List of works - Cynthia Sharma

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

scientific article published on 23 September 2020

A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence

scientific article published on 27 May 2020

A non‐coding RNA from the intercellular adhesion ( ica ) locus of Staphylococcus epidermidis controls polysaccharide intercellular adhesion (PIA)‐mediated biofilm formation

scientific article published on 06 April 2019

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

scientific article

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

scientific article published on 18 February 2020

A variable homopolymeric G-repeat defines small RNA-mediated posttranscriptional regulation of a chemotaxis receptor in Helicobacter pylori

scientific article

An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains.

scientific article published on 10 September 2012

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

scientific article published on August 24, 2012

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

scientific article

Argonaute proteins affect siRNA levels and accumulation of a novel extrachromosomal DNA from the Dictyostelium retrotransposon DIRS-1

scientific article

Automated transcription start site prediction for comparative Transcriptomics using the SuperGenome

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

scientific article

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

scientific article published in March 2018

Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity

scientific article published on 17 April 2014

Contribution of Hfq to photooxidative stress resistance and global regulation in Rhodobacter sphaeroides

scientific article published on 27 April 2011

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

scientific article

Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability.

scientific article

Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes

scientific article

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

scientific article published on 16 February 2012

Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome

scientific article

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

scientific article published on May 2011

Differences in the Transcriptomic Response of Campylobacter coli and Campylobacter lari to Heat Stress

scientific article published on 27 March 2020

Differential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori.

scientific article published on 16 June 2015

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

scientific article

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

scientific article published on June 2014

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

scientific article

Experimental approaches for the discovery and characterization of regulatory small RNA.

scientific article

Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism

scientific article

Experimental tools to identify RNA-protein interactions in Helicobacter pylori.

scientific article

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

scientific article

Functional characterization of the RNA chaperone Hfq in the opportunistic human pathogen Stenotrophomonas maltophilia

scientific article

Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq)

scientific article (publication date: 12 August 2016)

Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions

scientific article

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

scientific article

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

scientific article

HRIBO - High-throughput analysis of bacterial ribosome profiling data

scientific article published on 11 November 2020

HRIBO - High-throughput analysis of bacterial ribosome profiling data

scientific article published on 29 April 2020

Helicobacter pylori interferes with an embryonic stem cell micro RNA cluster to block cell cycle progression

scientific article published on 25 October 2011

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

scientific article

How to find small non-coding RNAs in bacteria

scientific article

Identification of regulatory RNAs in Bacillus subtilis

scientific article

Identification of the RNA Pyrophosphohydrolase RppH of Helicobacter pylori and Global Analysis of Its RNA Targets

scientific article published on 14 December 2016

In vivo and in vitro analysis of 6S RNA-templated short transcripts in Bacillus subtilis

scientific article

In vivo mapping of RNA-RNA interactions in Staphylococcus aureus using the endoribonuclease III.

scientific article

Interesting twists on small RNA themes in Pseudomonas aeruginosa ⬇️

scientific article published on March 28, 2011

Interplay of two small RNAs fine-tunes hierarchical flagellar gene expression in the foodborne pathogen Campylobacter jejuni

scientific article published on 22 April 2023

Investigating CRISPR RNA Biogenesis and Function Using RNA-seq

scientific article published on January 2015

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

scientific article published on 28 May 2021

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

scientific article published on 27 July 2011

Photooxidative stress-induced and abundant small RNAs in Rhodobacter sphaeroides

scientific article

Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis

scientific article (publication date: 16 August 2014)

Profound impact of Hfq on nutrient acquisition, metabolism and motility in the plant pathogen Agrobacterium tumefaciens

scientific article

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

scientific article published on 3 April 2014

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

scientific article

RNA Localization in Bacteria

scientific article published on 01 September 2018

RNA recording in single bacterial cells using reprogrammed tracrRNAs

scientific article published in August 2023

RNase III-mediated processing of a trans -acting bacterial sRNA and its cis -encoded antagonist

scientific article published on 19 March 2021

RNase III-mediated processing of a trans-acting bacterial sRNA and its cis-encoded antagonist

scientific article published in 2021

RiboReport - Benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria

scientific article published on 9 June 2021

Ribosome-controlled transcription termination is essential for the production of antibiotic microcin C.

scientific article published on October 2014

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

scientific article

Small RNA mediated gradual control of lipopolysaccharide biosynthesis affects antibiotic resistance in Helicobacter pylori

scientific article published on 21 July 2021

Small RNAs and virulence in bacterial pathogens

scientific article published on 01 April 2012

Small RNAs in Bacterial Virulence and Communication.

scientific article published on June 2016

Small RNAs of theBradyrhizobium/Rhodopseudomonaslineage and their analysis

article

Small RNAs that target G‐rich sequences are generated by diverse biogenesis pathways in Epsilonproteobacteria

scientific article published in January 2022

Stable isotope labeling by amino acids in cell culture based proteomics reveals differences in protein abundances between spiral and coccoid forms of the gastric pathogen Helicobacter pylori

scientific article published on 12 May 2015

Structural insights into the AapA1 toxin of Helicobacter pylori

scientific article published on 30 August 2019

Target recognition, RNA methylation activity and transcriptional regulation of the Dictyostelium discoideum Dnmt2-homologue (DnmA)

scientific article

Tetrachloroethene respiration in Sulfurospirillum species is regulated by a two‐component system as unraveled by comparative genomics, transcriptomics, and regulator binding studies

scientific article

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

scientific article published on 27 May 2016

The Rsm (Csr) post-transcriptional regulatory pathway coordinately controls multiple CRISPR-Cas immune systems

scientific article published on 01 September 2021

The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella Typhimurium during invasion gene expression

scientific article

The primary transcriptome of barley chloroplasts: numerous noncoding RNAs and the dominating role of the plastid-encoded RNA polymerase

scientific article

The primary transcriptome of the Escherichia coli O104:H4 pAA plasmid and novel insights into its virulence gene expression and regulation

scientific article (publication date: 17 October 2016)

The primary transcriptome of the major human pathogen Helicobacter pylori

scientific article

The small non-coding RNA RsaE influences extracellular matrix composition in Staphylococcus epidermidis biofilm communities

scientific article published in March 2019

Transcriptome complexity and riboregulation in the human pathogen Helicobacter pylori

scientific article

dRNA-seq transcriptional profiling of the FK506 biosynthetic gene cluster in Streptomyces tsukubaensis NRRL18488 and general analysis of the transcriptome

article

tRNA epitranscriptome determines pathogenicity of the opportunistic pathogen <i>Pseudomonas aeruginosa</i>

scientific article published on 7 March 2024

List of works by Cynthia Sharma

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

A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence

A non‐coding RNA from the intercellular adhesion ( ica ) locus of Staphylococcus epidermidis controls polysaccharide intercellular adhesion (PIA)‐mediated biofilm formation

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

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

A variable homopolymeric G-repeat defines small RNA-mediated posttranscriptional regulation of a chemotaxis receptor in Helicobacter pylori

An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains.

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

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

Argonaute proteins affect siRNA levels and accumulation of a novel extrachromosomal DNA from the Dictyostelium retrotransposon DIRS-1

Automated transcription start site prediction for comparative Transcriptomics using the SuperGenome

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

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

Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity

Contribution of Hfq to photooxidative stress resistance and global regulation in Rhodobacter sphaeroides

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

Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability.

Deep sequencing of Salmonella RNA associated with heterologous Hfq proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes

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

Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome

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

Differences in the Transcriptomic Response of Campylobacter coli and Campylobacter lari to Heat Stress

Differential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori.

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

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

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

Experimental approaches for the discovery and characterization of regulatory small RNA.

Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism

Experimental tools to identify RNA-protein interactions in Helicobacter pylori.

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

Functional characterization of the RNA chaperone Hfq in the opportunistic human pathogen Stenotrophomonas maltophilia

Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq)

Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions

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

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

HRIBO - High-throughput analysis of bacterial ribosome profiling data

HRIBO - High-throughput analysis of bacterial ribosome profiling data

Helicobacter pylori interferes with an embryonic stem cell micro RNA cluster to block cell cycle progression

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

How to find small non-coding RNAs in bacteria

Identification of regulatory RNAs in Bacillus subtilis

Identification of the RNA Pyrophosphohydrolase RppH of Helicobacter pylori and Global Analysis of Its RNA Targets

In vivo and in vitro analysis of 6S RNA-templated short transcripts in Bacillus subtilis

In vivo mapping of RNA-RNA interactions in Staphylococcus aureus using the endoribonuclease III.

Interesting twists on small RNA themes in Pseudomonas aeruginosa ⬇️

Interplay of two small RNAs fine-tunes hierarchical flagellar gene expression in the foodborne pathogen Campylobacter jejuni

Investigating CRISPR RNA Biogenesis and Function Using RNA-seq

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

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

Photooxidative stress-induced and abundant small RNAs in Rhodobacter sphaeroides

Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis

Profound impact of Hfq on nutrient acquisition, metabolism and motility in the plant pathogen Agrobacterium tumefaciens

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

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

RNA Localization in Bacteria

RNA recording in single bacterial cells using reprogrammed tracrRNAs

RNase III-mediated processing of a trans -acting bacterial sRNA and its cis -encoded antagonist

RNase III-mediated processing of a trans-acting bacterial sRNA and its cis-encoded antagonist

RiboReport - Benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria

Ribosome-controlled transcription termination is essential for the production of antibiotic microcin C.

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

Small RNA mediated gradual control of lipopolysaccharide biosynthesis affects antibiotic resistance in Helicobacter pylori

Small RNAs and virulence in bacterial pathogens

Small RNAs in Bacterial Virulence and Communication.

Small RNAs of theBradyrhizobium/Rhodopseudomonaslineage and their analysis

Small RNAs that target G‐rich sequences are generated by diverse biogenesis pathways in Epsilonproteobacteria

Stable isotope labeling by amino acids in cell culture based proteomics reveals differences in protein abundances between spiral and coccoid forms of the gastric pathogen Helicobacter pylori

Structural insights into the AapA1 toxin of Helicobacter pylori

Target recognition, RNA methylation activity and transcriptional regulation of the Dictyostelium discoideum Dnmt2-homologue (DnmA)

Tetrachloroethene respiration in Sulfurospirillum species is regulated by a two‐component system as unraveled by comparative genomics, transcriptomics, and regulator binding studies

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

The Rsm (Csr) post-transcriptional regulatory pathway coordinately controls multiple CRISPR-Cas immune systems

The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella Typhimurium during invasion gene expression

The primary transcriptome of barley chloroplasts: numerous noncoding RNAs and the dominating role of the plastid-encoded RNA polymerase

The primary transcriptome of the Escherichia coli O104:H4 pAA plasmid and novel insights into its virulence gene expression and regulation

The primary transcriptome of the major human pathogen Helicobacter pylori

The small non-coding RNA RsaE influences extracellular matrix composition in Staphylococcus epidermidis biofilm communities

Transcriptome complexity and riboregulation in the human pathogen Helicobacter pylori

dRNA-seq transcriptional profiling of the FK506 biosynthetic gene cluster in Streptomyces tsukubaensis NRRL18488 and general analysis of the transcriptome