C. Sharma

发表

RNA Localization in Bacteria.

Jingyi Fei, C. Sharma, 2018, Microbiology spectrum.

Identification of small regulatory RNAs and their targets in bacteria

C. Sharma, 2009 .

Small RNAs in Bacterial Virulence and Communication.

C. Sharma, S. L. Svensson, Sarah L. Svensson, 2016, Microbiology spectrum.

Deep Sequencing Analysis of Small Noncoding RNA and mRNA Targets of the Global Post-Transcriptional Regulator, Hfq

J. Vogel, T. Binnewies, K. Papenfort, 2008, PLoS genetics.

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

J. Vogel, C. Sharma, A. Sittka, 2009, RNA biology.

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

J. Vogel, C. Sharma, 2009, Current opinion in microbiology.

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

J. Vogel, C. Sharma, F. Darfeuille, 2007, Genes & development.

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

J. Vogel, C. Sharma, K. Nierhaus, 2008, Molecular cell.

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

J. Vogel, R. Schmitz, C. Sharma, 2009, Proceedings of the National Academy of Sciences.

Identification of regulatory RNAs in Bacillus subtilis

J. Vogel, Irnov Irnov, W. Winkler, 2010, Nucleic acids research.

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

J. Vogel, K. Papenfort, C. Sharma, 2010, Proceedings of the National Academy of Sciences.

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

J. Vogel, B. Voß, W. Hess, 2011, Proceedings of the National Academy of Sciences.

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

J. Vogel, E. Charpentier, Krzysztof Chylinski, 2011, Nature.

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

J. Vogel, H. Mollenkopf, K. Papenfort, 2011, Molecular microbiology.

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

P. Stadler, J. Vogel, Sven Findeiß, 2011, Nucleic acids research.

Global Transcriptional Start Site Mapping Using Differential RNA Sequencing Reveals Novel Antisense RNAs in Escherichia coli

Kay Nieselt, Konrad U. Förstner, Thorsten Bischler, 2014, Journal of bacteriology.

High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates

Kay Nieselt, Konrad U. Förstner, Richard Reinhardt, 2013, PLoS genetics.

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

Amy K. Cain, A. Westermann, J. Vogel, 2020 .

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

Amy K. Cain, A. Westermann, J. Vogel, 2020, bioRxiv.

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

Sascha Dietrich, C. Sharma, Sandy R. Pernitzsch, 2020, Molecular cell.

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

Konrad U. Förstner, J. Vogel, A. Mellmann, 2016, Scientific Reports.

HRIBO: high-throughput analysis of bacterial ribosome profiling data

R. Backofen, C. Sharma, Florian Eggenhofer, 2020, bioRxiv.

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

K. Nieselt, C. Sharma, T. Bischler, 2015, Methods.

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

Konrad U. Förstner, A. Marchfelder, A. Becker, 2016, BMC Genomics.

Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis

Konrad U. Förstner, J. Reeve, C. Sharma, 2014, BMC Genomics.

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

Andreas S. Richter, R. Backofen, R. Schmitz, 2012, Nucleic acids research.

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

Konrad U. Förstner, C. Sharma, K. Förstner, 2019, PLoS pathogens.

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

Konrad U. Förstner, S. Engelmann, K. Thormann, 2019, Molecular microbiology.

Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their analysis

J. Vogel, R. Reinhardt, G. Pessi, 2012, RNA biology.

Structural insights into the AapA1 toxin of Helicobacter pylori.

I. Alves, G. Salgado, C. Sharma, 2019, Biochimica et biophysica acta. General subjects.

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

C. Sharma, D. Beier, Sandy R. Pernitzsch, 2014, Proceedings of the National Academy of Sciences.

The Primary Transcriptome of Barley Chloroplasts: Numerous Noncoding RNAs and the Dominating Role of the Plastid-Encoded RNA Polymerase[C][W][OA]

Konrad U. Förstner, J. Vogel, C. Sharma, 2012, Plant Cell.

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

P. Sergiev, K. Severinov, M. Djordjevic, 2014, Nucleic acids research.

Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome

Jörg Vogel, Richard Reinhardt, Cynthia M. Sharma, 2009, Nucleic acids research.

Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni

R. Backofen, S. Engelmann, C. Sharma, 2022, bioRxiv.

Small proteome of the nitrogen-fixing plant symbiont Sinorhizobium meliloti

R. Backofen, C. Ahrens, D. Becher, 2022, bioRxiv.

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

J. Vogel, F. Lottspeich, G. Klug, 2011, Molecular microbiology.

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.

P. Uetz, S. Kalkhof, C. Sharma, 2015, Journal of proteomics.

Functional Characterization of the RNA Chaperone Hfq in the Opportunistic Human Pathogen Stenotrophomonas maltophilia

Konrad U. Förstner, Valerio Costa, Cynthia M. Sharma, 2012, Journal of bacteriology.

How to find small non-coding RNAs in bacteria

Jörg Vogel, J. Vogel, C. Sharma, 2005, Biological chemistry.

Going Deeper : Global Sequencing Approaches Identify Numerous sRNA Candidates and Place Riboregulators Centrally into Posttranscriptional Regulatory Networks

C. Sharma, Sarah L. Svensson, 2016 .

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

C. Sharma, Sarah L. Svensson, 2021, Molecular microbiology.

An RNase III processed, antisense RNA pair regulates a Campylobacter jejuni colonization factor

C. Sharma, Sarah L. Svensson, 2021 .

Argonaute Proteins Affect siRNA Levels and Accumulation of a Novel Extrachromosomal DNA from the Dictyostelium Retrotransposon DIRS-1*

Konrad U. Förstner, C. Sharma, K. Förstner, 2014, The Journal of Biological Chemistry.

Regulatory Mechanisms of Special Significance: Role of Small RNAs in Virulence Regulation

J. Vogel, C. Sharma, A. Böhm, 2013 .

The primary transcriptome of the major human pathogen Helicobacter pylori

Kristin Reiche, Peter F. Stadler, Steve Hoffmann, 2010, Nature.

Global Regulatory Functions of the Staphylococcus aureus Endoribonuclease III in Gene Expression

J. Vogel, F. Vandenesch, P. Romby, 2012, PLoS genetics.

Spacer prioritization in CRISPR-Cas9 immunity is enabled by the leader RNA

Chase L. Beisel, Omer S. Alkhnbashi, R. Backofen, 2022, Nature Microbiology.

Investigating CRISPR RNA Biogenesis and Function Using RNA-seq.

J. Vogel, C. Sharma, Nadja Heidrich, 2015, Methods in molecular biology.

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

C. Sharma, Sahil Sharma, 2021, Methods in molecular biology.

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

Konrad U. Förstner, K. Nieselt, C. Sharma, 2017, RNA biology.

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

Konrad U. Förstner, B. Bassler, C. Sharma, 2015, Proceedings of the National Academy of Sciences.

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

M. Nowrousian, C. Sharma, F. Narberhaus, 2012, RNA biology.

Differential RNA Sequencing (dRNA‐Seq): Deep‐Sequencing‐Based Analysis of Primary Transcriptomes

Jörg Vogel, Cynthia M. Sharma, J. Vogel, 2012 .

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

J. Vogel, R. Reinhardt, C. Sharma, 2012, The EMBO journal.

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

R. Reinhardt, M. Sauer, C. Sharma, 2016, Nature Communications.

Experimental tools to identify RNA-protein interactions in Helicobacter pylori

J. Vogel, R. Reinhardt, C. Sharma, 2012, RNA biology.

The Primary Transcriptome and Noncoding RNA Repertoire of Helicobacter pylori

C. Sharma, F. Darfeuille, Sandy R. Pernitzsch, 2016 .

Small RNAs and virulence in bacterial pathogens

C. Sharma, Nadja Heidrich, 2012, RNA biology.

Transcriptome Complexity and Riboregulation in the Human Pathogen Helicobacter pylori

Cynthia M. Sharma, C. Sharma, Sandy R. Pernitzsch, 2012, Front. Cell. Inf. Microbio..

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

Arthur Thompson, Neil Shearer, Cynthia M Sharma, 2012, BMC Genomics.

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

Peter F. Stadler, Steve Hoffmann, Christian Otto, 2009, PLoS Comput. Biol..

Automated transcription start site prediction for comparative Transcriptomics using the SuperGenome

Kay Nieselt, Cynthia M. Sharma, Alexander Herbig, 2013 .

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

D. Mathews, B. Suess, Z. Xu, 2011, RNA biology.

Photooxidative stress‐induced and abundant small RNAs in Rhodobacter sphaeroides

J. Vogel, G. Klug, C. Sharma, 2009, Molecular microbiology.

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

Jörg Vogel, Cynthia M Sharma, J. Vogel, 2014, Current opinion in microbiology.

The transcriptional landscape of Chlamydia pneumoniae

Jörg Vogel, Tobias Müller, Richard Reinhardt, 2011, Genome Biology.

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

C. Sharma, H. de Reuse, Sandy R. Pernitzsch, 2021, Nature Communications.

Identifying Small Open Reading Frames in Prokaryotes with Ribosome Profiling

Allen R. Buskirk, A. Mankin, N. Vázquez-Laslop, 2021 .

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

Omer S. Alkhnbashi, R. Backofen, C. Sharma, 2021, bioRxiv.

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

C. Sharma, T. Bischler, P. C. Fineran, 2021, Nucleic acids research.

RNA recording in single bacterial cells using reprogrammed tracrRNAs

Chase L. Beisel, A. Westermann, J. Vogel, 2023, Nature Biotechnology.

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

Chase L. Beisel, C. Beisel, C. Sharma, 2021, Science.

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

D. Gautheret, J. Vogel, B. Felden, 2010, Nucleic acids research.

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

A. Marchfelder, A. Becker, F. Pfeiffer, 2016, BMC Genomics.

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

Konrad U. Förstner, Jörg Vogel, Cynthia M. Sharma, 2014, bioRxiv.

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

Konrad U. Förstner, C. Sharma, K. Förstner, 2020, MicrobiologyOpen.

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

C. Sharma, H. Walles, M. Schweinlin, 2020, PLoS pathogens.

Profound Impact of Hfq on Nutrient Acquisition, Metabolism and Motility in the Plant Pathogen Agrobacterium tumefaciens

Konrad U. Förstner, C. Sharma, K. Förstner, 2014, PloS one.

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

Thorsten Bischler, Chase L Beisel, Ryan T. Leenay, 2018, Molecular cell.

HRIBO: high-throughput analysis of bacterial ribosome profiling data

Rolf Backofen, Rick Gelhausen, Florian Eggenhofer, 2020, Bioinformatics.

Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity

Björn Voß, Wolfgang R Hess, Claudia Steglich, 2014, The ISME Journal.

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

Quansheng Liu, J. Belasco, C. Sharma, 2016, The Journal of Biological Chemistry.

Global Transcriptional Start Site Mapping Using Differential RNA Sequencing Reveals Novel Antisense RNAs in Escherichia coli

G. Storz, A. Zhang, K. Nieselt, 2014 .

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

B. Beckmann, E. Kubareva, R. Hartmann, 2011, RNA biology.

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

H. Margalit, Y. Altuvia, P. Romby, 2013, Methods.

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

C. Sharma, Sarah L. Svensson, Fabian König, 2023, bioRxiv.

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

C. Sharma, Sarah L. Svensson, 2021, bioRxiv.

Unraveling the small proteome of the plant symbiont Sinorhizobium meliloti by ribosome profiling and proteogenomics

R. Backofen, C. Ahrens, D. Becher, 2023, microLife.

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

Konrad U. Förstner, A. Jeltsch, R. Gräf, 2013, Nucleic acids research.

Revealing the small proteome of Haloferax volcanii by combining ribosome profiling and small-protein optimized mass spectrometry

Omer S. Alkhnbashi, A. Marchfelder, R. Backofen, 2023, microLife.

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

J. Vogel, C. Sharma, C. Staedel, 2011, Silence.

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

J. Vogel, C. Sharma, 2009, Current opinion in microbiology.

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

Konrad U. Förstner, C. Sharma, T. Alter, 2020, Frontiers in Microbiology.

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

Konrad U. Förstner, J. Vogel, C. Sharma, 2014, bioRxiv.

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

C. Sharma, D. Beier, Sandy R. Pernitzsch, 2014, Proceedings of the National Academy of Sciences.

Interesting twists on small RNA themes in Pseudomonas aeruginosa

G. Storz, C. Sharma, Gisela Storz, 2011, Molecular microbiology.

Small RNAs in Bacterial Virulence and Communication

C. Sharma, Sarah L. Svensson, 2016, Microbiology spectrum.

Identifying Small Open Reading Frames in Prokaryotes with Ribosome Profiling

Allen R. Buskirk, A. Mankin, N. Vázquez-Laslop, 2021, Journal of bacteriology.