Target prediction for small, noncoding RNAs in bacteria (Q24544245)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16717284 AND SRC:MED&resulttype=core&format=json

28 January 2020

title

Target prediction for small, noncoding RNAs in bacteria (English)

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28 January 2020

1 reference

2

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28 January 2020

Maude Guillier

4

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28 January 2020

Gisela Storz

7

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28 January 2020

author name string

Brian Tjaden

1

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28 January 2020

Jason A Opdyke

3

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28 January 2020

Daniel X Fu

5

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28 January 2020

Susan Gottesman

6

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28 January 2020

language of work or name

English

0 references

publication date

22 May 2006

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28 January 2020

published in

Nucleic Acids Research

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28 January 2020

volume

34

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28 January 2020

issue

9

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28 January 2020

page(s)

2791-2802

1 reference

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DINAMelt web server for nucleic acid melting prediction

28 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

24 March 2017

Human MicroRNA targets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Fast and effective prediction of microRNA/target duplexes

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

MicroRNA targets in Drosophila

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Identification of Drosophila MicroRNA targets

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Computational identification of Drosophila microRNA genes

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Mfold web server for nucleic acid folding and hybridization prediction

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Identification of the Hfq-binding site on DsrA RNA: Hfq binds without altering DsrA secondary structure

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Spot 42 RNA mediates discoordinate expression of the E. coli galactose operon

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

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

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

The Escherichia coli OxyS regulatory RNA represses fhlA translation by blocking ribosome binding

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Riboregulation in Escherichia coli: DsrA RNA acts by RNA:RNA interactions at multiple loci

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Combinatorial microRNA target predictions

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Prediction of mammalian microRNA targets

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Identification of common molecular subsequences

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Vienna RNA secondary structure server

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Remodelling of the Escherichia coli outer membrane by two small regulatory RNAs

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Effect of RyhB small RNA on global iron use in Escherichia coli

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Regulation and mode of action of the second small RNA activator of RpoS translation, RprA

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Prediction of plant microRNA targets

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

The gcvB gene encodes a small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

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

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

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

24 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

A combined computational-experimental approach predicts human microRNA targets

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

An efficient recombination system for chromosome engineering in Escherichia coli

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Incorporating structure to predict microRNA targets

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulator

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Local alignment statistics

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

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

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

The function of micF RNA. micF RNA is a major factor in the thermal regulation of OmpF protein in Escherichia coli.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1464411

Secondary structure prediction of interacting RNA molecules

19 June 2018

1 reference

Regulation by iron: RNA rules the rust

21 January 2018

1 reference

PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes

21 January 2018

1 reference

Identification and characterization of novel small RNAs in the aspS-yrvM intergenic region of the Bacillus subtilis genome

21 January 2018

1 reference

A nonlinear measure of subalignment similarity and its significance levels

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16717284

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

fhlA repression by OxyS RNA: kissing complex formation at two sites results in a stable antisense-target RNA complex

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/16717284

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKL356

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16717284 AND SRC:MED&resulttype=core&format=json

28 January 2020

1 reference

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:16717284 AND SRC:MED&resulttype=core&format=json

28 January 2020

PubMed publication ID

16717284

2 references