Jiao C, Rechstadt C, König F, Homberger C, Yu J, Vogel J, Westermann AJ, Sharma CM, Beisel CL (2022)
RNA recording in single bacterial cells using reprogrammed tracrRNAs
Nature Biotechnology doi: 10.1038/s41587-022-01604-8 (Online ahead of print)

Liao C, Sharma S, Svensson SL, Kibe A, Weinberg Z, Alkhnbashi OS, Bischler T, Backofen R, Caliskan N, Sharma CM, Beisel CL (2022)
Spacer prioritization in CRISPR-Cas9 immunity is enabled by the leader RNA
Nature Microbiology 7(4):530-541

Pernitzsch SR, Alzheimer M, Bremer BU, Robbe-Saule M, de Reuse H, Sharma CM (2021)
Small RNA mediated gradual control of lipopolysaccharide biosynthesis control affects antibiotic resistance in Helicobacter pylori
Nature Communications 12, 4433 (2021) doi.org/10.1038/s41467-021-24689-2

Jiao C, Sharma S†, Dugar G†, Peeck NL, Bischler T, Wimmer F, Yu Y, Barquist L, Schoen C, Kurzai C, Sharma CM*, Beisel CL* (2021) † Equally contributing; * Corresponding authors
Non-canonical crRNAs derived from host transcripts enable multiplexable RNA detection by Cas9
Science 372(6545):941-948

Eisenbart SK†, Alzheimer M†, Pernitzsch SR, Dietrich S, Stahl S, Sharma CM (2020) † Equally contributing
A repeat-associated small RNA controls the major virulence factors of Helicobacter pylori
Molecular Cell 80(2):210-226, doi: 10.1016/j.molcel.2020.09.009

Svensson SL, Sharma CM (2021)
RNase III-mediated processing of a trans-acting bacterial sRNA and its cis-encoded antagonist
eLife doi.org/10.7554/eLife.69064

Svensson SL, Sharma CM (2021)
Small RNAs that target G-rich sequences are generated by diverse biogenesis pathways in Epsilonproteobacteria
Molecular Microbiology doi.org/10.1111/mmi.14850

Campa AR, Smith LM, Hampton HG, Sharma S, Jackson SA, Bischler T, Sharma CM, Fineran PC (2021)
The Rsm (Csr) post-transcriptional regulatory pathway coordinately controls multiple CRISPR-Cas immune systems
Nucleic Acids Research 49(16):9508-9525

Vazquez-Laslop N, Sharma CM, Mankin A, Buskirk AR (2021)
Identifying small ORFs in prokaryotes with ribosome profiling
Journal of Bacteriology  doi: 10.1128/JB.00294-21

Gelhausen R, Müller Teresa, Svensson SL, Alkhnbashi O, Sharma CM, Eggenhofer F, Backofen R (2021)
RiboReport - Benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria
Briefings in Bioinformatics 23(2): bbab549

Svensson SL & Sharma CM (2021)
An RNase III processed, antisense RNA pair regulates a Campylobacter jejuni colonization factor
bioRxiv  doi: https://doi.org/10.1101/2021.03.19.434396

Korkut DN, Alves ID, Vogel A, Chabas S, Sharma CM, Martinez D, Loquet A, Salgado GF, Darfeuille F (2020)
Structural insights into the AapA1 toxin of Helicobacter pylori
Biochim Biophys Acta Gen Subj 1864(1):129423

Schmidtke C, Findeiss S, Sharma CM, Kuhfuss J, Hoffmann S, Vogel J, Stadler PF, Bonas U (2020)
Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions
Nucleic Acids Research 40(5):2020-31

Riedel C, Förstner KU, Püning C, Alter T, Sharma CM, Gölz G (2020)
Differences in the Transcriptomic Response of Campylobacter coli and Campylobacter lari to Heat Stress
Front Microbiology 11:523

Alzheimer M, Svensson SL, König F, Schweinlin M, Metzger M, Walles H, Sharma CM  (2020)
A three-dimensional intestinal tissue model reveals factors and small regulatory RNAs important for colonization with Campylobacter jejuni
PLoS Pathogen 16(2):e1008304

Lerch MF, Schoenfelder SMK, Marincola G, Wencker FDR, Eckart M, Förstner KU, Sharma CM, Thormann KM, Kucklick M, Engelmann S, Ziebuhr W (2019)
A non-coding RNA from the intercellular adhesion (ica) locus of Staphylococcus epidermidis controls
polysaccharide intercellular adhesion (PIA)-mediated biofilm formation
Molecular Microbiology 1111(6):1571-1591

Schoenfelder SMK, Lange C, Prakash SA, Marincola G, Lerch MF, Wencker FDR, Förstner KU, Sharma CM, Ziebuhr W (2019)
The small non-coding RNA RsaE influences extracellular matrix composition in Staphylococcus epidermidis biofilm communities
PLoS Pathogens 15(3):e1007618

Fei J, Sharma CM (2018)
RNA Localization in Bacteria
Microbiol Spectrum 6(5) doi.org/10.1128/microbiolspec.RWR-0024-2018

Dugar G, Leenay RT, Eisenbart SK, Bischler T, Aul BU, Beisel CL, Sharma CM (2018)
CRISPR RNA-Dependent Binding and Cleavage of Endogenous RNAs by the Campylobacter jejuni Cas9
Molecular Cell 69(5):893-905

Bischler T, Hsieh PK, Resch M, Liu O, Tan HS, Foley PL, Hartleib A, Sharma CM, Belasco JG (2017)
Identification of the RNA pyrophosphohydrolase RppH of Helicobacter pylori and global analysis of its RNA targets
Journal of Biological Chemistry 292(5):1934-1950

Babski J, Haas KA, Näther-Schindler D, Pfeiffer F, Förstner KU, Hammelmann M, Hilker R, Becker A, Sharma CM, Marchfelder A, Soppa J (2016)
Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq)
BMC Genomics 17(1):629

Dugar G, Svensson SL, Bischler T, Wäldchen S, Reinhardt R, Sauer M, Sharma CM (2016)
The CsrA-FliW network controls polar localization of the dual-function flagellin mRNA in Campylobacter jejuni
Nature Communications 7:11667

Svensson SL & Sharma CM (2016)
Small RNAs in Bacterial Virulence and Communication
Microbial Spectrum 4(3)

Bischler T, Tan HS, Nieselt K, Sharma CM (2015)
Differential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori
Methods 86:89-101

Müller SA, Pernitzsch SR, Haange SB, Uetz P, von Bergen M, Sharma CM, Kalkhof S (2015)
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
Journal of Proteomics 126:34-45

Papenfort K, Förstner KU, Cong JP, Sharma CM, Bassler BL (2015)
Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm formation
PNAS 112:E766-75

Boesler B,  Meier D,  Förstner KU, Friedrich M, Hammann C, Sharma CM, Nellen W (2014)
Argonaute proteins affect siRNA levels and accumulation of a novel extrachromosomal DNA
from the Dictyostelium retrotransposon DIRS-1
Journal of Biological Chemistry 289(51):35124-38

Thomason MK*, Bischler T*, Eisenbart SK, Förstner KU, Zhang A, Herbig A,  Nieselt K, Sharma CM#, Storz G# (2014) *Equally contributing authors, #Corresponding authors
Global transcriptional start site mapping using dRNA-seq reveals novel antisense RNAs in Escherichia coli
J Bacteriology, 197(1):18-28

Zukher I, Novikova M, Tikhonov A, Nesterchuk M, Osterman I, Djordjevic M, Sergiev P, Sharma CM, Severinov K (2014)
Ribosome-controlled transcription termination is essential for the production of antibiotic microcin C
Nucleic Acids Research 42(19):11891-902

Möller M, Overlöper A, Förstner KU, Wen TN, Sharma CM, Lai EM, Narberhaus F (2014)
Profound impact of Hfq on nutrient acquisition, metabolism and motility in the plant pathogen Agrobacterium tumefaciens
PLoS One 9(10):e110427

Förstner KU, Vogel J, Sharma CM (2014)
READemption – A tool for the computational analysis of deep-sequencing based transcriptome data
Bioinformatics 30(23):3421-3

Sharma CM# & Vogel J#  (2014) #Corresponding authors
Differential RNA-seq: the approach behind and the biological insight gained
Current Opinion in Microbiology 19C:97-105

Jäger D, Förstner KU, Sharma CM, Santangelo TJ, Reeve JN  (2014)
Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis
BMC Genomics, 15(1):684

Voigt K, Sharma CM, Mitschke M, Lambrecht SJ, Voß B, Hess WR and Steglich C (2014)
Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity
SME Journal doi: 10.1038/ismej.2014.57

Heidrich N, Dugar G, Vogel J, Sharma CM (2014)
Investigating CRISPR RNA biogenesis and function using RNA-seq
Methods in Molecular Biology, in press

Pernitzsch SR, Tirier S, Beier D, Sharma CM  (2014)
A variable homopolymeric G-repeat defines small RNA-mediated post-transcriptional regulation of a chemotaxis receptor in Helicobacter pylori
PNAS 111(4):E501-10

Papenfort K, Corcoran CP, Gupta SK, Miyakoshi M, Heidrich N, Chao Y, Fröhlich KS, Sharma CM, Ziebuhr W, Böhm A, Vogel J (2013)
Regulatory Mechanisms of Special Significance: The role of sRNAs in Virulence
In: Regulation of Bacterial Virulence (eds. Darwin AJ, Vasil ML), ASM Press, pp493-527

Müller S, Windhof I, Maximov V, Jurkowski TP, Jeltsch A, Förstner KU, Sharma CM, Gräf R, Nellen W (2013)
Target recognition, RNA methylation activity and transcriptional regulation of the Dictyostelium discoideum Dnmt2-homologue (DnmA)
Nucleic Acids Research 41(18):8615-27

Lioliou E, Sharma CM, Altuvia Y, Caldelari I, Romilly C, Helfer AC, Margalit H, Romby H (2013)
In vivo mapping of RNA-RNA interactions in Staphylococcus aureus using the endoribonuclease III
Methods Jul 9. doi:pii: S1046-2023

Dugar G, HerbigA, Förstner KU, Heidrich N, Reinhardt R, Nieselt K, Sharma CM (2013)
High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates
PLoS Genetics 9(5): e1003495

Jäger D, Pernitzsch SR, Richter AS, Backofen R, Sharma CM, Schmitz RA (2012)
An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains
Nucleic Acids Research 40(21):10964-79

Roscetto E, Angrisano T, Costa V, Casalino M, Förstner KU, Sharma CM, Di Nocera PP, De Gregorio E (2012)
Functional characterization of the RNA chaperone Hfq in opportunistic human pathogen Stenotrophomonas maltophilia
J Bacteriology 194(21):5864-74

Chao Y, Papenfort K, Reinhardt R, Sharma CM, Vogel J (2012)
An atlas of Hfq-bound transcripts reveals 3' UTRs as a genomic reservoir of regulatory small RNAs
EMBO J 17;31(20):4005-19

Lioliou E, Sharma CM, Caldelari I, Helfer AC, Fechter P, Vandenesch F, Vogel J, Romby P  (2012)
Global regulatory functions of the of Staphylococcus aureus endoribonuclease III in gene expression
PLoS Genetics 8(6):e1002782

Sharma CM, Heidrich N (2012)
Small RNAs and virulence in bacterial pathogens
RNA Biology 9(4):361-363

Zhelyazkova P, Sharma CM, Förstner KU, Liere K, Vogel J, Börner T (2012)
The primary transcriptome of barley chloroplasts: numerous non-coding RNAs and the dominating role of the plastid-encoded RNA polymerase
Plant Cell 24(1):123-36

Rieder R, Reinhardt R, Sharma C, Vogel J (2012)
Experimental tools to identify RNA-protein interactions in Helicobacter pylori
RNA Biol 9(4):520-31

Pernitzsch SR, Sharma CM (2012)
Transcriptome Complexity and Riboregulation in the Human Pathogen Helicobacter pylori
Front Cell Infect Microbiol 2:14

Schmidtke C, Findeiß S, Sharma CM, Kuhfuß J, Hoffmann S, Vogel J, Stadler PF, Bonas U (2012)
Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions
Nucleic Acids Research 40(5):2020-31

Ramachandran VK, Shearer N, Jacob JJ, Sharma CM, Thompson A (2012)
The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella Typhimurium during invasion gene expression
BMC Genomics 17;13:25

Wilms I, Overlöper A, Nowrousian M, Sharma CM, Narberhaus F (2012)
SF RNA Virulence: Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens
RNA Biology 9(4):446-457

Madhugiri R, Pessi G, Voss B, Hahn J, Sharma CM, Reinhardt R, Vogel J, Hess WR, Fischer HM, Evguenieva-Hackenberg E (2012)
Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their analysis
RNA Biology 9(1):47-58

Albrecht M, Sharma CM, Dittrich MT, Müller T, Reinhardt R, Vogel J, Rudel T (2011)
The Transcriptional Landscape of Chlamydia pneumoniae.
Genome Biology 12(10):R98

Belair C, Baud J, Chabas S, Sharma CM, Vogel J, Staedel C, Darfeuille F (2011)
Helicobacter pylori interferes with an embryonic stem cell miRNA cluster to block cell cycle progression
Silence 2(1):7

Sharma CM, Papenfort K, Pernitzsch SR, Mollenkopf HJ, Hinton JC, Vogel J. (2011)
Pervasive post-transcriptional control of genes involved in amino acid metabolism by the Hfq-dependentGcvB small RNA
Molecular Microbiol 81(5):1144-65

Beckmann BM, Burenina OY, Hoch PG, Kubareva EA, Sharma CM,  Hartmann RK (2011)
In vivo and in vitro analysis of 6S RNA-templated short transcripts in Bacillus subtili
RNA Biology 8(5)

Berghoff BA, Glaeser J, Sharma CM, Zobawa M, Lottspeich F, Vogel J, Klug G (2011)
Contribution of Hfq to photooxidative stress resistance and global regulation in Rhodobacter sphaeroides
Molecular Microbiol 80(6):1479-1495

Deltcheva E, Chylinski K*, Sharma CM * , Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E (2011) *Equally contributing authors
CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III
Nature 471(7340):602-7

Sharma CM & Storz G (2011)
Interesting Twists on small RNA themes in Pseudomonas aeruginosa
Mol Microbiol  80(4):855-9

Mitschke J, Georg J, Scholz I, Sharma CM , Dienst D, Bantscheff J, Voß B, Steglich C, Wilde A, Vogel J, Hess WR (2011)
An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803
PNAS USA 1;108(5):2124-9 (Link)

Vockenhuber M-P, Sharma CM, Statt MG, Schmidt D, Xu Z, Dietrich S, Liesegang H, Mathews DH, Suess B (2011)
Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor
RNA Biology 8(3):468-77 (Link)

Papenfort K, Bouvier M, Mika F, Sharma CM, Vogel J (2010)
Evidence for an autonomous 5' target recognition domain in an Hfq-associated small RNA
PNAS 107(47):20435-40 (Link)

Irnov I, Sharma CM, Vogel J, Winkler W (2010)
Identification of regulatory RNAs in Bacillus subtilis
Nucleic Acids Research 38(19):6637-51 .(Link)

Bohn C, Rigoulay C, Chabelskaya S, Sharma CM, Marchais A, Skorski P, Borezee-Durant B, Barbet R, Jacquet E, Jacq A, Gautheret D, Felden B, Vogel J, Bouloc P (2010)
Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism
Nucleic Acids Research 38(19):6620-36 (Link)

Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiß S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF & Vogel J (2010)
The primary transcriptome of the major human pathogen Helicobacter pylori
Nature 464(7286):250-5. (Link)

Albrecht M, Sharma CM, Reinhardt R, Vogel J, Rudel T (2010)
Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome
Nucleic Acids Research, 38(3):868-77. (Link)

Jäger D*, Sharma CM*, Thomsen J, Ehlers C, Vogel J, Schmitz RA (2009) *Equally contributing authors
Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability
PNAS 106(51):21878-82

Berghoff BA, Glaeser J, Sharma CM, Vogel J, Klug G (2009)
Photooxidative stress induced and abundant small RNAs in Rhodobacter sphaeroides
Mol Microbiology 74(6):1497-1512

Sharma CM, Vogel J (2009)
Experimental approaches for the discovery and characterization of regulatory small RNA
Current Opinion in Microbiology 12(5):536-46

Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermüller J (2009)
Fast mapping of short sequences with mismatches, insertions and deletions using index structures
PLoS Computational Biology 5(9):e1000502

Sittka A, Sharma CM, Rolle K, Vogel J (2009)
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
RNA Biology 6(3):266-275

Bouvier M, Sharma CM, Mika F, Nierhaus KH, Vogel J (2008)
Small RNA binding to 5’ mRNA coding region inhibits translational initiation
Molecular Cell 32(6):827-37

Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT, Hinton JC, Vogel J (2008)
Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq
PLoS Genetics  4(8):e1000163

Sharma CM, Darfeuille F, Plantinga T, Vogel J (2007)
A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome binding sites
Genes & Development 21(21):2804-2817

Vogel J & Sharma CM (2005)
How to find small noncoding RNAs in bacteria
Biological Chemistry 386(11):1219-38

BOOK CHAPTERS

Sharma S, Sharma CM (2021)
Identification of RNA binding partners of CRISPR-Cas proteins in prokaryotes using RIP-seq
In: Post-Transcriptional Gene Regulation. Methods in Molecular Biology (eds. Dassi E), Humana Press USA, vol 2404:111-133

Papenfort K, Corcoran CP, Gupta SK, Miyakoshi M, Heidrich N, Chao Y, Fröhlich KS, Sharma CM, Ziebuhr W, Böhm A, Vogel J (2013)
Regulatory Mechanisms of Special Significance: The role of sRNAs in Virulence Regulation
In: Regulation of Bacterial Virulence (eds. Darwin AJ, Vasil ML), ASM Press, pp493-527

Borries A, Vogel J, Sharma CM (2012)
Differential RNA Sequencing (dRNA-Seq): Deep-Sequencing-Based Analysis of Primary Transcriptomes.
In: Tag-based Approaches for Next-Generation Sequencing (eds. M. Harbers, G. Kahl) Wiley-Blackwell-VCH (978-3-527-32819-2)

Heidrich N, Dugar G, Vogel J, Sharma CM (2015)
Investigating CRISPR RNA biogenesis and function using RNA-seq
In: CRISPR. Methods in Molecular Biology (eds. Lundgren M, Charpentier E, Fineran P), Humana Press USA, vol 1311:1-21