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Differential RNA-seq: the approach behind and the biological insight gained

Current opinion in microbiology, 2014-06, Vol.19, p.97-105

2014

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

PLoS genetics, 2008-08, Vol.4 (8), p.e1000163-e1000163

2008

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High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates

PLoS genetics, 2013-05, Vol.9 (5), p.e1003495-e1003495

2013

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

Nature (London), 2011-03, Vol.471 (7340), p.602-607

2011

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An atlas of Hfq-bound transcripts reveals 3′ UTRs as a genomic reservoir of regulatory small RNAs

The EMBO journal, 2012-10, Vol.31 (20), p.4005-4019

2012

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Fast mapping of short sequences with mismatches, insertions and deletions using index structures

PLoS computational biology, 2009-09, Vol.5 (9), p.e1000502-e1000502

2009

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Global regulatory functions of the Staphylococcus aureus endoribonuclease III in gene expression

PLoS genetics, 2012-06, Vol.8 (6), p.e1002782-e1002782

2012

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Noncanonical crRNAs derived from host transcripts enable multiplexable RNA detection by Cas9

Science (American Association for the Advancement of Science), 2021-05, Vol.372 (6545), p.941-948

2021

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Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli

Journal of bacteriology, 2015-01, Vol.197 (1), p.18-28

2015

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Experimental approaches for the discovery and characterization of regulatory small RNA

Current opinion in microbiology, 2009-10, Vol.12 (5), p.536-546

2009

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Identification of RNA Binding Partners of CRISPR-Cas Proteins in Prokaryotes Using RIP-Seq

Methods in molecular biology (Clifton, N.J.), 2022, Vol.2404, p.111

2022

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Interplay of two small RNAs fine-tunes hierarchical flagella gene expression in Campylobacter jejuni

Nature communications, 2024-06, Vol.15 (1), p.5240-21, Article 5240

2024

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READemption-a tool for the computational analysis of deep-sequencing-based transcriptome data

Bioinformatics, 2014-12, Vol.30 (23), p.3421-3423

2014

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Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm formation

Proceedings of the National Academy of Sciences - PNAS, 2015-02, Vol.112 (7), p.E766-E775

2015

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The primary transcriptome of the major human pathogen Helicobacter pylori

Nature (London), 2010-03, Vol.464 (7286), p.250-255

2010

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Identification of regulatory RNAs in Bacillus subtilis

Nucleic acids research, 2010-10, Vol.38 (19), p.6637-6651

2010

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Identifying Small Open Reading Frames in Prokaryotes with Ribosome Profiling

Journal of bacteriology, 2022-01, Vol.204 (1), p.e0029421

2022

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A Repeat-Associated Small RNA Controls the Major Virulence Factors of Helicobacter pylori

Molecular cell, 2020-10, Vol.80 (2), p.210-226.e7

2020

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A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites

Genes & development, 2007-11, Vol.21 (21), p.2804-2817

2007

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The CsrA-FliW network controls polar localization of the dual-function flagellin mRNA in Campylobacter jejuni

Nature communications, 2016-05, Vol.7 (1), p.11667-11667, Article 11667

2016

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CRISPR RNA-Dependent Binding and Cleavage of Endogenous RNAs by the Campylobacter jejuni Cas9

Molecular cell, 2018-03, Vol.69 (5), p.893-905.e7

2018

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experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803

Proceedings of the National Academy of Sciences - PNAS, 2011-02, Vol.108 (5), p.2124-2129

2011

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Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis

BMC genomics, 2014-08, Vol.15 (1), p.684-684

2014

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A three-dimensional intestinal tissue model reveals factors and small regulatory RNAs important for colonization with Campylobacter jejuni

PLoS pathogens, 2020-02, Vol.16 (2), p.e1008304-e1008304

2020

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Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome

Nucleic acids research, 2010-01, Vol.38 (3), p.868-877

2010

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Differential RNA-seq: the approach behind and the biological insight gained

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

High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates

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

An atlas of Hfq-bound transcripts reveals 3′ UTRs as a genomic reservoir of regulatory small RNAs

Fast mapping of short sequences with mismatches, insertions and deletions using index structures

Global regulatory functions of the Staphylococcus aureus endoribonuclease III in gene expression

Noncanonical crRNAs derived from host transcripts enable multiplexable RNA detection by Cas9

Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli

Experimental approaches for the discovery and characterization of regulatory small RNA

Identification of RNA Binding Partners of CRISPR-Cas Proteins in Prokaryotes Using RIP-Seq

Interplay of two small RNAs fine-tunes hierarchical flagella gene expression in Campylobacter jejuni

READemption-a tool for the computational analysis of deep-sequencing-based transcriptome data

Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm formation

The primary transcriptome of the major human pathogen Helicobacter pylori

Identification of regulatory RNAs in Bacillus subtilis

Identifying Small Open Reading Frames in Prokaryotes with Ribosome Profiling

A Repeat-Associated Small RNA Controls the Major Virulence Factors of Helicobacter pylori

A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites

The CsrA-FliW network controls polar localization of the dual-function flagellin mRNA in Campylobacter jejuni

CRISPR RNA-Dependent Binding and Cleavage of Endogenous RNAs by the Campylobacter jejuni Cas9

experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803

Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis

A three-dimensional intestinal tissue model reveals factors and small regulatory RNAs important for colonization with Campylobacter jejuni

Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome

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