Browsing by UMinho authors 3148

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Issue DateTitleAuthor(s)TypeAccess
21-Feb-2019The metabolic model of the Quercus suber (cork oak tree) leafDemirci, H.; Dias, Oscar; Chaves, Inês; Miguel, Célia; Rocha, Miguel, et al.AbstractOpen access
2019Modulation of the central carbon metabolism of Corynebacterium glutamicum improves malonyl-CoA availability and increases plant polyphenol synthesisMilke, Lars; Ferreira, Patrícia; Kallscheuer, Nicolai; Braga, Adelaide; Vogt, Michael, et al.ArticleOpen access
16-Nov-2018Production of mannosylglycerate in Saccharomyces cerevisiae by metabolic engineering and bioprocess optimizationFaria, Cristiana; Borges, Nuno; Rocha, I.; Santos, HelenaArticleOpen access
16-Nov-2018Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotesXavier, Joana C.; Patil, Kiran Raosaheb; Rocha, I.ArticleOpen access
10-Oct-2018Yeast chassis design for production of dicarboxylic acidsPereira, F.; Lopes, Hélder; Maia, Paulo; Meyer, B.; Konstantinidis, D., et al.AbstractOpen access
Aug-2018Heterologous production of resveratrol in bacterial hosts: currentstatus and perspectivesBraga, Adelaide; Ferreira, Patrícia; Oliveira, J.; Rocha, I.; Faria, N.ArticleOpen access
31-Jul-2018Methods for automated genome-scale metabolic model reconstructionFaria, José P.; Rocha, Miguel; Rocha, Isabel; Henry, Christopher S.ArticleRestricted access (UMinho)
24-Jun-2018Yeast chassis design for dicarboxylic acids productionPereira, Filipa; Lopes, Helder; Maia, Paulo; Meyer, Britta; Konstantinidis, Dimitrios, et al.AbstractOpen access
24-Jun-2018Development of novel genome-scale reconstruction strategies for production of terpenoids in Saccharomyces cerevisiaeDrescher, Paul; Vilaça, P.; Carreira, Rafael; Rocha, I.AbstractOpen access
30-May-2018Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130ZPereira, Bruno; Miguel, Joana; Vilaça, Paulo; Soares, Simão; Rocha, I., et al.ArticleOpen access
Apr-2018Metabolite secretion in microorganisms: the theory of metabolic overflow put to the testPinu, Farhana R.; Granucci, Ninna; Daniell, James; Han, Ting-Li; Carneiro, Sónia, et al.ArticleOpen access
29-Mar-2018Integrated metabolic flux and omics analysis of leishmania major metabolismShakyawar, S.; Rocha, I.; Carneiro, SóniaConference paperOpen access
Feb-2018Quantitative physiology and elemental composition of Kluyveromyces lactis CBS 2359 during growth on glucose at different specific growth ratesDias, Oscar; Basso, Thiago O.; Rocha, I.; Ferreira, Eugénio C.; Gombert, Andreas K.ArticleOpen access
Feb-2018Erratum to: Quantitative physiology and elemental composition of Kluyveromyces lactis CBS 2359 during growth on glucose at different specific growth ratesDias, Oscar; Basso, Thiago O.; Rocha, I.; Ferreira, Eugénio C.; Gombert, Andreas K.CorrigendumOpen access
10-Jan-2018Impact of the cultivation strategy on resveratrol production from glucose in engineered Corynebacterium glutamicumBraga, Adelaide; Oliveira, J.; Silva, Rita M.; Ferreira, Patrícia; Rocha, Isabel, et al.ArticleOpen access
7-Jan-2018Reconstructing high-quality large-scale metabolic models with merlinDias, Oscar; Rocha, Miguel; Ferreira, Eugénio C.; Rocha, IsabelBook partRestricted access (UMinho)
2018Analyzing and designing cell factories with OptFluxVilaça, Paulo Ricardo Carvalho; Maia, Paulo; Giesteira, Hugo Miguel Melo; Rocha, Isabel; Rocha, MiguelBook partRestricted access (UMinho)
2018BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruitsDudnik, Alexey; Almeida, A. Filipa; Andrade, Ricardo; Avila, Barbara; Bañados, Pilar, et al.ArticleRestricted access (UMinho)
2018An adsorptive bioprocess for production and recovery of resveratrol with Corynebacterium glutamicumBraga, Adelaide; Silva, Marcelo; Oliveira, Joana Filipa Azevedo; Silva, Rita M.; Ferreira, Patrícia, et al.ArticleOpen access
7-Dec-2017In silico design of improved cell factories - New methods and experimental validationRocha, I.AbstractOpen access
Aug-2017Genome-scale modeling of yeast: chronology, applications and critical perspectivesLopes, Hélder; Rocha, IsabelArticleOpen access
6-Jul-2017In silico metabolic engineering: from research to the marketRocha, I.AbstractOpen access
6-Jul-2017Combining high-value biotechnological processes: from wastewaters bioremediation to bacterial bioenergy feedstock productionCastro, Rita; Castro, P.; Silva, P.; Alves, M. M.; Rocha, I., et al.AbstractOpen access
6-Jul-2017Eicosapentaenoic acid (EPA) production in silico by Pythium irregulare, as value-added product, using sugarcane vinasse as carbon sourceFernandes, Bruna S.; Dias, Oscar; Zaiat, Marcelo; Pradella, José G. C.; Rocha, I.AbstractOpen access
Mar-2017Development of a framework for metabolic pathway analysis-driven strain optimization methodsVieira, Vítor; Maia, Paulo; Rocha, Isabel; Rocha, MiguelArticleOpen access
2017Genome-wide semi-automated annotation of transporter systemsDias, Oscar; Gomes, Daniel G.; Vilaça, P.; Cardoso, João; Rocha, Miguel, et al.ArticleOpen access
2017Integration of biomass formulations of genome-scale metabolic models with experimental data reveals universally essential cofactors in prokaryotesXavier, Joana Rute Calça; Patil, Kiran Raosaheb; Rocha, IsabelArticleOpen access
2017Identification of robust strain designs via tandem pFBA/LMOMA phenotype predictionMaia, Paulo; Rocha, Isabel Cristina Santos; Rocha, MiguelConference paperOpen access
Dec-2016Rhodococcus opacus B4: a promising bacterium for production of biofuels and biobased chemicalsCastro, Ana Rita; Rocha, I.; Alves, M. M.; Pereira, M. A.ArticleOpen access
Dec-2016Improving the flux distributions simulated with genome-scale metabolic models of Saccharomyces cerevisiaePereira, R.; Nielsen, Jens; Rocha, IsabelArticleOpen access
27-Nov-2016Estimation of biomass composition from genomic and transcriptomic informationSantos, Sophia; Rocha, IsabelArticleOpen access
24-Nov-2016Computing and applying atomic regulons to understand gene expression and regulationFaria, J.; Davis, James J.; Edirisinghe, Janaka N.; Taylor, Ronald C.; Weisenhorn, Pamela, et al.ArticleOpen access
Oct-2016Stoichiometric representation of geneproteinreaction associations leverages constraint-based analysis from reaction to gene-level phenotype predictionMachado, Daniel; Herrgård, Markus J.; Rocha, IsabelArticleOpen access
Oct-2016Current state and challenges for dynamic metabolic modelingVasilakou, Eleni; Machado, Daniel; Theorell, Axel; Rocha, Isabel; Nöh, Katharina, et al.ArticleOpen access
19-Jul-2016Yeast metabolic chassis designs for diverse biotechnological productsJouhten, Paula; Boruta, T.; Andrejev, S.; Pereira, Filipa; Rocha, Isabel, et al.ArticleOpen access
11-Jul-2016Towards an improved version of Kluyveromyces lactis genome-scale metabolic modelDias, Oscar; Santos, Sophia Torres; Ferreira, Eugénio C.; Rocha, I.AbstractOpen access
11-Jul-2016Predicting and modeling genotype-phenotype associations in yeast metabolic networksLopes, Hélder Moisés Gonçalves Pinheiro; Ramalho, Fábio; Rocha, I.AbstractOpen access
11-Jul-2016In silico metabolic engineering: from research to the marketRocha, I.AbstractOpen access
26-Jun-2016Rational modular design of yeast strains towards overproduction of industrially relevant productsLopes, H.; Maia, Paulo; Patil, Kiran Raosaheb; Rocha, IsabelAbstractOpen access
Jun-2016A computation tool for the estimation of biomass composition from genomic and transcriptomic informationSantos, Sophia Torres; Rocha, IsabelConference paperRestricted access (UMinho)
Jun-2016Development of an integrated framework for minimal cut set enumeration in constraint-based modelsVieira, Vítor; Maia, Paulo; Rocha, Isabel; Rocha, MiguelConference paperRestricted access (UMinho)
Mar-2016In silico constraint-based strain optimization methods: the quest for optimal cell factoriesSilva, P.; Rocha, Miguel; Rocha, I.ArticleRestricted access (UMinho)
18-Feb-2016A metabolic integrated yeast knowledgebase (MIYEASTK)Santos, Sophia; Liu, Filipe Alexandre Wang; Costa, Christopher; Vilaça, Paulo Ricardo Carvalho; Rocha, Miguel, et al.AbstractOpen access
2016A comparative analysis of dynamic models of the central carbon metabolism of Escherichia coliLima, Ana Patrícia; Baixinho, Vítor; Machado, Daniel; Rocha, IsabelArticleOpen access
2016Reconstruction of the regulatory network for Bacillus subtilis and reconciliation with gene expression dataFaria, J.; Overbeek, Ross; Taylor, Ronald C; Conrad, Neal; Vonstein, Veronika, et al.ArticleOpen access
2016A comparative proteome analysis of Escherichia coli ΔrelA mutant cellsCarneiro, S.; Villas-Bôas, Silas; Ferreira, Eugénio C.; Rocha, IsabelArticleOpen access
10-Dec-2015The effect of hydrodynamic conditions in Corynebacterium glutamicum growthOliveira, J. A.; Braga, Adelaide; Rocha, I.; Faria, Nuno Filipe MonteiroAbstractOpen access
Dec-2015Developing novel strains for butanol productionFerreira, Sofia; Pereira, Rui; Rocha, I.AbstractOpen access
Dec-2015Development of computational and experimental methods for biomass composition and evaluation of its impact in genome-scale models predictionSantos, Sophia Torres; Rocha, I.AbstractOpen access
3-Nov-2015Extracting kinetic information from literature with KineticREFreitas, Ana Alão; Costa, Hugo; Rocha, Miguel; Rocha, I.ArticleOpen access
8-Oct-2015Modeling the contribution of allosteric regulation for flux control in the central carbon metabolism of E. coliMachado, Daniel; Herrgard, Markus; Rocha, I.ArticleOpen access
18-Sep-2015Assessing the reliability of genome-scale metabolic models in the prediction of gene knockout phenotypesLopes, H.; Maia, Paulo; Patil, Kiran; Rocha, I.AbstractOpen access
18-Sep-2015Reconstruction of regulatory network models and reconciliation with gene expression dataFaria, J. P.; Overbeek, Ross; Taylor, Ronald C.; Conrad, Neal; Vonstein, Veronika, et al.AbstractOpen access
18-Sep-2015Comparing knockout strategies from in silico rational strain design toolsVieira, José Vítor Castro; Maia, Paulo; Rocha, Miguel; Rocha, I.AbstractOpen access
17-Sep-2015Universally essential cofactors in prokaryotesXavier, Joana Rute Calça; Patil, Kiran; Rocha, I.AbstractOpen access
16-Sep-2015Reconciling experimental data with in silico predictions in metabolic engineering applicationsRocha, I.AbstractOpen access
16-Sep-2015Integrating kinetic and constraint-based models of metabolismMachado, D.; Lima, Patrícia; Rocha, I.AbstractOpen access
16-Sep-2015Towards a genome-scale metabolic model of the Streptococcus pneumoniae R6 avirulent strainDias, Oscar; Saraiva, João; Ferreira, Eugénio C.; Rocha, I.AbstractOpen access
Sep-2015Salmonella typhimurium and Escherichia coli dissimilarity: closely related bacteria with distinct metabolic profilesSargo, Cíntia R .; Campani, Gilson; Silva, Gabriel G.; Giordano, Roberto C.; Silva, Adilson J. da, et al.ArticleOpen access
Sep-2015Produção e consumo de acetato em cultivos de Salmonella typhimurium em condições aeróbiasSargo, Cíntia R .; Silva, Adilson J.; Giordano, Roberto C; Ferreira, Eugénio C.; Rocha, I., et al.Conference paperOpen access
21-Jun-2015In silico design of Saccharomyces cerevisiae strains for production of industrial compounds derived from TCA cycleLopes, H.; Silva, P.; Patil, Kiran R.; Rocha, I.AbstractOpen access
12-Jun-2015Transcriptional vs post-transcriptional regulation of the central carbon metabolism of E. coliMachado, C. D.; Rocha, I.; Herrgård, MarkusAbstractOpen access
8-Jun-2015Reconciling gene expression data with regulatory network modelsFaria, José P.; Overbeek, Ross; Taylor, Ronald C.; Goelzer, Anne; Fromion, Vincent, et al.AbstractOpen access
8-Jun-2015Merlin latest developments for pathways analysisDias, Oscar; Rocha, Miguel; Ferreira, E. C.; Rocha, I.AbstractOpen access
8-Jun-2015Enhancing the production of mannosylglycerate in s. cerevisiae through in silico driven metabolic engineeringFaria, Cristiana; Borges, Nuno; Rocha, I.; Santos, HelenaAbstractOpen access
8-Jun-2015Analysis of Salmonella typhimurium pathways and metabolic model improvementSargo, Cíntia R .; Correia, Daniela M.; Giordano, R. C.; Ferreira, E. C.; Rocha, I., et al.AbstractOpen access
8-Jun-2015Reconstruction and validation of iTR383, a genome-scale metabolic model for Helicobacter pylori 26695Resende, Tiago; Correia, Daniela M.; Santos, Sophia Torres; Rocha, I.AbstractOpen access
8-Jun-2015TDPS - Turnover dependent phenotypic simulation: a quantitative constraint-based simulation method that accommodates all main strain design strategiesPereira, R. M.; Vilaça, Paulo; Nielsen, Jens; Rocha, I.AbstractOpen access
8-Jun-2015Analysis of 140 published GSMs and identification of the most common representation problemsVilaça, P.; Cardoso, João; Rocha, I.; Rocha, MiguelAbstractOpen access
Jun-2015Integration of biomass functions of genome-scale metabolic models with experimental data reveals universally essential cofactors in prokaryotesXavier, Joana Rute Calça; Patil, Kiran; Rocha, I.AbstractOpen access
Jun-2015Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenesCarneiro, Sónia; Miguel, Joana; Carreira, Rafael; Vilaça, Paulo Ricardo Carvalho; Rocha, I.AbstractOpen access
Jun-2015Visualizing omics data in the OptFlux workbenchMaia, Paulo; Vilaça, Paulo; Rocha, I.; Rocha, MiguelAbstractOpen access
Jun-2015Uncovering the metabolic capacities of H. pylori 26695 using 13C labeling experimentsCorreia, Daniela M.; Carreira, Rafael; Azevedo, Nuno Filipe; Rocha, I.AbstractOpen access
17-May-2015Metabolic models reconstruction using genome scale information (merlin): assessment and validationDias, Oscar; Rocha, Miguel; Ferreira, E. C.; Rocha, I.AbstractOpen access
17-May-2015Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenesCarneiro, S.; Miguel, J.; Carreira, R.; Vilaça, P.; Rocha, I.AbstractOpen access
11-May-2015Modelling allosteric regulation for prediction of flux control in the central carbon metabolism of E. coliMachado, C. D.; Herrgård, Markus; Rocha, I.AbstractOpen access
9-Apr-2015A text mining approach for the extraction of kinetic information from literatureFreitas, Ana A.; Costa, Hugo; Rocha, Miguel; Rocha, I.AbstractOpen access
9-Apr-2015Reconstruction and validation of a genome-scale metabolic model for Helicobacter pylori 26695Resende, Tiago; Correia, Daniela M.; Santos, Sophia; Rocha, I.AbstractOpen access
Feb-2015Development and application of efficient pathway enumeration algorithms for metabolic engineering applicationsLiu, Filipe; Vilaça, Paulo; Rocha, I.; Rocha, MiguelArticleOpen access
2015In silico modular design of Saccharomyces cerevisiae strains for enhanced production of organic acidsLopes, H.; Maia, Paulo; Patil, Kiran R.; Rocha, I.AbstractOpen access
2015A text mining approach for the extraction of kinetic information from literatureFreitas, Ana A.; Costa, Hugo; Rocha, Miguel; Rocha, I.Conference paperRestricted access (UMinho)
2015Reconstructing genome-scale metabolic models with merlinDias, Oscar; Rocha, Miguel; Ferreira, E. C.; Rocha, I.ArticleOpen access
Jul-2014Dietary sugars analysis : quantification of fructooligossacharides during fermentation by HPLC-RI methodCorreia, Daniela M.; Dias, Luís G.; Veloso, Ana C. A.; Dias, T.; Rocha, I., et al.ArticleOpen access
15-Jun-2014Flexible and user friendly tools for the incorporation of fluxomics data into metabolic modelsCarreira, Rafael; Pont, M.; Villas-Bôas, S. G.; Rocha, Miguel; Rocha, I.AbstractOpen access
8-Apr-2014Reconciling gene expression data with regulatory network models – a stimulon-based approach for integrated metabolic and regulatory modeling of Bacillus subtilisFaria, José P.; Overbeek, Ross; Taylor, Ronald C.; Goelzer, Anne; Fromion, Vincent, et al.AbstractOpen access
26-Mar-2014Yeast metabolomics : sample preparation for a GC/MS-based analysisCarneiro, S.; Pereira, R. M.; Rocha, I.Book partRestricted access (UMinho)
1-Jan-2014What is the relationship between intracellular and extracellular metabolites? The theory of "metabolic overflow" put into testVillas-Boas, S.; Han, Ting-Li; Liu, Tim; Kim, Sang; Carneiro, S., et al.AbstractOpen access
2014Vascular cells derived from Hutchinson-Gilford progeria syndrome (HGPS) inducible pluripotent stem cellsPitrez, Patricia R.; Vazão, Helena; Nissan, Xavier; Ferreira, Lino; Rocha, I.AbstractOpen access
2014Prediction of protein subunits using KEGG BRITEDias, Oscar; Liu, Filipe; Rocha, Miguel; Ferreira, E. C.; Rocha, I.AbstractOpen access
2014Improving the internal flux distributions from genome scale metabolic models of S. cerevisiaePereira, R. M.; Nielsen, Jens; Rocha, I.AbstractOpen access
2014Standardization and comparison of the biomass objective functions of manually curated genome-scale metabolic modelsXavier, Joana Rute Calça; Patil, Kiran Raosaheb; Rocha, I.AbstractOpen access
2014Modeling the contribution of allosteric regulation for flux control in the central carbon metabolism of E. coliMachado, C. D.; Herrgård, Markus; Rocha, I.AbstractOpen access
2014On the effects of phenotype prediction methods over strain design algorithms. A multi-objective approachMaia, Paulo; Rocha, Miguel; Rocha, I.AbstractOpen access
2014Optimization of fed-batch fermentation processes with bio-inspired algorithmsRocha, Miguel; Mendes, Rui; Rocha, Orlando; Rocha, I.; Ferreira, E. C.ArticleOpen access
2014CBFA : phenotype prediction integrating metabolic models with constraints derived from experimental dataCarreira, Rafael; Evangelista, Pedro; Maia, Paulo; Vilaça, Paulo; Pont, M., et al.ArticleOpen access
2014Evaluating pathway enumeration algorithms in metabolic engineering case studiesLiu, Filipe; Vilaça, Paulo; Rocha, I.; Rocha, MiguelConference paperOpen access
2014Systems biology perspectives on minimal and simpler cellsXavier, Joana Rute Calça; Patil, Kiran Raosaheb; Rocha, I.ArticleRestricted access (UMinho)
2014Visualization plugin for Optflux: tools for the creation of metabolic layouts and analysis of flux distributionsVilaça, Paulo Ricardo Carvalho; Noronha, Alberto Miguel Silva; Rocha, I.; Rocha, MiguelAbstractOpen access
2014iOD907, the first genome-scale metabolic model for the milk yeast Kluyveromyces lactisDias, Oscar; Pereira, R. M.; Gombert, Andreas Karoly; Ferreira, E. C.; Rocha, I.ArticleOpen access
2014Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic modelsFaria, J. P.; Overbeek, R.; Xia, F.; Rocha, Miguel; Rocha, I., et al.ArticleOpen access