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Isabel Rocha is Vice-Rector at NOVA University Lisbon, coordinating the Second and Third Missions, including the areas of Research, Innovation, entrepreneurship, technology and knowledge transfer, and the Institute of Arts and Technology . She is Principal Investigator at ITQB NOVA, coordinating a Research Laboratory in Systems and Synthetic Biology. She obtained her PhD at the University of Minho in Chemical and Biological Engineering and did a post-doctorate at the Technical University of Denmark. Her research in Biotechnology covers the topics of Bioinformatics, Metabolic Engineering, Synthetic Biology and Systems Biology, and she has published more than 140 complete articles in international magazines, books and conferences. She is the scientific coordinator, among others, of the Shikifactory100 Project (Shikifactory100.eu). She was from 2019 to 2022 the national representative on the executive board of the European Bioinformatics Infrastructure (ELIXIR). She is also an evaluator for several funding agencies, including the European Commission and the European Innovation Council. During 2007, she was a visiting professor at MIT, USA, as part of the MIT-Portugal Program and, from 2007 to 2017, she was part of the faculty at MIT-Portugal, being responsible for an educational innovation program involving 4 universities and 2 PhD programs - the i-teams. She was President of P-Bio, Portuguese Association of Bioindustries and is one of the founders of the companies Biotempo and SilicoLife. She was Chairman of the Board of the CoLab InnovPlantProtect (2011-2021), in crop protection, and is Vice-Chairman of the CoLab BIOREF in Biorefineries, and is also a member of the Board of Directors of Madan Parque, NOVA's technology-based incubator.
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Identification

Personal identification

Full name
Isabel Rocha

Citation names

  • Rocha, Isabel
  • Rocha, I.

Author identifiers

Ciência ID
7711-3969-7806
ORCID iD
0000-0001-9494-3410
Google Scholar ID
https://scholar.google.com/citations?user=ZgGREPcAAAAJ&hl=en
Researcher Id
A-4279-2013
Scopus Author Id
35238052200

Websites

Knowledge fields

  • Engineering and Technology - Industrial Biotechnology
  • Engineering and Technology - Industrial Biotechnology - Biofuels
  • Engineering and Technology - Industrial Biotechnology - Fermentation
  • Engineering and Technology - Industrial Biotechnology - Bioprocessing Technologies
  • Natural sciences - Biological Sciences - Molecular Biology
  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Engineering and Technology - Other Engineering and Technologies

Languages

Language Speaking Reading Writing Listening Peer-review
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Portuguese (Mother tongue)
Spanish; Castilian Advanced (C1) Advanced (C1) Upper intermediate (B2) Proficiency (C2) Advanced (C1)
French Intermediate (B1) Upper intermediate (B2) Intermediate (B1) Intermediate (B1) Intermediate (B1)
Education
Degree Classification
2003
Concluded
 Doutoramento em Engenharia Química e Biológica (Doutoramento)
Universidade do Minho Escola de Engenharia, Portugal
"Model-based strategies for computer-aided operation of a recombinant E. coli fermentation" (THESIS/DISSERTATION)
 Não Aplicável
1997
Concluded
 Engenharia Biológica (Licenciatura)
Universidade do Minho Escola de Engenharia, Portugal
"N/A" (THESIS/DISSERTATION)
 17 valores
Affiliation

Science

Category
Host institution 		Employer
2019/03/01 - Current Principal Investigator (Research) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Universidade Nova de Lisboa, Portugal
2003/12/01 - 2004/07/31 Postdoc (Research) Danmarks Tekniske Universitet, Denmark

Teaching in Higher Education

Category
Host institution 		Employer
2007/09/01 - 2017/09/14 Assistant Professor (University Teacher) Universidade do Minho Departamento de Engenharia Biológica, Portugal
2004/11/01 - 2007/08/31 Assistant (University Teacher) Universidade do Minho Departamento de Engenharia Biológica, Portugal
2002/09/01 - 2003/08/31 Assistant (University Teacher) Universidade do Minho, Portugal

Positions / Appointments

Category
Host institution 		Employer
2021/10/20 - Current Vice-Rector Universidade Nova de Lisboa, Portugal
2019/06/01 - Current Vice-President BIOREF Colab, Portugal
2018/11/15 - Current Member of the Board Madan Parque, Portugal
2019/11/15 - 2022/12/31 Vice-President ELIXIR - Distributed Infrastructure for Biological Data, United Kingdom
2019/02/01 - 2022/03/31 President InnovPlantProtect CoLab, Portugal
2017/09/15 - 2021/10/20 Pro-Rector Universidade Nova de Lisboa, Portugal
2009/03/01 - 2011/02/28 President APBio - Portuguese Bioindustries Association (now P-Bio), Portugal

Others

Category
Host institution 		Employer
2010/05/01 - Current Founder, Scientific Advisor and member of the Board SilicoLife, Portugal
2007/01/01 - 2017/09/14 Member of the Faculty MIT Portugal Program, Portugal
2002/01/01 - 2015/12/31 Founder and Chief Scientific Officer Biotempo, Ltd, Portugal
2012/09/01 - 2015/08/31 Member of the Scientific Advisory Board of the ERA-SynBio, an European effort to promote projects and initiatives in Synthetic Biology ERA SynBio - Synthetic Biology, Belgium
2007/02/01 - 2007/05/31 Visiting Scholar Massachusetts Institute of Technology, United States
1999/01/01 - 2003/10/31 Trainer and consultant in the fields of ISO 9000 and ISO 14000 implementation Several, Portugal
1998/05/01 - 2003/10/31 PhD Student Universidade do Minho Centro de Engenharia Biológica, Portugal
Projects

Grant

Designation Funders
2019/01/01 - 2023/03/31 SHIKIFACTORY100 - Modular cell factories for the production of 100 compounds from the shikimate pathway
grant agreement number 814408
Principal investigator
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
 European Commission
Ongoing
2019/07/01 - 2022/06/30 Machine learning and deep learning approaches to industrial biotechnology applications
NORTE-01-0247-FEDER-039831
Principal investigator
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
 Agência Nacional de Inovação SA
Ongoing
2021/02/01 - 2022/02/28 Using computational and experimental methods to provide a global characterization of viral fusion peptides
PTDC/CCI-BIO/28200/2017
Universidade de Lisboa Instituto de Medicina Molecular João Lobo Antunes, Portugal

Universidade Nova de Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2018/10/01 - 2021/09/30 MIXED-UP - Targeting pathogenesis and engineering cell factories: developing mixed regulatory
PTDC/BII-BIO/28216/2017
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
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
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
 European Commission
Concluded
2017/04 - 2019/05 Bio.Data – Portuguese Biological Data Network
ROTEIRO/0098/2013
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
2015/04/01 - 2018/12/31 DYNAMICS - Analysis and optimization of industrial microorganisms under dynamic process conditions
ERA-IB-2014
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2014/04/01 - 2017/12/31 DeYeastLibrary - Designer Yeast Strain Library Optimized for Metabolic Engineering Applications
ERA-IB-2/0003/2013
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2013/10/01 - 2017/08/31 Microbial cell factory and processes development for sugarcane hemicellulose hydrolysate valorization
MEC/MCTI/CAPES/CNPq/FAPs Nº 71/2013
Principal investigator
Concluded
2013/11/01 - 2016/10/31 BACterial Hosts for production of Bioactive phenolics from bERRY fruits
FP7-KBBE-2013-7
Principal investigator
Biotempo, Ltd, Portugal
 European Commission
Concluded
2012/07/01 - 2015/06/30 PEM – A platform for Metabolic engineering
FEDER, project 23060 (ANI)
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Agência Nacional de Inovação SA
Concluded
2012/04/01 - 2015/03/31 Finding the naturally evolved design principles of prevalent metabolic circuits
PTDC/QUI-BIQ/119657/2010
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2011/01/01 - 2013/12/31 In silico reconstruction of Streptococcus pneumoniae cellular networks and their impact on virulence.
FCT PTDC/EBB-EBI/113824/2009
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2010/04/01 - 2013/12/31 HeliSysBio - Molecular Systems Biology in Helicobacter pylori
FCT PTDC/EBB-EBI/104235/2008
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2008/11/01 - 2011/10/31 SYSINBIO- Systems Biology as a Driver for Industrial Biotechnology
call FP7-KBBE-2007-1
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
 European Commission
Concluded
2008/09/01 - 2010/08/31 Propolis efficacy for the control of American Foulbrood: evaluation in controlled regions
Measure 6A
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
Concluded

Contract

Designation Funders
2023/09/01 - Current Life Sciences for a Healthy and Sustainable Future
LA/P/0087/2020
10.54499/LA/P/0087/2020
Instituto Português de Oncologia de Lisboa Francisco Gentil EPE, Portugal

Universidade Nova de Lisboa Molecular Structural and Cellular Microbiology, Portugal

Universidade Nova de Lisboa, Portugal

Instituto de Biologia Experimental e Tecnológica, Portugal

Instituto Gulbenkian de Ciência, Portugal

Universidade de Lisboa Centro de Estudos Comparatistas, Portugal

BioResources 4 Sustainability, Portugal

Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, 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
2023/01/01 - 2025/12/31 Modelling vitamins B1 and B2 biosynthesis and biofortification in rice
2022.02916.PTDC
Universidade Nova de Lisboa, Portugal

Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2010/05 - 2013/11 SYNBIOBACTHER - Synthetic biology approaches to engineer "therapeutic" bacteria
102863
Provided by PTCRIS: 102863
PTDC/EBB-BIO/102863/2008
Universidade do Minho, Portugal

Instituto de Biotecnologia e Bioengenharia, Portugal

Universidade de Lisboa Instituto Superior Técnico, Portugal

Universidade do Porto Faculdade de Engenharia, 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

Instituto de Biotecnologia e Bioengenharia, Portugal

Universidade do Algarve, Portugal

Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal

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

Fundação Gaspar Frutuoso, Portugal

Universidade de Lisboa Instituto Superior Técnico, Portugal

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

Universidade dos Açores, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2009/04/01 - 2012/09/30 Bridging Systems and Synthetic Biology for the development of Improved Microbial Cell Factories
MIT-Pt/BS-BB/0082/2008
Provided by PTCRIS: 84035
Universidade do Minho, Portugal

Instituto de Biologia Experimental e Tecnológica, Portugal

Universidade do Minho Centro de Engenharia Biológica, Portugal

Universidade do Porto Faculdade de Engenharia, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2007/11/01 - 2009/10/31 Development of a user-friendly software platform for the rational design of improved microbial strains
Dupont Science and Engineering Program
Principal investigator
Universidade do Minho Centro de Engenharia Biológica, Portugal
Concluded
Outputs

Publications

Book
  1. Vilaça, P.; Maia, P.; Giesteira, H.; Rocha, I.; Rocha, M.. Analyzing and designing cell factories with OptFlux. 2018.
    10.1007/978-1-4939-7528-0_2
  2. Dias, O.; Rocha, M.; Ferreira, E.C.; Rocha, I.. Reconstructing high-quality large-scale metabolic models with merlin. 2018.
    10.1007/978-1-4939-7528-0_1
  3. Santos, S.; Rocha, I.. A computation tool for the estimation of biomass composition from genomic and transcriptomic information. 2016.
    10.1007/978-3-319-40126-3_17
  4. Vieira, V.; Maia, P.; Rocha, I.; Rocha, M.. Development of an integrated framework for minimal cut set enumeration in constraint-based models. 2016.
    10.1007/978-3-319-40126-3_20
  5. Freitas, A.A.; Costa, H.; Rocha, M.; Rocha, I.. A text mining approach for the extraction of kinetic information from literature. 2015.
    10.1007/978-3-319-19776-0_10
  6. Liu, F.; Vilaça, P.; Rocha, I.; Rocha, M.. Evaluating pathway enumeration algorithms in metabolic engineering case studies. 2014.
    10.1007/978-3-319-07581-5_26
  7. Carneiro, S.; Pereira, R.; Rocha, I.. Yeast metabolomics: Sample preparation for a GC/MS-based analysis. 2014.
    10.1007/978-1-4939-0563-8_12
  8. Resende, T.; Correia, D.M.; Rocha, I.. Assignment of Novel Functions to Helicobacter pylori 26695's Genome. 2013.
    10.1007/978-3-319-00578-2_5
  9. Gonçalves, E.; Rocha, I.; Rocha, M.. Computational tools for strain optimization by tuning the optimal level of gene expression. 2012.
    10.1007/978-3-642-28839-5_29
  10. Pinto, J.P.; Rocha, I.; Rocha, M.. Highlighting metabolic strategies using network analysis over strain optimization results. 2011.
    10.1007/978-3-642-24855-9_10
  11. Carneiro, S.; Ferreira, E.C.; Rocha, I.; Carneiro, Sonia; Ferreira, Eugenio C.; Rocha, Isabel; Rocha, MP; et al. A systematic modeling approach to elucidate the triggering of the stringent response in recombinant E. coli systems. 2011.
    10.1007/978-3-642-19914-1_41
  12. Lourenço, A.; Carneiro, S.; Pinto, J.P.; Rocha, M.; Ferreira, E.C.; Rocha, I.. Interpreting the regulatory interplay in E. Coli metabolic pathways. 2011.
    10.1007/978-3-642-19914-1_40
  13. Vilaça, P.; Maia, P.; Rocha, I.; Rocha, M.. Metaheuristics for strain optimization using transcriptional information enriched metabolic models. 2010.
    10.1007/978-3-642-12211-8-18
  14. Pinto, J.P.; Dias, O.; Lourenço, A.; Carneiro, S.; Ferreira, E.C.; Rocha, I.; Rocha, M.; et al. Data integration issues in the reconstruction of the genome-scale metabolic model of Zymomonas mobillis. 2009.
    10.1007/978-3-540-85861-4_12
  15. Rocha, O.; Nobre, C.; Dominguez, A.; Torres, D.; Faria, N.; Rodrigues, L.; Teixeira, J.A.; Ferreira, E.C.; Rocha, I.. A dynamical model for the fermentative production of fructooligosaccharides. 2009.
    10.1016/S1570-7946(09)70695-9
  16. Lourenço, A.; Carneiro, S.; Ferreira, E.C.; Carreira, R.; Rocha, L.M.; Glez-Peña, D.; Méndez, J.R.; et al. Biomedical text mining applied to document retrieval and semantic indexing. 2009.
    10.1007/978-3-642-02481-8_146
  17. Machado, D.; Costa, R.S.; Rocha, M.; Rocha, I.; Tidor, B.; Ferreira, E.C.. A critical review on modelling formalisms and simulation tools in computational biosystems. 2009.
    10.1007/978-3-642-02481-8_161
  18. Evangelista, P.; Rocha, I.; Ferreira, E.C.; Rocha, M.. Evolutionary approaches for strain optimization using dynamic models under a metabolic engineering perspective. 2009.
    10.1007/978-3-642-01184-9_13
  19. Valente, E.; Rocha, M.; Ferreira, E.C.; Rocha, I.. Modelling of biotechnological processes -An approach based on artificial neural networks. 2009.
    10.1007/978-3-642-01888-6_11
  20. Evangelista, P.; Rocha, I.; Ferreira, E.C.; Rocha, M.. A software tool for the simulation and optimization of dynamic metabolic models. 2009.
    10.1007/978-3-642-02481-8_162
  21. Mendes, R.; Rocha, I.; Pinto, J.P.; Ferreira, E.C.; Rocha, M.. Differential evolution for the offline and online optimization of fed-batch fermentation processes. 2008.
    10.1007/978-3-540-68830-3_13
Book chapter
  1. Braga, A.; Rocha, I.; Faria, N.; Braga, A; Faria, N. C. M. Corresponding author: Braga, A. "Microbial hosts as a promising platform for polyphenol production". In Natural Bio-active Compounds: Volume 1: Production and Applications, 71-103. Springer, 2019.
    Published
  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
  3. Rocha, Miguel; Pinto, Jose P.; Rocha, Isabel; Ferreira, Eugnio C.; Marchiori, E; Moore, JH; Rajapakse, JC. "Evaluating Evolutionary Algorithms and Differential Evolution for the online optimization of fermentation processes". 236-246. 2007.
  4. Rocha, Miguel; Mendes, Rui; Maia, Paulo; Pinto, Jose P.; Rocha, Isabel; Ferreira, Eugenio C.; Neves, J; Santos, MF; Machado, JM. "Evaluating simulated annealing algorithms in the optimization of bacterial strains". 473-484. 2007.
  5. Rocha, M; Neves, J; Veloso, ACA; Ferreira, EC; Rocha, I; Ribeiro, B; Albrecht, RF; et al. "Evolutionary algorithms for static and dynamic optimization of fed-batch fermentation processes". 288-291. 2005.
    10.1007/3-211-27389-1_69
  6. Rocha, M; Neves, J; Rocha, I; Ferreira, EC; Raidl, GR. "Evolutionary algorithms for optimal control in fed-batch fermentation processes". 84-93. 2004.
  7. Rocha, I; Ferreira, EC; Dochain, D; Perrier, M. "An integrated system for advanced monitoring and control of fed-batch fermentations of recombinant E-coli". 349-354. 2002.
Conference abstract
  1. Foito, A.; Menezes, R.; Kallscheuer, N.; Dobson, G; Austin, C; da Silva, M.H.; Braga, A.; et al. "From fruits to compounds: the importance of metabolomics in bioprospection studies". Paper presented in Malta Polyphenols 2019 - 13th World Congress on Polyphenols Application, Valletta, 2019.
    Published
  2. 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
  3. Resende, Tiago; Correia, Daniela M.; Santos, Sophia Torres; Rocha, I.. "Reconstruction and validation of iTR383, a genome-scale metabolic model for Helicobacter pylori 26695". Paper presented in MPA2015 - Metabolic Pathway Analysis, Braga, 2015.
    Published
  4. Correia, Daniela M.; Carreira, Rafael; Azevedo, Nuno Filipe; Rocha, I.. "Uncovering the metabolic capacities of H. pylori 26695 using 13C labeling experiments". Paper presented in MPA2015 - Metabolic Pathway Analysis, Braga, 2015.
    Published
  5. Resende, Tiago; Correia, Daniela M.; Santos, Sophia; Rocha, I.. "Reconstruction and validation of a genome-scale metabolic model for Helicobacter pylori 26695". Paper presented in BOD 2015 - Bioinformatics Open Days 2015, Braga, 2015.
    Published
  6. 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
  7. 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
  8. 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
  9. 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
  10. Sargo, Cíntia R .; Correia, Daniela M.; Giordano, R. C.; Ferreira, E. C.; Rocha, I.; Silva, Adilson J.; Zangirolami, T. C.. "Analysis of Salmonella typhimurium pathways and metabolic model improvement". Paper presented in MPA2015 - Metabolic Pathway Analysis, Braga, 2015.
    Published
  11. Resende, Tiago F.; Correia, Daniela M.; Santos, Sophia; Rocha, Isabel. "Reconstruction of metabolic models using genome information: A case study with Helicobacter pylori 26695". Paper presented in São Paulo Advanced School on the Present and Future of Bioenergy, Campinas, 2014.
  12. 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
  13. Correia, Daniela M.; Resende, T.; Rocha, I.. "Assignment of novel functions to Helicobacter pylori 26695's genome and reconstruction of a genome-scale metabolic model". Paper presented in Assignment of novel functions to Helicobacter pylori 26695’s genome and reconstruction of a genome-scale metabolic model, Copenhagen, 2013.
  14. 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
  15. Rodrigues, J. L.; Rodrigues, L. R.; Machado, C. D.; Kluskens, L. D.; Mota, M.; Rocha, I.; Ferreira, E. C.. "Synbiobacther - Engineering "therapeutic" bacteria". Paper presented in 3rd Meeting of the Institute for Biotechnology and Bioengineering, Lisboa, 2012.
    Published
  16. 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
  17. Nobre, C; Dominguez, A; Torres, Duarte; Rocha, O.; Rocha, I.; Ferreira, EC; Teixeira, JA; Rodrigues, LR. "Optimization of a fructooligosaccharides purification method using activated charcoal". Paper presented in MicroBiotech¿09, 2009.
  18. Nobre, C; Santos, MJ; Dominguez, A; Torres, Duarte; Rodrigues, L.R.; Rocha, I.; Teixeira, JA; Ferreira, EC. "Fractionation of fructo-oligosaccharides by gel filtration". Paper presented in 10th International Chemical and Biological Engineering Conference CHEMPOR, Braga, 2008.
  19. Torres, Duarte; Dominguez, A.; Rodrigues, LR; Rocha, I.; Cardoso, SM; Silva, AMS; Domingues, MRM; et al. "Experimental approach for prebiotic oligosaccharides fractionation and chemical characterization". Paper presented in Functional Foods in Europe ¿ International Developments in Science and Health Claims, 2007.
  20. Dominguez, A.; Nobre, C.; Torres, Duarte; Rocha, O.; Rodrigues, LR; Rocha, I.; Ferreira, EC; Lima, N.; Teixeira, JA. "Production of fructooligosaccharides by Aureobasidium sp. and Aspergillus sp,". Paper presented in Annual Meeting of the Institute of Food Technologists, Chicago, 2007.
  21. Rocha, O.; Dominguez, A.; Nobre, C.; Torres, Duarte; Rodrigues, LR; Rocha, I.; Teixeira, JA. "Modeling and simulation of fructo-oligosaccharides production". Paper presented in 2nd FEBS Advanced Lecture Course on Systems Biology. FEBS-SysBio2007: from molecules to life, Gosau, 2007.
  22. Nobre, C.; Dominguez, A.; Rocha, O.; Torres, Duarte; Rodrigues, LR; Rocha, I.; Teixeira, JA; Ferreira, EC. "Purification of fructo-oligosaccharides by adsorption onto charcoal filters". Paper presented in 4th Probiotics, Prebiotics and New Foods jointly with XXX International Congress on Microbial Ecology And Disease, Roma, 2007.
  23. Nobre, C.; Dominguez, A.; Torres, Duarte; Rocha, O.; Rodrigues, LR; Rocha, I.; Teixeira, JA; Ferreira, EC. "Purification of fructo-oligosaccharides by nanofiltration". Paper presented in 13th World Congress of Food Science and Technology, Nantes, 2006.
  24. Dominguez, A.; Nobre, C.; Torres, Duarte; Rodrigues, LR; Rocha, I.; Teixeira, JA; Lima, N.; Ferreira, EC. "Optimization of fermentation conditions for fructooligosaccharides productivity by Aureobasidium". Paper presented in World Congress on Industrial Biotechnology and Bioprocessing, Toronto, 2006.
  25. Torres, Duarte; Dominguez, A.; Rodrigues, LR; Rocha, I.; Teixeira, JA; Lima, N.; Ferreira, EC. "Prebiotics ¿ from concept to product. The BIOLIFE Project". Paper presented in Micro¿05-Biotech¿05, Póvoa de Varzim, 2005.
Conference paper
  1. 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.
  2. Fonseca, A.; Rocha, I.. "Strain optimization for aromatic amino acids using an Escherichia coli kinetic model". 2022.
    10.1016/j.ifacol.2022.07.524
  3. 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.
  4. Demirci, H.; Dias, Oscar; Chaves, Inês; Miguel, Célia; Rocha, Miguel; Rocha, I.. "The metabolic model of the Quercus suber (cork oak tree) leaf". 2019.
  5. Viana, Romeu; Dias, Oscar; Bastos, José; Lagoa, Davide Rafael Santos; Galocha, Mónica; Rocha, I.; Teixeira, Miguel Cacho. "Genome-scale metabolic model of the human pathogen C. albicans: aiming the identification of promising new drug targets". 2019.
  6. Shakyawar, S.; Rocha, I.; Carneiro, S.. "Integrated metabolic flux and omics analysis of leishmania major metabolism". 2018.
  7. Maia, P.; Rocha, I.; Rocha, M.. "Identification of robust strain designs via tandem pFBA/LMOMA phenotype prediction". 2017.
    10.1145/3067695.3082542
  8. Castro, Rita; Castro, P.; Silva, P.; Alves, M. M.; Rocha, I.; Pereira, M. A.. "Combining high-value biotechnological processes: from wastewaters bioremediation to bacterial bioenergy feedstock production". 2017.
  9. Dias, Oscar; Castro, Rita; Pereira, M. A.; Rocha, Isabel. "Towards the identification of pathways for lipids biosynthesis in HCB". 2017.
  10. 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.
  11. Lopes, H.; Maia, P.; Patil, K.R.; Rocha, I.. "Rational modular design of yeast strains towards overproduction of industrially relevant products". 2016.
  12. Dias, Oscar; Santos, Sophia Torres; Ferreira, Eugénio C.; Rocha, I.. "Towards an improved version of Kluyveromyces lactis genome-scale metabolic model". 2016.
  13. 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.
  14. Silva, A.; Sargo, Cintia Regina; Zangirolami, Teresa Cristina; Giordano, Roberto de Campos; Rocha, Isabel; Ferreira, Eugénio C.. "Metabolic profiling of secreted fermentative byproducts by Salmonella typhimurium". 2014.
  15. Portela, C.; Villas-Bôas, S.; Rocha, I.; Ferreira, E.C.; Portela, Carla; Villas-Bôas, S. G.; Ferreira, E. C.; et al. "Genome scale metabolic network reconstruction of the pathogen Enterococcus faecalis". 2013.
    10.3182/20131216-3-IN-2044.00067
  16. Carreira, R.; Rocha, M.; Villas-Bôas, S.G.; Rocha, I.. "Algorithms to infer metabolic flux ratios from fluxomics data". 2013.
    10.1109/BIBM.2013.6732490
  17. Evangelista, P.; Rocha, M.; Rocha, I.. "Evolutionary computation for predicting optimal reaction knockouts and enzyme modulation strategies". 2013.
    10.1109/CEC.2013.6557705
  18. Maia, P.; Rocha, I.; Rocha, M.. "An integrated framework for strain optimization". 2013.
    10.1109/CEC.2013.6557571
  19. Dias, Oscar; Gombert, Andreas Karoly; Ferreira, Eugénio C.; Rocha, I.. "iOD962 - the first genome-scale metabolic model of Kluyveromyces lactis". 2013.
  20. Dias, Oscar; Rocha, Miguel; Ferreira, Eugénio C.; Rocha, I.. "Assembling genome-wide transporter system annotations". 2012.
  21. Portela, Carla Andreia Freixo; Villas-Bôas, S. G.; Rocha, I.; Ferreira, E. C.. "Super model of the world : Enterococcus faecalis". 2012.
  22. Carvalho, A. R.; Castro, Paulo; Rocha, I.; Alves, M. M.; Pereira, M. A.. "Selective enrichment of hydrocarbonoclastic bacteria producing storage compounds of biotechnological relevance". 2012.
  23. 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
  24. 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
  25. 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
  26. 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.
  27. Aggio, R. B. M.; Carreira, R.; Carneiro, S.; Liu, T.; Portela, Carla Andreia Freixo; Rocha, I.; Rocha, Miguel; Ferreira, E. C.; Villas-Bôas, S. G.. "Comparing results obtained from the Pathway Activity Profiling (PAPi) algorithm with 13C-based metabolic flux analysis". 2011.
  28. Correia, Daniela M.; Bessa, L. J.; Azevedo, N. F.; Vieira, M. J.; Rocha, I.. "Growth assessment of Helicobacter pylori in liquidmedium – effect of aggregation". 2011.
  29. Correia, Daniela M.; Bessa, L. J.; Azevedo, N. F.; Vieira, M. J.; Rocha, I.. "Growth assessment methods for Helicobacter pylori in liquid medium". 2011.
  30. Pinto, J.P.; Rocha, I.; Rocha, M.. "A software tool for network topology analysis under a Metabolic Engineering perspective". 2010.
    10.1145/1854776.1854884
  31. Costa, R.S.; Machado, D.; Ferreira, E.C.; Rocha, I.. "Evaluating the integration of proteomic data for the prediction of intracellular fluxes after knockout experiments". 2010.
    10.3182/20100707-3-BE-2012.0108
  32. Machado, D.; Costa, R.S.; Rocha, M.; Rocha, I.; Tidor, B.; Ferreira, E.C.. "Model transformation of metabolic networks using a Petri net based framework". 2010.
  33. Dias, O.; Rocha, M.; Ferreira, E.C.; Rocha, I.. "Merlin: Metabolic models reconstruction using genome-scale information". 2010.
    10.3182/20100707-3-BE-2012.0076
  34. Soons, Z.I.T.A.; Ferreira, E.C.; Rocha, I.. "Selection of elementary modes for bioprocess control". 2010.
    10.3182/20100707-3-BE-2012.0019
  35. Rocha, I.; Dias, Oscar; Rocha, Miguel; Ferreira, Eugénio C.. "Genome-scale metabolic models reconstruction of less characterized organisms with Merlin". 2010.
  36. Correia, Daniela M.; Azevedo, N. F.; Vieira, M. J.; Rocha, I.. "System analysis of metabolism in Helicobacter pylori". 2010.
  37. Rocha, O.; Maia, P.; Rocha, I.; Rocha, M.. "Optferm-a computational platform for the optimization of fermentation processes". 2009.
  38. Azeredo, Joana; Henriques, Mariana; Rocha, I.; Ferreira, E. C.; Oliveira, Rosário. "Monoclonal antibodies production in wave and stirred tank bioreactors". 2009.
  39. Nobre, Clarisse; Santos, M.J.; Dominguez, Ana; Torres, Duarte; Peres, António M.; Rocha, Isabel; Ferreira, Eugénio C.; Rodrigues, Lígia R.; Teixeira, José A.. "Adsorption equilibrium of fructose, glucose, and sucrose for cationic resins in the sodium and potassium form". 2009.
  40. Loureno, A.; Carreira, R.; Carneiro, S.; Maia, P.; Glez-Peña, D.; Fdez-Riverola, F.; Ferreira, E.C.; Rocha, I.; Rocha, M.. "A framework for the development of biomedical text mining software tools". 2008.
    10.1109/BIBE.2008.4696707
  41. Mendes, R.; Lourenço, A.; Carneiro, S.; Rocha, M.; Rocha, I.; Ferreira, E.C.. "A framework for the integrated analysis of metabolic and regulatory networks". 2008.
    10.1109/BIBE.2008.4696727
  42. Rocha, I.; Veloso, A.; Carneiro, S.; Ferreira, E.; Costa, R.. "Implementation of a specific rate controller in a fed-batch E. coli fermentation". 2008.
    10.3182/20080706-5-KR-1001.3513
  43. Maia, P.; Rocha, I.; Ferreira, E.C.; Rocha, M.. "Evaluating evolutionary multiobjective algorithms for the in silico optimization of mutant strains". 2008.
    10.1109/BIBE.2008.4696733
  44. Vilas-Boas, Miguel; Veloso, Ana C.A.; Peres, António M.; Dias, L.G.; Dias, Teresa; Cardoso, Susana M.; Kluskens, L.; Rocha, Isabel. "Eficácia da própolis no controlo da loque americana. Avaliação em zonas controladas". 2008.
  45. Lourenço, Anália; Carreira, Rafael; Carneiro, Sónia; Maia, Paulo; Ferreira, Eugénio C.; Glez-Peña, D.; Fdez-Riverola, F.; Rocha, Miguel; Rocha, I.. "The @Note biomedical text mining workbench". 2008.
  46. Carneiro, S.; Lourenço, Anália; Mendes, Rui; Rocha, Miguel; Ferreira, Eugénio C.; Rocha, I.. "Network analysis of an integrated metabolic/regulatory model of Escherichia coli". 2008.
  47. Veloso, A.C.A.; Rocha, I.; Ferreira, E.C.. "Estimation of biomass concentration using interval observers in an E. coli fed-batch fermentation". 2007.
  48. Mendes, R.; Rocha, I.; Ferreira, E.C.; Rocha, M.. "A comparison of algorithms for the optimization of fermentation processes". 2006.
  49. Carneiro, S.; Rocha, I.; Ferreira, Eugénio C.. "A systems biology approach for the characterization of metabolic bottlenecks in recombinant protein production processes". 2005.
  50. Veloso, A.C.A.; Rocha, I.; Ferreira, E.C.. "Identification of yield coefficients in an E. coli model - An optimal experimental design using genetic algorithms". 2004.
  51. Rocha, I.; Ferreira, E.C.. "Model-based adaptive control of acetate concentration during the production of recombinant proteins with E. coli". 2002.
Conference poster
  1. Faustino, Maria V.; Lourenço, Tiago; Strobbe, Simon; Da Cao; Fonseca, André; Rocha, Isabel; Dominique Van Der Straeten; Oliveira, M.Margarida. "Unlocking the Potential of OsRibA1 for Riboflavin Enhancement in Rice". Paper presented in 20th International Symposium on Rice Functional Genomics (ISRFG2023), 2023.
  2. Faustino, Maria; Lourenço, Tiago Filipe; Strobbe, Simon; Da Cao; Fonseca, André; Rocha, Isabel; Dominique Van Der Straeten; Oliveira, M.Margarida. "Identification and characterization of OsRibA1, a gene involved in riboflavin biosynthesis in rice (Oryza sativa L.)". Paper presented in Iberian Plant Biology 2023, 2023.
  3. Faustino, M. ; Lourenço, Tiago Filipe; Strobbe, Simon; Cao, D; Fonseca, André; Rocha, Isabel; Van Der Straeten, Dominique; Oliveira, M.Margarida. "OsTH1, a new potential target for thiamin biofortification in rice". Paper presented in Plant Biology Europe, FESPB Federation of the European Societies of Plant Biology (3-6 July). Marseille, France, 2023.
  4. Correia, João; Caio S. Souza; Migle A. Bartels; Ferreira, Sofia; Lousa, Diana; Rocha, Isabel; Soares, Claudio M.. "Improving phenylalanine hydroxylase catalytic activity for tryptophan using an automated platform of structure-based enzyme engineering". Paper presented in Bioinformatics Open Days 2023, 2023.
  5. Buga, Carolina C.; Valério, Mariana; Balola, Alexandra; Ferreira, Ana S.; Sequeira, Ana M.; Rocha, Miguel; Vicente, João B.; et al. "Molecular determinants of the SARS-CoV-2 fusion peptide activity". Paper presented in Bioinformatics Open Days X, Braga, 2021.
  6. Oliveira, J. A.; Braga, A.; Rocha, I.; Faria, N.; Oliveira, J.A.; Braga, A.. "The effect of hydrodynamic conditions in Corynebacterium glutamicum growth". Paper presented in MicroBiotec'15 - Congress of Microbiology and Biotechnology 2015, 2015.
  7. Duarte, S. O. D.; Paulo, J.; Machado, D.; Rocha, I.; Mergulhão, F. J. M.; Rodrigues, L. R; Monteiro, G. A.. "A synthetic biology approach to engineer "therapeutic" bacteria". Paper presented in MicroBiotec’13 Congress of Microbiology and Biotechnology 2013, 2013.
  8. Nobre, Clarisse; Dominguez, Ana; Torres, D; Rocha, O.; Rocha, I.; José António Couto Teixeira; Ferreira, E.C.; Rodrigues, L.R.. "Determination of fructo-oligosaccharides adsorption parameters using ion-exchange resins". Paper presented in 21st International Ion Chromatography Symposium (IICS 2009), 2009.
  9. Dominguez, A.; Nobre, Clarisse; Torres, D.; Rodrigues, L.; Rocha, I.; Teixeira, J.A.; Lima, Nelson; Ferreira, E.C.. "Optimization of fermentation conditions for fructooligosaccharides production by Aureobasidium". Paper presented in , World Congress on Industrial Biotechnology and Bioprocessing, Toronto, Canada, 2006.
Journal article
  1. 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
  2. Viana, Romeu; Carreiro, Tiago; Couceiro, Diogo; Dias, Oscar; Rocha, Isabel; Teixeira, Miguel Cacho. "Metabolic reconstruction of the human pathogen Candida auris: using a cross-species approach for drug target prediction". FEMS Yeast Research 23 (2023): http://dx.doi.org/10.1093/femsyr/foad045.
    10.1093/femsyr/foad045
  3. "A Genome-Scale Metabolic Model for the Human Pathogen Candida Parapsilosis and Early Identification of Putative Novel Antifungal Drug Targets". Genes 13 2 (2022): 303-303. http://dx.doi.org/10.3390/genes13020303.
    10.3390/genes13020303
  4. van den Berg, N.I.; Machado, D.; Santos, S.; Rocha, I.; Chacón, J.; Harcombe, W.; Mitri, S.; Patil, K.R.. "Ecological modelling approaches for predicting emergent properties in microbial communities". Nature Ecology and Evolution 6 7 (2022): 855-865. http://www.scopus.com/inward/record.url?eid=2-s2.0-85130101018&partnerID=MN8TOARS.
    10.1038/s41559-022-01746-7
  5. Fonseca, André; Rocha, Isabel. "Strain optimization for aromatic amino acids using an Escherichia coli kinetic model". IFAC-PapersOnLine 55 7 (2022): 691-696. http://dx.doi.org/10.1016/j.ifacol.2022.07.524.
    10.1016/j.ifacol.2022.07.524
  6. "Model-guided development of an evolutionarily stable yeast chassis". Molecular Systems Biology 17 7 (2021): http://dx.doi.org/10.15252/msb.202110253.
    10.15252/msb.202110253
  7. Diana Széliová; Jason M. Haugh; Jerneja Štor; Isabella Thiel; Marcus Weinguny; Michael Hanscho; Gabriele Lhota; et al. "Inclusion of maintenance energy improves the intracellular flux predictions of CHO". PLOS Computational Biology 17 6 (2021): e1009022-e1009022. https://doi.org/10.1371/journal.pcbi.1009022.
    10.1371/journal.pcbi.1009022
  8. "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.
    10.1016/j.procbio.2020.11.013
  9. "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
  10. "Genome-Scale Metabolic Model of the Human Pathogen Candida albicans: A Promising Platform for Drug Target Prediction". Journal of Fungi 6 3 (2020): 171-171. http://dx.doi.org/10.3390/jof6030171.
    10.3390/jof6030171
  11. "Metabolic engineering strategies for butanol production in Escherichia coli". Biotechnology and Bioengineering 117 8 (2020): 2571-2587. http://dx.doi.org/10.1002/bit.27377.
    10.1002/bit.27377
  12. "Key Challenges in Designing CHO Chassis Platforms". Processes 8 6 (2020): 643-643. http://dx.doi.org/10.3390/pr8060643.
    10.3390/pr8060643
  13. Lieven, C.; Beber, M.E.; Olivier, B.G.; Bergmann, F.T.; Ataman, M.; Babaei, P.; Bartell, J.A.; et al. "MEMOTE for standardized genome-scale metabolic model testing". Nature Biotechnology 38 3 (2020): 272-276. http://www.scopus.com/inward/record.url?eid=2-s2.0-85081212273&partnerID=MN8TOARS.
    10.1038/s41587-020-0446-y
  14. Lieven, C.; Beber, M.E.; Olivier, B.G.; Bergmann, F.T.; Ataman, M.; Babaei, P.; Bartell, J.A.; et al. "Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing (Nature Biotechnology, (2020), 38, 3, (272-276), 10.1038/s41587-020-0446-y)". Nature Biotechnology 38 4 (2020): 504-504. http://www.scopus.com/inward/record.url?eid=2-s2.0-85082184324&partnerID=MN8TOARS.
    10.1038/s41587-020-0477-4
  15. Sofia Ferreira; Rui Pereira; Filipe Liu; Paulo Vilaça; Isabel Rocha. "Discovery and implementation of a novel pathway for n-butanol production via 2-oxoglutarate". Biotechnology for Biofuels 12 1 (2019): https://doi.org/10.1186/s13068-019-1565-x.
    10.1186/s13068-019-1565-x
  16. Cruz, F.; Lagoa, D.; Mendes, J.; Rocha, I.; Ferreira, E.C.; Rocha, M.; Dias, O.. "SamPler - a novel method for selecting parameters for gene functional annotation routines". BMC bioinformatics 20 1 (2019): 454-454. http://www.scopus.com/inward/record.url?eid=2-s2.0-85071772242&partnerID=MN8TOARS.
    10.1186/s12859-019-3038-4
  17. Milke, L.; Ferreira, P.; Kallscheuer, N.; Braga, A.; Vogt, M.; Kappelmann, J.; Oliveira, J.; et al. "Modulation of the central carbon metabolism of Corynebacterium glutamicum improves malonyl-CoA availability and increases plant polyphenol synthesis". Biotechnology and Bioengineering 116 6 (2019): 1380-1391. http://www.scopus.com/inward/record.url?eid=2-s2.0-85062368820&partnerID=MN8TOARS.
    10.1002/bit.26939
  18. Dias, O.; Saraiva, J.; Faria, C.; Ramirez, M.; Pinto, F.; Rocha, I.. "IDS372, a phenotypically reconciled model for the metabolism of streptococcus pneumoniae strain R6". Frontiers in Microbiology 10 JUN (2019): http://www.scopus.com/inward/record.url?eid=2-s2.0-85069038937&partnerID=MN8TOARS.
    10.3389/fmicb.2019.01283
  19. Kallscheuer, N.; Menezes, R.; Foito, A.; Da Silva, M.H.; Braga, A.; Dekker, W.; Sevillano, D.M.; et al. "Identification and microbial production of the raspberry phenol salidroside that is active against huntington’s disease". Plant Physiology 179 3 (2019): 969-985. http://www.scopus.com/inward/record.url?eid=2-s2.0-85062940979&partnerID=MN8TOARS.
    10.1104/pp.18.01074
  20. Pereira, R.; Vilaça, P.; Maia, P.; Nielsen, J.; Rocha, I.. "Turnover Dependent Phenotypic Simulation: A Quantitative Constraint-Based Simulation Method That Accommodates All Main Strain Design Strategies". ACS Synthetic Biology 8 5 (2019): 976-988. http://www.scopus.com/inward/record.url?eid=2-s2.0-85064968102&partnerID=MN8TOARS.
    10.1021/acssynbio.8b00248
  21. Correia, D.M.; Sargo, C.R.; Silva, A.J.; Santos, S.T.; Giordano, R.C.; Ferreira, E.C.; Zangirolami, T.C.; Ribeiro, M.P.A.; Rocha, I.. "Mapping Salmonella typhimurium pathways using 13C metabolic flux analysis". Metabolic Engineering 52 (2019): 303-314. http://www.scopus.com/inward/record.url?eid=2-s2.0-85059931870&partnerID=MN8TOARS.
    10.1016/j.ymben.2018.11.011
  22. Vieira, V.; Maia, P.; Rocha, M.; Rocha, I.. "Comparison of pathway analysis and constraint-based methods for cell factory design". BMC Bioinformatics 20 1 (2019): http://www.scopus.com/inward/record.url?eid=2-s2.0-85067639944&partnerID=MN8TOARS.
    10.1186/s12859-019-2934-y
  23. Fernandes, B.S.; Dias, O.; Costa, G.; Kaupert Neto, A.A.; Resende, T.F.C.; Oliveira, J.V.C.; Riaño-Pachón, D.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://www.scopus.com/inward/record.url?eid=2-s2.0-85068192963&partnerID=MN8TOARS.
    10.1186/s12896-019-0529-3
  24. Cristiana Faria; Nuno Borges; Isabel Rocha; Helena Santos. "Production of mannosylglycerate in Saccharomyces cerevisiae by metabolic engineering and bioprocess optimization". Microbial Cell Factories 17 1 (2018): https://doi.org/10.1186/s12934-018-1023-7.
    10.1186/s12934-018-1023-7
  25. Joana C. Xavier; Costas D. Maranas; Kiran Raosaheb Patil; Isabel Rocha. "Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes". PLOS Computational Biology 14 11 (2018): e1006556-e1006556. https://doi.org/10.1371/journal.pcbi.1006556.
    10.1371/journal.pcbi.1006556
  26. Braga, A.; Oliveira, J.; Silva, R.; Ferreira, P.; Rocha, I.; Kallscheuer, N.; Marienhagen, J.; Faria, N.. "Impact of the cultivation strategy on resveratrol production from glucose in engineered Corynebacterium glutamicum". Journal of Biotechnology 265 (2018): 70-75. http://www.scopus.com/inward/record.url?eid=2-s2.0-85034851295&partnerID=MN8TOARS.
    10.1016/j.jbiotec.2017.11.006
  27. Faria, J.P.; Rocha, M.; Rocha, I.; Henry, C.S.. "Methods for automated genome-scale metabolic model reconstruction". Biochemical Society Transactions 46 4 (2018): 931-936. http://www.scopus.com/inward/record.url?eid=2-s2.0-85052068503&partnerID=MN8TOARS.
    10.1042/BST20170246
  28. Pinu, F.R.; Granucci, N.; Daniell, J.; Han, T.-L.; Carneiro, S.; Rocha, I.; Nielsen, J.; Villas-Boas, S.G.. "Metabolite secretion in microorganisms: the theory of metabolic overflow put to the test". Metabolomics 14 4 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85042796931&partnerID=MN8TOARS.
    10.1007/s11306-018-1339-7
  29. Braga, A.; Ferreira, P.; Oliveira, J.; Rocha, I.; Faria, N.. "Heterologous production of resveratrol in bacterial hosts: current status and perspectives". World Journal of Microbiology and Biotechnology 34 8 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85050923667&partnerID=MN8TOARS.
    10.1007/s11274-018-2506-8
  30. Pereira, B.; Miguel, J.; Vilaça, P.; Soares, S.; Rocha, I.; Carneiro, S.. "Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z". BMC Systems Biology 12 1 (2018): http://www.scopus.com/inward/record.url?eid=2-s2.0-85047736095&partnerID=MN8TOARS.
    10.1186/s12918-018-0585-7
  31. Braga, A.; Silva, M.; Oliveira, J.; Silva, A.R.; Ferreira, P.; Ottens, M.; Rocha, I.; Faria, N.. "An adsorptive bioprocess for production and recovery of resveratrol with Corynebacterium glutamicum". Journal of Chemical Technology and Biotechnology 93 6 (2018): 1661-1668. http://www.scopus.com/inward/record.url?eid=2-s2.0-85045614118&partnerID=MN8TOARS.
    10.1002/jctb.5538
  32. Dias, O.; Basso, T.O.; Rocha, I.; Ferreira, E.C.; Gombert, A.K.. "Erratum to: 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): http://www.scopus.com/inward/record.url?eid=2-s2.0-85031425390&partnerID=MN8TOARS.
    10.1007/s10482-017-0948-x
  33. Dudnik, A.; Almeida, A.F.; Andrade, R.; Avila, B.; Bañados, P.; Barbay, D.; Bassard, J.-E.; et al. "BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits". Phytochemistry Reviews (2017): 1-36. http://www.scopus.com/inward/record.url?eid=2-s2.0-85028994529&partnerID=MN8TOARS.
    10.1007/s11101-017-9532-2
  34. 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
  35. Vieira, V.; Maia, P.; Rocha, I.; Rocha, M.. "Development of a Framework for Metabolic Pathway Analysis-Driven Strain Optimization Methods". Interdisciplinary Sciences: Computational Life Sciences 9 1 (2017): 46-55. http://www.scopus.com/inward/record.url?eid=2-s2.0-85016115248&partnerID=MN8TOARS.
    10.1007/s12539-017-0218-7
  36. Xavier, J.C.; Patil, K.R.; Rocha, I.. "Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes". Metabolic Engineering 39 (2017): 200-208. http://www.scopus.com/inward/record.url?eid=2-s2.0-85009252978&partnerID=MN8TOARS.
    10.1016/j.ymben.2016.12.002
  37. Dias, O.; Gomes, D.; Vilaça, P.; Cardoso, J.; Rocha, M.; Ferreira, E.C.; Rocha, I.. "Genome-Wide Semi-Automated Annotation of Transporter Systems". IEEE/ACM Transactions on Computational Biology and Bioinformatics 14 2 (2017): 443-456. http://www.scopus.com/inward/record.url?eid=2-s2.0-85017164643&partnerID=MN8TOARS.
    10.1109/TCBB.2016.2527647
  38. Lopes, H.; Rocha, I.. "Genome-scale modeling of yeast: chronology, applications and critical perspectives". FEMS yeast research 17 5 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85042164575&partnerID=MN8TOARS.
    10.1093/femsyr/fox050
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  100. Lourenço, A.; Carreira, R.; Carneiro, S.; Maia, P.; Glez-Peña, D.; Fdez-Riverola, F.; Ferreira, E.C.; Rocha, I.; Rocha, M.. "@Note: A workbench for Biomedical Text Mining". Journal of Biomedical Informatics 42 4 (2009): 710-720. http://www.scopus.com/inward/record.url?eid=2-s2.0-67649367551&partnerID=MN8TOARS.
    10.1016/j.jbi.2009.04.002
  101. Nobre, C.; Santos, M.J.; Dominguez, A.; Torres, D.; Rocha, O.; Peres, A.M.; Rocha, I.; et al. "Comparison of adsorption equilibrium of fructose, glucose and sucrose on potassium gel-type and macroporous sodium ion-exchange resins". Analytica Chimica Acta 654 1 (2009): 71-76. http://www.scopus.com/inward/record.url?eid=2-s2.0-70350111317&partnerID=MN8TOARS.
    10.1016/j.aca.2009.06.043
  102. Valente, Eduardo; Rocha, Isabel; Rocha, Miguel; Corchado, JM; DePaz, JF; Rocha, MP; Riverola, FF; et al. "Modelling Fed-Batch Fermentation Processes: An Approach Based on Artificial Neural Networks". 2nd International Workshop on Practical Applications of Computational Biology and Bioinformatics (Iwpacbb 2008) 49 (2009): 30-39. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000262505800004&KeyUID=WOS:000262505800004.
  103. Correia, D. M.; Cunha, M. L. R.; Azevedo, N. F.; Vieira, M. J.; Rocha, I.. "Comparison of H. pylori in Silico Metabolic Model Predictions with Experimental Data". Helicobacter 14 4 (2009): 388-388. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000268269300225&KeyUID=WOS:000268269300225.
  104. Evangelista, Pedro; Rocha, Isabel; Ferreira, Eugenio C.; Rocha, Miguel; Pizzuti, C; Ritchie, MD; Giacobini, M. "Evolutionary Approaches for Strain Optimization Using Dynamic Models under a Metabolic Engineering Perspective". Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, Proceedings 5483 (2009): 140-151. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000265955000013&KeyUID=WOS:000265955000013.
  105. Evangelista, Pedro; Rocha, Isabel; Ferreira, Eugenio C.; Rocha, Miguel; Omatu, S; Rocha, MP; Bravo, J; et al. "A Software Tool for the Simulation and Optimization of Dynamic Metabolic Models". Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living, Pt Ii, Proceedings 5518 (2009): 1071-1078. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000271116900162&KeyUID=WOS:000271116900162.
  106. Rocha, O.; Nobre, C.; Dominguez, A.; Torres, D.; Faria, N.; Rodrigues, L.; Teixeira, J. A.; et al. "A Dynamical Model for the Fermentative Production of Fructooligosaccharides". 10th International Symposium on Process Systems Engineering 27 (2009): 1827-1832. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000287727800305&KeyUID=WOS:000287727800305.
  107. Machado, Daniel; Costa, Rafael S.; Rocha, Miguel; Rocha, Isabel; Tidor, Bruce; Ferreira, Eugenio C.; Omatu, S; et al. "A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems". Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living, Pt Ii, Proceedings 5518 (2009): 1063-1070. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000271116900161&KeyUID=WOS:000271116900161.
  108. Lourenco, Analia; Carneiro, Sonia; Ferreira, Eugenio C.; Carreira, Rafael; Rocha, Luis M.; Glez-Pena, Daniel; Mendez, Jose R.; et al. "Biomedical Text Mining Applied to Document Retrieval and Semantic Indexing". Distributed Computing, Artificial Intelligence, Bioinformatics, Soft Computing, and Ambient Assisted Living, Pt Ii, Proceedings 5518 (2009): 954-963. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000271116900146&KeyUID=WOS:000271116900146.
  109. Lourenço, A.; Carneiro, S.; Carreira, R.; Rocha, M.; Rocha, I.; Ferreira, E.. "A tool for the automatic and manual annotation of biomedical documents". 3rd International Symposium on Semantic Mining in Biomedicine, SMBM 2008 - Proceedings (2008): 85-92. http://www.scopus.com/inward/record.url?eid=2-s2.0-84874276771&partnerID=MN8TOARS.
  110. Maia, Paulo; Rocha, Isabel; Ferreira, Eugenio C.; Rocha, Miguel; IEEE. "Evaluating Evolutionary Multiobjective Algorithms for the in silico Optimization of Mutant Strains". 8th Ieee International Conference on Bioinformatics and Bioengineering, Vols 1 and 2 (2008): 509-514. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000263828500085&KeyUID=WOS:000263828500085.
  111. Lourenco, Analia; Carreira, Rafael; Carneiro, Sonia; Maia, Paulo; Glez-Pena, Daniel; Fdez-Riverola, Florentino; Ferreira, Eugenio C.; et al. "A Framework for the Development of Biomedical Text Mining Software Tools". 8th Ieee International Conference on Bioinformatics and Bioengineering, Vols 1 and 2 (2008): 352-357. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000263828500059&KeyUID=WOS:000263828500059.
  112. Mendes, Rui; Lourenco, Analia; Carneiro, Sonia; Rocha, Miguel; Rocha, Isabel; Ferreira, Eugenio C.; IEEE. "A Framework for the Integrated Analysis of Metabolic and Regulatory Networks". 8th Ieee International Conference on Bioinformatics and Bioengineering, Vols 1 and 2 (2008): 474-479. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000263828500079&KeyUID=WOS:000263828500079.
  113. Mendes, Rui; Rocha, Isabel; Pinto, Jose P.; Ferreira, Eugenio C.; Rocha, Miguel; Chakraborty, UK. "Differential Evolution for the Offline and Online Optimization of Fed-Batch Fermentation Processes". Advances in Differential Evolution 143 (2008): 299-317. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000271449500013&KeyUID=WOS:000271449500013.
  114. Rocha, M.; Maia, P.; Mendes, R.; Pinto, J.P.; Ferreira, E.C.; Nielsen, J.; Patil, K.R.; Rocha, I.. "Natural computation meta-heuristics for the in silico optimization of microbial strains". BMC Bioinformatics 9 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-58149307906&partnerID=MN8TOARS.
    10.1186/1471-2105-9-499
  115. Rocha, Miguel; Pinto, Jose P.; Rocha, Isabel; Ferreira, Eugenio; IEEE; Rocha, M.; Pinto, J.P.; Rocha, I.; Ferreira, E.. "Optimization of bacterial strains with variable-sized evolutionary algorithms". 2007 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (2007): 331-337. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000248516200045&KeyUID=WOS:000248516200045.
  116. Rocha, M.; Mendes, R.; Maia, P.; Pinto, J.P.; Rocha, I.; Ferreira, E.C.. "Evaluating simulated annealing algorithms in the optimization of bacterial strains". Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 4874 LNAI (2007): 473-484. http://www.scopus.com/inward/record.url?eid=2-s2.0-38349011053&partnerID=MN8TOARS.
  117. Rocha, I.; Förster, J.; Nielsen, J.; Rocha, Isabel; Forster, Jochen; Nielsen, Jens. "Design and application of genome-scale reconstructed metabolic models". Methods in Molecular Biology 416 (2007): 409-431. http://www.scopus.com/inward/record.url?eid=2-s2.0-40549127097&partnerID=MN8TOARS.
    10.1007/978-1-59745-321-9_29
  118. Rocha, M.; Pinto, J.P.; Rocha, I.; Ferreira, E.C.. "Evaluating evolutionary algorithms and differential evolution for the online optimization of fermentation processes". Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 4447 LNCS (2007): 236-246. http://www.scopus.com/inward/record.url?eid=2-s2.0-38049043980&partnerID=MN8TOARS.
  119. Mendes, Rui; Rocha, Isabel; Ferreira, Eugenio C.; Rocha, Miguel; IEEE. "A comparison of algorithms for the optimization of fermentation processes". 2006 Ieee Congress on Evolutionary Computation, Vols 1-6 (2006): 2003-2010. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000245414203047&KeyUID=WOS:000245414203047.
  120. Rocha, M; Rocha, I; Ferreira, E; IEEE. "New representation in evolutionary algorithms for the optimization of bioprocesses". 2005 Ieee Congress on Evolutionary Computation, Vols 1-3, Proceedings (2005): 484-490. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000232173100063&KeyUID=WOS:000232173100063.
  121. Patil, K.R.; Rocha, I.; Förster, J.; Nielsen, J.. "Evolutionary programming as a platform for in silico metabolic engineering". BMC Bioinformatics 6 (2005): http://www.scopus.com/inward/record.url?eid=2-s2.0-30044437327&partnerID=MN8TOARS.
    10.1186/1471-2105-6-308
  122. Rocha, M.; Rocha, I.; Ferreira, E.. "A new representation in Evolutionary Algorithms for the optimization of bioprocesses". 2005 IEEE Congress on Evolutionary Computation, IEEE CEC 2005. Proceedings 1 (2005): 484-490. http://www.scopus.com/inward/record.url?eid=2-s2.0-27144478281&partnerID=MN8TOARS.
  123. Veloso, A.C.A.; Rocha, I.; Ferreira, E.C.. "Design of on-line state estimators for a recombinant E. coli FED-batch fermentation". IFAC Proceedings Volumes (IFAC-PapersOnline) 16 (2005): 67-72. http://www.scopus.com/inward/record.url?eid=2-s2.0-79960723278&partnerID=MN8TOARS.
  124. Rodrigues, L.; Rocha, I.; Torres, Duarte. "Alimentos funcionais - uma área estratégica para a BIOTEMPO". Boletim de Biotecnologia 82 (2005): 3-12.
  125. Rocha, M.; Neves, J.; Rocha, I.; Ferreira, E.C.. "Evolutionary algorithms for optimal control in fed-batch fermentation processes". Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 3005 (2004): 84-93. http://www.scopus.com/inward/record.url?eid=2-s2.0-27144481879&partnerID=MN8TOARS.
  126. Lubenova, V.; Rocha, I.; Ferreira, E.C.. "Estimation of multiple biomass growth rates and biomass concentration in a class of bioprocesses". Bioprocess and Biosystems Engineering 25 6 (2003): 395-406. http://www.scopus.com/inward/record.url?eid=2-s2.0-0042629838&partnerID=MN8TOARS.
    10.1007/s00449-003-0325-1
  127. Rocha, I.; Ferreira, E.C.. "On-line simultaneous monitoring of glucose and acetate with FIA during high cell density fermentation of recombinant E. coli". Analytica Chimica Acta 462 2 (2002): 293-304. http://www.scopus.com/inward/record.url?eid=2-s2.0-0036644636&partnerID=MN8TOARS.
    10.1016/S0003-2670(02)00347-1
Preprint
  1. Emanuel Cunha; Miguel Silva; Ines Chaves; Huseyin Demirci; Davide Rafael Lagoa; Diogo Lima; Miguel Rocha; Isabel Rocha; Oscar Dias. "The first multi-tissue diel genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber". 2021. https://doi.org/10.1101/2021.03.09.434537.
    10.1101/2021.03.09.434537
Thesis / Dissertation
  1. Portela, Carla Andreia Freixo; Ferreira, E. C.; Rocha, I.; Villas-Bôas, S. G.. "In vivo metabolic pathway analysis of Enterococcus faecalis for uncovering key pathogenicity factors". PhD, 2013. http://hdl.handle.net/1822/28768.

Other

Other output
  1. Inclusion of maintenance energy improves the intracellular flux predictions of CHO. 2020. Diana Széliová; Jerneja Štor; Isabella Thiel; Marcus Weinguny; Michael Hanscho; Gabriele Lhota; Nicole Borth; et al. https://doi.org/10.1101/2020.12.21.423738.
    10.1101/2020.12.21.423738
  2. Memote: A community driven effort towards a standardized genome-scale metabolic model test suite. 2018. Lieven, C.; Beber, M.E.; Olivier, B.G.; Bergmann, F.T.; Ataman, M.; Babaei, P.; Bartell, J.A.; et al. http://www.scopus.com/inward/record.url?eid=2-s2.0-85093368412&partnerID=MN8TOARS.
    10.1101/350991
  3. Minimal cut set enumeration plugin for OptFlux. Software. 2016. Vieira, Vítor; Maia, Paulo; Rocha, Miguel; Rocha, Isabel. https://sourceforge.net/p/optflux/optflux-mcs/.
  4. Análise de fluxos metabólicos com substrato isotopicamente marcado (13C-MFA) em S. typhimurium. Linhagens atenuadas de Salmonella têm sido estudadas para produção e veiculação de substâncias com fins terapêuticos. Modelos metabólicos à escala genômica são ferramentas importantes no desenvolvimento de estratégias de engenharia metabólica. Este trabalho teve por objetivo obter dados experimentais para aprimorar o modelo metabólico e aprofundar o conhecimento do metabolismo de S. typhimurium (S. 2016. Correia, D. M.; Sargo, Cintia Regina; Giordano, Roberto de Campos; Rocha, Isabel; Silva, A. J.; Zangirolami, Teresa Cristina. http://hdl.handle.net/1822/44529.
  5. Produção e consumo de acetato em cultivos de Salmonella typhimurium em condições aeróbias. Linhagens atenuadas de Salmonella typhimurium têm sido amplamente estudadas para o desenvolvimento de diversas vacinas e no tratamento do câncer. No entanto, ainda há poucas informações a respeito de seu metabolismo. S. typhimurium e Escherichia coli apresentam grande similaridade em seus genomas e redes metabólicas. Com o intuito de avaliar o metabolismo da Salmonella sob condições aeróbias, real. 2015. Sargo, Cíntia R .; Silva, Adilson J.; Giordano, Roberto C; Ferreira, Eugénio C.; Rocha, I.; Zangirolami, Teresa C.. http://hdl.handle.net/1822/37804.
  6. Specific growth rate regulation in a fed-batch E. coli fermentation. Invested Lecture at Automatic Control Unit of Cinvestav - Centro de Investigación y Estudios Avanzados. 2007. Rocha, Isabel; Ferreira, Eugénio C.. http://hdl.handle.net/1822/59534.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2018/10 Computer-based Synthetic Biology strategies for novel Cell Factories. Invited plenary speaker at Synthetic Biology – Resource allocation in natural and unnatural systems (Nature Conferences). Shanghai, China. October 15-17 2018. Resource allocation in natural and unnatural systems
Nature Conferences (Shangai, China)
2018/03 Kinetic Modelling and Strain Design. Invited plenary speaker at the Workshop Challenges in Applied Systems Biology. Science Center Delft. March 15, 2018. Workshop Challenges in Applied Systems Biology
Science Center Delft (Delft, Netherlands)
2017/12 In silico design of improved cell factories – New methods and experimental validation. Invited speaker at Microbiotec'17 - Congress of Microbiology and Biotechnology 2017. Porto, Portugal, Dec 7-9, 28, 2017. Microbiotec'17 - Congress of Microbiology and Biotechnology
(Porto, Portugal)
2017/05 New Tools for improving metabolic annotations. Invited plenary speaker at Copenhagen Biosciences Conferences - 11th Conference: Data-Driven Biotechnology, Bench, Bioreactor and Bedside. Copenhagen, Denmark, 7-11 May, 2017 11th Conference: Data-Driven Biotechnology
Copenhagen Biosciences Conferences (Copenhagen, Denmark)
2017/04 Rational design of microbes for competitive biotechnological processes. Invited plenary speaker at SynBioBeta London 2017 – Imperial College, UK, April 4-6 2017. SynBioBeta
(United Kingdom)
2016/07 In silico design of cell factories. Invited speaker at Ciência 2016 – National Science Meeting – Lisbon, Portugal, July 6 2016. National Science Meeting
(lisbon, Portugal)
2016/07 In silico Metabolic Engineering: from research to the market. Invited plenary speaker at PYFF6 - 6th Conference on Physiology of Yeast and Filamentous Fungi – Lisbon, Portugal, July 11-14 2016. PYFF6 - 6th Conference on Physiology of Yeast and Filamentous Fungi
(Lisbon, Portugal)
2016/06 Metabolic Systems Biology: tools for model-based analysis and design of microbial systems. Invited plenary speaker at the 5th International Iberian Biophysics Congress, Porto, Portugal, 15-17 June 2016. 5th International Iberian Biophysics Congress
(Porto, Portugal)
2015/10 Melhoramento das predições in sílico para assistência ao desenvolvimento de estratégias de engenharia metabólica. Invited plenary speaker at the V Encontro da Escola Brasileira de Química Verde, Campinas, Brasil, October 20 2015. V Encontro da Escola Brasileira de Química Verde
(Campinas, Brazil)
2015/09 Reconciling Experimental Data With in Silico Predictions In Metabolic Engineering Applications. Invited plenary speaker at the 4th COBRA Conference on Constraint-Based Reconstruction and Analysis, Heidelberg, Germany, 16-18 September 2015. 4th COBRA Conference on Constraint-Based Reconstruction and Analysis
(Heidelberg, Germany)
2015/06 Improved in silico strain design by a combined approach to simulation and optimization. Invited plenary speaker at the EMBO |EMBL Symposium “Enabling Technologies for Eukaryotic Synthetic Biology”, Heidelberg, Germany, June 21-23 2015. EMBO |EMBL Symposium “Enabling Technologies for Eukaryotic Synthetic Biology”
EMBL (Heidelberg, Germany)
2013/09 Improving in silico predictions in Metabolic Engineering problems. Invited plenary speaker at the Metabolic Pathways Analysis Conference, Oxford, UK, September 16-20 2013. Metabolic Pathways Analysis Conference
(Oxford, United Kingdom)
2013/08 Systems Biology for the development of microbial cell factories. Invited speaker at the XIX Sinaferm – Simpósio Nacional de Bioprocesso, Foz do Iguaçu, Brazil, July 30 – August 2 2013 XIX Sinaferm – Simpósio Nacional de Bioprocesso
(Brazil)
2011/12 New tools for the simulation and optimization of microbes in metabolic engineering problems. Invited speaker at the Conference MicroBiotec'11. Braga, Portugal, 1-3 December, 2011. Conference MicroBiotec'11
(Portugal)
2010/12 Rational strain improvement through Metabolic Systems Biology. Invited plenary speaker at the conference Joint meeting of the NZ Microbiological Society and NZ Society for Biochemistry & Molecular Biology: Small Things, Big Ideas, Auckland, New Zealand, December 2-4 2010. Joint meeting of the NZ Microbiological Society and NZ Society for Biochemistry & Molecular Biology: Small Things, Big Ideas
(Auckland, New Zealand)
2009/07 Systems Biology for the development of microbial cell factories. Invited speaker at the National Science Meeting 2009, Lisbon, Portugal, July 30 2009. National Science Meeting
(Portugal)
2006/09 Systems Biology of Recombinant Organisms. Invited plenary speaker at the European Biopharm Scale-up Congress, Geneva, Switzerland, September 12-14 2006. European Biopharm Scale-up Congress
(Switzerland)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2011/10 - Current Computer Aided Design of Metabolic Pathways. Co-supervision with Miguel Rocha, DI, UMinho.
Co-supervisor
 PhD in Computer Science (MAP-i) (PhD)
Universidade do Minho, Portugal
2019/06 - 2023/05 Development of hybrid metabolic models for the optimization of production of aromatic compounds derived from shikimate. Co-supervision with Sónia Carneiro, SilicoLife, Portugal.
Supervisor
 Molecular BioSciences PhD Program (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2018/11 - 2022/12 Metagenomics Analysis in Extreme Environments for the discovery of novel enzymes and pathways. Co-Supervision with José Pereira Leal, CEDOC, NOVA University Lisbon.
Supervisor
 Molecular BioSciences PhD Program (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2018/01 - 2021/12 Development of Genome-scale reconstruction strategies. Program. Co-supervision with Rafael Carreira (SilicoLIfe)
Supervisor
 PhD in Chemical and Biological Engineering (PhD)
Universidade do Minho, Portugal
2018/01 - 2020/12 Metabolic Engineering aided by computer-guided enzyme engineering for the optimization of cell factories. Co-supervision with Cláudio Soares (ITQB NOVA).
Supervisor
 PhD in Bioengineering (MIT-Portugal Program) (PhD)
Universidade do Minho, Portugal
2017/01 - 2020/12 Design and optimization of microbial communities
Supervisor
 PhD in BioEngineering (PhD)
Universidade do Minho, Portugal
2017/09 - 2020/09 Optimization of organic acids titers in Saccharomyces cerevisiae chassis cells. Co-Supervision with Lucília Domingues (CEB-UMINHO)
Supervisor
 PhD in Chemical and Biological Engineering (PhD)
Universidade do Minho, Portugal
2017/09 - 2020/09 Development of chemically defined medium for biopharmaceuticals production using mammalian cell lines guided through metabolic modelling tools and metabolomics measurements.
Supervisor
 PhD in Bioengineering (MIT-Portugal Program) (PhD)
Universidade do Minho, Portugal
2015/01 - 2019/12 Metabolic Systems Biology of Leishmania major. Co-supervision with Sónia Carneiro, SilicoLife,
Co-supervisor
 PhD in Chemical and Biological Engineering (PhD)
Universidade do Minho, Portugal
2017/12 - 2019/06 Building a database and development of a machine learning algorithm to identify and characterize viral fusion peptides. Co-supervision with Diana Lousa (ITQB NOVA).
Co-supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2017/02 - 2019/01 Otimização da fermentação para a produção industrial de compostos fenólicos. Co-supervision with Adelaide Braga (University of Minho) and Nuno Faria (Biotempo, Lda).
Supervisor
 Integrated Master in Biological Engineering (Master)
Universidade do Minho, Portugal
2014/01 - 2018/12 Development of novel strains for the production of biofuels. Co-supervision with Aljoscha Whal, Technical University of Delft, The Netherlands and Rui Pereira (Chalmers, Sweden). Currently Post-Doc at ITQB NOVA
Supervisor
 PhD in Bioengineering (MIT-Portugal Program) (PhD)
Universidade do Minho, Portugal
2014/01 - 2018/12 Accelerating Metabolic Engineering tasks by the in silico development of libraries of strains. Co-supervision with Kiran Patil, EMBL, Germany. Currently Advisor for Technology Transfer at NOVA University
Supervisor
 PhD in Bioengineering (MIT-Portugal Program) (PhD)
Universidade do Minho, Portugal
2014/01 - 2018/12 Improving Predictions in Metabolic Engineering problems by incorporating enzyme structural information. Co-supervision with Cláudio Soares, ITQB, Portugal. Currently working at the Biotech multinational company Amyris, Porto, Portugal
Supervisor
 PhD in Bioengineering (MIT-Portugal Program) (PhD)
Universidade do Minho, Portugal
2013/10 - 2018/07 Evaluation and development of algorithms and computational tools for metabolic pathway optimization. Co-supervision with Miguel Rocha, DI, UMinho. Currently Post-Doc researcher at the Argonne National Laboratory, USA
Co-supervisor
 PhD in Computer Science (MAP-i) (PhD)
Universidade do Minho, Portugal
2016/12 - 2017/10 Reconstructing the metabolic network of Lactobacillus helveticus on a genome-wide scale. Co-supervision with Óscar Manuel Lima Dias (University of Minho) and Ahmad Adel Zeidan (Chr Hansen A/S, Denmark).
Supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2016/12 - 2017/10 Genome-Scale Metabolic Network Reconstruction of the dairy bacterium Streptococcus thermophiles. Co-supervision with Óscar Manuel Lima Dias (University of Minho) and Ahmad Adel Zeidan (Chr Hansen A/S, Denmark).
Co-supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2012/01 - 2017/10 Development of cell factories for the efficient production of mannosylglycerate, a thermolyte with great potential in biotechnology. Co-supervision with Helena Santos and Nuno Borges, ITQB, Portugal. Currently Head of Development at SilicoLife, Ltd, Braga.
Co-supervisor
 PhD in Bioengineering (MIT-Portugal Program) (PhD)
Universidade do Minho, Portugal
2012/01 - 2017/05 Systems analysis of metabolic network origin and evolution in prokaryotes. Co-supervision with Kiran Patil, EMBL, Germany. Currently POst-Doc reseracher at Heinrich Heine Universität Düsseldorf
Supervisor
 PhD in Chemical and Biological Engineering (PhD)
Universidade do Minho, Portugal
2015/02 - 2017/03 Optimization of the production of bioplastics using Metabolic Engineering. Co-supervision with Rui Pereira, SilicoLife, Ltd.
Supervisor
 Integrated Master in Biological Engineering (Master)
Universidade do Minho, Portugal
2005 - 2017 Supervision of over 80 researchers (Bachelor or Master level) under the scope of the funded research projects. Supervision of 1st year PhD students of the PhD program in Bioengineering in their 6-weeks lab rotation – 20 students 2007-2017. Supervision of 5th year graduate students of Biological Engineering (pre-Bologna) in their industrial training period – 4 students 2005-2007. Supervision of 4th year graduate students in process design projects in the Master Program in Biological Engineering (since 2005) – 6 groups of students 2005-2017
Supervisor
 Several (Other)
Universidade do Minho, Portugal
2016/02 - 2016/10 Preparation and presentation of a plan to improve the fast cooling process in a unit of human food production. Co-supervision with Pedro Lorga (Pingo Doce, S. A.)
Supervisor
 Integrated Master in Biological Engineering (Master)
Universidade do Minho, Portugal
2016/02 - 2016/10 Aplicação do Sistema HACCP no caso de estudo de fiambres fatiados. Co-supervision with Juliana Martins (Salsicharia Limiana, Lda).
Supervisor
 Integrated Master in Biological Engineering (Master)
Universidade do Minho, Portugal
2009/09 - 2016/09 Development of Dynamic Multi-Layered Cell Models based on Cellular Automata. Co-Supervision with Miguel Rocha, DI, UMinho and Bruce Tidor, MIT, USA. Currently Data Scientist at HOLD Platform Limited.
Supervisor
 PhD in Bioengineering (MIT-Portugal program) (PhD)
Universidade do Minho, Portugal
2014/12 - 2016/01 Evolutionary Engineering of Lactic Acid Bacteria. Co-supervision with Jochen Foster, DTU, Denmark.
Supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2014/12 - 2015/12 Analysis and optimization of industrial microorganisms under dynamic process conditions. – University of Minho. Co-supervision with Carlos Daniel Machado, CEB, UMinho.
Supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2010/01 - 2015/12 Hydrocarbonoclastic bacteria: from bioremediation to bioenergy feedstock. Co-supervision with Alcina Pereira, DEB, UMinho. Currently Post-Doc Reseacrher at UMinho
Co-supervisor
 PhD in Chemical and Biological Engineering (PhD)
Universidade do Minho, Portugal
2014/12 - 2015/10 Regulatory modelling of Saccharomyces cerevisiae. Co-supervision with Kiran R. Patil, EMBL, Germany.
Supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2014/12 - 2015/10 Development of a dynamic model for the production of phenolic compounds. Co-supervision with Nuno Faria, Biotempo.
Supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2014/12 - 2015/10 Development of metabolic pathway analysis based algorithms for strain optimization. Co-supervision with Miguel Rocha, DI, UMinho.
Co-supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2010/09 - 2015/07 Optimization of the Production Active Pharmaceutical Ingredients with E.coli. Co-supervision with Jens Nielsen, Chalmers, Sweden. Currently Post-Doc at Chalmers, Sweden.
Supervisor
 PhD in Bioengineering (MIT-Portugal program) (PhD)
Universidade do Minho, Portugal
2013/12 - 2015/06 In silico optimization of organic acids production. Co-supervision with Simão Soares, SilicoLife.
Supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2010/09 - 2015/06 Understanding the evolution and conservation of regulatory mechanisms through reconstruction and comparison of metabolic regulatory networks. Co-Supervision with Miguel Rocha, DI, UMinho and Chris Henry, Argonne National Laboratory, USA. Currently Researcher at Argonne National Laboratory and University of Chicago, USA
Supervisor
 PhD in Bioengineering (MIT-Portugal program) (PhD)
Universidade do Minho, Portugal
2009/09 - 2015/06 Developing Computational Tools to Explore the Synergies between Systems Biology and Metabolome Analysis. Co-supervision with Miguel Rocha, DI, UMinho and Silas Villas-Bôas, University of Auckland, New Zealand. Currently Head of Development at SilicoLife, Ltd, Braga, Portugal
Co-supervisor
 PhD in Biomedical Engineering
Universidade do Minho, Portugal
2009/09 - 2015/06 Metabolic Control Analysis as a Framework for Strain Optimization. Co-Supervision with Miguel Rocha, DI, UMinho. Currently Head of Development at SilicoLife, Ltd, Braga, Portugal
Supervisor
 PhD in Bioengineering (MIT-Portugal program) (PhD)
Universidade do Minho, Portugal
2013/12 - 2015/04 Analysis of output properties of Peroxiredoxin / Thioredoxin /thioredoxin reductase system. Co-supervision with Armindo Machado, CNC, Coimbra University.
Co-supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2014/02 - 2014/10 Desenho e Visualização de Vias Metabólicas para Análise de Soluções de Otimização de Estirpes. – University of Minho. Co-supervision with Sónia Carneiro, SilicoLife, Ltd.
Supervisor of Ana Isabel Lobo Castro
 Integrated Master in Biological Engineering (Master)
Universidade do Minho, Portugal
2014/02 - 2014/10 Reconstrução do modelo metabólico do Actinobacillus succionogenes. – University of Minho. Co-supervision with Sónia Carneiro, SilicoLife, Ltd.
Supervisor
 Integrated Master in Biological Engineering (Master)
Universidade do Minho, Portugal
2014/02 - 2014/10 Implementation of the fermentation strategies for lactic acid bacteria. Co-supervision with Nuno Faria, Biotempo, Ltd.
Supervisor
 Integrated Master in Biological Engineering (Master)
Universidade do Minho, Portugal
2014/02 - 2014/10 Importância do pH na carne de bovino embalada. Co-supervision with Graciete Machado, Centralcarnes, Ltd.
Supervisor
 Integrated Master in Biological Engineering (Master)
Universidade do Minho, Portugal
2013/12 - 2014/10 Extraction of kinetic information from literature. Co-supervision with Miguel Rocha, DI, UMinho.
Supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2009/02 - 2014/06 Systems analysis of metabolism in Helicobacter pylori. Co-Supervision with Maria João Vieira, DEB, University of Minho and Nuno Azevedo, Faculty of Engineering, University of Porto. Currently Head of R&D at the Perfume company Nortempresa, Ltd, Braga, Portugal.
Supervisor
 PhD in Chemical and Biological Engineering (PhD)
Universidade do Minho, Portugal
2009/03 - 2013/12 In vivo metabolic pathway analysis of Enterococcus faecalis for uncovering key pathogenicity factors. Co-Supervision with Eugénio Ferreira, DEB, UMinho and Silas Vilas-Boas, Univ. Auckland, New Zealand. Currently employed at the Value Creation Office at NOVA University Lisbon, Portugal.
Supervisor
 PhD in Chemical and Biological Engineering (PhD)
Universidade do Minho, Portugal
2013/02 - 2013/11 Sistemas de Segurança Alimentar e de Controlo de Qualidade na Cerealis Produtos Alimentares S.A. Co-supervision with Cláudia Torres, Cerealis, Ltd. Role: Main supervisor. February – October 2013 (concluded).
Supervisor
 Integrated Master in Biological Engineering (Master)
Universidade do Minho, Portugal
2013/02 - 2013/10 Estudo das análises microbiológicas realizadas no Departamento Alimentar dos SASUM, no âmbito do respetivo SGSA. Co-supervision with Raquel Lopes, Biotempo, Ltd.
Supervisor
 Integrated Master in Biological Engineering (Master)
Universidade do Minho, Portugal
2013/02 - 2013/10 Metabolic engineering – In silico fumaric acid production. Co-supervision with Sónia Carneiro, SilicoLife, Ltd.
Supervisor
 Integrated Master in Biological Engineering (Master)
Universidade do Minho, Portugal
2013/02 - 2013/10 Revisão do SGQ e Segurança Alimentar em empresas do Grupo IDIS. Co-supervision with Sara Antunes, Idis, Ltd.
Supervisor
 Integrated Master in Biological Engineering (Master)
Universidade do Minho, Portugal
2013/02 - 2013/10 Metabolic Engineering – Itaconic Acid Production in Escherichia coli. Co-supervision with Sónia Carneiro, SilicoLife, Ltd.
Supervisor
 Integrated Master in Biological Engineering (Master)
Universidade do Minho, Portugal
2012/12 - 2013/10 Computational tools for pathway optimization towards metabolic engineering applications. Co-supervision with Miguel Rocha, DI, UMinho.
Supervisor of Filipe Alexandre Wang Liu
 MSc in Informatics (Master)
Universidade do Minho, Portugal
2012/12 - 2013/10 Development of computational methods for the determination of biomass composition and evaluation of its impact in genome-scale models predictions.
Supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2012/12 - 2013/10 Genome reannotation and genome-scale metabolic model reconstruction of Helicobacter pylori 26695.
Supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2012/12 - 2013/10 Investigação da produção do ácido itacónico pela bactéria Escherichia coli. Co-supervision with Sónia Carneiro, CEB, UMinho.
Co-supervisor
 MSc in Bioengineering (Master)
Universidade do Minho, Portugal
2009/02 - 2013/06 Reconstruction of the Genome-scale Metabolic Network of Kluyveromyces lactis. Co-Supervision with Eugénio Ferreira, DEB, UMinho and Andreas Gombert, University of Sao Paulo, Brazil. Currently Assistant Researcher at University of Minho.
Supervisor
 PhD in Chemical and Biological Engineering (PhD)
Universidade do Minho, Portugal
2007/12 - 2012/12 Computational tools for large-scale biological network analysis. Co-supervision with Miguel Rocha, DI, UMinho. Currently Post-Doc researcher at the University of Algarve.
Co-supervisor
 PhD in Informatics (PhD)
Universidade do Minho, Portugal
2012/02 - 2012/10 Desenvolvimento de metodologias para a optimização operacional de uma linha de produção de Galactooligossacarídeos e Frutooligossacarídeos. Co-supervision with Nuno Faria, Biotempo, Ltd.
Supervisor
 Integrated Master in Biological Engineering (Master)
Universidade do Minho, Portugal
2011/12 - 2012/10 Reconstruction of a generic metabolic model for Streptococcus pneumonia. Co-supervision with Francisco Pinto, University of Lisbon, Portugal.
Supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2009/12 - 2012/06 Connecting design and function in moiety-transfer cycles: functional implications of product inhibition by cycled intermediates. – University of Minho. Co-supervision with Armindo Salvador, CNC, Portugal.
Co-supervisor
 MSc Bioinformatics (Master)
Universidade do Minho, Portugal
2008/09 - 2012/06 Extracção e Classificação de Relações Biologicamente Relevantes da Literatura Biomédica. Co-supervision with Anália Lourenço, IBB,
Supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2008/09 - 2012/01 Novel modelling formalisms and simulation tools in Computational Biosystems. Co-supervision with Eugénio Ferreira, DEB, UMinho and Bruce Tidor, MIT, USA. Currently Post-Doc at EMBL, Heidelberg, Germany.
Co-supervisor
 PhD in Bioengineering (MIT-Portugal program) (PhD)
Universidade do Minho, Portugal
2006/01 - 2011/11 Systems analysis and metabolic network modeling in Escherichia coli. Co-supervision with Eugénio Ferreira, DEB, UMinho). Currently Researcher at FCT NOVA.
Co-supervisor
 PhD in Chemical and Biological Engineering (PhD)
Universidade do Minho, Portugal
2011/02 - 2011/10 Integração Energética de um Processo Industrial de Valorização de Soro de Queijo. – University of Minho. Co-supervision with Nuno Faria, Biotempo, Ltd.
Supervisor
 Integrated Master in Biological Engineering (Master)
Universidade do Minho, Portugal
2010/12 - 2011/10 Analysis of the kinetic response of S. cerevisiae to dynamic feast/famine conditions. Co-supervision with Aljoscha Wahl, Delft University of Technology, The Netherlands.
Co-supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2010/12 - 2011/10 Reconstruction, refinement and validation of a genome-scale metabolic model for the biosynthesis of triacylglycerols in Rhodococcus opacus. Co-supervision with Alcina Pereira, IBB, University of Minho.
Supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2010/10 - 2011/10 Desenvolvimento de ferramentas computacionais para otimização de estirpes por adição de reacções ao modelo metabólico. Co-supervision with Miguel Rocha, DI, UMinho.
Co-supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2011/03 - 2011/06 Systems analysis of metabolic networks’ origin and evolution.
Supervisor
 Integrated Master Program in Bioengineering (Master)
Universidade do Porto, Portugal
2006/01 - 2010/12 A Systems Biology approach for the characterization of metabolic bottlenecks in recombinant protein production processes. Co-supervision with Eugenio Ferreira, DEB, UMinho. Currently Head of Development at SilicoLife, Ltd, Braga, Portugal.
Supervisor
 PhD in Chemical and Biological Engineering (PhD)
Universidade do Minho, Portugal
2009/12 - 2010/10 Uncovering metabolic and regulatory signatures in H. pylori infection by integration of “omics” data and metabolic models. Co-supervision with Kiran Patil, Technical University of Denmark.
Supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2008/02 - 2010/01 Engenharia Genética de Escherichia coli com vista ao melhoramento do processo de produção de proteínas recombinantes. Co-supervision with Lucília Domingues, IBB, University of Minho.
Co-supervisor
 Integrated Master in Biological Engineering (Master)
Universidade do Minho, Portugal
2009/02 - 2009/12 Measurement and Control of Glucose Concentration in Mammalian Cultivations using Mid-IR Spectroscopy. Co-supervision with Mats Akesson, NovoNordisk, Inc, Denmark.
Co-supervisor
 Integrated Master in Biological Engineering (Master)
Universidade do Minho, Portugal
2008/01 - 2009/12 Implementação de um Sistema Integrado de Gestão da Qualidade e Ambiental numa empresa transformadora de madeira. Co-supervision with Maria Olívia Pereira, DEB, University of Minho.
Co-supervisor
 MSc in Environmental Management Systems (Master)
Universidade do Minho, Portugal
2009/02 - 2009/11 Physiological characterization of PUFA producing microorganisms. Co-supervision with Jochen Forster, Fluxome Sciences, Denmark.
Co-supervisor
 Integrated Master in Biological Engineering (Master)
Universidade do Minho, Portugal
2008/10 - 2009/11 Desenvolvimento de ferramentas computacionais para a optimização de processos de fermentação em Biotecnologia. - University of Minho. Co-supervision with Miguel Rocha, DI, University of Minho.
Co-supervisor
 MSc in Informatics (Master)
Universidade do Minho, Portugal
2008/12 - 2009/10 Semi-automatic reconstruction of the metabolic network of three different strains of the Streptococcus pneumoniae (TIGR4, R6 and G54). Co-supervision with Francisco Pinto, University of Lisbon.
Supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2008/12 - 2009/10 Identifying metabolic and regulatory signatures of type 2 diabetes by integration of gene expression data and genome-scale metabolic networks. Co-supervision with Kiran Patil, Technical University of Denmark.
Co-supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2008/12 - 2009/09 Multi-Objective Evolutionary Algorithms for the in silico Optimization of Mutant Strains. Co-supervision with Miguel Rocha, DI, University of Minho.
Co-supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2008/12 - 2009/09 Computational Tools for the Simulation and Optimization of Biological processes with Dynamical Models. Co-supervision with Miguel Rocha, DI, University of Minho.
Supervisor
 MSc in Bioinformatics (Master)
Universidade do Minho, Portugal
2008/02 - 2009/07 Optimization of the production of fructo-oligosaccharides with Aspergillus spp. Co-supervision with Lígia Rodrigues, IBB, University of Minho.
Co-supervisor
 Integrated Master in Biological Engineering (Master)
Universidade do Minho, Portugal
2007/10 - 2009/07 Monitoring and modelling of recombinant E. coli fermentation. Co-supervision with E. C. Ferreira, DEB, University of Minho.
Supervisor
 MSc in Biotechnology (Master)
Universidade do Minho, Portugal
2007/11 - 2008/10 Computational Tools for the Reconstruction of Genome-scale Metabolic Models. Co-supervision with Miguel Rocha, DI, University of Minho.
Co-supervisor
 MSc in Informatics (Master)
Universidade do Minho, Portugal
2007/02 - 2007/12 Application of Bioinformatics tools to the optimization of an Industrial Biotechnology Process. - University of Minho. Co-supervision with Miguel Rocha, DI, University of Minho.
Supervisor
 Integrated Master in Biological Engineering (Master)
Universidade do Minho, Portugal
2007/02 - 2007/12 Online optimization of the production of functional food ingredients. - University of Minho. Co-supervision with Duarte Torres, Biotempo, Ltd.
Supervisor
 Integrated Master in Biological Engineering (Master)
Universidade do Minho, Portugal
2006/10 - 2007/12 Modelling of Biotechnological Processes - an approach based on Artificial Neural Networks. Co-supervision with Miguel Rocha, DI, University of Minho.
Co-supervisor
 MSc in Informatics (Master)
Universidade do Minho, Portugal
2005/10 - 2006/06 Implementation of an Environmental Management System in a company producing package material and its integration with quality and health management systems. Co-supervision with Maria Olívia Pereira, DEB, University of Minho.
Co-supervisor
 MSc in Environmental Management Systems (Master)
Universidade do Minho, Portugal

Jury of academic degree

Topic
Role 		Candidate name (Type of degree)
Institution / Organization
2019/10 Analysis of metabolic heterogeneity over cell division cycle in non-synchronized yeast
(Thesis) Main arguer
 Inês Vasconcelos Miranda Santos (PhD)
Universidade de Coimbra, Portugal
2019/07 New constraint-based methods to characterize Chinese hamster ovary cell metabolism
(Thesis) Main arguer
 Sarah Noel Galleguillos Rioboo (PhD)
Universität für Bodenkultur Wien, Austria
2018/10/03 A mathematical model of the phosphoinositide pathway in human pulmonary epithelial cells
(Thesis) Main arguer
 Daniel Olivença (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2018/10 Analysis, mathematical modeling and optimization of mammalian cell cultures in perfused bioreactors. University of Mons, Belgium, October 2018. Member of jury as opponent.
(Thesis) Main arguer
 Sofia Afonso Fernandes de Sousa (PhD)
2017 Developing strategies for systems metabolic engineering of Pichia pastoris
(Thesis) Main arguer
 Màrius Tomàs Gamisans (PhD)
Universitat Autònoma de Barcelona, Spain
2016/12 Network Inference for Logic-Based Ordinary Differential Equations
(Thesis) Arguer
 David Saque Henriques (PhD)
Universidade do Minho, Portugal
2016/11 Seeking general principles in the design of defense systems against hydrogen peroxide
(Thesis) Main arguer
 Gianluca Selvaggio (PhD)
Universidade Nova de Lisboa, Portugal
2016/09 Development of Dynamic Multi-Layered Cell Models based on Cellular Automata
Supervisor
 Pedro Tiago Evangelista (PhD)
Universidade do Minho, Portugal
2016/05 Systems analysis of metabolic network origin and evolution in prokaryotes
Supervisor
 Joana Rute Calça Xavier (PhD)
Universidade do Minho, Portugal
2015/09 Rational design of insect cell-based vaccine production: Bridging metabolomics with mathematical tools to study virus-host interactions.
(Thesis) Main arguer
 Francisca Sarreira Simões Horta Monteiro (PhD)
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2015/07 Improvement of in silico strain engineering methods in S. cerevisiae
Supervisor
 Rui Miguel Pinheiro Silva Pereira (PhD)
Universidade do Minho, Portugal
2015/06 Modelling microbes: new methods for integrated metabolic and regulatory network reconstruction
Supervisor
 José Pedro Lopes Faria (PhD)
Universidade do Minho, Portugal
2014/06 Systems analysis of metabolism in Helicobacter pylori
Supervisor
 Daniela Matilde Marques Correia (PhD)
Universidade do Minho, Portugal
2013/12 In vivo metabolic pathway analysis of Enterococcus faecalis for uncovering key pathogenicity factors
Supervisor
 Carla Andreia Freixo Portela (PhD)
Universidade do Minho, Portugal
2013/06 Reconstruction of the Genome-scale Metabolic Network of Kluyveromyces lactis
Supervisor
 Óscar Manuel Lima Dias (PhD)
Universidade do Minho, Portugal
2013/03 Management and characterization of Helicobacter pylori in vitro growth: new insights into its free-living and biofilm modes of growth
(Thesis) Main arguer
 Lucinda Janete da Silva Bessa (PhD)
University D’ANNUNZIO, Italy
2013/01 Design and engineering of a cyanobacterial photoautotrophic chassis and parts for synthetic biology applications
(Thesis) Main arguer
 Filipe José Vilarinho Pinto (PhD)
Universidade do Porto, Portugal
2012/12 Computational Tools for Data Integration and Regulatory Network Inference in Systems Biology
Supervisor
 José Pedro Basto Gouveia Pereira Pinto (PhD)
Universidade do Minho, Portugal
2012/06 . Investigating genotype-phenotype relationships in Saccharomyces cerevisiae metabolic network through stoichiometric modeling
(Thesis) Main arguer
 Ana Rita Brochado (PhD)
Danmarks Tekniske Universitet, Denmark
2012/01 Novel modelling formalisms and simulation tools in Computational Biosystems
Supervisor
 Carlos Daniel Moutinho Machado (PhD)
Universidade do Minho, Portugal
2010/12 From Genome-scale Models of Microorganisms to Process Control and Optimization - Application to Recombinant Protein Production
Supervisor
 Rafael Sousa Costa (PhD)
Universidade do Minho, Portugal
2010/12 Characterization of a Salmonella phage using omic tools and mathematical models to predict host-phage interaction
(Thesis) Arguer
 Sílvio Roberto Branco dos Santos (PhD)
Universidade do Minho, Portugal
2010/12 A Systems Biology approach for the characterization of metabolic bottlenecks in recombinant protein production processes
Supervisor
 Sónia Madalena Azevedo Carneiro (PhD)
Universidade do Minho, Portugal
2010/06 Model discrimination in time-course kinetics: the glyoxalase pathway in Saccharomyces cerevisiae
(Thesis) Main arguer
 Nuno Filipe Gonçalves Lages (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2010/03 Production of Galacto-Oligosaccharides - Physicochemical and Functional Characterization
(Thesis) Arguer
 Duarte Paulo Martins Torres (PhD)
Universidade do Minho, Portugal
2007 Feed Strategies Optimization for Parameter Identification in a E. coli Fermentation Model for Monitoring and Control
(Thesis) Arguer
 Ana Cristina Araújo Veloso (PhD)
Universidade do Minho, Portugal

Committee member

Activity description
Role 		Institution / Organization
2019/10/14 - 2019/10/19 8th International Conference Foundations of Systems Biology in Engineering, FOSBE 2019. Valencia, Spain, October 14-19 2019. Vice-chair for Industry of the Program committee.
Member
2019/08 - 2019/08 MPA 2019 – Metabolic Pathway Analysis 2019, Riga, Latvia, August 2019. Member of the organizing committee.
Member
2018/09 - 2018/09 2nd DD-DeCaF workshop – Data driven cell factory design (http://dd-decaf.eu/2018/09/18/2nd-workshop.html), Oeiras, September 18-19 2018. Co-head of the organizing committee.
Member
2018 - 2018 Metabolic Engineering 12 - Systems Metabolic Engineering for Superior Bio-Production, The Westin Grand Munich, Munich, Germany, June 24-28, 2018. Member of the Organizing Committee.
2015 - 2015 MPA 2015 – Metabolic Pathway Analysis 2015 (http://www.mpa15.org), Braga, June 8-12 2015. Head of the organizing committee.
President / Vice-president
2008 - 2008 CHEMPOR 2008 - 10th International Chemical and Biological Engineering Conference, Braga, Portugal, September 4-6 2008. Member of the Organizing Committee.
Member
2007 - 2007 Workshop on Computational Methods in Bioinformatics and Systems Biology, 13th Portuguese Conference on Artificial Intelligence, Guimarães, Portugal, December 3-7 2007. Member of the Organizing Committee.
Member

Conference scientific committee

Conference name Conference host
2018/06 - 2018/06 12th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB'18), Toledo, Spain, June 20-22 2018. Member of the Scientific Committee.
2017 - 2017 11th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB’17), Polytechnic of Porto – Porto, Portugal. June 21-23, 2017. Member of the Scientific Committee.
2016 - 2016 XIX National Biochemistry Congress (Portugal), University of Minho, Guimarães, Portugal, December 8-10 2016. Member of the Scientific Committee.
2016 - 2016 6th International Conference Foundations of Systems Biology in Engineering, FOSBE 2016. Otto-von-Guericke University and the Max Planck Institute, Magdeburg, Germany, October 9-12 2016. Member of the Programme Committee.
2016 - 2016 10th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB'16). Seville, Spain. June 1-3, 2016. Member of the Scientific Committee.
2015 - 2015 9th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB'15), Salamanca, Spain, June 3-5 2015. Member of the Scientific Committee.
2015 - 2015 MPA 2015 – Metabolic Pathway Analysis 2015 (http://www.mpa15), Braga, June 8-12 2015. Member of the scientific committee.
2014 - 2014 8th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB'14), Salamanca, Spain, June 4-6 2014. Member of the Scientific Committee.
2014 - 2014 Bioinformatics 2014 – 5th International Conference on Bioinformatics models, methods and algorithms, Angers, France, March 3-6 2014. Member of the Program Committee.
2013 - 2013 7th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB'13), Salamanca, Spain, May 22-24 2013. Member of the Scientific Committee.
2012 - 2012 6th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB 2012), Salamanca, Spain, March 28-30 2012. Member of the Scientific Committee.
2011 - 2011 5th International Conference on Practical Applications of Computational Biology and Bioinformatics (PACBB 2011), Salamanca, Spain, April 6-8 2011. Member of the Scientific Committee.
2010 - 2010 X Jornadas de Bioinformática, Malaga, Spain, October 27-29 2010. Member of the Scientific Committee.
2010 - 2010 4th International Workshop on Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2010), Guimarães, Portugal, June 16-18 2010. Member of the Scientific Committee.
2009 - 2009 2nd Workshop on Computational Methods in Bioinformatics and Systems Biology, 14th Portuguese Conference on Artificial Intelligence, Aveiro, Portugal, October 12-15 2009. Member of the Program Committee.
2009 - 2009 3rd International Workshop Practical Applications Computational Biology and Bioinformatics (IWPACBB 2009), Salamanca, Spain, June 10-12 2009. Member of the Scientific Committee.
2008 - 2008 2nd International Workshop Practical Applications of Computational Biology and Bioinformatics (IWPACBB 2008), Salamanca, Spain, October 22-24 2008. Member of the Scientific Committee.

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2017/10 - Current Course coordination and teaching of the module Systems Biology at the PhD Program in Molecular Biosciences, 1.5 credits (6 hours of teaching, 35 hours total) PhD Program in Molecular Biosciences (Doutoramento) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2009/09 - 2017/08 Master in Bioengineering - Bioinformatics and Systems Biology. Discipline part of the Curricular Unit Bioprocess Engineering (UCE Engenharia de Bioprocessos). 5 credits. 1st year. 1st Semester. Compulsory Discipline. Typology: 50% T + 50% TP. Role: Coordinator since the launch of the discipline (2009/2010). Responsible for the design and implementation of the program Average number of students: 20. MSc Bioengineering (Mestrado) Universidade do Minho, Portugal
2007/09 - 2017/08 PhD in Bioengineering (MIT-Portugal): - Bio-Teams (Bioengenharia de sistemas: da Ideia à Inovação). 1st year. 2nd semester. Compulsory Discipline. Typology: 40% T + 60% TP. Role: Coordinator. Responsible for the design and implementation of the program. Average number of students: 30. - Lab Rotations (Rotação Laboratorial). 1st year. Compulsory Discipline. Typology: 50% P + 50% OT. Role: lecturer. Average number of students: 5. PhD Bioengineering (Doutoramento) Universidade do Minho, Portugal
2007/09 - 2017/08 PhD in Bioengineering (MIT-Portugal): - Computational Biosystems (Ciência e Engenharia de Biosistemas). 1st year. 1st Semester. Compulsory Discipline. Typology: 40% T + 60% TP. Role: lecturer. Coordinator in 2016/2017. Co-responsible for the design of the program. Average number of students: 20. - Innovation in Bioengineering (Inovação em Bioengenharia). 1st year. 1st semester. Compulsory Discipline. Typology: 100% T. Role: lecturer. Average number of students: 20. PhD Bioengineering (Doutoramento) Universidade do Minho, Portugal
2007/09 - 2017/08 - Systems Biology. 5 credits. 1st year. 1st Semester. Compulsory Discipline. Typology: 50% T + 50% TP. Role: Coordinator since the launch of the Master Program (2007/2008). Responsible for the design and implementation of the program. Average number of students: 30. - Modeling of Biological Processes 5 credits. 1st year. 2st Semester. Compulsory Discipline. Typology: 50% T + 50% TP. Role: Coordinator since 2010/2011. Co-responsible for the design and implementation of the program. Average number of students: 30. MSc Bioinformatics (Mestrado) Universidade do Minho, Portugal
2007/09 - 2017/08 Master in Bioinformatics: - Project in Bioinformatics and Systems Biology 10 credits. 1st year. 2nd Semester. Compulsory Discipline. Typology: 100% PL. Role: Coordinator since 2007/2008. Co-responsible for the design and implementation of the program. Average number of students: 30. - Entrepreneurship in Biotechology and Bioinformatics 5 credits. 2nd year. 1st Semester. Compulsory Discipline. Typology: 100% T. Role: Coordinator since. Co-responsible for the design and implementation of the program. Average number of students: 30. MSc Bioinformatics (Mestrado) Universidade do Minho, Portugal
2007/09 - 2017/08 Master in Bioinformatics: - Biochemical Engineering 5 credits. 1st year. 1st Semester. Compulsory Discipline. Typology: 100% TP. Role: Lecturer. Average number of students: 5. - Research methods and tools in Research in Bioinformatics 5 credits. 2nd year. 1st Semester. Compulsory Discipline. Typology: 50% T + 50% TP. Role: Lecturer. Average number of students: 30. - Bioinformatics Laboratories 5 credits. 1st year. 1st Semester. Compulsory Discipline. Typology: 100% PL. Role: Lecturer. Average number of students: 30. MSc Bioinformatics (Mestrado) Universidade do Minho, Portugal
2005/02 - 2017/08 Integrated Master in Biological Engineering: - Process Control and Instrumentation. 5 credits. 4th year. 2nd Semester. Compulsory Discipline. Typology: 40% T + 10% TP + 40% OT. Role: Coordinator from 2010/2011 to 2012/2013 and in 2016/2017. Average number of students: 60. MSc Biological Engineering (Mestrado integrado) Universidade do Minho, Portugal
2013 - 2013 Course coordination and teaching of the Course on “Metabolic Engineering with OptFlux”, offered at the Sinaferm Conference 2013 (6 hours), Foz de Iguaçu, Brazil, July 30 2013. Post-Graduation course (Outros)

Other jury / evaluation

Activity description Institution / Organization
2019/04 - 2019/04 Evaluator DFB - Deutsche Forschungsgemeinschaft: Review Panel for the Priority Programme “Novel production processes and multi-scale analysis, modelling and design of cell-cell and cell-bioreactor interactions (InterZell).
2019 - 2019 Evaluator for the European Commission Horizon 2020 call SC1-BHC-02-2019: 'Systems approaches for the discovery of combinatorial therapies for complex disorders'.
2019 - 2019 Evaluation of PhD Grants for FCT in Portugal - Bioengineering and Biotechnology panel
2019 - 2019 Evaluator for the European Commission Horizon 2020 call CE-Biotec-05-2019: Microorganism communities for plastics bio-degradation (RIA). Single Stage. 4 full proposals.
2019 - 2019 Evaluator for the Portuguese Science Foundation (FCT) of the Research Infrastructures (panel coordinator)
2017 - 2017 Evaluator for the European Commission Horizon 2020 call SC1-PM-02-2017: New Concepts in Patient Stratification – stage 1 (22 proposals) and stage 2 (6 proposals).
2016 - 2016 Evaluator for the European Commission for COST Actions Open Call OC-2016-2 (1 proposal).
2015 - 2015 Evaluator for the European Commission Horizon 2020 call PHC2 – 2015: "Understanding disease: systems medicine" – stage 1 (18 proposals) and stage 2 (8 proposals).
2014 - 2014 Evaluator for the ERASynBio call on collaborative projects – 2014 (1 proposal).
2014 - 2014 Evaluator for the Czech Ministry of Education (Czech-Norwegian Research Programme), Czech Republic, 2014
2007 - 2014 Evaluator for the Biotechnology and Biological Sciences Research Council grants (United Kingdom). 2007, 2009 and 2014.
2013 - 2013 Evaluator for the BBRSC (Multidisciplinary Research Centres in Synthetic Biology), UK, 2013.
2013 - 2013 Evaluator for the Portuguese Innovation Agency, Portugal, 2013
2013 - 2013 Evaluator for the Latvian Science Council (national call), Latvia, 2013
2012 - 2012 Evaluator for the Polish-Norwegian Research Programme, The National Centre for Research and Development, Poland, 2012.
2011 - 2012 Evaluator for the EU 7th Framework Programme in the area of Systems Medicine (European Union). 2011 and 2012.
2011 - 2011 Evaluator for the Research Council of K.U.Leuven. (Belgium). 2011.
2010 - 2010 Evaluator for the Research Foundation - Flanders, (FWO). (Belgium). 2010.
2010 - 2010 Evaluator for the ERA-IB 2nd Call - Industrial biotechnology for Europe: an integrated approach (European Union). 2010.
2008 - 2009 Evaluator for the Chilean Research Fund Council (FONDECYT) – Initiation projects (Chile). 2008 and 2009.
2007 - 2009 Evaluator for the Biotechnology and Biological Sciences Research Council grants (United Kingdom). 2007 and 2009.
Distinctions

Other distinction

2010 Atreve-te Award to the best entrepreneurial project to SilicoLife (sponsored by the President of the Portuguese Republic)
Caixa Geral de Depositos, Portugal
2009 1st Annual 2009 MIT-Portugal Education Innovation Award
2007 Dupont Science & Engineering Award
EI Dupont de Nemours and Co, United States
1997 University of Minho Award
Universidade do Minho, Portugal
1997 Rotary Club Foundation Prize
1996 University/Industry Prize