Title: Revisiting operons: an analysis of the landscape of transcriptional units in E. coli

Journal Article · · BMC Bioinformatics

Not Available

Sponsoring Organization:
USDOE
OSTI ID:
1618519
Journal Information:
BMC Bioinformatics, Journal Name: BMC Bioinformatics Journal Issue: 1 Vol. 16; ISSN 1471-2105
Publisher:
Springer Science + Business MediaCopyright Statement
Country of Publication:
United Kingdom
Language:
English

References (35)

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The size of the transcription unit in balbiani ring 2 of Chironomus tentans as derived from analysis of the primary transcript and 75 S RNA journal September 1978
Differential Translation Tunes Uneven Production of Operon-Encoded Proteins journal September 2013
Global Genomic Arrangement of Bacterial Genes Is Closely Tied with the Total Transcriptional Efficiency journal February 2013
The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: A molecular perspective journal November 2006
Gene Ontology: tool for the unification of biology journal May 2000
Prevalence of transcription promoters within archaeal operons and coding sequences journal January 2009
The transcription unit architecture of the Escherichia coli genome journal November 2009
Bacterial nucleoid-associated proteins, nucleoid structure and gene expression journal February 2010
Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome journal March 2010
Operons in Escherichia coli: Genomic analyses and predictions journal May 2000
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles journal April 1999
Physical descriptions of the bacterial nucleoid at large scales, and their biological implications journal June 2012
The EcoCyc Database journal January 2002
Connected gene neighborhoods in prokaryotic genomes journal May 2002
Prediction of functional modules based on comparative genome analysis and Gene Ontology application journal May 2005
Operon prediction using both genome-specific and general genomic information journal December 2006
Detecting uber-operons in prokaryotic genomes journal April 2006
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information journal October 2007
DOOR: a database for prokaryotic operons journal November 2008
OperonDB: a comprehensive database of predicted operons in microbial genomes journal January 2009
Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes journal September 2011
RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more journal November 2012
Computational analyses of transcriptomic data reveal the dynamic organization of the Escherichia coli chromosome under different conditions journal April 2013
Computational analysis of bacterial RNA-Seq data journal May 2013
Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum journal March 2015
Genome-wide detection of novel regulatory RNAs in E. coli journal June 2011
Genomewide Function Conservation and Phylogeny in the Herpesviridae journal January 2001
The pdhR?aceEF?lpd operon of Escherichia coli expresses the pyruvate dehydrogenase complex journal April 1994
Unprecedented High-Resolution View of Bacterial Operon Architecture Revealed by RNA Sequencing journal July 2014
A Universal Operon Predictor for Prokaryotic Genomes journal February 2009
Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study journal January 2011
Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling journal January 2013
A high resolution map of a cyanobacterial transcriptome journal January 2011
Genome‐wide study of mRNA degradation and transcript elongation in E scherichia coli journal January 2015

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