Identifying and characterizing Hfq-RNA interactions (Q34740470)

4 August 2017

title

Identifying and characterizing Hfq-RNA interactions (English)

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4 August 2017

M A Faner

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4 August 2017

A L Feig

series ordinal

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4 August 2017

publication date

23 May 2013

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4 August 2017

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4 August 2017

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4 August 2017

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4 August 2017

page(s)

144-159

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Predicting sRNAs and their targets in bacteria

4 August 2017

cites work

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7 July 2018

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7 July 2018

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7 July 2018

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Essential Requirements for Robust Signaling in Hfq Dependent Small RNA Networks

7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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PolyU tail of rho-independent terminator of bacterial small RNAs is essential for Hfq action

7 July 2018

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Hfq and its constellation of RNA

7 July 2018

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Structural basis for RNA 3'-end recognition by Hfq

7 July 2018

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Major role for mRNA binding and restructuring in sRNA recruitment by Hfq.

7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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RNAs actively cycle on the Sm-like protein Hfq.

7 July 2018

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Evidence for an autonomous 5' target recognition domain in an Hfq-associated small RNA

7 July 2018

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Recognition of heptameric seed sequence underlies multi-target regulation by RybB small RNA in Salmonella enterica

7 July 2018

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Studying RNA-RNA and RNA-protein interactions by isothermal titration calorimetry.

7 July 2018

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An upstream Hfq binding site in the fhlA mRNA leader region facilitates the OxyS-fhlA interaction

7 July 2018

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Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA

7 July 2018

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Base pairing small RNAs and their roles in global regulatory networks

7 July 2018

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7 July 2018

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The response regulator SprE (RssB) is required for maintaining poly(A) polymerase I-degradosome association during stationary phase

7 July 2018

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7 July 2018

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7 July 2018

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Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts

7 July 2018

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A minimal base-pairing region of a bacterial small RNA SgrS required for translational repression of ptsG mRNA

7 July 2018

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7 July 2018

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Proteomic alterations explain phenotypic changes in Sinorhizobium meliloti lacking the RNA chaperone Hfq.

7 July 2018

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The role of Hfq in bacterial pathogens

7 July 2018

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Structure of Escherichia coli Hfq bound to polyriboadenylate RNA

7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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7 July 2018

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Multiple target regulation by small noncoding RNAs rewires gene expression at the post-transcriptional level

7 July 2018

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Global systems-level analysis of Hfq and SmpB deletion mutants in Salmonella: implications for virulence and global protein translation

7 July 2018

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7 July 2018

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Small RNA binding to 5' mRNA coding region inhibits translational initiation

7 July 2018

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The 5' end of two redundant sRNAs is involved in the regulation of multiple targets, including their own regulator

7 July 2018

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IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions

7 July 2018

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Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools

7 July 2018

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7 July 2018

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

7 July 2018

1 reference

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The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA

7 July 2018

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High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis

7 July 2018

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7 July 2018

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High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states

7 July 2018

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Systematic deletion of Salmonella small RNA genes identifies CyaR, a conserved CRP-dependent riboregulator of OmpX synthesis

7 July 2018

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The RNA binding protein Hfq interacts specifically with tRNAs.

7 July 2018

1 reference

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

7 July 2018

1 reference

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Sm-like protein Hfq: location of the ATP-binding site and the effect of ATP on Hfq-- RNA complexes.

7 July 2018

1 reference

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SigmaE-dependent small RNAs of Salmonella respond to membrane stress by accelerating global omp mRNA decay

7 July 2018

1 reference

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Regulatory mechanisms employed by cis-encoded antisense RNAs

7 July 2018

1 reference

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Mechanism of RNA silencing by Hfq-binding small RNAs

7 July 2018

1 reference

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Translational control and target recognition by Escherichia coli small RNAs in vivo

7 July 2018

1 reference

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Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

7 July 2018

1 reference

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The RNA chaperone Hfq is essential for the virulence of Salmonella typhimurium

7 July 2018

1 reference

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Hfq modulates the sigmaE-mediated envelope stress response and the sigma32-mediated cytoplasmic stress response in Escherichia coli

7 July 2018

1 reference

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From ribosome to riboswitch: control of gene expression in bacteria by RNA structural rearrangements

7 July 2018

1 reference

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Base-pairing requirement for RNA silencing by a bacterial small RNA and acceleration of duplex formation by Hfq

7 July 2018

1 reference

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Identification of small Hfq-binding RNAs in Listeria monocytogenes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

Escherichia coli Hfq binds A18 and DsrA domain II with similar 2:1 Hfq6/RNA stoichiometry using different surface sites

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

Facilitating RNA structure prediction with microarrays

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

CLIP: a method for identifying protein-RNA interaction sites in living cells

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

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

7 July 2018

1 reference

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RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs

7 July 2018

1 reference

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Bacterial small RNA regulators

7 July 2018

1 reference

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RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE)

7 July 2018

1 reference

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Interaction network containing conserved and essential protein complexes in Escherichia coli

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

Cycling of the Sm-like protein Hfq on the DsrA small regulatory RNA

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

The RNA-binding protein Hfq of Listeria monocytogenes: role in stress tolerance and virulence

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

Global analysis of small RNA and mRNA targets of Hfq

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

A survey of small RNA-encoding genes in Escherichia coli

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

Kinetic studies of RNA-protein interactions using surface plasmon resonance.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

Lead(II) as a probe for investigating RNA structure in vivo

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

Identification of novel small RNAs using comparative genomics and microarrays

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

Methods and statistics for combining motif match scores

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

The E. coli signal recognition particle is required for the insertion of a subset of inner membrane proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

AU-rich elements: characterization and importance in mRNA degradation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

Regulation of the Escherichia coli hfq gene encoding the host factor for phage Q beta

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

Characterization of broadly pleiotropic phenotypes caused by an hfq insertion mutation in Escherichia coli K-12.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

Functional analysis of reverse transcription by a frameshift pol mutant of murine leukemia virus

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

RNA SHAPE analysis in living cells

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

Experimental identification of small non-coding regulatory RNAs in the opportunistic human pathogen Burkholderia cenocepacia J2315.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependent GcvB small RNA.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

Construction of two mathematical models for prediction of bacterial sRNA targets.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

The Sm-like protein Hfq regulates polyadenylation dependent mRNA decay in Escherichia coli.

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

Hfq is essential for Vibrio cholerae virulence and downregulates sigma expression

26 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3787079

The host factor required for RNA phage Qbeta RNA replication in vitro. Intracellular location, quantitation, and purification by polyadenylate-cellulose chromatography

26 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23707622

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.YMETH.2013.04.023

1 reference

4 August 2017

1 reference

4 August 2017

1 reference