(Q37787963)

23 August 2017

Genome-scale metabolic networks (English)

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23 August 2017

Marco Terzer

1

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23 August 2017

Nathaniel D Maynard

series ordinal

2

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23 August 2017

Markus W Covert

series ordinal

3

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23 August 2017

Jörg Stelling

series ordinal

4

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23 August 2017

1 November 2009

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Wiley interdisciplinary reviews. Systems biology and medicine

23 August 2017

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23 August 2017

1

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23 August 2017

285-297

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23 August 2017

3

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Genome-scale models of microbial cells: evaluating the consequences of constraints

23 August 2017

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Design and application of genome-scale reconstructed metabolic models.

21 January 2018

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Linking data to models: data regression

21 January 2018

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Metabolic modeling of microbial strains in silico.

21 January 2018

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UniProt: the Universal Protein knowledgebase

21 January 2018

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BRENDA, enzyme data and metabolic information

21 January 2018

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Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

21 January 2018

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KEGG: Kyoto Encyclopedia of Genes and Genomes

21 January 2018

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The ENZYME database in 2000

21 January 2018

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13C metabolic flux analysis

21 January 2018

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Towards multidimensional genome annotation

21 January 2018

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A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information

21 January 2018

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Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling

21 January 2018

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A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

21 January 2018

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Thirteen years of building constraint-based in silico models of Escherichia coli

21 January 2018

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The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

21 January 2018

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Cleaning up with genomics: applying molecular biology to bioremediation

21 January 2018

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Geobacter sulfurreducens strain engineered for increased rates of respiration

21 January 2018

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Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae

21 January 2018

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Metabolic functions of duplicate genes in Saccharomyces cerevisiae

21 January 2018

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MetaCyc: a multiorganism database of metabolic pathways and enzymes

21 January 2018

1 reference

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

21 January 2018

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Conservation analysis in biochemical networks: computational issues for software writers

21 January 2018

1 reference

The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools

21 January 2018

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Co-regulation of metabolic genes is better explained by flux coupling than by network distance

21 January 2018

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Flux coupling analysis of genome-scale metabolic network reconstructions.

21 January 2018

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The effects of alternate optimal solutions in constraint-based genome-scale metabolic models

21 January 2018

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Detection of stoichiometric inconsistencies in biomolecular models.

21 January 2018

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Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli

21 January 2018

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Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism

21 January 2018

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Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism

21 January 2018

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Effect of Escherichia coli biomass composition on central metabolic fluxes predicted by a stoichiometric model

21 January 2018

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In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data

21 January 2018

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Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth

21 January 2018

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Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states

21 January 2018

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Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes

21 January 2018

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A MILP-based flux alternative generation and NMR experimental design strategy for metabolic engineering.

21 January 2018

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Conservation of expression and sequence of metabolic genes is reflected by activity across metabolic states

21 January 2018

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Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli.

21 January 2018

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Dynamic flux balance analysis of diauxic growth in Escherichia coli

21 January 2018

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Something from nothing: bridging the gap between constraint-based and kinetic modelling.

21 January 2018

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Hybrid dynamic/static method for large-scale simulation of metabolism

21 January 2018

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The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities

21 January 2018

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Analysis of optimality in natural and perturbed metabolic networks

21 January 2018

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Regulatory on/off minimization of metabolic flux changes after genetic perturbations

21 January 2018

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Computation of elementary modes: a unifying framework and the new binary approach

21 January 2018

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Large-scale computation of elementary flux modes with bit pattern trees

21 January 2018

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Two approaches for metabolic pathway analysis?

21 January 2018

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The geometry of the flux cone of a metabolic network

21 January 2018

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Combinatorial complexity of pathway analysis in metabolic networks.

21 January 2018

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Reconstructing metabolic flux vectors from extreme pathways: defining the alpha-spectrum

21 January 2018

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Metabolic network structure determines key aspects of functionality and regulation

21 January 2018

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Minimal cut sets in biochemical reaction networks.

21 January 2018

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Generalized concept of minimal cut sets in biochemical networks.

21 January 2018

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Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization

21 January 2018

1 reference

The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis

21 January 2018

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Regulation of gene expression in flux balance models of metabolism

21 January 2018

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Constraints-based models: regulation of gene expression reduces the steady-state solution space

21 January 2018

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Integrating high-throughput and computational data elucidates bacterial networks

21 January 2018

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Transcriptional regulation in constraints-based metabolic models of Escherichia coli

21 January 2018

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Integration of gene expression data into genome-scale metabolic models

21 January 2018

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A predictive model for transcriptional control of physiology in a free living cell.

21 January 2018

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The Pathway Tools software

21 January 2018

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The KEGG databases at GenomeNet

21 January 2018

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PUMA2--grid-based high-throughput analysis of genomes and metabolic pathways

21 January 2018

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Genome-scale microbial in silico models: the constraints-based approach.

21 January 2018

1 reference

Correcting ligands, metabolites, and pathways

21 January 2018

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Metabolic networks are NP-hard to reconstruct

21 January 2018

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Systems approach to refining genome annotation

21 January 2018

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Toward the automated generation of genome-scale metabolic networks in the SEED.

21 January 2018

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GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes

21 January 2018

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Identifying metabolic enzymes with multiple types of association evidence

21 January 2018

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Filling gaps in a metabolic network using expression information.

21 January 2018

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Optimization based automated curation of metabolic reconstructions

21 January 2018

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Hierarchical structure and the prediction of missing links in networks

21 January 2018

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Optimization-based framework for inferring and testing hypothesized metabolic objective functions.

21 January 2018

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Predicting biological system objectives de novo from internal state measurements

21 January 2018

1 reference

OptStrain: a computational framework for redesign of microbial production systems.

21 January 2018

1 reference

Evolutionary programming as a platform for in silico metabolic engineering

21 January 2018

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Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation

21 January 2018

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Integrating cybernetic modeling with pathway analysis provides a dynamic, systems-level description of metabolic control

21 January 2018

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Formulating genome-scale kinetic models in the post-genome era.

21 January 2018

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Analysis of global control of Escherichia coli carbohydrate uptake

21 January 2018

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Dynamic analysis of integrated signaling, metabolic, and regulatory networks

21 January 2018

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Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data

21 January 2018

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Bringing metabolic networks to life: convenience rate law and thermodynamic constraints

21 January 2018

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Ensemble modeling of metabolic networks

21 January 2018

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Understanding bistability in complex enzyme-driven reaction networks

21 January 2018

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Subnetwork analysis reveals dynamic features of complex (bio)chemical networks

21 January 2018

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Conservation analysis of large biochemical networks.

21 January 2018

1 reference

21 January 2018

Identifiers

DOI

10.1002/WSBM.37

1 reference

23 August 2017

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