19 documents found, page 1 of 2
Development of an integrated metabolic and transcriptional regulatory model for...
Drescher, Paul; Carreira, Rafael Castro; Vilaça, Paulo; Rocha, Isabel Cristina SantosSaccharomyces cerevisiae (S. cerevisiae) is commonly used as a cell factory for research and industrial applications. The development of optimization strategies for S. cerevisiae was extensively driven by the establishment of genome-scale metabolic models. Additionally, to aid metabolic modeling, multiple attempts to infer transcriptional regulatory networks from expression data have been made. However, these d...
Reconstruction of a genome-scale metabolic model for Actinobacillus succinogene...
Pereira, Bruno; Miguel, Joana; Vilaça, Paulo; Soares, Simão; Rocha, I.; Carneiro, SóniaBackground Actinobacillus succinogenes is a promising bacterial catalyst for the bioproduction of succinic acid from low-cost raw materials. In this work, a genome-scale metabolic model was reconstructed and used to assess the metabolic capabilities of this microorganism under producing conditions. Results The model, iBP722, was reconstructed based on the functional reannotation of the complete genome sequence ...
Visualizing omics data in the OptFlux workbench
Maia, Paulo; Vilaça, Paulo; Rocha, I.; Rocha, MiguelOptFlux is an open-source and extensible workbench for Metabolic Engineering (ME) tasks. Since 2012, OptFlux adoption has been steadily increasing among users, making it one of the reference go-to platforms among the ME community. The workbench supports common ME tasks such as phenotype prediction for both wild-type and mutant genotypes, metabolic control analysis and pathway analysis as well as strain optimiza...
Development and application of efficient pathway enumeration algorithms for met...
Liu, Filipe; Vilaça, Paulo; Rocha, I.; Rocha, MiguelMetabolic Engineering (ME) aims to design microbial cell factories towards the production of valuable compounds. In this endeavor, one important task relates to the search for the most suitable heterologous pathway(s) to add to the selected host. Different algorithms have been developed in the past towards this goal, following distinct approaches spanning constraint-based modelling, graph-based methods and know...
TDPS - Turnover dependent phenotypic simulation: a quantitative constraint-base...
Pereira, R. M.; Vilaça, Paulo; Nielsen, Jens; Rocha, I.Constraint-based modelling methodologies can expedite the strain engineering process by helping in the search for interesting genetic modification targets. Although the search for gene knock-outs is fairly established with in silico methodologies, most computational strain design methods still model gene up/down-regulations by forcing the corresponding flux values to pre-calculated levels without considering th...
Reg4OptFlux: an OptFlux plug-in that comprises meta-heuristics approaches for m...
Rocha, Orlando; Vilaça, Paulo; Rocha, Miguel; Mendes, RuiMetabolic engineering (ME) strategies have been implemented over the last few years, in order to improve microbial strains of interest in industrial biotechnology. With the advent of experimental data concerning to regulatory aspects, several efforts have been conducted to incorporate this information in genome-scale metabolic models, aiming at the improvement of phenotype simulation methods. However, most of t...
CBFA: phenotype prediction integrating metabolic models with constraints derive...
Carreira, Rafael; Evangelista, Pedro; Maia, Paulo; Vilaça, Paulo; Pont, M.; Tomb, J. F.; Rocha, I.; Rocha, MiguelBackground Flux analysis methods lie at the core of Metabolic Engineering (ME), providing methods for phenotype simulation that allow the determination of flux distributions under different conditions. Although many constraint-based modeling software tools have been developed and published, none provides a free user-friendly application that makes available the full portfolio of flux analysis methods. Results T...
An integrated network visualization framework towards metabolic engineering app...
Noronha, Alberto; Vilaça, Paulo; Rocha, MiguelBackground Over the last years, several methods for the phenotype simulation of microorganisms, under specified genetic and environmental conditions have been proposed, in the context of Metabolic Engineering (ME). These methods provided insight on the functioning of microbial metabolism and played a key role in the design of genetic modifications that can lead to strains of industrial interest. On the other ha...
Evaluating pathway enumeration algorithms in metabolic engineering case studies
Liu, Filipe; Vilaça, Paulo; Rocha, I.; Rocha, MiguelThe design of cell factories for the production of compounds involves the search for suitable heterologous pathways. Different strategies have been proposed to infer such pathways, but most are optimization approaches with specific objective functions, not suited to enumerate multiple pathways. In this work, we analyze two pathway enumeration algorithms based on graph representations: the Solution Structure Gen...
OptFlux3: an improved platform for in silico design of cellular factories
Rocha, I.; Vilaça, Paulo; Maia, P.; Soares, Simão; Rocha, MiguelThe rational design of cellular factories for industrial biotechnology aims to create optimized organisms for the production of bulk chemicals, pharmaceuticals, food ingredients and enzymes, among others. Metabolic engineering (ME) plays a key role in this process, supported by the latest advances in genetic engineering in combination with computational tools to define targets for strain improvement. OptFlux is...