Analysis of optimality in natural and perturbed metabolic networks
An important goal of whole-cell computational modeling is to integrate detailed biochemical
information with biological intuition to produce testable predictions. Based on the premise …
information with biological intuition to produce testable predictions. Based on the premise …
Finding elementary flux modes in metabolic networks based on flux balance analysis and flux coupling analysis: application to the analysis of Escherichia coli …
S Tabe-Bordbar, SA Marashi - Biotechnology letters, 2013 - Springer
Elementary modes (EMs) are steady-state metabolic flux vectors with minimal set of active
reactions. Each EM corresponds to a metabolic pathway. Therefore, studying EMs is helpful …
reactions. Each EM corresponds to a metabolic pathway. Therefore, studying EMs is helpful …
Comparing methods for metabolic network analysis and an application to metabolic engineering
Bioinformatics tools have facilitated the reconstruction and analysis of cellular metabolism of
various organisms based on information encoded in their genomes. Characterization of …
various organisms based on information encoded in their genomes. Characterization of …
Modeling the Contribution of Allosteric Regulation for Flux Control in the Central Carbon Metabolism of E. coli
Modeling cellular metabolism is fundamental for many biotechnological applications,
including drug discovery and rational cell factory design. Central carbon metabolism (CCM) …
including drug discovery and rational cell factory design. Central carbon metabolism (CCM) …
Use of randomized sampling for analysis of metabolic networks
J Schellenberger, BØ Palsson - Journal of biological chemistry, 2009 - ASBMB
Genome-scale metabolic network reconstructions in microorganisms have been formulated
and studied for about 8 years. The constraint-based approach has shown great promise in …
and studied for about 8 years. The constraint-based approach has shown great promise in …
CASOP GS: Computing intervention strategies targeted at production improvement in genome-scale metabolic networks
Metabolic engineering aims to improve the production of desired biochemicals and proteins
in organisms and therefore, plays a central role in Biotechnology. However, the design of …
in organisms and therefore, plays a central role in Biotechnology. However, the design of …
Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems
The elucidation of organism‐scale metabolic networks necessitates the development of
integrative methods to analyze and interpret the systemic properties of cellular metabolism …
integrative methods to analyze and interpret the systemic properties of cellular metabolism …
The activity reaction core and plasticity of metabolic networks
Understanding the system-level adaptive changes taking place in an organism in response
to variations in the environment is a key issue of contemporary biology. Current modeling …
to variations in the environment is a key issue of contemporary biology. Current modeling …
Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets
D Hartleb, F Jarre, MJ Lercher - PLoS computational biology, 2016 - journals.plos.org
Constraint-based metabolic modeling methods such as Flux Balance Analysis (FBA) are
routinely used to predict the effects of genetic changes and to design strains with desired …
routinely used to predict the effects of genetic changes and to design strains with desired …
EColiCore2: a reference network model of the central metabolism of Escherichia coli and relationships to its genome-scale parent model
Genome-scale metabolic modeling has become an invaluable tool to analyze properties
and capabilities of metabolic networks and has been particularly successful for the model …
and capabilities of metabolic networks and has been particularly successful for the model …