The life-cycle of operons (Q33247453)

24 July 2017

title

The life-cycle of operons (English)

1 reference

24 July 2017

Adam P Arkin

0 references

Eric J Alm

1 reference

24 July 2017

Morgan N Price

1 reference

24 July 2017

language of work or name

1 reference

23 June 2006

1 reference

24 July 2017

1 reference

24 July 2017

1 reference

24 July 2017

1 reference

24 July 2017

page(s)

e96

1 reference

Creative Commons Attribution 4.0 International

24 July 2017

start time

23 June 2006

1 reference

April 2022 Public Data File from Crossref

copyrighted

0 references

cites work

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14 July 2018

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Evolutionary conservation of bacterial operons: does transcriptional connectivity matter?

14 July 2018

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Prediction of transcriptional terminators in Bacillus subtilis and related species

14 July 2018

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14 July 2018

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14 July 2018

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Operon formation is driven by co-regulation and not by horizontal gene transfer

14 July 2018

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Transcriptome analysis of Shewanella oneidensis MR-1 in response to elevated salt conditions

14 July 2018

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A novel method for accurate operon predictions in all sequenced prokaryotes

14 July 2018

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Interaction network containing conserved and essential protein complexes in Escherichia coli

14 July 2018

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Selection-driven transcriptome polymorphism in Escherichia coli/Shigella species

14 July 2018

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Differences in LexA regulon structure among Proteobacteria through in vivo assisted comparative genomics

14 July 2018

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Global transcriptome analysis of the heat shock response of Shewanella oneidensis

14 July 2018

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Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism

14 July 2018

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Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli

14 July 2018

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Evidence against the selfish operon theory

14 July 2018

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Integrating high-throughput and computational data elucidates bacterial networks

14 July 2018

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Just-in-time transcription program in metabolic pathways

14 July 2018

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MUSCLE: multiple sequence alignment with high accuracy and high throughput

14 July 2018

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In silico analysis reveals substantial variability in the gene contents of the gamma proteobacteria LexA-regulon

14 July 2018

1 reference

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Genome-Scale Analysis of the Uses of the Escherichia coli Genome: Model-Driven Analysis of Heterogeneous Data Sets

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Experimental Determination and System Level Analysis of Essential Genes in Escherichia coli MG1655

14 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=1480536

From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria

14 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=1480536

Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Parallel changes in gene expression after 20,000 generations of evolution in Escherichiacoli

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

CDD: a curated Entrez database of conserved domain alignments

14 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=1480536

ASAP, a systematic annotation package for community analysis of genomes

14 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=1480536

The Stanford Microarray Database: data access and quality assessment tools

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Factors influencing the identification of transcription factor binding sites by cross-species comparison.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

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14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Likelihood-based tests of topologies in phylogenetics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Co-expression pattern from DNA microarray experiments as a tool for operon prediction

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Connected gene neighborhoods in prokaryotic 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=1480536

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Deletional bias and the evolution of bacterial 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=1480536

Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Prediction of operons in microbial 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=1480536

The COG database: new developments in phylogenetic classification of proteins from complete 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=1480536

Predicting protein function by genomic context: quantitative evaluation and qualitative inferences

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Operons in Escherichia coli: genomic analyses and predictions

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

opdA, a Salmonella enterica serovar Typhimurium gene encoding a protease, is part of an operon regulated by heat shock

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Finding families for genomic ORFans

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Initiation of translation in prokaryotes and eukaryotes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

The use of gene clusters to infer functional coupling

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Components of the Salmonella flagellar export apparatus and classification of export substrates

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Conservation of gene order: a fingerprint of proteins that physically interact

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Selfish operons: horizontal transfer may drive the evolution of gene clusters

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Molecular characterization of the Salmonella typhimurium flhB operon and its protein products

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

The distance between Escherichia coli genes is related to gene expression levels

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

recD: the gene for an essential third subunit of exonuclease V

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Nucleotide sequence of the dapF gene and flanking regions from Escherichia coli K12

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Heterologous expression and regulation of the lysA genes of Pseudomonas aeruginosa and Escherichia 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=1480536

Structure and regulation of the Escherichia coli ruv operon involved in DNA repair and recombination.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Cloning and nucleotide sequencing of the genes rimI and rimJ which encode enzymes acetylating ribosomal proteins S18 and S5 of Escherichia coli K12.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Vitamin B12 transport in Escherichia coli K12 does not require the btuE gene of the btuCED operon

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Recombination at ColE1 cer requires the Escherichia coli xerC gene product, a member of the lambda integrase family of site-specific recombinases

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Efficient attenuation of stochasticity in gene expression through post-transcriptional control.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

A powerful non-homology method for the prediction of operons in prokaryotes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Distributional profiles of homologous open reading frames among bacterial phyla: implications for vertical and lateral transmission

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Translation at higher than an optimal level interferes with coupling at an intercistronic junction.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Regulation of diaminopimelate decarboxylase synthesis in Escherichia coli. III. Nucleotide sequence and regulation of the lysR gene

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Inference and Analysis of the Relative Stability of Bacterial Chromosomes

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Analysis of the Cellular Functions of Escherichia coli Operons and Their Conservation in Bacillus subtilis

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1480536

Divergent transcriptional and translational signals in Archaea

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16789824

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Leaderless transcripts of the crenarchaeal hyperthermophile Pyrobaculum aerophilum

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16789824

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

On dynamics of overlapping genes in bacterial genomes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16789824

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PGEN.0020096

1 reference

24 July 2017

1 reference

24 July 2017

1 reference