(Q34001909)

30 July 2017

title

Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli (English)

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30 July 2017

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8

Hirotada Mori

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30 July 2017

Atsuko Shinhara

1

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30 July 2017

Motomu Matsui

2

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30 July 2017

Kiriko Hiraoka

3

1 reference

30 July 2017

Wataru Nomura

4

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30 July 2017

Reiko Hirano

5

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30 July 2017

Kenji Nakahigashi

6

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30 July 2017

Masaru Tomita

7

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30 July 2017

Akio Kanai

9

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30 July 2017

language of work or name

English

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publication date

24 August 2011

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30 July 2017

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30 July 2017

volume

12

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30 July 2017

page(s)

428

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Genome-wide detection of novel regulatory RNAs in E. coli

30 July 2017

cites work

1 reference

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5 July 2018

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Studying bacterial transcriptomes using RNA-seq

5 July 2018

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Widespread antisense transcription in Escherichia coli.

5 July 2018

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Identification of regulatory RNAs in Bacillus subtilis

5 July 2018

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The primary transcriptome of the major human pathogen Helicobacter pylori

5 July 2018

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A broadening world of bacterial small RNAs

5 July 2018

1 reference

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The transcription unit architecture of the Escherichia coli genome

5 July 2018

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5 July 2018

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Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli

5 July 2018

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Next generation sequencing of microbial transcriptomes: challenges and opportunities.

5 July 2018

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Small stress response proteins in Escherichia coli: proteins missed by classical proteomic studies

5 July 2018

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Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation

5 July 2018

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A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi

5 July 2018

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Structure and complexity of a bacterial transcriptome.

5 July 2018

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Regulatory RNAs in bacteria

5 July 2018

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Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing

5 July 2018

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Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing

5 July 2018

1 reference

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Small membrane proteins found by comparative genomics and ribosome binding site models.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Repression of small toxic protein synthesis by the Sib and OhsC small RNAs

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

SOAP: short oligonucleotide alignment program

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Small RNAs making a small protein

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

A dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Regulating bacterial transcription with small RNAs.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Phage regulatory circuits and virulence gene expression

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Involvement of a novel transcriptional activator and small RNA in post-transcriptional regulation of the glucose phosphoenolpyruvate phosphotransferase system

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

The small RNA regulators of Escherichia coli: roles and mechanisms*

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

GadY, a small-RNA regulator of acid response genes in Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Java Treeview--extensible visualization of microarray data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Open source clustering software

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Global analysis of small RNA and mRNA targets of Hfq

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Prophages and bacterial genomics: what have we learned so far?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

A survey of small RNA-encoding genes in Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Molecular characterization of long direct repeat (LDR) sequences expressing a stable mRNA encoding for a 35-amino-acid cell-killing peptide and a cis-encoded small antisense RNA in Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Small RNAs in bacteria: diverse regulators of gene expression in response to environmental changes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

BLAT—The BLAST-Like Alignment Tool

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

RNAMotif, an RNA secondary structure definition and search algorithm

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

A computational approach to identify genes for functional RNAs in genomic sequences

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Computational identification of noncoding RNAs in E. coli by comparative genomics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Prediction of rho-independent transcriptional terminators in Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Novel small RNA-encoding genes in the intergenic regions of Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Identification of novel small RNAs using comparative genomics and microarrays

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Multiple hok genes on the chromosome of Escherichia coli

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

A small, stable RNA induced by oxidative stress: role as a pleiotropic regulator and antimutator

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

A flexible motif search technique based on generalized profiles.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Escherichia colipromoter sequences predictin vitroRNA polymerase selectivity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Genetic evidence that DicF, a second division inhibitor encoded by the Escherichia coli dicB operon, is probably RNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Regulation of the expression of the cell-cycle gene ftsZ by DicF antisense RNA. Division does not require a fixed number of FtsZ molecules

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Guidelines for bacteriophage characterization

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3175480

Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model.

5 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1471-2164-12-428

A probabilistic method for identifying start codons in bacterial genomes.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186%2F1471-2164-12-428

21 January 2018

Identifiers

DOI

10.1186/1471-2164-12-428

1 reference

30 July 2017

1 reference

30 July 2017

1 reference