cruz; João Capela; João C. Sequeira; Marta Sampaio; Cláudia Sampaio; Oscar Dias. "Systematic assessment of template-based genome-scale metabolic models created with the BiGG Integration Tool". Journal of Integrative Bioinformatics (2022): https://doi.org/10.1515/jib-2022-0014.
    10.1515/jib-2022-0014
  11. Capela, João; Lagoa, Davide; Rodrigues, Ruben; Cunha, Emanuel; Cruz, Fernando; Barbosa, Ana; Bastos, José; et al. Corresponding author: Dias, O.. "merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models". Nucleic Acids Research 50 11 (2022): 6052-6066. http://dx.doi.org/10.1093/nar/gkac459.
    Open access • Published • 10.1093/nar/gkac459
  12. Oliveira, Ricardo; Pinho, Eva; Sousa, Ana Luísa; Dias, O.; Azevedo, Nuno Filipe; Almeida, Carina. "Modelling aptamers with nucleic acid mimics (NAM): From sequence to three-dimensional docking". PLOS ONE 17 3 (2022): e0264701. http://dx.doi.org/10.1371/journal.pone.0264701.
    10.1371/journal.pone.0264701
  13. Viana, Romeu; Couceiro, Diogo; Carreiro, Tiago; Dias, Oscar; Rocha, Isabel; Teixeira, Miguel Cacho. "A Genome-Scale Metabolic Model for the Human Pathogen Candida Parapsilosis and Early Identification of Putative Novel Antifungal Drug Targets". Genes 13 2 (2022): 303. http://dx.doi.org/10.3390/genes13020303.
    10.3390/genes13020303
  14. Marta Sampaio; Miguel Rocha; Oscar Dias; Sampaio, Marta; Rocha, Miguel; Dias, Oscar. "Exploring synergies between plant metabolic modelling and machine learning". Computational and Structural Biotechnology Journal (2022): https://hdl.handle.net/1822/77194.
    Accepted • 10.1016/j.csbj.2022.04.016
  15. Saraiva, João Pedro; Bartholomäus, Alexandre; Kallies, René; Gomes, Marta; Bicalho, Marcos; Coelho Kasmanas, Jonas; Vogt, Carsten; et al. "OrtSuite: from genomes to prediction of microbial interactions within targeted ecosystem processes". Life Science Alliance 4 12 (2021): e202101167. http://dx.doi.org/10.26508/lsa.202101167.
    10.26508/lsa.202101167
  16. Pinto, Graça; Sampaio, Marta; Dias, Oscar; Almeida, Carina; Azeredo, Joana; Oliveira, Hugo. "Insights into the genome architecture and evolution of Shiga toxin encoding bacteriophages of Escherichia coli". BMC Genomics 22 1 (2021): http://dx.doi.org/10.1186/s12864-021-07685-0.
    Published • 10.1186/s12864-021-07685-0
  17. Oliveira, Alexandre; Rodrigues, Joana; Ferreira, Eugénio Campos; Rodrigues, Lígia; Dias, Oscar; Alexandre Oliveira; Joana Rodrigues; et al. "A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli". PLOS Computational Biology 17 3 (2021): e1008704. http://dx.doi.org/10.1371/journal.pcbi.1008704.
    10.1371/journal.pcbi.1008704
  18. Alves, Rafael F.; Zetty-Arenas, Ana M.; Demirci, Huseyin; Dias, Oscar; Rocha, Isabel; Basso, Thiago O.; Freitas, Sindelia. "Enhancing acetic acid and 5-hydroxymethyl furfural tolerance of C. saccharoperbutylacetonicum through adaptive laboratory evolution". Process Biochemistry 101 (2021): 179-189. http://dx.doi.org/10.1016/j.procbio.2020.11.013.
    Published • 10.1016/j.procbio.2020.11.013
  19. Fernando João Pereira da Cruz; João Capela; Ferreira, Eugénio Campos; Miguel Rocha; Dias, O.. "BioISO: an objective-oriented application for assisting the curation of genome-scale metabolic models". bioRxiv (2021): https://www.biorxiv.org/content/10.1101/2021.03.07.434259v1.
    Open access • Published • 10.1101/2021.03.07.434259
  20. Emanuel Cunha; Miguel Silva; Ines Chaves; Huseyin Demirci; Davide Lagoa; Diogo Lima; Miguel Rocha; Isabel Cristina Pereira da Rocha; Dias, O.. "iEC7871 Quercus suber model: the first multi-tissue diel cycle genome-scale metabolic model of a woody tree". bioRxiv (2021): https://doi.org/10.1101/2021.03.09.434537.
    Open access • Published • 10.1101/2021.03.09.434537
  21. Cruz, Fernando; Faria, José P.; Rocha, Miguel; Rocha, Isabel; Dias, Oscar. "A review of methods for the reconstruction and analysis of integrated genome-scale models of metabolism and regulation". Biochemical Society Transactions 48 5 (2020): 1889-1903. http://dx.doi.org/10.1042/bst20190840.
    10.1042/bst20190840
  22. Viana, Romeu; Dias, Oscar; Lagoa, Davide; Galocha, Mónica; Rocha, Isabel; Teixeira, Miguel Cacho. "Genome-Scale Metabolic Model of the Human Pathogen Candida albicans: A Promising Platform for Drug Target Prediction". Journal of Fungi 6 3 (2020): 171. http://dx.doi.org/10.3390/jof6030171.
    10.3390/jof6030171
  23. Oliveira, Hugo; Pinto, Graça; Mendes, Bruna; Dias, O.; Hendrix, Hanne; Akturk, Ergun; Noben, Jean-Paul; et al. "A Tailspike with Exopolysaccharide Depolymerase Activity from a New Providencia stuartii Phage Makes Multidrug-Resistant Bacteria Susceptible to Serum-Mediated Killing". Applied and Environmental Microbiology 86 13 (2020): http://dx.doi.org/10.1128/aem.00073-20.
    10.1128/aem.00073-20
  24. Cruz, Fernando; Lagoa, Davide; Mendes, João; Rocha, Isabel; Ferreira, Eugénio C.; Rocha, Miguel; Dias, Oscar. "SamPler - a novel method for selecting parameters for gene functional annotation routines". BMC Bioinformatics 20 1 (2019): http://dx.doi.org/10.1186/s12859-019-3038-4.
    10.1186/s12859-019-3038-4
  25. Sampaio, Marta; Rocha, Miguel; Oliveira, Hugo; Dias, Oscar. "Predicting promoters in phage genomes using PhagePromoter". Bioinformatics (2019): http://dx.doi.org/10.1093/bioinformatics/btz580.
    10.1093/bioinformatics/btz580
  26. Fernandes, Bruna S.; Dias, Oscar; Costa, Gisela; Kaupert Neto, Antonio A.; Resende, Tiago F. C.; Oliveira, Juliana V. C.; Riaño-Pachón, Diego M.; et al. "Genome-wide sequencing and metabolic annotation of Pythium irregulare CBS 494.86: understanding Eicosapentaenoic acid production". BMC Biotechnology 19 1 (2019): http://dx.doi.org/10.1186/s12896-019-0529-3.
    10.1186/s12896-019-0529-3
  27. Dias, Oscar; Saraiva, João; Faria, Cristiana; Ramirez, Mario; Pinto, Francisco; Rocha, Isabel. "iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6". Frontiers in Microbiology 10 (2019): http://dx.doi.org/10.3389/fmicb.2019.01283.
    10.3389/fmicb.2019.01283
  28. Oliveira, Hugo; Sampaio, Marta; Melo, Luís D. R.; Dias, Oscar; Pope, Welkin H.; Hatfull, Graham F.; Azeredo, Joana. "Staphylococci phages display vast genomic diversity and evolutionary relationships". BMC Genomics 20 1 (2019): http://dx.doi.org/10.1186/s12864-019-5647-8.
    10.1186/s12864-019-5647-8
  29. Dias, O.; Basso, T.O.; Rocha, I.; Ferreira, E.C.; Gombert, A.K.. "Quantitative physiology and elemental composition of Kluyveromyces lactis CBS 2359 during growth on glucose at different specific growth rates". Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology (2017): 1-13. http://www.scopus.com/inward/record.url?eid=2-s2.0-85029147316&partnerID=MN8TOARS.
    10.1007/s10482-017-0940-5
  30. Dias, Oscar; Gomes, Daniel; Vilaca, Paulo; Cardoso, Joao; Rocha, Miguel; Ferreira, Eugénio C.; Rocha, Isabel. "Genome-wide Semi-automated Annotation of Transporter Systems". IEEE/ACM Transactions on Computational Biology and Bioinformatics 1 (2016): 1-1. https://www.computer.org/csdl/trans/tb/preprint/07403958-abs.html.
    Published • 10.1109/TCBB.2016.2527647
  31. Dias, Oscar; Rocha, Miguel; Ferreira, Eugénio C.; Rocha, Isabel. "Reconstructing genome-scale metabolic models with merlin". Nucleic Acids Research 43 8 (2015): 3899-3910.
    Published • 10.1093/nar/gkv294
  32. Dias, Oscar; Pereira, Rui; Gombert, Andreas K.; Ferreira, Eugénio C.; Rocha, Isabel. "iOD907, the first genome-scale metabolic model for the milk yeast Kluyveromyces lactis". Biotechnology Journal 9 6 (2014): 776-790. http://onlinelibrary.wiley.com/doi/10.1002/biot.201300242/abstract.
    Published • 10.1002/biot.201300242
  33. Gomes, Daniel; Aguiar, Tatiana Q; Dias, Oscar; Ferreira, Eugénio C.; Rocha, Isabel. "Genome-wide metabolic re-annotation of Ashbya gossypii: new insights into its metabolism through a comparative analysis with Saccharomyces cerevisiae and Kluyveromyces lactis". BMC Genomics 15 1 (2014): 810-810.
    Published • 10.1186/1471-2164-15-810
  34. Dias, Oscar; Gombert, Andreas K.; Ferreira, Eugénio C.; Rocha, Isabel. "Genome-wide metabolic (re-) annotation of Kluyveromyces lactis". BMC Genomics 13 1 (2012): 517-517. http://www.biomedcentral.com/1471-2164/13/517/abstract.
    Published • 10.1186/1471-2164-13-517
  35. Mesquita, Daniela P.; Dias, Oscar; Amaral, António L.; Ferreira, Eugénio C.. "A Comparison between Bright Field and Phase-Contrast Image Analysis Techniques in Activated Sludge Morphological Characterization". Microscopy and Microanalysis 16 02 (2010): 166-174.
    Published • 10.1017/S1431927609991358
  36. Mesquita, Daniela P.; Dias, Oscar; Elias, R.A.V.; Amaral, António L.; Ferreira, Eugénio C.. "Dilution and Magnification Effects on Image Analysis Applications in Activated Sludge Characterization". Microscopy and Microanalysis 16 05 (2010): 561-568.
    Published • 10.1017/S1431927610093785
  37. Mesquita, Daniela P.; Dias, Oscar; Amaral, António L.; Ferreira, Eugénio C.. "Correlation between sludge settling ability and image analysis information using partial least squares". Analytica Chimica Acta 642 1-2 (2009): 94-101. http://hdl.handle.net/1822/9469.
    Published • 10.1016/j.aca.2009.03.023
  38. Mesquita, Daniela P.; Dias, Oscar; Amaral, António L.; Ferreira, Eugénio C.. "Monitoring of activated sludge settling ability through image analysis: validation on full-scale wastewater treatment plants". Bioprocess and Biosystems Engineering 32 3 (2008): 361-367.
    Published • 10.1007/s00449-008-0255-z
Online resource
  1. Davide Lagoa; José P. Faria; Filipe Liu; Emanuel Cunha; Christopher S. Henry; Oscar Dias. TranSyT, the Transport Systems Tracker. 2021. https://transyt.bio.di.uminho.pt/.
Preprint
  1. Raman, Karthik; Kratochvil, Miroslav; Olivier, Brett G.; Konig, Matthias; Sengupta, Pratyay; Baskaran, Dinesh Kumar Kuppa; Nguyen, Tung V N; et al. "FROG analysis ensures the reproducibility of genome scale metabolic models". 2024. https://hdl.handle.net/1822/93169.
    10.1101/2024.09.24.614797
  2. Márcia R. Couto; Joana L. Rodrigues; Oscar Dias; Lígia R Rodrigues. "In Silico Design of Saccharomyces cerevisiae Strains for Improved Production of Chondroitin". 2023. https://doi.org/10.20944/preprints202312.1479.v1.
    10.20944/preprints202312.1479.v1
  3. Maria Vieira; José Duarte; Rita Domingues; Hugo Oliveira; Oscar Dias. "PhageDPO: Phage Depolymerase Finder". 2023. https://doi.org/10.1101/2023.02.24.529883.
    10.1101/2023.02.24.529883
Thesis / Dissertation
  1. Sampaio, Marta Sofia Costa. "M3L: exploring synergies between metabolic modelling and machine learning for studying plants". PhD, 2024. https://hdl.handle.net/1822/93519.
  2. Santos, Sophia Torres. "Design and optimization of microbial communities". PhD, 2024. https://hdl.handle.net/1822/91621.
  3. Moura, José Diogo Cruz de. "Development and integration of topology-based methods for gap-filling of metabolic networks". Master, 2023. https://hdl.handle.net/1822/92681.
  4. Duarte, António Nuno Carrilho Canatário. "PhageAnnotate viral genome classifier". Master, 2023. https://hdl.handle.net/1822/92817.
  5. Castro, Rute Salomé Pires de. "Development of an artificial intelligence breast cancer diagnostic tool". Master, 2023. https://hdl.handle.net/1822/92793.
  6. Macedo, Diogo Duarte Pinto. "Development of deep learning models for scRNA data analysis". Master, 2023. https://hdl.handle.net/1822/86515.
  7. Babo, Ana Camila Ribeiro de. "Integrating machine learning and mechanistic modeling towards adaptation of plants to climate change". Master, 2023. https://hdl.handle.net/1822/92829.
  8. Leiras, Mónica Rafaela Machado. "Development of a serious game to stimulate the learning of genome-scale metabolic modeling concepts". Master, 2023. https://hdl.handle.net/1822/92794.
  9. Cruz, Fernando João Pereira. "Blueprint: documenting the complexity of metabolic regulation by reconstruction of integrated metabolic-regulatory models". PhD, 2023. https://hdl.handle.net/1822/86184.
  10. Esperança, Alexandre Miguel Magalhães. "PhageSNP: prediction of the effect of hypermutable phage proteins along Staphylococcus genus". Master, 2023. https://hdl.handle.net/1822/92811.
  11. Machado, Tiago Moreira. "Development and analysis of mathematical models to study metabolic constraints and capacities in different photosynthetic types". Master, 2022. https://hdl.handle.net/1822/84566.
  12. Pereira, Juliana Marques. "Ecological modelling to describe the role of light on microbial interactions in Ulva spp. with implications in aquaculture". Master, 2022. https://hdl.handle.net/1822/84490.
  13. Rocha, Miguel Alexandre Oliveira. "Development and implementation of methodologies for integrating omics data with genomic-scaled metabolic models". Master, 2022. https://hdl.handle.net/1822/84479.
  14. Faria, Maria Inês Alves. "Multi-view learning for multiomics data integration for the study of plants". Master, 2022. https://hdl.handle.net/1822/78318.
  15. Nunes, Rui Ricardo Barros. "Genome-scale metabolic modelling of an extremophile microbial community". Master, 2022. https://hdl.handle.net/1822/87188.
  16. Abreu, João Nuno Cardoso Gonçalves de. "Development of DNA sequence classifiers based on deep learning". Master, 2022. https://hdl.handle.net/1822/84065.
  17. Silva, Carla Rafaela Mendes da. "Development of a framework for the classification of antibiotics adjuvants". Master, 2022. https://hdl.handle.net/1822/84505.
  18. Barros, Miguel Ângelo Pereira. "Development of a deep learning-based computational framework for the classification of protein sequences". Master, 2022. https://hdl.handle.net/1822/84576.
  19. Lopes, Maria João Mogadouro. "Bioinformatics approaches for engineering L-tyrosine production in Escherichia coli". Master, 2022. https://hdl.handle.net/1822/83545.
  20. Duarte, José Alexandre Graça. "PhageDPO: phage depolymerase finder". Master, 2021. http://hdl.handle.net/1822/77372.
  21. Dias, João Pedro Porto. "PhagePro: prophage finding tool". Master, 2021. https://hdl.handle.net/1822/82764.
  22. Fernandes, Ana Isabel Gomes. "Unveiling the production of metabolites with flavor enhancement through genome-scale metabolic modelling of a lambic beer microbial community". Master, 2021. https://hdl.handle.net/1822/80397.
  23. Ribeiro, João Manuel Capela Araújo. "Biochemical complex data generation and integration in genome-scale metabolic models". Master, 2021. https://hdl.handle.net/1822/81195.
  24. Lima, Diogo Batista. "Development and implementation of a repository for transcriptional regulatory information". Master, 2019. https://hdl.handle.net/1822/79880.
  25. Silva, Andrea Ferreira Meireles. "Identification and classification of transporter proteins using deep learning models". Master, 2019. https://hdl.handle.net/1822/79910.
  26. Pereira, Sofia Raquel Lages. "Implementation of the object-relational mapping tool Hibernate in merlin’s framework". Master, 2019. https://hdl.handle.net/1822/80047.
  27. Mendes, João Pedro Bernardo. "Reconstructing of the metabolic network of Lactobacillus rhamnosus". Master, 2019. http://hdl.handle.net/1822/66520.
  28. Cunha, Emanuel Rodrigues da. "Genome-scale reconstruction of the metabolic model of the probiotic bacterium Lactobacillus acidophilus". Master, 2019. https://hdl.handle.net/1822/80307.
  29. Sousa, José Miguel Dantas de. "In silico objective-driven optimization of microbial communities". Master, 2019. http://hdl.handle.net/1822/74173.
  30. Oliveira, Alexandre Rafael Machado. "A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli". Master, 2019. https://hdl.handle.net/1822/79954.
  31. Gomes, Marta Lopes. "In silico characterization of microbial communities interaction in soil samples". Master, 2019. https://hdl.handle.net/1822/79891.
  32. Silva, Miguel Ângelo Fernandes da. "Genome-scale metabolic modelling of the pathogen Xylella fastidiosa". Master, 2019. https://hdl.handle.net/1822/80753.
  33. Isabelinho, Tiago Filipe Pereira. "Comparative analysis and characterization of industrial Streptococcus thermophilus genomes". Master, 2019. https://hdl.handle.net/1822/79890.
  34. Bastos, José Jorge Sampaio. "Modelling interspecies interactions of syntrophic communities of Syntrophobacter fumaroxidans and Methanospirillum hungatei". Master, 2019. https://hdl.handle.net/1822/66580.
  35. Cruz, Renato Alexandre Azevedo. "Nitrobacter vulgaris: genome-scale model reconstruction and interactions with Nitrosomonas europaea". Master, 2018. https://hdl.handle.net/1822/79790.
  36. Morais, José Amaro Ferreira. "Development of bioinformatics tools to accelerate the reconstruction of genome-scale models". Master, 2018. https://hdl.handle.net/1822/79708.
  37. Sampaio, Marta Sofia Costa. "PhagePromoter: phage promoters online analysis tool". Master, 2018. https://hdl.handle.net/1822/64122.
  38. Raposo, Pedro Miguel Brígida. "Reconstruction of the genome-scale metabolic model of Nitrosomonas europaea". Master, 2017. http://hdl.handle.net/1822/56111.
  39. Dias, António Carlos Fortuna Ribeiro. "Development and implementation of bioinformatics tools for the reconstruction of GiSMos". Master, 2017. http://hdl.handle.net/1822/56103.
  40. Dias, José Miguel Gonçalves. "Reconstructing the metabolic network of Lactobacillus helveticus on a genome-wide scale". Master, 2017. https://hdl.handle.net/1822/56112.
  41. Faria, Daniel Torres Varzim. "Development of a computational approach for the identification and annotation of transport proteins". Master, 2016. http://hdl.handle.net/1822/47386.
  42. Dias, O.. "Reconstruction of the Genome-scale Metabolic Network of Kluyveromyces lactis". PhD, Universidade do Minho, 2013.
  43. Dias, Oscar. "Reconstruction of the genome-scale metabolic network of Kluyveromyces lactis". PhD, 2013. https://hdl.handle.net/1822/24859.

Other

Other output
  1. Towards a genome-scale metabolic model of Dunaliella salina. Dunaliella salina is a green algae known for its ability to produce carotenoids. However, maximizing its production while achieving significant biomass yields remains challenging, which can be addressed through systems biology tools like genome-scale metabolic models. This work presents the first genome-scale metabolic model for D. salina, enabling an in silico analysis and optimization of -carote. 2024. Cunha, Emanuel Rodrigues; Sousa, Vítor; Vicente, A. A.; Geada, Pedro Miguel Macedo; Dias, Oscar. https://hdl.handle.net/1822/93578.
    10.1016/j.ifacol.2024.10.007
  2. The Biochemical cOmplex data Integration in Metabolic Models at Genome-scale database and tool. 2021. boimmg. https://boimmg.bio.di.uminho.pt/.
  3. Quercus suber model - iEC7871. 2021. iEC7871.
  4. Biological networks constraint-based In Silico Optimization. BioISO is aimed at evaluating either the biomass or metabolic network formulation of a given constraint-based metabolic model. This computational tool is based on the Constraints-Based Reconstruction and Analysis (COBRA) and Flux Balance Analysis (FBA) frameworks.. 2019. BioISO. https://bioiso.bio.di.uminho.pt/.
  5. Transport Systems Tracker. The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes, based on the annotations of the Transporter Classification Database (TCDB). In addition, this tool also generates the respective transport reactions while providing the respective Gene-Protein-Reaction associations. TranSyT can receive as input the organism NCBI taxonomy. 2019. TranSyT. https://transyt.bio.di.uminho.pt/.
    10.1101/2021.04.29.441738
  6. ProTReND - online database of transcriptional regulatory networks. Transcriptional regulatory networks (TRN)s can be thought of as a group of transcription factors (regulatory proteins) that may activate and/or repress certain gene's expression.. 2019. ProTReND. https://protrend.bio.di.uminho.pt/.
  7. PhageSuite - phage processing tools. 2019. PhageSuite. https://galaxy.bio.di.uminho.pt/.
  8. A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli. Acrylic acid (AA) is an important chemical that can be used in the production of a broad spectrum of products used on a daily basis, such as diapers, coatings paints, adhesives, textiles, detergents and plastic additives [1]. In addition, this chemical can also be used in the production of a superabsorbent polymer, which further increases its worldwide demand and commercial value in the industrial. 2019. Oliveira, Alexandre; Rodrigues, L. R.; Rodrigues, Joana Lúcia Lima Correia; Dias, Oscar. http://hdl.handle.net/1822/61767.
  9. merlin - metabolic models reconstruction using genome-scale information. Software. 2010. Dias, Oscar; Rocha, Miguel; Ferreira, Eugénio C.; Rocha, Isabel. http://sysbio.uminho.pt/merlin/.
    10.3182/20100707-3-BE-2012.0076
  10. Correlation between sludge settleability and image analysis information using Partial Least Squares. CAC2008 - Proceedings of the 11th International Conference on Chemometrics in Analytical Chemistry. 2008. Mesquita, D. P.; Dias, Oscar; Dias, A. M. A.; Amaral, A. L.; Ferreira, Eugénio C.; Mesquita, Daniela P.; Amaral, António L.. https://hdl.handle.net/1822/8280.
  11. Evaluation of activated sludge systems by image analysis procedures. Biomass inspection under optical microscopy coupled to automated image analysis methodologies is, nowadays, increasingly used. Image analysis is presently considered a powerful tool to identify and quantify biomass morphological and physiological changes. In this work, an image analysis program was developed in Matlab environment, allowing the identification and characterization of microbial aggre. 2008. Mesquita, D. P.; Dias, Oscar; Amaral, A. L.; Ferreira, Eugénio C.. https://hdl.handle.net/1822/8121.
  12. Dilution effects on aggregates and filaments contents in automated image analysis methodologies. Monitoring activated sludge processes by microscopic observations and image analysis is a well established technique with the utmost importance for microbial community characterization. Occasionally, there are biological systems operating with high biomass concentrations that need to be diluted, causing reproducibility problems for the sampling and image analysis methodologies. In the current work. 2008. Dias, Oscar; Mesquita, D. P.; Amaral, A. L.; Ferreira, Eugénio C.. https://hdl.handle.net/1822/8119.
Spin-off company
  1. 2021. OMNIUMAI - INTELIGÊNCIA ARTIFICIAL E CIÊNCIAS DE DADOS, LDA. Artificial Intelligence; Bioinformatics; Data Sciences. https://www.omniumai.com/.
Standard or policy
  1. Transport Systems identification number. The Transport Systems Tracker (TranSyT) is a tool to identify transport systems and the compounds carried across membranes. This tool compiles a database that assigns identifiers to transport systems. 2020. TranSyT identifier. https://registry.identifiers.org/registry/transyt.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2023/03/23 Revolutionizing Bioinformatics with AI VIII Semana da Bioengenharia
Instituto Superior Técnico (Lisboa, Portugal)
2022/03/07 Tools for processing and analysing data Ready for BioData Management?: Data Stewardship for Life Sciences Training Program
Biodata.pt (Online, Portugal)
2021/06/22 iPlants@PT – a repository of in silico models of Portuguese plant life WATERMAN Web Seminar
Nadine Töpfer - IPK Leibniz Institute (Online, Germany)
2021/02/03 TBL in Systems Biology Docência+ Impacto 2021
University of Minho
2017/07/21 Reconstructing genome-scale metabolic models with merlin Seminar
Chris Henry (Chicago, United States)
2017/05/15 Reconstructing genome-scale metabolic models with merlin Seminar
Ahmad Zeidan (Copenhagen, Denmark)
2015 Towards a genome-scale metabolic model for the Kluyveromyces lactis yeast
(Netherlands)
2015 Reconstructing genome-scale metabolic models with merlin Seminar
Kiran Patil (Heidelberg, Germany)
2013 iOD962 - the first genome-scale metabolic model of Kluyveromyces lactis Bioinformatics Open Days 2013
(Braga, Portugal)
2012 Reconstructing genome-scale metabolic models with merlin: the Ashbya gossypii case study 3rd Meeting of the Institute for Biotechnology and Bioengineering
Institute for Biotechnology and Bioengineering (Lisboa, Portugal)
2010 Merlin: Metabolic models reconstruction using genome-scale information 11th International Symposium on Computer Applications in Biotechnology - CAB 2010
IFAC - International Federation of Automatic Control (Leuven, Belgium)
2008 Dilution effects on aggregates and filaments contents in automated image analysis methodologies International Symposium on Sanitary and Environmental Engineering : SIDISA 08
Andis Toscana - Associazione Nazionale di Ingegneria Sanitaria Ambientale Toscana (Florence, Italy)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2022/03/01 - Current AI2SM: Artificial Intelligence to expose plant Secondary Metabolism
Supervisor of João Manuel Capela Araújo Ribeiro
 Informática (PhD)
Universidade do Minho, Portugal
2022 - Current iCellulose - Reconstruction of an in silico model for the improvement of the bacterial cellulose yield of Komagataeibacter xylinus ATCC 700178
Co-supervisor of Miguel Monteiro Pacheco
 Engenharia Química e Biológica (PhD)
Universidade do Minho, Portugal
2022 - Current Development of a serious game for learning the basic concepts of genome-scale metabolic models
Supervisor of Mónica Rafaela Machado Leiras
 Bioinformática (Master)
Universidade do Minho, Portugal
2022 - Current Integrating machine learning and mechanistic modelling towards adaptation of plants to climate change
Supervisor of Ana Camila Ribeiro de Babo
 Bioinformática (Master)
Universidade do Minho, Portugal
2022 - Current Bioinformatics characterization of biodiversity in grapevines using NGS data
Supervisor of João António Soares Monteiro
 Bioinformática (Master)
Universidade do Minho, Portugal
2022 - Current Study SARS-CoV-2 infection using GECKO models to drive drug target discovery
Supervisor of Ruben André Pacheco Silva
 Bioinformática (Master)
Universidade do Minho, Portugal
2022 - Current Development and integration of topology and machine learning-based methods for gap filling of metabolic networks in merlin
Supervisor of José Diogo Cruz de Moura
 Bioinformática (Master)
Universidade do Minho, Portugal
2022 - Current PhageAnnotate: Viral Genome Classifier
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2022 - Current PhageSNP – Prediction of the effect of hypermutable phage proteins along Staphylococcus genus
Co-supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2021/02 - Current Development of highly effective microalgae processing strategies aiming at improving pigment and lipids production
Co-supervisor of Vitor Emanuel da Silva Sousa
 Engenharia Química e Biológica (PhD)
Universidade do Minho, Portugal
2021/01 - Current Development and implementation of methodologies for integrating omics data with GSM models
Supervisor of Miguel Alexandre Oliveira Rocha
 Bioinformática (Master)
Universidade do Minho, Portugal
2021 - Current Development and analysis of mathematical models to study metabolic constrains and capacities in different photosynthetic types
Supervisor of Tiago Moreira Machado
 Bioinformática (Master)
Universidade do Minho, Portugal
2021 - Current Development of a framework for the classification of antibiotics adjuvants
Supervisor of Carla Rafaela Mendes da Silva
 Bioinformática (Master)
Universidade do Minho, Portugal
2021 - Current Development of a deep learning-based computational framework for the classification of protein sequences
Co-supervisor of Miguel Ângelo Pereira Barros
 Bioinformática (Master)
Universidade do Minho, Portugal
2021 - Current Development of Genome-Scale Metabolic Models for methanogens and syntrophic cocultures
Supervisor of Mariana Sofia Gomes Coelho
 Bioinformática (Master)
Universidade do Minho, Portugal
2021 - Current Ecological modelling to describe the role of light on microbial interactions in Ulva spp. with implications in aquaculture
Supervisor of Juliana Marques Pereira
 Bioinformática (Master)
Universidade do Minho, Portugal
2021 - Current Bioinformatics approaches for prenylflavonoids production in Escherichia coli
Supervisor of André Maia Magalhães
 Bioinformática (Master)
Universidade do Minho, Portugal
2021 - Current Reconstruction of genome-scale metabolic models of microalgae for exploration of pigments and lipids production
Supervisor
 Engenharia Química e Biológica (PhD)
Universidade do Minho, Portugal
2020/10/01 - Current A Systems Biology approach to model COVID19 phenotypes and drive drug discovery
Supervisor of Alexandre Rafael Machado Oliveira
Universidade do Minho, Portugal
2020 - Current Bioinformatics approaches for engineering L-tyrosine production in Escherichia coli
Supervisor of Maria João Mogadouro Lopes
 Bioinformática (Master)
Universidade do Minho, Portugal
2019 - Current M3L: Exploring synergies between metabolic modeling and machine learning for studying plants
Supervisor of Marta Sofia Costa Sampaio
 Informática (PhD)
Universidade do Minho, Portugal
2019 - Current Genome-­scale metabolic model reconstruction of a symbiotic microbial community at an extreme environment
Supervisor of Joana Raquel da Rocha Santos
Bioinformática (Master)
Universidade do Minho, Portugal
2018/09/01 - Current Unravelling the consortium interactions of filamentous bacteria
Supervisor of Ana Margarida Torres Marques de Miranda
 Bioinformática (Master)
Universidade do Minho, Portugal
2017 - Current Design and optimization of microbial communities
Co-supervisor of Sophia Torres dos Santos
 Bioengenharia (PhD)
Universidade do Minho, Portugal
2022 - 2023/12 Adriano Miguel Pereira da Silva
Supervisor of Adriano Miguel Pereira da Silva
 Bioinformática (Master)
Universidade do Minho, Portugal
2021 - 2023/02 Development of Deep Learning Models for scRNA data analysis
Supervisor of Diogo Duarte Pinto Macedo
 Bioinformática (Master)
Universidade do Minho, Portugal
2018 - 2023 Blueprint: documenting the complexity of metabolic regulation by reconstruction of integrated metabolic-regulatory models
Supervisor of Fernando João Pereira da Cruz
 Engenharia Biomédica (PhD)
Universidade do Minho, Portugal
2020 - 2022/01 PhageDPO: Phage Depolymerase Finder
Co-supervisor of José Alexandre Graça Duarte
 Bioinformática (Master)
Universidade do Minho, Portugal
2022 - 2022 Genome-scale metabolic modelling of na extremophile microbial community
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2021/01 - 2022 Development of continuous integration workflows for merlin
Supervisor of Ana Carolina Costa Barbosa
 Bioinformática (Master)
Universidade do Minho, Portugal
2020/01 - 2022 Multi-view learning for multiomics data integration for the study of plants
Supervisor of Maria Inês Alves Faria
 Bioinformática (Master)
Universidade do Minho, Portugal
2019 - 2022 Genome-scale metabolic modelling of an extremophile microbial community
Supervisor of Rui Ricardo Barros Nunes
Bioinformática (Master)
Universidade do Minho, Portugal
2019 - 2021/10/13 Unveiling the production of metabolites with flavor enhancement through genome-scale metabolic modelling of a Lambic beer microbial community
Supervisor of Ana Isabel Gomes Fernandes
 Bioinformática (Master)
Universidade do Minho, Portugal
2019 - 2021/03/01 Development of bioinformatics tools towards the improvement of gap filling in metabolic models
Supervisor of João Manuel Capela Araújo Ribeiro
 Bioinformática (Master)
Universidade do Minho, Portugal
2021 - 2021 M3L: Exploring synergies between metabolic modelling and machine learning for studying plants.
Supervisor
 Informática (PhD)
Universidade do Minho, Portugal
2021 - 2021 Unveiling the production of metabolites with flavor enhancement through genome-scale metabolic modelling of a lambic beer microbial community
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2021 - 2021 Development of bioinformatics tools towards the imporvement of gap filling in metabolic models
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2021 - 2021 Bacteriophage-host determinants: identification of bacteriophage receptors through machine learning techniques
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2021 - 2021 Development of bioinformatics tools in prophage analysis
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2019 - 2021 Bacteriophage-host determinants: identification of bacteriophage receptors through machine learning techniques
Supervisor of Pedro Henrique Matela Aidos Manso de Araújo
 Bioinformática (Master)
Universidade do Minho, Portugal
2019 - 2021 Development of Bioinformatics tools in prophage analysis
Supervisor of João Pedro Porto Dias
 Bioinformática (Master)
Universidade do Minho, Portugal
2018/09/01 - 2020/07/31 Implementation of new tools and approaches for the reconstruction of genome-scale metabolic models
Supervisor of Cláudia Isabela Sampaio Ganâncio
 Bioinformática (Master)
Universidade do Minho, Portugal
2019/01/01 - 2020/04/09 Assessment of microbial community interactions using different tools
Supervisor of Catarina Moreira Ribeiro
 Bioinformática (Master)
Universidade do Minho, Portugal
2018/09/01 - 2020/02/18 In silico and in vitro analysis of microbial community interactions in fermented foods
Supervisor of Catarina Moreira Ribeiro
 Bioinformática (Master)
Universidade do Minho, Portugal
2018/09/01 - 2019/10/31 A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli
Supervisor of Alexandre Rafael Machado Oliveira
 Bioinformática (Master)
Universidade do Minho, Portugal
2018/09/01 - 2019/10/31 Identification and classification of transporter proteins using deep learning models
Co-supervisor of Andrea Ferreira Meireles da Silva
 Bioinformática (Master)
Universidade do Minho, Portugal
2018/09/01 - 2019/10/31 Development and implementation of a repository for transcriptional regulatory information
Supervisor of Diogo Batista Lima
 Bioinformática (Master)
Universidade do Minho, Portugal
2018/09/01 - 2019/10/31 Genome-scale reconstruction of the metabolic network of the probiotic bacterium Lactobacillus acidophilus
Supervisor of Emanuel Rodrigues da Cunha
 Bioinformática (Master)
Universidade do Minho, Portugal
2018/09/01 - 2019/10/31 In silico objective-driven optimization of microbial communities
Supervisor of José Miguel Dantas de Sousa
 Bioinformática (Master)
Universidade do Minho, Portugal
2018/09/01 - 2019/10/31 In silico characterization of microbial communities interaction in soil samples
Supervisor of Marta Lopes Gomes
 Bioinformática (Master)
Universidade do Minho, Portugal
2018/09/01 - 2019/10/31 Genome-Scale Metabolic Modelling of the pathogen Xylella fastidiosa
Supervisor of Miguel Ângelo Fernandes da Silva
 Bioinformática (Master)
Universidade do Minho, Portugal
2018/09/01 - 2019/10/31 Implementation of the object-relational mapping tool Hibernate in merlin’s framework
Supervisor of Sofia Raquel Lages Pereira
 Bioinformática (Master)
Universidade do Minho, Portugal
2017/09 - 2019/06 Comparative analysis and characterization of industrial Streptococcus thermophilus genomes
Supervisor of Tiago Filipe Pereira Isabelinho
Bioinformática (Master)
Universidade do Minho, Portugal
2017/09 - 2019/03 Reconstruction of the metabolic network of Lactobacillus rhamnosus
Co-supervisor of João Pedro Bernardo Mendes
 Bioinformática (Master)
Universidade do Minho, Portugal
2017/09 - 2019/03 Modelling interspecies interactions of syntrophic communities of Syntrophobacter fumaroxidans and Methanospirillum hungatei
Supervisor of José Jorge Sampaio Bastos
 Bioinformática (Master)
Universidade do Minho, Portugal
2019 - 2019 In silico characterization of microbial communities interaction in soil samples
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2017/09 - 2018/10 Development of Bioinformatics tools for the classification of transporter systems
Supervisor of Davide Rafael Santos Lagoa
 Bioinformática (Master)
Universidade do Minho, Portugal
2017/09 - 2018/10 Nitrobacter vulgaris: genome-scale model reconstruction and interactions with Nitrosomonas europaea
Supervisor of Renato Alexandre Azevedo Cruz
 Bioinformática (Master)
Universidade do Minho, Portugal
2017/09 - 2018/08 PhagePromoter: Phage Promoters Online Analysis Tool
Supervisor of Marta Sofia Costa Sampaio
 Bioinformática (Master)
Universidade do Minho, Portugal
2018 - 2018 PhagePromoter: Ferramenta online de análise de promotores de fagos
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2018 - 2018 Improving merlin´s framework for the reconstruction of treponema pallidum
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2018 - 2018 Nitrobacter vulgaris: genomic scale model reconstruction and interactions with nitrosomonas europaea
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2018 - 2018 improvement of the bionformatics tool TRIAGE for modelling transport systems
Supervisor
 Bioinformática (Master)
Universidade do Minho, Portugal
2017 - 2018 Development of bioinformatics tools to accelerate the reconstruction of genome-scale models
Supervisor of José Amaro Ferreira Morais
 Bioinformática (Master)
Universidade do Minho, Portugal
2016/09 - 2017/10 Comparação genómica de bacteriofagos responsaveis por injectar especies de providência
Supervisor of Bruna Lopes Mendes
 Bioinformática (Master)
Universidade do Minho, Portugal
2016/09 - 2017/10 Reconstrução do modelo matabólico à escala genómica de Nitrosomonas europaea
Supervisor of Pedro Miguel Brígida Raposo
 Bioinformática (Master)
Universidade do Minho, Portugal
2016 - 2017 Reconstructing the metabolic of Lactobacillus helveticus on a genome-wide scale
Supervisor of Jose Miguel Gonçalves Dias
 Bioinformática (Master)
Universidade do Minho, Portugal
2016 - 2017 Reconstrução da rede metalica à escala genómica de Streptococus thermophilus
Co-supervisor of Fernando João Pereira da Cruz
 Bioinformática (Master)
Universidade do Minho, Portugal
2016 - 2017 Desenvolvimento e implementação de ferramentas bioinformáticas para a reconstrução de GisMos
Supervisor of António Carlos Fortuna Ribeiro Dias
 Bioinformática (Master)
Universidade do Minho, Portugal
2015 - 2016 Development of a computational approach for the identification and annotation of transport proteins
Supervisor of Daniel Torres Varzim Faria
 Bioinformática (Master)
Universidade do Minho, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2020/06/29 - 2020/07/03 Summer School in Metabolic Modeling (2020/06/29 - 2020/07/03)
Workshop (President of the Organising Committee)
 Universidade do Minho Centro de Engenharia Biológica, Portugal
2019/07/03 - 2019/07/07 Summer School in Metabolic Modeling (2019/07/03 - 2019/07/07)
Workshop (President of the Organising Committee)
 Universidade do Minho Centro de Engenharia Biológica, Portugal
2015/06/08 - 2015/06/12 Metabolic Pathway Analysis 2015 (2015/06/08 - 2015/06/12)
Conference (Member of the Organising Committee)
 Biochemical Society, United Kingdom

Universidade do Minho Centro de Engenharia Biológica, Portugal

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2022/03/03 - 2022/03/05 Moderator of the Systems Biology panel.
Conference
 XI Bioinformatics Open Days
Universidade do Minho, Portugal
2021/10/07 - 2021/10/07 Chair at the PACBB: Bioinformatics and systems biology panel
Conference
 15th International Conference on Practical Applications of Computational Biology & Bioinformatics
Universidad de Salamanca, Spain
2021/02/03 - 2021/02/03 Participation in Docência+ Impacto 2021 https://api.eu.badgr.io/public/assertions/nVPMy2cTSwS9HbMDRO7Ocg?identity__email=odias%40deb.uminho.pt
Workshop
 Docência+ Impacto 2021
Universidade do Minho, Portugal
2020/12/04 - 2020/12/04 Pedagogical training: "Introductory activity on the construction of online concept maps in the CMap cloud and its use in the educational context, streamlined in a Flipped Webinar format" Formação pedagógica: "Atividade introdutória sobre a construção de mapas conceituais on-line no CMap cloud e seu uso no contexto educacional, dinamizada em formato de Flipped Webinar" https://api.eu.badgr.io/public/assertions/z-tIUONbQFK0O9IU4tm2sw?identity__email=odias%40deb.uminho.pt
Workshop
 Flipped Webinar: CMap cloud
Universidade do Minho, Portugal
2020/10/15 - 2020/10/15 Pedagogical training: Participation as a facilitator of the training program "Teaching +" (3rd edition) is certified. Formação pedagógica: Certifica-se a participação como facilitador do programa de formação "Docência +" (3.ª edição). https://api.eu.badgr.io/public/assertions/t0-B6vdvS1miSqX93ZI6fQ?identity__email=odias%40deb.uminho.pt docência+ (3.ª edição - 2020): Facilitador
Universidade do Minho, Portugal
2020/10/08 - 2020/10/08 Chair at the PACBB: Bioinformatics and Biomedical applications session.
Conference
 Practical Applications of Computational Biology & Bioinformatics
Università degli Studi dell'Aquila, Italy
2020/09/29 - 2020/09/29 Pedagogical training: Introductory activity on the educational use of TED-Ed, streamlined in a Flipped Webinar format Formação pedagógica: Atividade introdutória sobre o uso educacional do TED-Ed, dinamizada em formato de Flipped Webinar https://api.eu.badgr.io/public/assertions/bYkL15qdRSynqP6a8An8mg?identity__email=odias%40deb.uminho.pt
Workshop
 Flipped webinar: TED-Ed
Universidade do Minho, Portugal
2020/09/22 - 2020/09/22 Pedagogical training: Introductory activity on Open Badges (download, print) and their use in the educational context, streamlined in Flipped Webinar format. Formação pedagógica: Atividade introdutória sobre os Open Badges (download, impressão) e seu uso no contexto educacional, dinamizada em formato de Flipped Webinar https://api.eu.badgr.io/public/assertions/sVw3Ly5eTAuqX2VwNeMsPg?identity__email=odias%40deb.uminho.pt
Workshop
 Flipped Webinar: Open badges
Universidade do Minho, Portugal
2020/09/18 - 2020/09/18 Pedagogical training: Introductory activity on the Team-Based Learning (TBL) methodology, streamlined in a Flipped Webinar format. Formação pedagógica: Atividade introdutória sobre a metodologia Team-Based Learning (TBL), dinamizada em formato de Flipped Webinar. https://api.eu.badgr.io/public/assertions/rwfl_SQ3SxSnIQdhqAw8ug?identity__email=odias%40deb.uminho.pt
Workshop
 Flipped webinar: TBL
Universidade do Minho, Portugal
2020/07/24 - 2020/07/24 Pedagogical training: You have successfully completed the training program “Teaching +” (2nd edition), making a 20-hour workload, in distance learning regime. Formação pedagógica: Certifica-se que completou com sucesso o programa de formação “Docência +” (2.ª edição), perfazendo uma carga horária de 20 horas, em regime de ensino a distância. https://api.eu.badgr.io/public/assertions/WtdeLdeNRKyf1VAYlO6-Ig?identity__email=odias%40deb.uminho.pt
Workshop
 Docência + (edição 2020): Transformação
Universidade do Minho, Portugal
2020/07/10 - 2020/07/10 Participation in the webinar presented by Professor Roni Roberts, carried out during the "Docência +" training program (2nd edition), is certified. Certifica-se a participação no webinar apresentado pelo Professor Roni Roberts, realizado durante o programa de formação "Docência +" (2.ª edição). https://api.eu.badgr.io/public/assertions/Gsp07OK1TIGGKWhg-aS5Tw?identity__email=odias%40deb.uminho.pt
Seminar
 Webinar "Students as Partners: empowering students to actively improve their university experience"
Universidade do Minho, Portugal
2020/06/18 - 2020/06/18 Pedagogical training: Sharing IDEAS # 11: What will we take into account in the preparation of the new school year? Formação pedagógica: Partilhando IDEiAs #11: O que vamos ter em conta na preparação do novo ano letivo? https://api.eu.badgr.io/public/assertions/AufWWS7bRqOQDPoiJXXYKg?identity__email=odias%40deb.uminho.pt
Workshop
 Preparação do novo ano letivo
Universidade do Minho, Portugal
2020/05/28 - 2020/05/28 Pedagogical training: Sharing IDEAS # 09: What challenges and opportunities for the University in the context of the resumption of Pandemic: Teaching? Formação pedagógica: Partilhando IDEiAs #09: Que desafios e que oportunidades para a Universidade no contexto da retoma da Pandemia:o Ensino? https://api.eu.badgr.io/public/assertions/CiwO80i1ShOtCDlLtOn4aw?identity__email=odias%40deb.uminho.pt
Workshop
 Desafios e que oportunidades para a Universidade
Universidade do Minho, Portugal
2020/01/29 - 2020/01/29 Pedagogical training in "The classroom game: strategies for promoting participation in the classroom" - Formação pedagógica em "O jogo da aula: estratégias para a promoção da participação na sala de aula"
Seminar
 O jogo da aula: estratégias para a promoção da participação na sala de aula
Universidade do Minho, Portugal
2020/01/29 - 2020/01/29 Pedagogical Training in "Challenge Based Learning - A New Role for Universities to Contribute to Social Transformation and Public Good" - Formação pedagógica em "Challenge Based Learning - A New Role for Universities to Contribute to Social Transformation and Public Good"
Seminar
 Challenge Based Learning - A New Role for Universities to Contribute to Social Transformation and Public Good
Universidade do Minho, Portugal
2020/01/29 - 2020/01/29 Pedagogical training in "Practical Workshop for the Construction of Multiple Choice Questions to test objectives of greater complexity (2nd Ed.)" - Formação pedagógica em "Workshop prático de construção de Perguntas de Escolha Múltipla para testar objectivos de maior complexidade (2ª Ed.)"
Workshop
 Workshop prático de construção de Perguntas de Escolha Múltipla para testar objectivos de maior complexidade (2ª Ed.)
Universidade do Minho, Portugal
2019/09/27 - 2019/09/27 Pedagogical training in "Workshop: Blackboard in everyday life: Essential tools" - Formação pedagógica em "Workshop: Blackboard no dia a dia: ferramentas Essenciais"
Workshop
 Workshop: Blackboard no dia a dia: ferramentas Essenciais
Universidade do Minho, Portugal
2019/09/24 - 2019/09/24 Pedagogical training in "More interactive classes with" Team Based Learning "(TBL) - 3rd Edition" - Formação pedagógica em "Aulas mais interativas com "Team Based Learning" (TBL) - 3ª Edição"
Workshop
 Aulas mais interativas com "Team Based Learning" (TBL) - 3ª Edição
Universidade do Minho, Portugal
2018/07/20 - 2018/07/20 Pedagogical Training in "Occupational Stress in Higher Education Teachers" - Formação Pedagógica em "Organização e gestão do trabalho"
Seminar
 Organização e gestão do trabalho
Universidade do Minho, Portugal
2018/07/10 - 2018/07/10 Pedagogical Training in "Introduction to Mindfulness" - Formação Pedagógica em "Introdução ao Mindfulness"
Seminar
 Introdução ao Mindfulness
Universidade do Minho, Portugal
2018/07/09 - 2018/07/09 Pedagogical Training in "Occupational Stress in Higher Education Teachers" - Formação Pedagógica em "Stress ocupacional em docentes do ensino superior"
Seminar
 Stress ocupacional em docentes do ensino superior
Universidade do Minho, Portugal
2018/07/05 - 2018/07/05 Pedagogical training in the "use of Idea Puzzle® software in the research process" - Formação Pedagógica na "utilização do software Idea Puzzle® no processo de investigação"
Seminar
 A utilização do software Idea Puzzle® no processo de investigação de doutoramento
Universidade do Minho, Portugal
2018/06/19 - 2018/06/19 Pedagogical Training in "Soft Skills of Pedagogical Communication" - Formação Pedagógica em "Soft Skills de Comunicação Pedagógica"
Seminar
 Soft Skills de Comunicação Pedagógica
Universidade do Minho, Portugal

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2023/03/24 Metabolomics-Based Approaches For Food Authentication and Traceability
(Thesis) Arguer
 Rebeca Tatiana de Souto Santos (PhD)
Universidade do Minho, Portugal
2022/03/12 Developing deep learning methods to predict phenotypes and clinical outcomes from transcriptomics data
President of the jury
 Maria Fernanda Silva Vieira (Master)
Universidade do Minho, Portugal
2022/03 To be or NOT to be: The Impact of Negative Annotation in Biomedical Semantic Similarity
(Thesis) Main arguer
 Lina Andreia Gama Aveiro (Master)
Universidade de Lisboa, Portugal
2022/02/18 Characterization of the choroid plexus cells transcriptome during development
President of the jury
 Miguel Monteiro Pacheco (Master)
Universidade do Minho, Portugal
2021/12/13 A model validation pipeline for healthy tissue genome-scale metabolic models
President of the jury
 Maria Adília Balacó Chócha Pessoa Monteiro (Master)
Universidade do Minho, Portugal
2021/10/13 Computacional Approaches for the integration of in vitro chemical and screening data sets
President of the jury
 Ana Beatriz Gonçalves da Cunha (Master)
Universidade do Minho, Portugal
2021/10 Produção de para-aminobenzoato a partir de Corynebacterium glutamicum
(Thesis) Main arguer
 Ana Filipa Baptista Fernandes (Master)
Universidade do Minho, Portugal
2021/09/16 Analysis of metabolic pathways of Saccharomyces cerevisiae in alcoholic fermentation to mitigate glucose rise in grapes due to global warming effects
(Thesis) Main arguer
 João Pedro Zamith Piedade Ribeiro Magalhães (Master)
Universidade de Trás-os-Montes e Alto Douro, Portugal
2021/04/14 Development of deep learning-based tools for the design of new compounds with desired biological activities
President of the jury
 Tiago Filipe Escairo Sousa (Master)
Universidade do Minho, Portugal
2021/03/29 Dynamic genome-scale modelling of the Saccharomyces non-cerevisiae yeasts metabolism in wine fermentation
(Thesis) Main arguer
 David Miguel Ferreira dos Santos (Master)
Universidade do Minho, Portugal
2021/03/15 Computational methods for the identification of genetic variants in complex diseases
President of the jury
 Débora Alves Antunes (Master)
Universidade do Minho, Portugal
2021/03/09 Avian genomics: Insight into bitter taste receptors
President of the jury
 Raquel Sofia Vasconcelos Cardoso (Master)
Universidade do Minho, Portugal
2021/03/02 Implementing a webserver for managing and detecting viral fusion proteins
President of the jury
 Pedro Daniel Martins Moreira (Master)
Universidade do Minho, Portugal
2020/11/09 “Development of a Tool based on Deep Learning able to classify Biomedical Literature
President of the jury
 Nuno Miguel Caetano Alves (Master)
Universidade do Minho, Portugal
2019/11/28 Analysis of Human Metabolic Models Using Machine Learning Techniques
(Thesis) Main arguer
 Pedro Miguel Serra Morim (Master)
Universidade do Minho, Portugal
2018/10/08 Development of a tool for partial automated annotation of metabolic reactions
(Thesis) Main arguer
 Pedro Miguel Teixeira Queirós (Master)
Universidade do Minho, Portugal
2016 Systems Analysis of Minimal Metabolic Networks in Prokaryotes
(Thesis) Arguer
 Joana Rute Calça Xavier (PhD)
Universidade do Minho, Portugal
2015 Algorithms and Computational Tools for Metabolic Flux Analysis
(Thesis) Arguer
 Rafael de Castro Carreira (PhD)
Universidade do Minho, Portugal
2015 Analysis of transcriptomic data for inference of the function of the ATXN3 gene in neuronal cells
(Thesis) Main arguer
 Manuel José Gil Nogueira Ferreira (Master)
Universidade do Minho, Portugal
2015 In silico Optimization of organic acids production
(Thesis) Main arguer
 Bárbara Correia Brito (Master)
Universidade do Minho, Portugal
2014 Reconstrução do Modelo Metabólico do Actinobaccilus succinogenes
(Thesis) Main arguer
 Joana Margarida Miguel (Master)
Universidade do Minho, Portugal
2014 Development of an integrated platform for the in silico phenotype simulation of microbial strains
(Thesis) Main arguer
 Hugo Miguel Melo Giesteira (Master)
Universidade do Minho, Portugal
2013 PGP: Prokaryote Gene Prediction software
(Thesis) Main arguer
 José Carlos Ribeiro Pacheco (Master)
Universidade do Minho, Portugal

Ad Hoc journal article review

Journal title (ISSN) Publisher
2021 - Current Metabolites (2218-1989) MDPI
2021 - Current npj systems biology and applications (2056-7189) Nature Publishing Group
2020 - Current Computers in Biology and Medicine (0010-4825) Elsevier
2020 - Current Frontiers in Bioengineering and Biotechnology (2296-4185) Frontiers Media
2020 - Current Transactions on Computational Biology and Bioinformatics (1545-5963) IEEE xplore
2020 - Current Scientific reports (2045-2322) Nature Publishing Group
2019 - Current Biotechnology Journal (1860-7314) Wiley Online Library
2019 - Current BMC Bioinformatics (1471-2105) Springer Nature
2019 - Current Frontiers in Genetics (1664-8021) Frontiers Media
2019 - Current BioMed Research International (2314-6141) Hindawi
2018 - Current Bioinformatics (1367-4811) Oxford

Committee member

Activity description
Role 		Institution / Organization
2022 - Current Review Editor for the Synthetic Biology of the Frontiers in Bioengineering and Biotechnology journal
Member
 Frontiers Media SA, Switzerland
2021 - Current Guest Editor for MDPI Genes Special issue on Reconstruction of Genome-Scale Metabolic Models
Coordinator
 MDPI AG, Switzerland
2021 - Current Outreach activities - ICEBreak is a cycle of online webinars, bringing together researchers, students and the general public to share and discuss science at CEB. With a duration of 30 min.
Coordinator
 Universidade do Minho Centro de Engenharia Biológica, Portugal

Conference scientific committee

Conference name Conference host
2022/07/13 - 2022/07/15 16th International Conference on Practical Applications of Computational Biology & Bioinformatics University of L'Aquila, Italy
2021/10/06 - 2021/10/08 15h International Conference on Practical Applications of Computational Biology & Bioinformatics University of Salamanca, Spain
2020/10/07 - 2020/10/09 14th International Conference on Practical Applications of Computational Biology & Bioinformatics University of L'Aquila, Italy
2019/09/05 - 2019/09/06 INForum - Simpósio de Informática
2019/06/26 - 2019/06/28 13th International Conference on Practical Applications of Computational Biology & Bioinformatics High technical school of Ávila, University of Salamanca, Spain
2018/06/20 - 2018/06/22 12th International Conference on Practical Applications of Computational Biology & Bioinformatics Campus Tecnológico de la Fábrica de Armas University of Castilla-La Mancha, Spain
2017/06/21 - 2017/06/23 11th International Conference on Practical Applications of Computational Biology & Bioinformatics Polytechnic of Porto, Portugal
2016/06/01 - 2016/06/03 10th International Conference on Practical Applications of Computational Biology & Bioinformatics University of Sevilla, Spain
2015/06/03 - 2015/06/05 9th International Conference on Practical Applications of Computational Biology & Bioinformatics University of Salamanca, Spain

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2017/02 - Current Biological Process Modeling Master's in Bioinformatics (Mestrado) Universidade do Minho Departamento de Engenharia Biológica, Portugal
2017/02 - Current Project on Bioinformatics and Systems Biology Master's in Bioinformatics (Mestrado) Universidade do Minho Departamento de Engenharia Biológica, Portugal
2016/09/01 - Current Systems Biology Master's in Bioinformatics (Mestrado) Universidade do Minho Departamento de Engenharia Biológica, Portugal
2016/09 - Current Bioinformatics and Systems Biology Master's in Biological Engineering (Mestrado integrado) Universidade do Minho Departamento de Engenharia Biológica, Portugal

Evaluation committee

Activity description
Role 		Institution / Organization Funding entity
2022/02/06 - 2022/02/15 Evaluator for the assessment of applications for exceptional extension «COVID grants» panel
Evaluator
 Fundação para a Ciência e a Tecnologia, Portugal

Mentoring / Tutoring

Topic Student name
2018/09 - Current Reconstruction and computational analysis of metabolism associated with the production of xylitol of Candida tropicalis Diana Carolina Tusso Pinzon
2019/01 - 2021 Construction of metabolic models of Candida albicans and Candida glabrata Romeu Filipe Nobre Viana
2017/10 - 2019 Evolutionary engineering of Clostridium saccharoperbutylacetonicum for enhanced tolerance toward lignocellulosic inhibitors in butanol production Rafael Ferraz Alves
2016/12 - 2017/12 Evaluation of lipid production in silico, eicosapentaenoic acid (EPA), by Pythium irregulare as value added product, from vinasse Bruna Soares Fernandes
Distinctions

Award

2019 Best poster award at MicroBiotec'19 - Congress of Microbiology and Biotechnology
Universidade de Coimbra, Portugal

Other distinction

2020 Spotlight recognition - Oliveira H et al. AEM journal. doi: 10.1128/AEM.00073-20
2012 Highly Accessed - Dias O et al. BMC Genomics journal. doi: 10.1186/1471-2164-13-517