(Q35221569)

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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

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scholarly article

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Europe PubMed Central

PubMed publication ID

7 August 2017

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

1 reference

Europe PubMed Central

PubMed publication ID

7 August 2017

Desulfovibrio vulgaris

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Desulfovibrio vulgaris

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based on heuristic

inferred from title

author name string

Lei Nie

1

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Europe PubMed Central

PubMed publication ID

7 August 2017

Gang Wu

2

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Europe PubMed Central

PubMed publication ID

7 August 2017

Weiwen Zhang

3

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Europe PubMed Central

PubMed publication ID

7 August 2017

language of work or name

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publication date

8 October 2006

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Europe PubMed Central

PubMed publication ID

7 August 2017

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Europe PubMed Central

PubMed publication ID

7 August 2017

174

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Europe PubMed Central

PubMed publication ID

7 August 2017

4

1 reference

Europe PubMed Central

PubMed publication ID

7 August 2017

2229-2243

1 reference

Europe PubMed Central

PubMed publication ID

7 August 2017

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

LC-MS/MS based proteomic analysis and functional inference of hypothetical proteins in Desulfovibrio vulgaris

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Integrated analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: zero-inflated Poisson regression models to predict abundance of undetected proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Memory efficient folding algorithms for circular RNA secondary structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Differences in codon bias cannot explain differences in translational power among microbes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Integrative analysis of genome-scale data by using pseudoinverse projection predicts novel correlation between DNA replication and RNA transcription

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Changes in the protein expression of yeast as a function of carbon source

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Interplay of transcriptomics and proteomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Hierarchy of sequence-dependent features associated with prokaryotic translation

1 reference

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13 July 2018

Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria

1 reference

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13 July 2018

Comparing protein abundance and mRNA expression levels on a genomic scale

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Translational selection and yeast proteome evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Vienna RNA secondary structure server

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Bacterial translational control at atomic resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Termination of translation: interplay of mRNA, rRNAs and release factors?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Gene expression analysis using oligonucleotide arrays produced by maskless photolithography

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Global analysis of gene expression in yeast

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

The use of accurate mass tags for high-throughput microbial proteomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Non-canonical mechanism for translational control in bacteria: synthesis of ribosomal protein S1.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Integrated genomic and proteomic analyses of a systematically perturbed metabolic network

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Codon bias at the 3'-side of the initiation codon is correlated with translation initiation efficiency in Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

A sampling of the yeast proteome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Translation in Bacillus subtilis: roles and trends of initiation and termination, insights from a genome analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Correlation between protein and mRNA abundance in yeast

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Decoding the translational termination signal: the polypeptide chain release factor in Escherichia coli crosslinks to the base following the stop codon.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

The translational stop signal: codon with a context, or extended factor recognition element?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Translational termination efficiency in both bacteria and mammals is regulated by the base following the stop codon

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

The identity of the base following the stop codon determines the efficiency of in vivo translational termination in Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Prokaryotic translation: the interactive pathway leading to initiation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Codon bias in Escherichia coli may modulate translation initiation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Identification and characterization of E.coli ribosomal binding sites by free energy computation

1 reference

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13 July 2018

Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Codon usage and tRNA content in unicellular and multicellular organisms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Directional mutation pressure and neutral molecular evolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Influence of the codon following the AUG initiation codon on the expression of a modified lacZ gene in Escherichia coli

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Selection of the mRNA translation initiation region by Escherichia coli ribosomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

The maximum rate of gene expression is dependent on the downstream context of unfavourable codons.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Secondary structure of the ribosome binding site determines translational efficiency: a quantitative analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Sequence analysis suggests that tetra-nucleotides signal the termination of protein synthesis in eukaryotes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Eukaryotic start and stop translation sites.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

13 July 2018

Codon choice and potential complementarity between mRNA downstream of the initiation codon and bases 1471 –1480 in 16S ribosomal RNA affects expression ofglnS

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The influence of ribosome-binding-site elements on translational efficiency in Bacillus subtilis and Escherichia coli in vivo

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13 July 2018

Global transcriptomic analysis of Desulfovibrio vulgaris on different electron donors.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

26 September 2018

The genus desulfovibrio: the centennial

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

26 September 2018

Relationships among stop codon usage bias, its context, isochores, and gene expression level in various eukaryotes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

26 September 2018

Proteome composition in Plasmodium falciparum: higher usage of GC-rich nonsynonymous codons in highly expressed genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

26 September 2018

Gene expression levels influence amino acid usage and evolutionary rates in endosymbiotic bacteria.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

26 September 2018

Probability-based evaluation of peptide and protein identifications from tandem mass spectrometry and SEQUEST analysis: the human proteome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

26 September 2018

Post-transcriptional expression regulation in the yeast Saccharomyces cerevisiae on a genomic scale.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

26 September 2018

Comprehensive sequence analysis of translation termination sites in various eukaryotes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

26 September 2018

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

26 September 2018

Translational initiation on structured messengers. Another role for the Shine-Dalgarno interaction.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

26 September 2018

The cellular concentration of the sigma S subunit of RNA polymerase in Escherichia coli is controlled at the levels of transcription, translation, and protein stability

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

26 September 2018

A proteomic view ofDesulfovibrio vulgaris metabolism as determined by liquid chromatography coupled with tandem mass spectrometry

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698625

15 November 2018

Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting tran

1 reference

https://pubmed.ncbi.nlm.nih.gov/17028312

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Relation between mRNA expression and sequence information in Desulfovibrio vulgaris: combinatorial contributions of upstream regulatory motifs and coding sequence features to variations in mRNA abundance

1 reference

https://pubmed.ncbi.nlm.nih.gov/17028312

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/17028312

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Oxidative stress and heat-shock responses in Desulfovibrio vulgaris by genome-wide transcriptomic analysis

1 reference

https://pubmed.ncbi.nlm.nih.gov/17028312

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Codon usage determines translation rate in Escherichia coli

1 reference

https://pubmed.ncbi.nlm.nih.gov/17028312

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotes

1 reference

https://pubmed.ncbi.nlm.nih.gov/17028312

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1534/GENETICS.106.065862

1 reference

Europe PubMed Central

PubMed publication ID

7 August 2017

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

7 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

7 August 2017

ResearchGate publication ID

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