(Q34722556)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675309%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

title

Genome-wide identification of regulatory RNAs in the human pathogen Clostridium difficile (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675309%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

main subject

Clostridium difficile

0 references

author

Olga Soutourina

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675309%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Marc Monot

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675309%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

author name string

Pierre Boudry

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675309%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Laure Saujet

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675309%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Christophe Pichon

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675309%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Odile Sismeiro

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675309%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Ekaterina Semenova

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675309%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Konstantin Severinov

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675309%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Chantal Le Bouguenec

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675309%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Jean-Yves Coppée

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675309%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Bruno Dupuy

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675309%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Isabelle Martin-Verstraete

12

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675309%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

publication date

9 May 2013

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675309%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675309%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

volume

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675309%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

issue

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675309%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

page(s)

e1003493

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675309%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

1 March 2020

copyright license

start time

9 May 2013

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome

7 July 2018

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Cyclic diguanylate inversely regulates motility and aggregation in Clostridium difficile

7 July 2018

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Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens

7 July 2018

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Identification of 88 regulatory small RNAs in the TIGR4 strain of the human pathogen Streptococcus pneumoniae.

7 July 2018

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Essential features and rational design of CRISPR RNAs that function with the Cas RAMP module complex to cleave RNAs.

7 July 2018

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An in silico model for identification of small RNAs in whole bacterial genomes: characterization of antisense RNAs in pathogenic Escherichia coli and Streptococcus agalactiae strains

7 July 2018

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CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation

7 July 2018

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Cyclic di-GMP, an established secondary messenger still speeding up.

7 July 2018

1 reference

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Mechanism for gene control by a natural allosteric group I ribozyme

7 July 2018

1 reference

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Hfq and its constellation of RNA

7 July 2018

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7 July 2018

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Clostridium difficile has two parallel and essential Sec secretion systems

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

The key sigma factor of transition phase, SigH, controls sporulation, metabolism, and virulence factor expression in Clostridium difficile

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Evolution and classification of the CRISPR-Cas systems

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor.

7 July 2018

1 reference

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c-di-GMP turn-over in Clostridium difficile is controlled by a plethora of diguanylate cyclases and phosphodiesterases

7 July 2018

1 reference

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The human gut mobile metagenome: a metazoan perspective.

7 July 2018

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CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Reannotation of the genome sequence of Clostridium difficile strain 630.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

An expanding universe of small 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=3649979

Small RNAs in the genus Clostridium

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Comparative genome-wide analysis of small RNAs of major Gram-positive pathogens: from identification to application

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

RNase III participates in GadY-dependent cleavage of the gadX-gadW mRNA.

7 July 2018

1 reference

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Cyclic-di-GMP reaches out into the bacterial RNA world

7 July 2018

1 reference

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Studying bacterial transcriptomes using RNA-seq

7 July 2018

1 reference

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Integration of metabolism and virulence by Clostridium difficile CodY

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Bacterial antisense RNAs: how many are there, and what are they doing?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

An allosteric self-splicing ribozyme triggered by a bacterial second messenger

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Regulatory RNA in bacterial pathogens

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Transcription, processing and function of CRISPR cassettes 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=3649979

Stabilization of Clostridium perfringens collagenase mRNA by VR-RNA-dependent cleavage in 5' leader sequence

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Freiburg RNA Tools: a web server integrating INTARNA, EXPARNA and LOCARNA

7 July 2018

1 reference

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Virulence factor p60 of Listeria monocytogenes modulates innate immunity by inducing tumor necrosis factor alpha

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

The T box mechanism: tRNA as a regulatory molecule

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

A single-base resolution map of an archaeal transcriptome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Activation of gene expression by small 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=3649979

An overview of RNAs with regulatory functions in gram-positive 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=3649979

A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Characterization of the sporulation initiation pathway of Clostridium difficile and its role in toxin production

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

RNase Y, a novel endoribonuclease, initiates riboswitch turnover in Bacillus subtilis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

The Sequence Alignment/Map format and SAMtools

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

New trends in Clostridium difficile virulence and pathogenesis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Regulatory RNAs 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=3649979

Rfam: updates to the RNA families database

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

High-throughput, kingdom-wide prediction and annotation of bacterial non-coding 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=3649979

Riboswitches in eubacteria sense the second messenger cyclic di-GMP

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Clostridium difficile toxin synthesis is negatively regulated by TcdC.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Comparative genomic analysis of T-box regulatory systems 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=3649979

CRISPR--a widespread system that provides acquired resistance against phages in bacteria and archaea

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Proteins that interact with bacterial small RNA regulators

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Regulatory mechanisms employed by cis-encoded antisense 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=3649979

6S RNA: a small RNA regulator 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=3649979

Construction and analysis of chromosomal Clostridium difficile mutants

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Target prediction for small, noncoding RNAs 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=3649979

RNase P cleaves transient structures in some riboswitches

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Ribonucleases J1 and J2: two novel endoribonucleases in B.subtilis with functional homology to E.coli RNase E.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

A highly conserved 6S RNA structure is required for regulation 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=3649979

Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

The riboswitch control of bacterial metabolism

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Mfold web server for nucleic acid folding and hybridization prediction

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

The VirR/VirS regulatory cascade affects transcription of plasmid-encoded putative virulence genes in Clostridium perfringens strain 13.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

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=3649979

Clostridial VirR/VirS regulon involves a regulatory RNA molecule for expression of toxins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Clostridium difficile cell attachment is modified by environmental factors

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Regulated transcription of Clostridium difficile toxin genes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

The lytE gene of Bacillus subtilis 168 encodes a cell wall hydrolase.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Glucosylation of Rho proteins by Clostridium difficile toxin B.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

Relapse of antibiotic associated colitis: endogenous persistence of Clostridium difficile during vancomycin therapy

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3649979

RNAs: regulators of bacterial virulence

7 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003493

Deep sequencing defines the transcriptional map of L. pneumophila and identifies growth phase-dependent regulated ncRNAs implicated in virulence

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003493

Multiple factors modulate biofilm formation by the anaerobic pathogen Clostridium difficile

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003493

Evaluation of candidate reference genes in Clostridium difficile for gene expression normalization

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PGEN.1003493

A P60 mutant of Listeria monocytogenes is impaired in its ability to cause infection in intragastrically inoculated mice

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23675309

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23675309

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Genetic evidence for involvement of the alternative sigma factor SigI in controlling expression of the cell wall hydrolase gene lytE and contribution of LytE to heat survival of Bacillus subtilis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23675309

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PGEN.1003493

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675309%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675309%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23675309%20AND%20SRC:MED&resulttype=core&format=json