(Q41994687)

15 October 2017

Predicting gene expression level from relative codon usage bias: an application to Escherichia coli genome (English)

1 reference

15 October 2017

1 reference

1 reference

Uttam Roymondal

1

1 reference

15 October 2017

Shibsankar Das

series ordinal

2

1 reference

15 October 2017

Satyabrata Sahoo

series ordinal

3

1 reference

15 October 2017

language of work or name

1 reference

8 January 2009

1 reference

15 October 2017

1 reference

15 October 2017

16

1 reference

15 October 2017

1

1 reference

15 October 2017

13-30

1 reference

Distinguishing features of delta-proteobacterial genomes

15 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Predicted highly expressed genes in archaeal genomes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Relationship between codon biased genes, microarray expression values and physiological characteristics of Streptococcus pneumoniae.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Comparative analysis of gene expression among low G+C gram-positive genomes.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

The signature of selection mediated by expression on human genes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Isochores and tissue-specificity

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Predicting gene expression levels from codon biases in alpha-proteobacterial genomes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Evolution of synonymous codon usage in metazoans

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Determinants of CpG islands: expression in early embryo and isochore structure

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Characterizations of highly expressed genes of four fast-growing bacteria

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Highly expressed and alien genes of the Synechocystis genome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Predicted highly expressed genes of diverse prokaryotic genomes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Nature and structure of human genes that generate retropseudogenes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Genome-wide expression profiling in Escherichia coli K-12

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Natural selection on synonymous sites is correlated with gene length and recombination in Drosophila.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Gene length and codon usage bias in Drosophila melanogaster, Saccharomyces cerevisiae and Escherichia coli

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

What drives codon choices in human genes?

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Synonymous codon bias is related to gene length in Escherichia coli: selection for translational accuracy?

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Protein identifications on O'Farrell two-dimensional gels: locations of 55 additional Escherichia coli proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Protein identifications of O'Farrell two-dimensional gels: locations of 81 Escherichia coli proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Codon usage in bacteria: correlation with gene expressivity

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Codon usage and gene expression

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

The 'effective number of codons' used in a gene

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Patterns of protein synthesis in E. coli: a catalog of the amount of 140 individual proteins at different growth rates

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Predicted highly expressed genes in the genomes of Streptomyces coelicolor and Streptomyces avermitilis and the implications for their metabolism

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

A survey of codon and amino acid frequency bias in microbial genomes focusing on translational efficiency.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Codon usages in different gene classes of the Escherichia coli genome.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Codon use and the rate of divergence of land plant chloroplast genes

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Codon usage in Kluyveromyces lactis and in yeast cytochrome c-encoding genes.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2646356

Inferring lifestyle from gene expression patterns

18 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19131380

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19131380

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19131380

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/DNARES/DSN029

1 reference

15 October 2017

1 reference

15 October 2017

PubMed publication ID

19131380

1 reference