(Q34268420)

1 August 2017

Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico (English)

1 reference

1 August 2017

1 reference

Michael J McAnulty

1

1 reference

1 August 2017

Jiun Y Yen

series ordinal

2

1 reference

1 August 2017

Benjamin G Freedman

series ordinal

3

1 reference

1 August 2017

Ryan S Senger

series ordinal

4

1 reference

1 August 2017

14 May 2012

1 reference

1 August 2017

1 reference

1 August 2017

6

1 reference

1 August 2017

42

1 reference

https://scigraph.springernature.com/pub.10.1186/1752-0509-6-42

1 August 2017

0 references

cites work

The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Systems-level metabolic flux profiling elucidates a complete, bifurcated tricarboxylic acid cycle in Clostridium acetobutylicum.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Biofuel production improvement with genome-scale models: The role of cell composition

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Genome scale reconstruction of a Salmonella metabolic model: comparison of similarity and differences with a commensal Escherichia coli strain

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Reconstruction of biochemical networks in microorganisms

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Genome-scale model for Clostridium acetobutylicum: Part II. Development of specific proton flux states and numerically determined sub-systems

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Aldehyde-alcohol dehydrogenase and/or thiolase overexpression coupled with CoA transferase downregulation lead to higher alcohol titers and selectivity in Clostridium acetobutylicum fermentations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Group contribution method for thermodynamic analysis of complex metabolic networks

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

The transcriptional program underlying the physiology of clostridial sporulation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

The genomic and epidemiological dynamics of human influenza A virus

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

NADH availability limits asymmetric biocatalytic epoxidation in a growing recombinant Escherichia coli strain.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Thermodynamics-based metabolic flux analysis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Matrix formalism to describe functional states of transcriptional regulatory systems

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Towards multidimensional genome annotation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Acetone and Butanol Production by Clostridium acetobutylicum in a Synthetic Medium.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Metabolic functions of duplicate genes in Saccharomyces cerevisiae

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Modeling Lactococcus lactis using a genome-scale flux model

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Comparison of network-based pathway analysis methods

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Antisense RNA downregulation of coenzyme A transferase combined with alcohol-aldehyde dehydrogenase overexpression leads to predominantly alcohologenic Clostridium acetobutylicum fermentations

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Metabolic pathways in the post-genome era.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Design of antisense RNA constructs for downregulation of the acetone formation pathway of Clostridium acetobutylicum

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Metabolic flux profiling of Escherichia coli mutants in central carbon metabolism using GC-MS.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

KEGG: kyoto encyclopedia of genes and genomes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Metabolic fluxes in riboflavin-producing Bacillus subtilis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

In vivo methylation in Escherichia coli by the Bacillus subtilis phage phi 3T I methyltransferase to protect plasmids from restriction upon transformation of Clostridium acetobutylicum ATCC 824

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Regulation of Clostridium acetobutylicum metabolism as revealed by mixed-substrate steady-state continuous cultures: role of NADH/NAD ratio and ATP pool

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3495714

Equations and calculations for fermentations of butyric acid bacteria.

6 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-6-42

Metabolic engineering of the non-sporulating, non-solventogenic Clostridium acetobutylicum strain M5 to produce butanol without acetone demonstrate the robustness of the acid-formation pathways and the importance of the electron balance

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-6-42

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/10.1186%2F1752-0509-6-42

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/10.1186%2F1752-0509-6-42

Reconstruction, modeling & analysis of Halobacterium salinarum R-1 metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-6-42

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-6-42

Genetic manipulation of acid formation pathways by gene inactivation in Clostridium acetobutylicum ATCC 824.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-6-42

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-6-42

Fermentation characterization and flux analysis of recombinant strains of Clostridium acetobutylicum with an inactivated solR gene

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-6-42

Stoichiometric modeling of Clostridium acetobutylicum fermentations with non-linear constraints

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-6-42

Characterization of recombinant strains of the Clostridium acetobutylicum butyrate kinase inactivation mutant: need for new phenomenological models for solventogenesis and butanol inhibition?

21 January 2018

1 reference

12 December 2020

Resolving the TCA cycle and pentose-phosphate pathway of Clostridium acetobutylicum ATCC 824: Isotopomer analysis, in vitro activities and expression analysis.

1 reference

12 December 2020

Targeting multiple targets in Pseudomonas aeruginosa PAO1 using flux balance analysis of a reconstructed genome-scale metabolic network

1 reference

12 December 2020

Metabolic flux analysis elucidates the importance of the acid-formation pathways in regulating solvent production by Clostridium acetobutylicum

1 reference

12 December 2020

Genome-scale metabolic network analysis and drug targeting of multi-drug resistant pathogen Acinetobacter baumannii AYE

1 reference

12 December 2020

Identifiers

DOI

10.1186/1752-0509-6-42

1 reference

journals/bmcsb/McAnultyYFS12

1 August 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

1 August 2017

1 reference