(Q33391538)

26 July 2017

3 references

19 September 2019

2 November 2019

2 September 2020

Genome-scale models of bacterial metabolism: reconstruction and applications (English)

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biomedical investigative technique

26 July 2017

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19 September 2019

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2 November 2019

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2 September 2020

Maxime Durot

1

1 reference

26 July 2017

Pierre-Yves Bourguignon

series ordinal

2

1 reference

26 July 2017

Vincent Schachter

series ordinal

3

1 reference

26 July 2017

3 December 2008

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FEMS Microbiology Reviews

26 July 2017

1 January 2009

3 references

19 September 2019

2 November 2019

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4 references

26 July 2017

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26 July 2017

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Creative Commons Attribution 2.5 Generic

26 July 2017

3 references

19 September 2019

2 November 2019

Ab initio prediction of metabolic networks using Fourier transform mass spectrometry data

2 September 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Microbial biodegradation of polyaromatic hydrocarbons

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

The Systems Biology Research Tool: evolvable open-source software

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Application of systems biology for bioprocess development

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Can single knockouts accurately single out gene functions?

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

The University of Minnesota pathway prediction system: predicting metabolic logic

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Estimating the size of the solution space of metabolic networks.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Dynamic analysis of integrated signaling, metabolic, and regulatory networks

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Context-specific metabolic networks are consistent with experiments

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

The evolution of modularity in bacterial metabolic networks.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Exploiting the pathway structure of metabolism to reveal high-order epistasis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Opportunities for renewable bioenergy using microorganisms

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

New insights into the alternative D-glucarate degradation pathway.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Metabolic flux analysis and metabolic engineering of microorganisms

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

KEGG for linking genomes to life and the environment

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Systems metabolic engineering of Escherichia coli for L-threonine production

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

The universal protein resource (UniProt)

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Annotation, comparison and databases for hundreds of bacterial genomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Estimation of the number of extreme pathways for metabolic networks

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Metabolite essentiality elucidates robustness of Escherichia coli metabolism

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Metabolic flux elucidation for large-scale models using 13C labeled isotopes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Modeling Neisseria meningitidis metabolism: from genome to metabolic fluxes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Observing metabolic functions at the genome scale

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Distinguishing enzymes using metabolome data for the hybrid dynamic/static method

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Structural and functional analysis of cellular networks with CellNetAnalyzer

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Metabolic flux analysis in a nonstationary system: fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Multiple high-throughput analyses monitor the response of E. coli to perturbations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Metabolic modeling of a mutualistic microbial community.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Applications of fluorescence microscopy to single bacterial cells

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

BRENDA, AMENDA and FRENDA: the enzyme information system in 2007

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Thermodynamics-based metabolic flux analysis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Systematic assignment of thermodynamic constraints in metabolic network models

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Metabolic networks in motion: 13C-based flux analysis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

STRING 7--recent developments in the integration and prediction of protein interactions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Systems approach to refining genome annotation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Experimental and computational assessment of conditionally essential genes in Escherichia coli

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

ScrumPy: metabolic modelling with Python

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Identification of genome-scale metabolic network models using experimentally measured flux profiles

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Review: on the analysis and interpretation of correlations in metabolomic data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Accelerating the reconstruction of genome-scale metabolic networks

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Metatool 5.0: fast and flexible elementary modes analysis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Production of the antimalarial drug precursor artemisinic acid in engineered yeast

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Chance and necessity in the evolution of minimal metabolic networks

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Identifying metabolic enzymes with multiple types of association evidence

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Metabolite coupling in genome-scale metabolic networks

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Systematic analysis of conservation relations in Escherichia coli genome-scale metabolic network reveals novel growth media

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Towards multidimensional genome annotation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

The University of Minnesota Biocatalysis/Biodegradation Database: the first decade

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

MetaCyc: a multiorganism database of metabolic pathways and enzymes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Evolutionary programming as a platform for in silico metabolic engineering

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Minimum information requested in the annotation of biochemical models (MIRIAM)

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Bacterial degradation of xenobiotic compounds: evolution and distribution of novel enzyme activities

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

In silico reconstruction of the metabolic pathways of Lactobacillus plantarum: comparing predictions of nutrient requirements with those from growth experiments.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Metabolic functions of duplicate genes in Saccharomyces cerevisiae

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Chemoinformatics: a new field with a long tradition

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

In silico genome-scale reconstruction and validation of the Staphylococcus aureus metabolic network.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Modeling Lactococcus lactis using a genome-scale flux model

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Measuring the metabolome: current analytical technologies

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Uncovering transcriptional regulation of metabolism by using metabolic network topology

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

k-Cone analysis: determining all candidate values for kinetic parameters on a network scale

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Assignment of endogenous substrates to enzymes by global metabolite profiling

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Elucidation and structural analysis of conserved pools for genome-scale metabolic reconstructions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Comparison of network-based pathway analysis methods

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

A computational approach to measuring coherence of gene expression in pathways

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

A Bayesian method for identifying missing enzymes in predicted metabolic pathway databases

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Advances in the prediction of protein targeting signals

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Integrating high-throughput and computational data elucidates bacterial networks

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Prolinks: a database of protein functional linkages derived from coevolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Use of genome-scale microbial models for metabolic engineering

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Global organization of metabolic fluxes in the bacterium Escherichia coli

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Flux coupling analysis of genome-scale metabolic network reconstructions.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Systematic genome-wide screens of gene function

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Comprehensive transposon mutant library of Pseudomonas aeruginosa

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

In Silico Atomic Tracing by Substrate-Product Relationships in Escherichia coli Intermediary Metabolism

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

AMIGene: Annotation of MIcrobial Genes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Metabolic pathways in the post-genome era.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Missing genes in metabolic pathways: a comparative genomics approach

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Essential Bacillus subtilis genes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Two approaches for metabolic pathway analysis?

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Analysis of optimality in natural and perturbed metabolic networks

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

The Pathway Tools software

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Genome-scale metabolic model of Helicobacter pylori 26695.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Energy balance for analysis of complex metabolic networks

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Regulation of gene expression in flux balance models of metabolism

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

A priori analysis of metabolic flux identifiability from (13)C-labeling data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

13C metabolic flux analysis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Phenotype microarrays for high-throughput phenotypic testing and assay of gene function

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

InterPro--an integrated documentation resource for protein families, domains and functional sites

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Gene ontology: tool for the unification of biology

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Improved microbial gene identification with GLIMMER

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Biochemical and molecular characterization of the Bacillus subtilis acetoin catabolic pathway.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Correlation between protein and mRNA abundance in yeast

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Utilization of energy for growth and maintenance in continuous and batch cultures of microorganisms. A reevaluation of the method for the determination of ATP production by measuring molar growth yields

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Toward a science of metabolic engineering

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Metabolic control analysis: a survey of its theoretical and experimental development

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Integration of gene expression data into genome-scale metabolic models

28 July 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Thermodynamic constraints for biochemical networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Predicting genes for orphan metabolic activities using phylogenetic profiles

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Mass spectrometry-based metabolomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Global functional profiling of gene expression.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

In silico design and adaptive evolution of Escherichia coli for production of lactic acid.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Computational prediction and experimental verification of the gene encoding the NAD+/NADP+-dependent succinate semialdehyde dehydrogenase in Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Essential genes on metabolic maps.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Detection of stoichiometric inconsistencies in biomolecular models.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Co-clustering of biological networks and gene expression data

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Exploring the diversity of complex metabolic networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Investigating metabolite essentiality through genome-scale analysis of Escherichia coli production capabilities

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Multidimensional annotation of the Escherichia coli K-12 genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Minimal cut sets in biochemical reaction networks.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

META. 1. A program for the evaluation of metabolic transformation of chemicals.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Optimization based automated curation of metabolic reconstructions

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Adaptive evolution of bacterial metabolic networks by horizontal gene transfer.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Elucidation of an alternate isoleucine biosynthesis pathway in Geobacter sulfurreducens

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Metabolomics approach for enzyme discovery.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Integrated network reconstruction, visualization and analysis using YANAsquare.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

From Annotated Genomes to Metabolic Flux Models and Kinetic Parameter Fitting

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

A genome-scale computational study of the interplay between transcriptional regulation and metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Systematic condition-dependent annotation of metabolic genes

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Metabolic network structure determines key aspects of functionality and regulation

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

IdentiCS--identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

High-throughput transposon mutagenesis of Corynebacterium glutamicum and construction of a single-gene disruptant mutant library

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Stoichiometric model for evaluating the metabolic capabilities of the facultative methylotroph Methylobacterium extorquens AM1, with application to reconstruction of C(3) and C(4) metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space.

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

Is maximization of molar yield in metabolic networks favoured by evolution?

21 January 2018

1 reference

https://api.crossref.org/works/10.1111%2FJ.1574-6976.2008.00146.X

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

LibSBML: an API library for SBML.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

The model organism as a system: integrating 'omics' data sets

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Horizontal gene transfer depends on gene content of the host.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Structural analysis of expanding metabolic networks.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Heuristics for chemical compound matching.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

MetaFluxNet, a program package for metabolic pathway construction and analysis, and its use in large-scale metabolic flux analysis of Escherichia coli.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

TransportDB: a relational database of cellular membrane transport systems

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Enzyme-specific profiles for genome annotation: PRIAM

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

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

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Ab initio reconstruction of metabolic pathways.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Characterizing the metabolic phenotype: a phenotype phase plane analysis

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Transcriptome meets metabolome: hierarchical and metabolic regulation of the glycolytic pathway

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Bidirectional reaction steps in metabolic networks: III. Explicit solution and analysis of isotopomer labeling systems.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

METATOOL: for studying metabolic networks.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2704943

Multiple knockout analysis of genetic robustness in the yeast metabolic network

31 October 2018

1 reference

12 December 2020

Heuristics for similarity searching of chemical graphs using a maximum common edge subgraph algorithm

1 reference

12 December 2020

Ab initio prediction of thermodynamically feasible reaction directions from biochemical network stoichiometry

1 reference

12 December 2020

Isotopomer subspaces as indicators of metabolic-pathway structure

1 reference

12 December 2020

Integration of the information from gene expression and metabolic fluxes for the analysis of the regulatory mechanisms in Synechocystis

1 reference

12 December 2020

10.1111/J.1574-6976.2008.00146.X

Identifiers

DOI

1 reference

26 July 2017

1 reference

26 July 2017

1 reference