(Q28538197)

April 2022 Public Data File from Crossref

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Inferring metabolic states in uncharacterized environments using gene-expression measurements

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Modeling phenotypic metabolic adaptations of Mycobacterium tuberculosis H37Rv under hypoxia

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Shrinking the metabolic solution space using experimental datasets

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

A whole-cell computational model predicts phenotype from genotype

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

What is flux balance analysis?

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

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

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Context-specific metabolic networks are consistent with experiments

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Ten simple rules for reproducible computational research

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Applications of genome-scale metabolic reconstructions

23 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

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

6 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Reconstruction of biochemical networks in microorganisms

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Assessment of transcript reconstruction methods for RNA-seq

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Systematic evaluation of spliced alignment programs for RNA-seq data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Analysis of omics data with genome-scale models of metabolism

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Genome-level transcription data of Yersinia pestis analyzed with a new metabolic constraint-based approach

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Temporal expression-based analysis of metabolism

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

The expanding scope of DNA sequencing

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Integration of expression data in genome-scale metabolic network reconstructions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Prediction of microbial growth rate versus biomass yield by a metabolic network with kinetic parameters

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Improving metabolic flux predictions using absolute gene expression data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Inferring carbon sources from gene expression profiles using metabolic flux models

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Modeling formalisms in Systems Biology

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Functional integration of a metabolic network model and expression data without arbitrary thresholding.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Metabolic and transcriptional response to cofactor perturbations in Escherichia coli.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Low oxygen levels as a trigger for enhancement of respiratory metabolism in Saccharomyces cerevisiae

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Oxygen dependence of metabolic fluxes and energy generation of Saccharomyces cerevisiae CEN.PK113-1A.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Strategies for systems-level metabolic engineering

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Integration of gene expression data into genome-scale metabolic models

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Dynamic flux balance analysis of diauxic growth in Escherichia coli

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

What mRNA Abundances Can Tell us about Metabolism

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3998872

Novel algorithms and the benefits of comparative validation.

3 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003580

Predicting metabolic fluxes using gene expression differences as constraints.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003580

Flux-coupled genes and their use in metabolic flux analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003580

Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A chemostat culture study.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003580

Metabolic reconfiguration precedes transcriptional regulation in the antioxidant response.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003580

Multidimensional optimality of microbial metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003580

ON ELEMENTARY FLUX MODES IN BIOCHEMICAL REACTION SYSTEMS AT STEADY STATE

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1003580

Somewhat in control--the role of transcription in regulating microbial metabolic fluxes

21 January 2018

1 reference

12 December 2020

iMAT: an integrative metabolic analysis tool

1 reference

12 December 2020

Network-based prediction of human tissue-specific metabolism

1 reference

12 December 2020

The dynamics of the macromolecular composition of biomass

1 reference

12 December 2020

10.1371/JOURNAL.PCBI.1003580

Identifiers

DOI

1 reference

journals/ploscb/MachadoH14

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

1 reference

PubMed publication ID

24762745

1 reference