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 17:629. doi: 10.1186

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
Mechanisms of Bacterial Pathogens, 5th edition, In press

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, in press

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
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)
Global transcriptional start site mapping using dRNA-seq reveals novel antisense RNAs in Escherichia coli
J Bacteriology, 197(1) in press (pii: JB.02096-14)*Equally contributing authors, #Corresponding authors

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, in press (pii: btu533)

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

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


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 2012;2:14. doi: 10.3389/fcimb.2012.00014. Epub 2012 Feb 21. (Link)

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

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 1;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)
CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III
Nature 471(7340):602-7 #Equally contributing authors

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 Volume 8 Issue 3 (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 USA  23; 107(47):20435-40 (Link)

Irnov I, Sharma CM, Vogel J, Winkler W (2010)
Identification of regulatory RNAs in Bacillus subtilis
Nucleic Acids Research 1;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 1;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)
Deep sequencing analysis of the Methanosarcina mazei Gö1 transcriptome in response to nitrogen availability
PNAS 106(51):21878-82. *Equally contributing authors

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



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
Investigating CRISPR RNA biogenesis and function using RNA-seq
CRISPR: Methods and Protocols in Methods in Molecular Biology, Humana Press USA