Constraint-based models predict metabolic and associated cellular functions. (Q38178893)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24430943%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

title

Constraint-based models predict metabolic and associated cellular functions (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24430943%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24430943%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

Zachary King

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24430943%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

4

Bernhard O Palsson

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24430943%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

author name string

Aarash Bordbar

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24430943%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

publication date

16 January 2014

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24430943%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

published in

Nature Reviews Genetics

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24430943%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

volume

15

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24430943%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

issue

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24430943%20AND%20SRC:MED&resulttype=core&format=json

5 March 2020

page(s)

107-120

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24430943%20AND%20SRC:MED&resulttype=core&format=json

Reconstruction of biochemical networks in microorganisms

5 March 2020

cites work

1 reference

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

31 March 2020

1 reference

Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods

31 March 2020

1 reference

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

31 March 2020

1 reference

Environments that induce synthetic microbial ecosystems

31 March 2020

1 reference

A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology

31 March 2020

1 reference

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

31 March 2020

1 reference

Large-scale in silico modeling of metabolic interactions between cell types in the human brain

31 March 2020

1 reference

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

31 March 2020

1 reference

Identification of potential pathway mediation targets in Toll-like receptor signaling

31 March 2020

1 reference

Functional states of the genome-scale Escherichia coli transcriptional regulatory system

31 March 2020

1 reference

Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization

31 March 2020

1 reference

Fat synthesis in adipose tissue. An examination of stoichiometric constraints

31 March 2020

1 reference

Simple constrained-optimization view of acetate overflow in E. coli.

31 March 2020

1 reference

Optimal selection of metabolic fluxes for in vivo measurement. II. Application to Escherichia coli and hybridoma cell metabolism

31 March 2020

1 reference

ON ELEMENTARY FLUX MODES IN BIOCHEMICAL REACTION SYSTEMS AT STEADY STATE

31 March 2020

1 reference

Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective

31 March 2020

1 reference

Pathway alignment: application to the comparative analysis of glycolytic enzymes

31 March 2020

1 reference

Pathway analysis, engineering, and physiological considerations for redirecting central metabolism.

31 March 2020

1 reference

Whole-genome random sequencing and assembly of Haemophilus influenzae Rd

31 March 2020

1 reference

Systems properties of the Haemophilus influenzae Rd metabolic genotype

31 March 2020

1 reference

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

31 March 2020

1 reference

Analysis of optimality in natural and perturbed metabolic networks

31 March 2020

1 reference

Metabolic network structure determines key aspects of functionality and regulation

31 March 2020

1 reference

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

31 March 2020

1 reference

Global organization of metabolic fluxes in the bacterium Escherichia coli

31 March 2020

1 reference

Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast

31 March 2020

1 reference

Adaptive evolution of bacterial metabolic networks by horizontal gene transfer.

31 March 2020

1 reference

Analysis of omics data with genome-scale models of metabolism

31 March 2020

1 reference

Uncovering transcriptional regulation of metabolism by using metabolic network topology

31 March 2020

1 reference

Expression dynamics of a cellular metabolic network

31 March 2020

1 reference

Network-based prediction of human tissue-specific metabolism

31 March 2020

1 reference

Context-specific metabolic networks are consistent with experiments

31 March 2020

1 reference

Fundamental Escherichia coli biochemical pathways for biomass and energy production: creation of overall flux states

31 March 2020

1 reference

Fundamental Escherichia coli biochemical pathways for biomass and energy production: identification of reactions

31 March 2020

1 reference

The ability of flux balance analysis to predict evolution of central metabolism scales with the initial distance to the optimum

31 March 2020

1 reference

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

31 March 2020

1 reference

Shifts in growth strategies reflect tradeoffs in cellular economics

31 March 2020

1 reference

Multidimensional optimality of microbial metabolism

31 March 2020

1 reference

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

31 March 2020

1 reference

Enzyme promiscuity: a mechanistic and evolutionary perspective

31 March 2020

1 reference

Network context and selection in the evolution to enzyme specificity.

31 March 2020

1 reference

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

31 March 2020

1 reference

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection

31 March 2020

1 reference

BRENDA, the enzyme information system in 2011

31 March 2020

1 reference

Integrative genomic analysis identifies isoleucine and CodY as regulators of Listeria monocytogenes virulence

31 March 2020

1 reference

The genetic landscape of a cell

31 March 2020

1 reference

A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae

31 March 2020

1 reference

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

31 March 2020

1 reference

Modular epistasis in yeast metabolism.

31 March 2020

1 reference

Plasticity of genetic interactions in metabolic networks of yeast

31 March 2020

1 reference

Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks

31 March 2020

1 reference

An integrated approach to characterize genetic interaction networks in yeast metabolism

31 March 2020

1 reference

Connecting extracellular metabolomic measurements to intracellular flux states in yeast

31 March 2020

1 reference

Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs.

31 March 2020

1 reference

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

31 March 2020

1 reference

Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns

31 March 2020

1 reference

Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata

31 March 2020

1 reference

Systematizing the generation of missing metabolic knowledge

31 March 2020

1 reference

Systems approach to refining genome annotation

31 March 2020

1 reference

Global reconstruction of the human metabolic network based on genomic and bibliomic data

31 March 2020

1 reference

Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity

31 March 2020

1 reference

KEGG for integration and interpretation of large-scale molecular data sets

31 March 2020

1 reference

Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism.

31 March 2020

1 reference

Systems biotechnology for strain improvement

31 March 2020

1 reference

Towards systems metabolic engineering of microorganisms for amino acid production

31 March 2020

1 reference

Economic and environmental impacts of microbial biodiesel

31 March 2020

1 reference

Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol

31 March 2020

1 reference

Exploring the diversity of complex metabolic networks.

31 March 2020

1 reference

New group contribution method for estimating properties of pure compounds

31 March 2020

1 reference

Ten years of pathway analysis: current approaches and outstanding challenges

31 March 2020

1 reference

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

31 March 2020

1 reference

Metabolically re-modeling the drug pipeline

31 March 2020

1 reference

Cancer cell metabolism: Warburg and beyond

31 March 2020

1 reference

Predicting selective drug targets in cancer through metabolic networks.

31 March 2020

1 reference

Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase

31 March 2020

1 reference

Computational reconstruction of tissue‐specific metabolic models: application to human liver metabolism

31 March 2020

1 reference

Metabolite essentiality elucidates robustness of Escherichia coli metabolism

31 March 2020

1 reference

Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery

31 March 2020

1 reference

Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production

31 March 2020

1 reference

In silico method for modelling metabolism and gene product expression at genome scale

31 March 2020

1 reference

Three-dimensional structural view of the central metabolic network of Thermotoga maritima

31 March 2020

1 reference

Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery

31 March 2020

1 reference

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

31 March 2020

1 reference

Diversity and versatility of the Thermotoga maritima sugar kinome

31 March 2020

1 reference

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

31 March 2020

1 reference

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis.

31 March 2020

1 reference

Integrating high-throughput and computational data elucidates bacterial networks

31 March 2020

1 reference

Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli

31 March 2020

1 reference

The molecular diversity of adaptive convergence.

31 March 2020

1 reference

A whole-cell computational model predicts phenotype from genotype

31 March 2020

1 reference

A community-driven global reconstruction of human metabolism.

31 March 2020

1 reference

Computational systems biology and in silico modeling of the human microbiome

31 March 2020

1 reference

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

31 March 2020

1 reference

Energy charge of the adenylate pool as a regulatory parameter. Interaction with feedback modifiers

31 March 2020

1 reference

Diffusion and chemical transformation

31 March 2020

1 reference

Shrinking the metabolic solution space using experimental datasets

31 March 2020

1 reference

Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production

31 March 2020

1 reference

What is flux balance analysis?

31 March 2020

1 reference

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

31 March 2020

1 reference

Stochastic modelling for quantitative description of heterogeneous biological systems

31 March 2020

1 reference

Computational approaches to the topology, stability and dynamics of metabolic networks.

31 March 2020

1 reference

Modeling and simulation of genetic regulatory systems: a literature review

31 March 2020

1 reference

Using Bayesian networks to analyze expression data

31 March 2020

1 reference

Bayesian statistical methods for genetic association studies

31 March 2020

1 reference

Differential network biology

31 March 2020

1 reference

Leveraging models of cell regulation and GWAS data in integrative network-based association studies

31 March 2020

1 reference

Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.

31 March 2020

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24430943

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

EFFECT OF TEMPERATURE ON THE COMPOSITION OF FATTY ACIDS IN ESCHERICHIA COLI

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24430943

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Pathway alignment: application to the comparative analysis of glycolytic enzymes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24430943