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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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Identificação

Identificação pessoal

Nome completo
Isabel Rocha

Nomes de citação

  • Rocha, Isabel
  • Rocha, I.

Identificadores de autor

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

Domínios de atuação

  • Ciências da Engenharia e Tecnologias - Biotecnologia Industrial
  • Ciências da Engenharia e Tecnologias - Biotecnologia Industrial - Biocombustíveis
  • Ciências da Engenharia e Tecnologias - Biotecnologia Industrial - Fermentação
  • Ciências da Engenharia e Tecnologias - Biotecnologia Industrial - Tecnologias de BioProcessamento
  • Ciências Naturais - Ciências Biológicas - Biologia Molecular
  • Ciências Exatas - Ciências da Computação e da Informação - Bioinformática
  • Ciências da Engenharia e Tecnologias - Outras Ciências da Engenharia e Tecnologias

Idiomas

Idioma Conversação Leitura Escrita Compreensão Peer-review
Inglês Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2)
Português (Idioma materno)
Espanhol; Castelhano Utilizador proficiente (C1) Utilizador proficiente (C1) Utilizador independente (B2) Utilizador proficiente (C2) Utilizador proficiente (C1)
Francês Utilizador independente (B1) Utilizador independente (B2) Utilizador independente (B1) Utilizador independente (B1) Utilizador independente (B1)
Formação
Grau Classificação
2003
Concluído
 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" (TESE/DISSERTAÇÃO)
 Não Aplicável
1997
Concluído
 Engenharia Biológica (Licenciatura)
Universidade do Minho Escola de Engenharia, Portugal
"N/A" (TESE/DISSERTAÇÃO)
 17 valores
Percurso profissional

Ciência

Categoria Profissional
Instituição de acolhimento 		Empregador
2019/03/01 - Atual Investigador principal (carreira) (Investigação) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Universidade Nova de Lisboa, Portugal
2003/12/01 - 2004/07/31 Pós-doutorado (Investigação) Danmarks Tekniske Universitet, Dinamarca

Docência no Ensino Superior

Categoria Profissional
Instituição de acolhimento 		Empregador
2007/09/01 - 2017/09/14 Professor Auxiliar (Docente Universitário) Universidade do Minho Departamento de Engenharia Biológica, Portugal
2004/11/01 - 2007/08/31 Assistente (Docente Universitário) Universidade do Minho Departamento de Engenharia Biológica, Portugal
2002/09/01 - 2003/08/31 Assistente (Docente Universitário) Universidade do Minho, Portugal

Cargos e Funções

Categoria Profissional
Instituição de acolhimento 		Empregador
2021/10/20 - Atual Vice-Reitor Universidade Nova de Lisboa, Portugal
2019/06/01 - Atual Vice-Presidente BIOREF Colab, Portugal
2018/11/15 - Atual Member of the Board Madan Parque, Portugal
2019/11/15 - 2022/12/31 Vice-Presidente ELIXIR - Distributed Infrastructure for Biological Data, Reino Unido
2019/02/01 - 2022/03/31 Presidente InnovPlantProtect CoLab, Portugal
2017/09/15 - 2021/10/20 Pró-Reitor Universidade Nova de Lisboa, Portugal
2009/03/01 - 2011/02/28 Presidente APBio - Portuguese Bioindustries Association (now P-Bio), Portugal

Outros

Categoria Profissional
Instituição de acolhimento 		Empregador
2010/05/01 - Atual 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, Bélgica
2007/02/01 - 2007/05/31 Visiting Scholar Massachusetts Institute of Technology, Estados Unidos
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
Projetos

Bolsa

Designação Financiadores
2019/01/01 - 2023/03/31 SHIKIFACTORY100 - Modular cell factories for the production of 100 compounds from the shikimate pathway
grant agreement number 814408
Investigador responsável
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
 European Commission
Em curso
2019/07/01 - 2022/06/30 Machine learning and deep learning approaches to industrial biotechnology applications
NORTE-01-0247-FEDER-039831
Investigador responsável
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
 Agência Nacional de Inovação SA
Em curso
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
Concluído
2018/10/01 - 2021/09/30 MIXED-UP - Targeting pathogenesis and engineering cell factories: developing mixed regulatory
PTDC/BII-BIO/28216/2017
Investigador responsável
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Em curso
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
Investigador responsável
Universidade do Minho Centro de Engenharia Biológica, Portugal
 European Commission
Concluído
2017/04 - 2019/05 Bio.Data – Portuguese Biological Data Network
ROTEIRO/0098/2013
Investigador responsável
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Em curso
2015/04/01 - 2018/12/31 DYNAMICS - Analysis and optimization of industrial microorganisms under dynamic process conditions
ERA-IB-2014
Investigador responsável
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2014/04/01 - 2017/12/31 DeYeastLibrary - Designer Yeast Strain Library Optimized for Metabolic Engineering Applications
ERA-IB-2/0003/2013
Investigador responsável
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
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
Investigador responsável
Concluído
2013/11/01 - 2016/10/31 BACterial Hosts for production of Bioactive phenolics from bERRY fruits
FP7-KBBE-2013-7
Investigador responsável
Biotempo, Ltd, Portugal
 European Commission
Concluído
2012/07/01 - 2015/06/30 PEM – A platform for Metabolic engineering
FEDER, project 23060 (ANI)
Investigador responsável
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Agência Nacional de Inovação SA
Concluído
2012/04/01 - 2015/03/31 Finding the naturally evolved design principles of prevalent metabolic circuits
PTDC/QUI-BIQ/119657/2010
Investigador responsável
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
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
Investigador responsável
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2010/04/01 - 2013/12/31 HeliSysBio - Molecular Systems Biology in Helicobacter pylori
FCT PTDC/EBB-EBI/104235/2008
Investigador responsável
Universidade do Minho Centro de Engenharia Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluído
2008/11/01 - 2011/10/31 SYSINBIO- Systems Biology as a Driver for Industrial Biotechnology
call FP7-KBBE-2007-1
Investigador responsável
Universidade do Minho Centro de Engenharia Biológica, Portugal
 European Commission
Concluído
2008/09/01 - 2010/08/31 Propolis efficacy for the control of American Foulbrood: evaluation in controlled regions
Measure 6A
Investigador responsável
Universidade do Minho Centro de Engenharia Biológica, Portugal
Concluído

Projeto

Designação Financiadores
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
Em curso
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
Concluído
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
Concluído
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
Concluído
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
Investigador responsável
Universidade do Minho Centro de Engenharia Biológica, Portugal
Concluído
Produções

Publicações

Artigo em conferência
  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". Trabalho apresentado em 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". Trabalho apresentado em 3rd Meeting of the Institute for Biotechnology and Bioengineering, Lisboa, 2012.
    Publicado
  24. Gomes, Daniel; Dias, Oscar; Ferreira, Eugénio C.; Rocha, Isabel. "Reconstruction of a genome-scale metabolic model for the riboflavin producer fungus Ashbya gossypii". Trabalho apresentado em EMBO Conference Series - From Functional Genomics to Systems Biology, Heidelberg, 2012.
    Publicado
  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". Trabalho apresentado em MicroBiotec'11, Braga, 2011.
    Publicado
  26. Dias, Oscar; Ferreira, Eugénio C.; Rocha, I.; Rocha, Isabel. "Towards genome-wide semi-automated transporter system annotations". Trabalho apresentado em 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. Pinto, J.P.; Rocha, I.; Rocha, M.. "A software tool for network topology analysis under a Metabolic Engineering perspective". 2010.
    10.1145/1854776.1854884
  29. 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
  30. 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.
  31. 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
  32. 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
  33. Rocha, I.; Dias, Oscar; Rocha, Miguel; Ferreira, Eugénio C.. "Genome-scale metabolic models reconstruction of less characterized organisms with Merlin". 2010.
  34. Rocha, O.; Maia, P.; Rocha, I.; Rocha, M.. "Optferm-a computational platform for the optimization of fermentation processes". 2009.
  35. Azeredo, Joana; Henriques, Mariana; Rocha, I.; Ferreira, E. C.; Oliveira, Rosário. "Monoclonal antibodies production in wave and stirred tank bioreactors". 2009.
  36. 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.
  37. 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
  38. 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
  39. 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
  40. 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
  41. 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.
  42. 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.
  43. 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.
  44. Veloso, A.C.A.; Rocha, I.; Ferreira, E.C.. "Estimation of biomass concentration using interval observers in an E. coli fed-batch fermentation". 2007.
  45. Mendes, R.; Rocha, I.; Ferreira, E.C.; Rocha, M.. "A comparison of algorithms for the optimization of fermentation processes". 2006.
  46. Carneiro, S.; Rocha, I.; Ferreira, Eugénio C.. "A systems biology approach for the characterization of metabolic bottlenecks in recombinant protein production processes". 2005.
  47. 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.
  48. Rocha, I.; Ferreira, E.C.. "Model-based adaptive control of acetate concentration during the production of recombinant proteins with E. coli". 2002.
Artigo em revista
  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
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  77. Maia, P.; Vilaça, P.; Rocha, I.; Pont, M.; Tomb, J.-F.; Rocha, M.. "An integrated computational environment for elementary modes analysis of biochemical networks". International Journal of Data Mining and Bioinformatics 6 4 (2012): 382-395. http://www.scopus.com/inward/record.url?eid=2-s2.0-84867003199&partnerID=MN8TOARS.
    10.1504/IJDMB.2012.049292
  78. Carneiro, Sonia; Lourenco, Analia; Ferreira, Eugenio C; Rocha, Isabel. "Stringent response of Escherichia coli: revisiting the bibliome using literature mining.". Microbial informatics and experimentation 1 1 (2011): 14-14. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=MEDLINE&KeyUT=MEDLINE:22587779&KeyUID=MEDLINE:22587779.
    10.1186/2042-5783-1-14
  79. Soons, Z.I.T.A.; Ferreira, E.C.; Rocha, I.. "Identification of minimal metabolic pathway models consistent with phenotypic data". Journal of Process Control 21 10 (2011): 1483-1492. http://www.scopus.com/inward/record.url?eid=2-s2.0-80054757888&partnerID=MN8TOARS.
    10.1016/j.jprocont.2011.05.012
  80. Lourenço, A.; Carneiro, S.; Pinto, J.P.; Rocha, M.; Ferreira, E.C.; Rocha, I.. "A study of the short and long-term regulation of E. coli metabolic pathways.". Journal of integrative bioinformatics 8 3 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-84855554919&partnerID=MN8TOARS.
  81. Machado, D.; Costa, R.S.; Rocha, M.; Ferreira, E.C.; Tidor, B.; Rocha, I.. "Modeling formalisms in systems biology". AMB Express 1 1 (2011): 1-14. http://www.scopus.com/inward/record.url?eid=2-s2.0-84867843623&partnerID=MN8TOARS.
    10.1186/2191-0855-1-45
  82. Carreira, R.; Carneiro, S.; Pereira, R.; Rocha, M.; Rocha, I.; Ferreira, E.C.; Lourenço, A.. "Semantic annotation of biological concepts interplaying microbial cellular responses". BMC Bioinformatics 12 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-82155187091&partnerID=MN8TOARS.
    10.1186/1471-2105-12-460
  83. Carneiro, S.; Villas-Bôas, S.G.; Ferreira, E.C.; Rocha, I.. "Metabolic footprint analysis of recombinant Escherichia coli strains during fed-batch fermentations". Molecular BioSystems 7 3 (2011): 899-910. http://www.scopus.com/inward/record.url?eid=2-s2.0-79951623012&partnerID=MN8TOARS.
    10.1039/c0mb00143k
  84. Costa, R.S.; Machado, D.; Rocha, I.; Ferreira, E.C.. "Critical perspective on the consequences of the limited availability of kinetic data in metabolic dynamic modelling". IET Systems Biology 5 3 (2011): 157-163. http://www.scopus.com/inward/record.url?eid=2-s2.0-79960940147&partnerID=MN8TOARS.
    10.1049/iet-syb.2009.0058
  85. Vilaça, P.; ocha, I.; Rocha, M.. "A computational tool for the simulation and optimization of microbial strains accounting integrated metabolic/regulatory information". BioSystems 103 3 (2011): 435-441. http://www.scopus.com/inward/record.url?eid=2-s2.0-79751525708&partnerID=MN8TOARS.
    10.1016/j.biosystems.2010.11.012
  86. Lourenço, A.; Carneiro, S.; Rocha, M.; Ferreira, E.C.; Rocha, I.. "Challenges in integrating Escherichia coli molecular biology data". Briefings in Bioinformatics 12 2 (2011): 91-103. http://www.scopus.com/inward/record.url?eid=2-s2.0-79953144460&partnerID=MN8TOARS.
    10.1093/bib/bbq067
  87. Maia, Paulo; Pont, Marcellinus; Tomb, Jean-Francois; Rocha, Isabel; Rocha, Miguel; Rocha, MP; Riverola, FF; Shatkay, H; Corchado, JM. "Enhancing Elementary Flux Modes Analysis Using Filtering Techniques in an Integrated Environment". Advances in Bioinformatics 74 (2010): 217-224. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000288875100028&KeyUID=WOS:000288875100028.
    10.1007/978-3-642-13214-8_28
  88. Vilaca, Paulo; Maia, Paulo; Rocha, Isabel; Rocha, Miguel; Pizzuti, C; Ritchie, MD; Giacobini, M. "Metaheuristics for Strain Optimization Using Transcriptional Information Enriched Metabolic Models". Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics, Proceedings 6023 (2010): 205-216. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000279043700018&KeyUID=WOS:000279043700018.
  89. Carneiro, Sonia; Villas-Boas, Silas G.; Rocha, Isabel; Ferreira, Eugenio C.; Rocha, MP; Riverola, FF; Shatkay, H; Corchado, JM. "Applying a Metabolic Footprinting Approach to Characterize the Impact of the Recombinant Protein Production in Escherichia coli". Advances in Bioinformatics 74 (2010): 193-200. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000288875100025&KeyUID=WOS:000288875100025.
    10.1007/978-3-642-13214-8_25
  90. Domingues, L.; Rocha, I.; Dourado, F.; Alves, M.; Ferreira, E.C.. "Virtual laboratories in (bio)chemical engineering education". Education for Chemical Engineers 5 2 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-77950861764&partnerID=MN8TOARS.
    10.1016/j.ece.2010.02.001
  91. Rocha, I.; Maia, P.; Evangelista, P.; Vilaça, P.; Soares, S.; Pinto, J.P.; Nielsen, J.; et al. "OptFlux: An open-source software platform for in silico metabolic engineering". BMC Systems Biology 4 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-77950960250&partnerID=MN8TOARS.
    10.1186/1752-0509-4-45
  92. Costa, R.S.; Machado, D.; Rocha, I.; Ferreira, E.C.. "Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis-Menten and approximate kinetic equations". BioSystems 100 2 (2010): 150-157. http://www.scopus.com/inward/record.url?eid=2-s2.0-77952953154&partnerID=MN8TOARS.
    10.1016/j.biosystems.2010.03.001
  93. Lourenço, A.; Carreira, R.; Glez-Peña, D.; Méndez, J.R.; Carneiro, S.; Rocha, L.M.; Díaz, F.; et al. "BioDR: Semantic indexing networks for biomedical document retrieval". Expert Systems with Applications 37 4 (2010): 3444-3453. http://www.scopus.com/inward/record.url?eid=2-s2.0-71349084312&partnerID=MN8TOARS.
    10.1016/j.eswa.2009.10.044
  94. Rocha, Orlando; Maia, Paulo; Rocha, Isabel; Rocha, Miguel; AlAkaidi, M. "OPTFERM - A COMPUTATIONAL PLATFORM FOR THE OPTIMIZATION OF FERMENTATION PROCESSES". European Simulation and Modelling Conference 2009 (2009): 5-9. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000280117100001&KeyUID=WOS:000280117100001.
  95. Carneiro, S.; Villas-Boas, S.; Rocha, I.; Ferreira, E. C.. "Metabolic footprinting of Escherichia coli grown in fed-batch fermentation during recombinant protein production". New Biotechnology 25 (2009): S342-S342. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000281760100826&KeyUID=WOS:000281760100826.
    10.1016/j.nbt.2009.06.828
  96. Carneiro, S.; Amaral, A.L.; Veloso, A.C.A.; Dias, T.; Peres, A.M.; Ferreira, E.C.; Rocha, I.. "Assessment of physiological conditions in E. Coli fermentations by epifluorescent microscopy and image analysis". Biotechnology Progress 25 3 (2009): 882-891. http://www.scopus.com/inward/record.url?eid=2-s2.0-67651093759&partnerID=MN8TOARS.
    10.1002/btpr.134
  97. Neri, D.F.M.; Balcão, V.M.; Costa, R.S.; Rocha, I.C.A.P.; Ferreira, E.M.F.C.; Torres, D.P.M.; Rodrigues, L.R.M.; Carvalho Jr., L.B.; Teixeira, J.A.. "Galacto-oligosaccharides production during lactose hydrolysis by free Aspergillus oryzae ß-galactosidase and immobilized on magnetic polysiloxane-polyvinyl alcohol". Food Chemistry 115 1 (2009): 92-99. http://www.scopus.com/inward/record.url?eid=2-s2.0-60749116567&partnerID=MN8TOARS.
    10.1016/j.foodchem.2008.11.068
  98. Dias, L.G.; Veloso, A.C.A.; Correia, D.M.; Rocha, O.; Torres, D.; Rocha, I.; Rodrigues, L.R.; Peres, A.M.. "UV spectrophotometry method for the monitoring of galacto-oligosaccharides production". Food Chemistry 113 1 (2009): 246-252. http://www.scopus.com/inward/record.url?eid=2-s2.0-54849163200&partnerID=MN8TOARS.
    10.1016/j.foodchem.2008.06.072
  99. Veloso, A.C.A.; Rocha, I.; Ferreira, E.C.. "Monitoring of fed-batch E. coli fermentations with software sensors". Bioprocess and Biosystems Engineering 32 3 (2009): 381-388. http://www.scopus.com/inward/record.url?eid=2-s2.0-62949142138&partnerID=MN8TOARS.
    10.1007/s00449-008-0257-x
  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
Capítulo de livro
  1. Braga, A.; Rocha, I.; Faria, N.; Braga, A; Faria, N. C. M. Autor correspondente: 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.
    Publicado
  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.
    Publicado
  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.
Livro
  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
Poster em conferência
  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". Trabalho apresentado em 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.)". Trabalho apresentado em Iberian Plant Biology 2023, 2023.
  3. 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". Trabalho apresentado em Bioinformatics Open Days 2023, 2023.
  4. 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". Trabalho apresentado em Bioinformatics Open Days X, Braga, 2021.
  5. Oliveira, J. A.; Braga, A.; Rocha, I.; Faria, N.; Oliveira, J.A.; Braga, A.. "The effect of hydrodynamic conditions in Corynebacterium glutamicum growth". Trabalho apresentado em MicroBiotec'15 - Congress of Microbiology and Biotechnology 2015, 2015.
  6. 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". Trabalho apresentado em 21st International Ion Chromatography Symposium (IICS 2009), 2009.
  7. 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". Trabalho apresentado em , World Congress on Industrial Biotechnology and Bioprocessing, Toronto, Canada, 2006.
Pré-impressão
  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
Resumo em conferência
  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". Trabalho apresentado em Malta Polyphenols 2019 - 13th World Congress on Polyphenols Application, Valletta, 2019.
    Publicado
  2. Vieira, Vítor; Maia, Paulo; Rocha, Miguel; Rocha, Isabel. "Development of pathway analysis based algorithms for strain optimization". Trabalho apresentado em Bioinformatics Open Days, Braga, 2016.
    Publicado
  3. Dias, Oscar; Rocha, Miguel; Ferreira, Eugénio C.; Rocha, Isabel; Rocha, I.. "MEtabolic models Reconstruction using genome scaLe INformation (merlin) - assessment and validation". Trabalho apresentado em Copenhagen Biosciences Conferences - 7th Conference: Cell Factories and Biosustainability, Copenhagen, 2015.
    Publicado
  4. Dias, Oscar; Rocha, Miguel; Ferreira, Eugénio C.; Rocha, Isabel; Rocha, I.. "Merlin Latest Developments for Pathways Analysis". Trabalho apresentado em MPA2015 - Metabolic Pathway Analysis 2015, Braga, 2015.
    Publicado
  5. Dias, Oscar; Saraiva, João; Ferreira, Eugénio C.; Rocha, Isabel. "Towards a Genome-Scale Metabolic Model of the Streptococcus Pneumoniae R6 Avirulent Strain". Trabalho apresentado em COBRA 2015 - 4th Conference on Constraint-Based Reconstruction and Analysis, Heidelberg, 2015.
    Publicado
  6. Vieira, Vítor; Maia, Paulo; Rocha, Miguel; Rocha, Isabel. "Comparing knockout strategies from in silico rational strain design tools". Trabalho apresentado em 4th Conference on Constraint-Based Reconstruction and Analysis (COBRA), Heidelberg, Alemanha, 2015.
    Publicado
  7. Gomes, Daniel; Dias, Oscar; Ferreira, Eugénio C.; Rocha, Isabel. "Reconstruction of a genome-scale metabolic model for the filamentous fungus Ashbya gossypii". Trabalho apresentado em PYFF5 - 5th Conference on Physiology of Yeast and Filamentous Fungi, Montpellier, 2014.
    Publicado
  8. Dias, Oscar; Gombert, Andreas K.; Ferreira, Eugénio C.; Rocha, Isabel. "Towards a genome-scale metabolic model for the Kluyveromyces lactis yeast.". Trabalho apresentado em 9th European Congress of Chemical Engineering / 2nd European Congress of Applied Biotechnology, The Hague, 2013.
    Publicado
  9. Rodrigues, J. L.; Rodrigues, L. R.; Machado, C. D.; Kluskens, L. D.; Mota, M.; Rocha, I.; Ferreira, E. C.. "Synbiobacther - Engineering "therapeutic" bacteria". Trabalho apresentado em 3rd Meeting of the Institute for Biotechnology and Bioengineering, Lisboa, 2012.
    Publicado
  10. 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.". Trabalho apresentado em JORNADAS DE BIOINFORMÁTICA, Lisboa, 2009.
    Publicado
  11. 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". Trabalho apresentado em MicroBiotech¿09, 2009.
  12. Nobre, C; Santos, MJ; Dominguez, A; Torres, Duarte; Rodrigues, L.R.; Rocha, I.; Teixeira, JA; Ferreira, EC. "Fractionation of fructo-oligosaccharides by gel filtration". Trabalho apresentado em 10th International Chemical and Biological Engineering Conference CHEMPOR, Braga, 2008.
  13. 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". Trabalho apresentado em Functional Foods in Europe ¿ International Developments in Science and Health Claims, 2007.
  14. 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,". Trabalho apresentado em Annual Meeting of the Institute of Food Technologists, Chicago, 2007.
  15. Rocha, O.; Dominguez, A.; Nobre, C.; Torres, Duarte; Rodrigues, LR; Rocha, I.; Teixeira, JA. "Modeling and simulation of fructo-oligosaccharides production". Trabalho apresentado em 2nd FEBS Advanced Lecture Course on Systems Biology. FEBS-SysBio2007: from molecules to life, Gosau, 2007.
  16. 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". Trabalho apresentado em 4th Probiotics, Prebiotics and New Foods jointly with XXX International Congress on Microbial Ecology And Disease, Roma, 2007.
  17. Nobre, C.; Dominguez, A.; Torres, Duarte; Rocha, O.; Rodrigues, LR; Rocha, I.; Teixeira, JA; Ferreira, EC. "Purification of fructo-oligosaccharides by nanofiltration". Trabalho apresentado em 13th World Congress of Food Science and Technology, Nantes, 2006.
  18. 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". Trabalho apresentado em World Congress on Industrial Biotechnology and Bioprocessing, Toronto, 2006.
  19. Torres, Duarte; Dominguez, A.; Rodrigues, LR; Rocha, I.; Teixeira, JA; Lima, N.; Ferreira, EC. "Prebiotics ¿ from concept to product. The BIOLIFE Project". Trabalho apresentado em Micro¿05-Biotech¿05, Póvoa de Varzim, 2005.
Tese / Dissertação
  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". Doutoramento, 2013. http://hdl.handle.net/1822/28768.

Outros

Outra produção
  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.
Atividades

Apresentação oral de trabalho

Título da apresentação Nome do evento
Anfitrião (Local do evento)
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, Países Baixos)
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, Dinamarca)
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
(Reino Unido)
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, Brasil)
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, Alemanha)
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, Alemanha)
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, Reino Unido)
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
(Brasil)
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, Nova Zelândia)
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
(Suiça)

Orientação

Título / Tema
Papel desempenhado 		Curso (Tipo)
Instituição / Organização
2011/10 - Atual Computer Aided Design of Metabolic Pathways. Co-supervision with Miguel Rocha, DI, UMinho.
Coorientador
 PhD in Computer Science (MAP-i) (Doutoramento)
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.
Orientador
 Molecular BioSciences PhD Program (Doutoramento)
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.
Orientador
 Molecular BioSciences PhD Program (Doutoramento)
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)
Orientador
 PhD in Chemical and Biological Engineering (Doutoramento)
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).
Orientador
 PhD in Bioengineering (MIT-Portugal Program) (Doutoramento)
Universidade do Minho, Portugal
2017/01 - 2020/12 Design and optimization of microbial communities
Orientador
 PhD in BioEngineering (Doutoramento)
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)
Orientador
 PhD in Chemical and Biological Engineering (Doutoramento)
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.
Orientador
 PhD in Bioengineering (MIT-Portugal Program) (Doutoramento)
Universidade do Minho, Portugal
2015/01 - 2019/12 Metabolic Systems Biology of Leishmania major. Co-supervision with Sónia Carneiro, SilicoLife,
Coorientador
 PhD in Chemical and Biological Engineering (Doutoramento)
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).
Coorientador
 MSc in Bioinformatics (Mestrado)
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).
Orientador
 Integrated Master in Biological Engineering (Mestrado)
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
Orientador
 PhD in Bioengineering (MIT-Portugal Program) (Doutoramento)
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
Orientador
 PhD in Bioengineering (MIT-Portugal Program) (Doutoramento)
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
Orientador
 PhD in Bioengineering (MIT-Portugal Program) (Doutoramento)
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
Coorientador
 PhD in Computer Science (MAP-i) (Doutoramento)
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).
Orientador
 MSc in Bioinformatics (Mestrado)
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).
Coorientador
 MSc in Bioinformatics (Mestrado)
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.
Coorientador
 PhD in Bioengineering (MIT-Portugal Program) (Doutoramento)
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
Orientador
 PhD in Chemical and Biological Engineering (Doutoramento)
Universidade do Minho, Portugal
2015/02 - 2017/03 Optimization of the production of bioplastics using Metabolic Engineering. Co-supervision with Rui Pereira, SilicoLife, Ltd.
Orientador
 Integrated Master in Biological Engineering (Mestrado)
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
Orientador
 Several (Outra)
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.)
Orientador
 Integrated Master in Biological Engineering (Mestrado)
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).
Orientador
 Integrated Master in Biological Engineering (Mestrado)
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.
Orientador
 PhD in Bioengineering (MIT-Portugal program) (Doutoramento)
Universidade do Minho, Portugal
2014/12 - 2016/01 Evolutionary Engineering of Lactic Acid Bacteria. Co-supervision with Jochen Foster, DTU, Denmark.
Orientador
 MSc in Bioinformatics (Mestrado)
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.
Orientador
 MSc in Bioinformatics (Mestrado)
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
Coorientador
 PhD in Chemical and Biological Engineering (Doutoramento)
Universidade do Minho, Portugal
2014/12 - 2015/10 Regulatory modelling of Saccharomyces cerevisiae. Co-supervision with Kiran R. Patil, EMBL, Germany.
Orientador
 MSc in Bioinformatics (Mestrado)
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.
Orientador
 MSc in Bioinformatics (Mestrado)
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.
Coorientador
 MSc in Bioinformatics (Mestrado)
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.
Orientador
 PhD in Bioengineering (MIT-Portugal program) (Doutoramento)
Universidade do Minho, Portugal
2013/12 - 2015/06 In silico optimization of organic acids production. Co-supervision with Simão Soares, SilicoLife.
Orientador
 MSc in Bioinformatics (Mestrado)
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
Orientador
 PhD in Bioengineering (MIT-Portugal program) (Doutoramento)
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
Coorientador
 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
Orientador
 PhD in Bioengineering (MIT-Portugal program) (Doutoramento)
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.
Coorientador
 MSc in Bioinformatics (Mestrado)
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.
Orientador de Ana Isabel Lobo Castro
 Integrated Master in Biological Engineering (Mestrado)
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.
Orientador
 Integrated Master in Biological Engineering (Mestrado)
Universidade do Minho, Portugal
2014/02 - 2014/10 Implementation of the fermentation strategies for lactic acid bacteria. Co-supervision with Nuno Faria, Biotempo, Ltd.
Orientador
 Integrated Master in Biological Engineering (Mestrado)
Universidade do Minho, Portugal
2014/02 - 2014/10 Importância do pH na carne de bovino embalada. Co-supervision with Graciete Machado, Centralcarnes, Ltd.
Orientador
 Integrated Master in Biological Engineering (Mestrado)
Universidade do Minho, Portugal
2013/12 - 2014/10 Extraction of kinetic information from literature. Co-supervision with Miguel Rocha, DI, UMinho.
Orientador
 MSc in Bioinformatics (Mestrado)
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.
Orientador
 PhD in Chemical and Biological Engineering (Doutoramento)
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.
Orientador
 PhD in Chemical and Biological Engineering (Doutoramento)
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).
Orientador
 Integrated Master in Biological Engineering (Mestrado)
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.
Orientador
 Integrated Master in Biological Engineering (Mestrado)
Universidade do Minho, Portugal
2013/02 - 2013/10 Metabolic engineering – In silico fumaric acid production. Co-supervision with Sónia Carneiro, SilicoLife, Ltd.
Orientador
 Integrated Master in Biological Engineering (Mestrado)
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.
Orientador
 Integrated Master in Biological Engineering (Mestrado)
Universidade do Minho, Portugal
2013/02 - 2013/10 Metabolic Engineering – Itaconic Acid Production in Escherichia coli. Co-supervision with Sónia Carneiro, SilicoLife, Ltd.
Orientador
 Integrated Master in Biological Engineering (Mestrado)
Universidade do Minho, Portugal
2012/12 - 2013/10 Computational tools for pathway optimization towards metabolic engineering applications. Co-supervision with Miguel Rocha, DI, UMinho.
Orientador de Filipe Alexandre Wang Liu
 MSc in Informatics (Mestrado)
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.
Orientador
 MSc in Bioinformatics (Mestrado)
Universidade do Minho, Portugal
2012/12 - 2013/10 Genome reannotation and genome-scale metabolic model reconstruction of Helicobacter pylori 26695.
Orientador
 MSc in Bioinformatics (Mestrado)
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.
Coorientador
 MSc in Bioengineering (Mestrado)
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.
Orientador
 PhD in Chemical and Biological Engineering (Doutoramento)
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.
Coorientador
 PhD in Informatics (Doutoramento)
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.
Orientador
 Integrated Master in Biological Engineering (Mestrado)
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.
Orientador
 MSc in Bioinformatics (Mestrado)
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.
Coorientador
 MSc Bioinformatics (Mestrado)
Universidade do Minho, Portugal
2008/09 - 2012/06 Extracção e Classificação de Relações Biologicamente Relevantes da Literatura Biomédica. Co-supervision with Anália Lourenço, IBB,
Orientador
 MSc in Bioinformatics (Mestrado)
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.
Coorientador
 PhD in Bioengineering (MIT-Portugal program) (Doutoramento)
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.
Coorientador
 PhD in Chemical and Biological Engineering (Doutoramento)
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.
Orientador
 Integrated Master in Biological Engineering (Mestrado)
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.
Coorientador
 MSc in Bioinformatics (Mestrado)
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.
Orientador
 MSc in Bioinformatics (Mestrado)
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.
Coorientador
 MSc in Bioinformatics (Mestrado)
Universidade do Minho, Portugal
2011/03 - 2011/06 Systems analysis of metabolic networks’ origin and evolution.
Orientador
 Integrated Master Program in Bioengineering (Mestrado)
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.
Orientador
 PhD in Chemical and Biological Engineering (Doutoramento)
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.
Orientador
 MSc in Bioinformatics (Mestrado)
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.
Coorientador
 Integrated Master in Biological Engineering (Mestrado)
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.
Coorientador
 Integrated Master in Biological Engineering (Mestrado)
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.
Coorientador
 MSc in Environmental Management Systems (Mestrado)
Universidade do Minho, Portugal
2009/02 - 2009/11 Physiological characterization of PUFA producing microorganisms. Co-supervision with Jochen Forster, Fluxome Sciences, Denmark.
Coorientador
 Integrated Master in Biological Engineering (Mestrado)
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.
Coorientador
 MSc in Informatics (Mestrado)
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.
Orientador
 MSc in Bioinformatics (Mestrado)
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.
Coorientador
 MSc in Bioinformatics (Mestrado)
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.
Coorientador
 MSc in Bioinformatics (Mestrado)
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.
Orientador
 MSc in Bioinformatics (Mestrado)
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.
Coorientador
 Integrated Master in Biological Engineering (Mestrado)
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.
Orientador
 MSc in Biotechnology (Mestrado)
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.
Coorientador
 MSc in Informatics (Mestrado)
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.
Orientador
 Integrated Master in Biological Engineering (Mestrado)
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.
Orientador
 Integrated Master in Biological Engineering (Mestrado)
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.
Coorientador
 MSc in Informatics (Mestrado)
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.
Coorientador
 MSc in Environmental Management Systems (Mestrado)
Universidade do Minho, Portugal

Júri de grau académico

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

Arbitragem científica em conferência

Nome da conferência Local da conferência
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.

Curso / Disciplina lecionado

Disciplina Curso (Tipo) Instituição / Organização
2017/10 - Atual 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)

Membro de comissão

Descrição da atividade
Tipo de participação 		Instituição / Organização
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.
Membro
2019/08 - 2019/08 MPA 2019 – Metabolic Pathway Analysis 2019, Riga, Latvia, August 2019. Member of the organizing committee.
Membro
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.
Membro
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.
Presidente / Vice-presidente
2008 - 2008 CHEMPOR 2008 - 10th International Chemical and Biological Engineering Conference, Braga, Portugal, September 4-6 2008. Member of the Organizing Committee.
Membro
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.
Membro

Outro júri / avaliação

Descrição da atividade Instituição / Organização
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.
Distinções

Outra distinção

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, Estados Unidos
1997 University of Minho Award
Universidade do Minho, Portugal
1997 Rotary Club Foundation Prize
1996 University/Industry Prize