(Q34741381)

4 August 2017

title

Integration of a constraint-based metabolic model of Brassica napus developing seeds with (13)C-metabolic flux analysis (English)

1 reference

4 August 2017

Brassica napus

1 reference

5

Hardy Rolletschek

1 reference

4 August 2017

Jordan O Hay

1

1 reference

4 August 2017

Hai Shi

2

1 reference

4 August 2017

Nicolas Heinzel

3

1 reference

4 August 2017

Inga Hebbelmann

4

1 reference

4 August 2017

Jorg Schwender

6

1 reference

4 August 2017

publication date

19 December 2014

1 reference

Frontiers in Plant Science

4 August 2017

published in

1 reference

4 August 2017

volume

5

1 reference

4 August 2017

page(s)

724

1 reference

Transcript abundance on its own cannot be used to infer fluxes in central metabolism

4 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Anthocyanin biosynthetic genes in Brassica rapa

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Phosphorylation of Arabidopsis transketolase at Ser428 provides a potential paradigm for the metabolic control of chloroplast carbon metabolism.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Path2Models: large-scale generation of computational models from biochemical pathway maps

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Software platforms to facilitate reconstructing genome-scale metabolic networks

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Systems analysis of metabolic phenotypes: what have we learnt?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Elucidating rice cell metabolism under flooding and drought stresses using flux-based modeling and analysis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Fast thermodynamically constrained flux variability analysis.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

A proof for loop-law constraints in stoichiometric metabolic networks.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Tissue-specific distribution of secondary metabolites in rapeseed (Brassica napus L.)

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

13CFLUX2--high-performance software suite for (13)C-metabolic flux analysis.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Syntenic gene analysis between Brassica rapa and other Brassicaceae species

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Shrinking the metabolic solution space using experimental datasets

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Plant genome-scale metabolic reconstruction and modelling

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Integration of expression data in genome-scale metabolic network reconstructions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Are we ready for genome-scale modeling in plants?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Flux-balance modeling of plant metabolism.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Experimental flux measurements on a network scale

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Metabolic modeling of Chlamydomonas reinhardtii: energy requirements for photoautotrophic growth and maintenance

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Frontiers in metabolic reconstruction and modeling of plant genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Identifiers.org and MIRIAM Registry: community resources to provide persistent identification

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

The genome of the mesopolyploid crop species Brassica rapa

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Comparative deep transcriptional profiling of four developing oilseeds

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Elimination of thermodynamically infeasible loops in steady-state metabolic models

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Expansion and subfunctionalisation of flavonoid 3',5'-hydroxylases in the grapevine lineage

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Prediction of metabolic fluxes by incorporating genomic context and flux-converging pattern analyses

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Metabolic network analysis integrated with transcript verification for sequenced genomes.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Metabolic flux analysis as a tool in metabolic engineering of plants

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

LibSBML: an API library for SBML.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Integration of gene expression data into genome-scale metabolic models

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Malate valves to balance cellular energy supply

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

AraCyc: a biochemical pathway database for Arabidopsis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4271587

Systematics and phylogeny of the Brassicaceae (Cruciferae): an overview

7 July 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

Plastidial NAD-dependent malate dehydrogenase is critical for embryo development and heterotrophic metabolism in Arabidopsis.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

Expa: a program for calculating extreme pathways in biochemical reaction networks

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

Seed architecture shapes embryo metabolism in oilseed rape.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

A method for accounting for maintenance costs in flux balance analysis improves the prediction of plant cell metabolic phenotypes under stress conditions.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

Incorporating metabolic flux ratios into constraint-based flux analysis by using artificial metabolites and converging ratio determinants.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

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/10.3389%2FFPLS.2014.00724

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

The plastidic pentose phosphate translocator represents a link between the cytosolic and the plastidic pentose phosphate pathways in plants

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

Changes in tocopherol and plastochromanol-8 contents in seeds and oil of oilseed rape (Brassica napus L.) during storage as influenced by temperature and air oxygen.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

Metabolic network reconstruction and flux variability analysis of storage synthesis in developing oilseed rape (Brassica napus L.) embryos.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

Analysis of metabolic flux phenotypes for two Arabidopsis mutants with severe impairment in seed storage lipid synthesis

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

Genetics. Predicting microbial growth

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

Combined noninvasive imaging and modeling approaches reveal metabolic compartmentation in the barley endosperm

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

Probing in vivo metabolism by stable isotope labeling of storage lipids and proteins in developing Brassica napus embryos

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

The plastid-localized NAD-dependent malate dehydrogenase is crucial for energy homeostasis in developing Arabidopsis thaliana seeds.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

Integration of genome-scale modeling and transcript profiling reveals metabolic pathways underlying light and temperature acclimation in Arabidopsis

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

A comprehensive analysis of the NADP-malic enzyme gene family of Arabidopsis

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

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/10.3389%2FFPLS.2014.00724

A genome-scale metabolic model accurately predicts fluxes in central carbon metabolism under stress conditions.

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

A Diel Flux Balance Model Captures Interactions between Light and Dark Metabolism during Day-Night Cycles in C3 and Crassulacean Acid Metabolism Leaves

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3389%2FFPLS.2014.00724

Flux balance analysis of barley seeds: a computational approach to study systemic properties of central metabolism

21 January 2018

1 reference

12 December 2020

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

1 reference

12 December 2020

Predictive modeling of biomass component tradeoffs in Brassica napus developing oilseeds based on in silico manipulation of storage metabolism

1 reference

12 December 2020

Flux variability analysis: application to developing oilseed rape embryos using toolboxes for constraint-based modeling

1 reference

12 December 2020

Computational analysis of storage synthesis in developing Brassica napus L. (oilseed rape) embryos: flux variability analysis in relation to ¹³C metabolic flux analysis

1 reference

12 December 2020

Proteomic Comparison of Plastids from Developing Embryos and Leaves ofBrassica napus

1 reference

12 December 2020

An in silico compartmentalized metabolic model of Brassica napus enables the systemic study of regulatory aspects of plant central metabolism

1 reference

12 December 2020

The colorless flavonoids of Arabidopsis thaliana (Brassicaceae). I. A model system to study the orthodihydroxy structure

1 reference

12 December 2020

Identifiers

DOI

10.3389/FPLS.2014.00724

1 reference

4 August 2017

1 reference

4 August 2017

1 reference