(Q30710200)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24314206%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

title

Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24314206%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24314206%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

Kaspar Valgepea

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24314206%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

John E. Beasley

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24314206%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

author name string

Jon Pey

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24314206%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

Francisco J Planes

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24314206%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

publication date

8 December 2013

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24314206%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24314206%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

volume

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24314206%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

page(s)

134

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24314206%20AND%20SRC:MED&resulttype=core&format=json

describes a project that uses

2 March 2020

limma

object named as

limma

2 references

22 June 2022

https://europepmc.org/article/PMC/3878952

inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

exact match

https://scigraph.springernature.com/pub.10.1186/1752-0509-7-134

0 references

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Selection of human tissue-specific elementary flux modes using gene expression data

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Integrating tracer-based metabolomics data and metabolic fluxes in a linear fashion via Elementary Carbon Modes.

14 July 2018

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14 July 2018

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14 July 2018

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Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase

14 July 2018

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SEAS: a system for SEED-based pathway enrichment analysis

14 July 2018

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Optimal regulatory strategies for metabolic pathways in Escherichia coli depending on protein costs.

14 July 2018

1 reference

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Path finding methods accounting for stoichiometry in metabolic networks.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Genetic architecture of regulatory variation in Arabidopsis thaliana

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Systems biology approach reveals that overflow metabolism of acetate in Escherichia coli is triggered by carbon catabolite repression of acetyl-CoA synthetase

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

EcoCyc: a comprehensive database of Escherichia coli biology

14 July 2018

1 reference

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Evidence for an alternative glycolytic pathway in rapidly proliferating cells

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Pathway discovery in metabolic networks by subgraph extraction

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Escherichia coli toxin/antitoxin pair MqsR/MqsA regulate toxin CspD.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

SubpathwayMiner: a software package for flexible identification of pathways

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Testing significance relative to a fold-change threshold is a TREAT.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

KEGG spider: interpretation of genomics data in the context of the global gene metabolic network

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Transcriptome analysis of the normal human mammary cell commitment and differentiation process

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Application of systems biology for bioprocess development

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

fdrtool: a versatile R package for estimating local and tail area-based false discovery rates

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Bioinformatics applications for pathway analysis of microarray data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Is proteomics the new genomics?

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Altered expression of mitochondrial and extracellular matrix genes in the heart of human fetuses with chromosome 21 trisomy

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Evidence of differential HLA class I-mediated viral evolution in functional and accessory/regulatory genes of HIV-1

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Observing metabolic functions at the genome scale

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

PathExpress: a web-based tool to identify relevant pathways in gene expression data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

A microRNA signature of hypoxia

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Recovering metabolic pathways via optimization.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Overflow metabolism in Escherichia coli during steady-state growth: transcriptional regulation and effect of the redox ratio

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Genomic analysis of metabolic pathway gene expression in mice

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Pathways to the analysis of microarray data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Integrating genomics and metabolomics for engineering plant metabolic pathways

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Identification and functional significance of genes regulated by structurally different histone deacetylase inhibitors

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Global analysis of protein expression in yeast

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Statistical tests for differential expression in cDNA microarray experiments

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Microarray data normalization and transformation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Pathway Processor: a tool for integrating whole-genome expression results into metabolic networks

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Metabolic control analysis in drug discovery and disease

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Metabolomics – the link between genotypes and phenotypes

14 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

14 July 2018

https://pubmed.ncbi.nlm.nih.gov/24314206

12 December 2020

inferred from PubMed ID database lookup

Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Whole-genome expression analysis: challenges beyond clustering

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Analysis of gene expression data with pathway scores.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

KEGG: kyoto encyclopedia of genes and genomes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Quantitative monitoring of gene expression patterns with a complementary DNA microarray

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Acetyl-phosphate is a critical determinant of lysine acetylation in E. coli.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Can sugars be produced from fatty acids? A test case for pathway analysis tools

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Simple constrained-optimization view of acetate overflow in E. coli.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

An integrated analysis of the effects of Esculentin 1–21 on Saccharomyces cerevisiae

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Global gene expression analysis of glucose overflow metabolism in Escherichia coli and reduction of aerobic acetate formation.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Effect of glycine on the cell yield and growth rate of Escherichia coli: evidence for cell-density-dependent glycine degradation as determined by (13)C NMR spectroscopy

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

Influence of acetic acid on the growth of Escherichia coli K12 during high-cell-density cultivation in a dialysis reactor.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3878952

A universal framework for 13C metabolic flux analysis

25 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24314206

12 December 2020

inferred from PubMed ID database lookup

Network-based prediction of human tissue-specific metabolism

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24314206

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1186/1752-0509-7-134

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24314206%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

DBLP publication ID

journals/bmcsb/PeyVRBP13

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24314206%20AND%20SRC:MED&resulttype=core&format=json

2 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24314206%20AND%20SRC:MED&resulttype=core&format=json