(Q38256965)

1 September 2017

1 reference

title

Generalized framework for context-specific metabolic model extraction methods (English)

1 reference

1 September 2017

Semidán Robaina Estévez

object named as

Semidán Robaina Estévez

series ordinal

1

0 references

Zoran Nikoloski

object named as

Zoran Nikoloski

series ordinal

2

0 references

publication date

19 September 2014

1 reference

Frontiers in Plant Science

1 September 2017

1 reference

1 September 2017

5

1 reference

1 September 2017

491

1 reference

Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism

1 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

k-OptForce: integrating kinetics with flux balance analysis for strain design

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Advancing metabolic models with kinetic information.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Fast reconstruction of compact context-specific metabolic network models

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Constraint-based models predict metabolic and associated cellular functions.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

The Gene Expression Barcode 3.0: improved data processing and mining tools

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Analysis of omics data with genome-scale models of metabolism

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Temporal expression-based analysis of metabolism

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Plant genome-scale metabolic reconstruction and modelling

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Integration of expression data in genome-scale metabolic network reconstructions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Improving metabolic flux predictions using absolute gene expression data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Flux-balance modeling of plant metabolism.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

AlgaGEM--a genome-scale metabolic reconstruction of algae based on the Chlamydomonas reinhardtii genome

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Model-based confirmation of alternative substrates of mitochondrial electron transport chain

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

From network models to network responses: integration of thermodynamic and kinetic properties of yeast genome-scale metabolic networks

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Zea mays iRS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Computationally efficient flux variability analysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Stochastic approaches in systems biology

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

What is flux balance analysis?

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Quantitation in mass-spectrometry-based proteomics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

AraGEM, a genome-scale reconstruction of the primary metabolic network in Arabidopsis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Context-specific metabolic networks are consistent with experiments

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

The future of metabolic phytochemistry: larger numbers of metabolites, higher resolution, greater understanding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Unraveling the complexity of flux regulation: a new method demonstrated for nutrient starvation in Saccharomyces cerevisiae

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

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

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Bottom-up Metabolic Reconstruction of Arabidopsis and Its Application to Determining the Metabolic Costs of Enzyme Production.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

C4GEM, a genome-scale metabolic model to study C4 plant metabolism

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

A genome-scale metabolic model of Arabidopsis and some of its properties

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Stochastic modelling for quantitative description of heterogeneous biological systems.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4168813

Responses to light intensity in a genome-scale model of rice metabolism

31 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.3389%2FFPLS.2014.00491

Multiscale metabolic modeling: dynamic flux balance analysis on a whole-plant scale

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25285097

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Network-based prediction of human tissue-specific metabolism

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25285097

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25285097

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.3389/FPLS.2014.00491

1 reference

1 September 2017

1 reference

PMC publication ID

4168813

1 September 2017

PubMed publication ID

25285097

1 reference

PMC publication ID

4168813