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Analyzing and Designing Cell Factories with OptFlux

author

Isabel Rocha

Miguel Rocha

published in: Methods in Molecular Biology

date of publication: 2018-01-01

language: English

Cites articles 68

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2016-01-04

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

Andreas Dräger, Joshua A. Lerman, Ali Ebrahim, Nathan E. Lewis
2016-03

In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories

Paulo Maia, Isabel Rocha, Miguel Rocha
2015-04-06

Reconstructing genome-scale metabolic models with merlin

Oscar Dias, Eugénio C. Ferreira, Isabel Rocha, Miguel Rocha
2015-08-27

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

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2014-05-01

Optimizing genome-scale network reconstructions.

Bernhard Palsson
2014-12-30

An integrated network visualization framework towards metabolic engineering applications

Miguel Rocha
2013-03-27

Metabolic engineering: past and future
2013-06-26

Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks

Steffen Klamt
2013-11-18

Software platforms to facilitate reconstructing genome-scale metabolic networks

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The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum

Jens Nielsen, Saeed Shoaie, Intawat Nookaew, Rasmus Agren, Wanwipa Vongsangnak
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A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes

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2013-10-03

An objective function exploiting suboptimal solutions in metabolic networks

Pamela Silver
2013-06

An integrated framework for strain optimization

Paulo Maia, Isabel Rocha, Miguel Rocha
2012-11-01

Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks

Sergej Andrejev, Ana Rita Brochado, Kiran R Patil, Costas D. Maranas
2012-02-01

Optimization approaches for the in silico discovery of optimal targets for gene over/underexpression.

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2010-01

A protocol for generating a high-quality genome-scale metabolic reconstruction

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2010-09

High-throughput generation, optimization and analysis of genome-scale metabolic models
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Pedro Mendes, Evangelos Simeonidis, Kieran Smallbone, Neil Swainston
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OptFlux: an open-source software platform for in silico metabolic engineering

Kiran R Patil, Isabel Rocha, Eugénio C. Ferreira, Jens Nielsen, Pedro Evangelista, Paulo Maia, Miguel Rocha
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AIBench: a rapid application development framework for translational research in biomedicine

Paulo Maia, Miguel Reboiro-Jato, Daniel Glez-Peña, Miguel Rocha, Florentino Fdez-Riverola
2010-04-29

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What is flux balance analysis?

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2010-04-27

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2010-07-01

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

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2010-01-01

Metabolic engineering of Escherichia coli for the production of polylactic acid and its copolymers

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2009-08

The Systems Biology Graphical Notation
2008-01-01

Design and application of genome-scale reconstructed metabolic models.

Isabel Rocha, Jens Nielsen
2008-02-05

LibSBML: an API library for SBML.

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2008-04-01

A strategy to calculate the patterns of nutrient consumption by microorganisms applying a two-level optimisation principle to reconstructed metabolic networks

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Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions

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Natural computation meta-heuristics for the in silico optimization of microbial strains

Jens Nielsen, Paulo Maia, Rui Mendes, Kiran R Patil, Isabel Rocha, Miguel Rocha, Eugénio C. Ferreira

Article - wd:Q47266625

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