publicações selecionadas
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artigo de conferência
- Identification of robust strain designs via tandem pFBA/LMOMA phenotype prediction 2017
- Savings in internal logistics using a RFID-based software system in a lean context 2017
- Savings in internal logistics using a RFID-based software system in a lean context 2017
- Development of an integrated framework for minimal cut set enumeration in constraint-based models. AI Communications. 2016
- An integrated framework for strain optimization 2013
- A study on the robustness of strain optimization algorithms 2011
- Enhancing Elementary Flux Modes analysis using filtering techniques in an integrated environment 2010
- Metaheuristics for strain optimization using transcriptional information enriched metabolic models. Computational Methods in Applied Sciences. 2010
- OptFlux: an open-source software platform for in silico metabolic engineering 2010
- Implementing metaheuristic optimization algorithms with JECoLi. International Conference on Intelligent Systems Design and Applications. 2009
- Optferm-a computational platform for the optimization of fermentation processes 2009
- A framework for the development of biomedical text mining software tools. IEEE International Conference on Bioinformatics and Bioengineering. 2008
- Evaluating evolutionary multiobjective algorithms for the in silico optimization of mutant strains. IEEE International Conference on Bioinformatics and Bioengineering. 2008
- The @Note biomedical text mining workbench 2008
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artigo de revista
- Model-guided development of an evolutionarily stable yeast chassis. Molecular Systems Biology. 2021
- Comparison of pathway analysis and constraint-based methods for cell factory design. BMC Bioinformatics. 2019
- Application of agent-based modelling to assess single-molecule transport across the cell envelope of E. coli. Computers in Biology and Medicine. 2019
- Turnover dependent phenotypic simulation: a quantitative constraint-based simulation method that accommodates all main strain design strategies. ACS Synthetic Biology. 2019
- A Review of Dynamic Modeling Approaches and Their Application in Computational Strain Optimization for Metabolic Engineering. Antibiotics. 2018
- Development of a Framework for Metabolic Pathway Analysis-Driven Strain Optimization Methods. Interdisciplinary Sciences-Computational Life Sciences. 2017
- PRESENCE OF ABNORMAL FINDINGS WITHIN SPORTS PRE-PARTICIPATION CARDIOVASCULAR SCREENING. British Journal of Sports Medicine. 2017
- CBFA: Phenotype prediction integrating metabolic models with constraints derived from experimental data. BMC Systems Biology. 2014
- OptFlux: An open-source software platform for in silico metabolic engineering. BMC Systems Biology. 2010
- @Note: A workbench for Biomedical Text Mining. Journal of Biomedical Informatics. 2009
- Natural computation meta-heuristics for the in silico optimization of microbial strains. BMC Bioinformatics. 2008
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capítulo de livro
- Analyzing and designing cell factories with OptFlux. Methods in Molecular Biology. 2018
- Evaluating Simulated Annealing Algorithms in the Optimization of Bacterial Strains. Computational Methods in Applied Sciences. 2007
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documento
- Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology. 2020
- MEMOTE for standardized genome-scale metabolic model testing. Nature Biotechnology. 2020
- Yeast chassis design for production of dicarboxylic acids. New Biotechnology. 2018
- Yeast chassis design for dicarboxylic acids production 2018
- Rational modular design of yeast strains towards overproduction of industrially relevant products 2016
- Development of pathway analysis based algorithms for strain optimization 2016
- Assessing the reliability of genome-scale metabolic models in the prediction of gene knockout phenotypes 2015
- Comparing knockout strategies from in silico rational strain design tools 2015
- Visualizing omics data in the OptFlux workbench 2015
- In silico modular design of Saccharomyces cerevisiae strains for enhanced production of organic acids 2015
- On the effects of phenotype prediction methods over strain design algorithms. A multi-objective approach 2014
- A generic multi-criterion approach for mutant strain optimization 2012
- OPTFERM - a computational platform for the optimization of fermentation processes 2012
- Optflux: an open-source software platform for in silico metabolic engineering 2010
- A study on the effects of using gene-reaction rules on in silico strain optimization 2009
- Multi-criterion approaches for the in silico optimization of mutant microorganisms 2009
- OptFlux: a software for metabolic engineering 2009
- OptGene: a framework for in silico metabolic engineering 2008
- Evolutionary multiobjective algorithms for in silico metabolic engineering 2008
- The @Note biomedical text mining workbench 2008
- Constraint-based approach for in silico Escherichia coli combined regulatory/metabolic modelling 2007
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livro
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poster de conferência
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teses