Codon usage variability determines the correlation between proteome and transcriptome fold changes (Q33830070)

29 July 2017

Codon usage variability determines the correlation between proteome and transcriptome fold changes (English)

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29 July 2017

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3

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29 July 2017

2

Sergio Bordel

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PubMed ID

21352515

Roberto Olivares-Hernández

29 July 2017

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Roberto Olivares-Hernández

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1

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publication date

25 February 2011

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29 July 2017

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29 July 2017

5

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29 July 2017

33

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PubMed ID

21352515

describes a project that uses

29 July 2017

Cytoscape

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Cytoscape

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9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

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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.10.1186/1752-0509-5-33

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cites work

Translation efficiency is determined by both codon bias and folding energy

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Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator

4 July 2018

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Universal function-specificity of codon usage

4 July 2018

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Design parameters to control synthetic gene expression in Escherichia coli

4 July 2018

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Coding-sequence determinants of gene expression in Escherichia coli

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058016

Effects of codon distributions and tRNA competition on protein translation

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058016

Characterization of global yeast quantitative proteome data generated from the wild-type and glucose repression saccharomyces cerevisiae strains: the comparison of two quantitative methods

4 July 2018

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Determinants of protein abundance and translation efficiency in S. cerevisiae

4 July 2018

1 reference

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Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis

4 July 2018

1 reference

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Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae

4 July 2018

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Integrative analysis of transcriptomic and proteomic data: challenges, solutions and applications

4 July 2018

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Posttranscriptional expression regulation: what determines translation rates?

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058016

Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation.

4 July 2018

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A model for protein translation: polysome self-organization leads to maximum protein synthesis rates.

4 July 2018

1 reference

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Correlation of mRNA expression and protein abundance affected by multiple sequence features related to translational efficiency in Desulfovibrio vulgaris: a quantitative analysis

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058016

An algorithmic framework for genome-wide modeling and analysis of translation networks

4 July 2018

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BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058016

Relative predicted protein levels of functionally associated proteins are conserved across organisms

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058016

Solving the riddle of codon usage preferences: a test for translational selection

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058016

Codon bias and heterologous protein expression

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058016

The molecular mechanics of eukaryotic translation

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058016

Hierarchy of sequence-dependent features associated with prokaryotic translation

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058016

Cytoscape: a software environment for integrated models of biomolecular interaction networks

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058016

Global analysis of protein expression in yeast

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058016

Comparing protein abundance and mRNA expression levels on a genomic scale

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058016

Translational selection and yeast proteome evolution

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058016

Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae

4 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058016

Eukaryotic translation initiation factors and regulators

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058016

Integrated genomic and proteomic analyses of a systematically perturbed metabolic network

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058016

A sampling of the yeast proteome

4 July 2018

1 reference

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Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation

4 July 2018

1 reference

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Correlation between protein and mRNA abundance in yeast

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058016

Simulation of prokaryotic genetic circuits

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058016

Stochastic mechanisms in gene expression

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3058016

The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications

4 July 2018

1 reference

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Insights into the relation between mRNA and protein expression patterns: I. Theoretical considerations.

4 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1752-0509-5-33

Analysis of growth rate effects on productivity of recombinant Escherichia coli populations using molecular mechanism models. Reprinted from Biotechnology and Bioengineering, Vol. 26, Issue 1, Pages 66-73 (1984).

21 January 2018

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Crossref

https://api.crossref.org/works/10.1186%2F1752-0509-5-33

Complementary profiling of gene expression at the transcriptome and proteome levels in Saccharomyces cerevisiae

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1752-0509-5-33

Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: a multiple regression to identify sources of variations

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21352515

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A mathematical model for elongation of a peptide chain

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21352515

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1752-0509-5-33

1 reference

journals/bmcsb/Olivares-HernandezBN11

29 July 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

29 July 2017

1 reference

PubMed ID

21352515