Prof Jörg Vogel


Prof. Jörg Vogel is the founding director of the Helmholtz Institute for RNA-based Infection Research (HIRI) as well as the director of the Institute of Molecular Infection Biology (IMIB) at the University of Würzburg, Germany. As world-leading scientist in the field of RNA biology, Jörg Vogel is considered a pioneer in the application and development of high-throughput sequencing methods for the analysis of individual infected cells as well as interactions between pathogenic bacteria and their hosts. 

Prof. Jörg Vogel studied biochemistry at Humboldt University, Berlin, Germany, and at Imperial College, London, UK. In 1999, he received his PhD from Humboldt University with a thesis on Group II intron splicing. He spent his postdoctoral years at Uppsala University, Sweden (2000-2001) and as an EMBO fellow at the Hebrew University, Jerusalem, Israel (2002-2003) before he started an Independent Junior Research Group at the Max Planck Institute for Infection Biology in Berlin, Germany (2004-2010). He became Full Professor and Director of the Institute for Molecular Infection Biology at the University of Würzburg in 2009. As of 2017, he is the Director of the Helmholtz Institute for RNA-based Infection Research (HIRI) in Würzburg.

Jörg Vogel is an elected member of EMBO, the German National Academy of Sciences, as well as the European and American Academies of Microbiology. In 2017, he received a Leibniz Prize, Germany’s most prestigious research award, for his ground-breaking contributions to the understanding of regulatory RNA molecules in infection biology.

Prof. Vogel’s group seek to understand the full (noncoding) RNA world of bacterial pathogens and use RNA-centric approaches to targeting pathogens and manipulating microbiota. A major innovative goal is the comprehensive simultaneous RNA-based profiling of the pathogen and the infected host in real time and at single-cell resolution; where applicable, this should also include co-colonizing microbiota. Researchers at the Vogel lab focus on the mode of action of those noncoding RNA molecules that are crucial for the virulence of the pathogen, differentially expressed upon exposure to the host, or impact gene expression in interacting members of the microbiota. The knowledge obtained will be exploited for therapeutic intervention with clinically relevant bacterial pathogens.


The CRISPR/Cas system in Neisseria meningitidis affects bacterial adhesion to human nasopharyngeal epithelial cells

Heidrich N, Hagmann A, Bauriedl S, Vogel J, Schoen C (2019)

RNA Biol, 16 (4): 390-396DOI: 10.1080/15476286.2018.1486660

The Major RNA-Binding Protein ProQ Impacts Virulence Gene Expression in Salmonella enterica Serovar Typhimurium

Westermann A, Venturini E, Sellin M, Förstner K, Hardt W, Vogel J (2019)

MBio, 10 (1): 02504-18DOI: 10.1128/mBio.02504-18

Functional expansion of a TCA cycle operon mRNA by a 3' end-derived small RNA

Miyakoshi M, Matera G, Maki K, Sone Y, Vogel J (2019)

Nucleic Acids Res, 47 (4): 2075-2088DOI: 10.1093/nar/gky1243


Global Maps of ProQ Binding In Vivo Reveal Target Recognition via RNA Structure and Stability Control at mRNA 3' Ends

Holmqvist E, Li L, Bischler T, Barquist L, Vogel J (2018)

Mol Cell, 70 (5): 971-982DOI: 10.1016/j.molcel.2018.04.017

CRP-cAMP mediates silencing of Salmonella virulence at the post-transcriptional level

El Mouali Y, Gaviria-Cantin T, Sánchez-Romero M, Gibert M, Westermann A, Vogel J, Balsalobre C (2018)

Plos Genet, 14 (6)DOI: 10.1371/journal.pgen.1007401

ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes

Yu S, Vogel J, Förstner K (2018)

Gigascience, 7 (9)DOI: 10.1093/gigascience/giy096

Salmonella persisters undermine host immune defenses during antibiotic treatment

Stapels D, Hill P, Westermann A, Fisher R, Thurston T, Saliba A, Blommestein I, Vogel J, Helaine S (2018)

Science, 362 (6419): 1156-1160DOI: 10.1126/science.aat7148

Nuclear lncRNA stabilization in the host response to bacterial infection

Munschauer M, Vogel J (2018)

EMBO J, 37 (13)DOI: 10.15252/embj.201899875

Genome organization and DNA accessibility control antigenic variation in trypanosomes

Müller L, Cosentino R, Förstner K, Guizetti J, Wedel C, Kaplan N, Janzen C, Arampatzi P, Vogel J, Steinbiss S, …, Sebra R, Siegel T (2018)

Nature, 563 (7729): 121-125DOI: 10.1038/s41586-018-0619-8

Bacterial RNA Biology on a Genome Scale

Hör J, Gorski S, Vogel J (2018)

Mol Cell, 70 (5): 785-799DOI: 10.1016/j.molcel.2017.12.023

Host-Pathogen Transcriptomics by Dual RNA-Seq

Westermann A, Vogel J (2018)

In: Arluison V., Valverde C. (eds) Bacterial Regulatory RNA, Methods Mol Biol (Methods in Molecular Biology), 1737: 59-75DOI: 10.1007/978-1-4939-7634-8_4

RNA-binding proteins in bacteria

Holmqvist E, Vogel J (2018)

Nat Rev Microbiol, 16 (10): 601-615DOI: 10.1038/s41579-018-0049-5

Stress-induced host membrane remodeling protects from infection by non-motile bacterial pathogens

Tawk C, Nigro G, Rodrigues Lopes I, Aguilar C, Lisowski C, Mano M, Sansonetti P, Vogel J, Eulalio A (2018)

EMBO J, 37 (23)DOI: 10.15252/embj.201798529


APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins

Sharan M, Förstner K, Eulalio A, Vogel J (2017)

Nucleic Acids Res, 45 (11)DOI: 10.1093/nar/gkx137

A systematic analysis of the RNA-targeting potential of secreted bacterial effector proteins

Tawk C, Sharan M, Eulalio A, Vogel J (2017)

Sci Rep, 7 (1)DOI: 10.1038/s41598-017-09527-0

Global snapshots of bacterial RNA networks

Hör J, Vogel J (2017)

EMBO J, 36 (3): 245-247DOI: 10.15252/embj.201696072

The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq

Heidrich N, Bauriedl S, Barquist L, Li L, Schoen C, Vogel J (2017)

Nucleic Acids Res, 45 (10): 6147-6167DOI: 10.1093/nar/gkx168

Molecular mechanism of mRNA repression in trans by a ProQ‐dependent small RNA

Smirnov A, Wang C, Drewry L, Vogel J (2017)

EMBO J, 36 (8): 1029-45DOI: 10.15252/embj.201696127

RNA-based recognition and targeting: sowing the seeds of specificity

Gorski S, Vogel J, Doudna J (2017)

Nat Rev Mol Cell Biol, 18 (4): 215-228DOI: 10.1038/nrm.2016.174

Discovery of new RNA classes and global RNA-binding proteins

Smirnov A, Schneider C, Hör J, Vogel J (2017)

Curr Opin Microbiol, 39: 152-160DOI: 10.1016/j.mib.2017.11.016

RNA target profiles direct the discovery of virulence functions for the cold-shock proteins CspC and CspE

Michaux C, Holmqvist E, Vasicek E, Sharan M, Barquist L, Westermann A, Gunn J, Vogel J (2017)

Proc Natl Acad Sci U S A, 114 (26): 6824-6829DOI: 10.1073/pnas.1620772114

Einzelzell-RNA-Sequenzierung beleuchtet den Infektionsprozess

Saliba A, Westermann A, Vogel J (2017)

Biospektrum, 23 (5): 525-528DOI: 10.1007/s12268-017-0836-y

Structure of the Escherichia coli ProQ RNA-binding protein

Gonzalez G, Hardwick S, Maslen S, Skehel J, Holmqvist E, Vogel J, Bateman A, Luisi B, Broadhurst R (2017)

RNA (New York, N.Y.C), 23 (5): 696-711DOI: 10.1261/rna.060343.116

New RNA-seq approaches for the study of bacterial pathogens

Saliba A, C Santos S, Vogel J (2017)

Curr Opin Microbiol, 35: 78-87DOI: 10.1016/j.mib.2017.01.001

In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways

Chao Y, Li L, Girodat D, Förstner K, Said N, Corcoran C, Smiga M, Papenfort K, Reinhardt R, Wieden H, Luisi B, Vogel J (2017)

Mol Cell, 65 (1): 39-51DOI: 10.1016/j.molcel.2016.11.002


Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo

Holmqvist E, Wright P, Li L, Bischler T, Barquist L, Reinhardt R, Backofen R, Vogel J (2016)

EMBO J, 35 (9): 991-1011DOI: 10.15252/embj.201593360

Natural mutations in a Staphylococcus aureus virulence regulator attenuate cytotoxicity but permit bacteremia and abscess formation

Das S, Lindemann C, Young B, Muller J, Österreich B, Ternette N, Winkler A, Paprotka K, Reinhardt R, Förstner K, …, Wyllie D, Fraunholz M (2016)

Proc Natl Acad Sci U S A, 113 (22): 3101-10DOI: 10.1073/pnas.1520255113

An NK Cell Perforin Response Elicited via IL-18 Controls Mucosal Inflammation Kinetics during Salmonella Gut Infection

Müller A, Dolowschiak T, Sellin M, Felmy B, Verbree C, Gadient S, Westermann A, Vogel J, LeibundGut-Landmann S, Hardt W (2016)

Plos Pathog, 12 (6)DOI: 10.1371/journal.ppat.1005723

A 3' UTR-Derived Small RNA Provides the Regulatory Noncoding Arm of the Inner Membrane Stress Response

Chao Y, Vogel J (2016)

Mol Cell, 61 (3): 352-363DOI: 10.1016/j.molcel.2015.12.023

Grad-seq guides the discovery of ProQ as a major small RNA-binding protein

Smirnov A, Förstner K, Holmqvist E, Otto A, Günster R, Becher D, Reinhardt R, Vogel J (2016)

Proc Natl Acad Sci U S A, 113 (41): 11591-11596DOI: 10.1073/pnas.1609981113

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Jiang Y, Oron T, Clark W, Bankapur A, D'Andrea D, Lepore R, Funk C, Kahanda I, Verspoor K, Ben-Hur A, …, Friedberg I, Radivojac P (2016)

Genome Biol, 17 (1)DOI: 10.1186/s13059-016-1037-6

Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella

Saliba A, Li L, Westermann A, Appenzeller S, Stapels D, Schulte L, Helaine S, Vogel J (2016)

Nat Microbiol, 2DOI: 10.1038/nmicrobiol.2016.206

The target spectrum of SdsR small RNA in Salmonella

Fröhlich K, Haneke K, Papenfort K, Vogel J (2016)

Nucleic Acids Res, 44 (21): 10406-22DOI: 10.1093/nar/gkw632

Molecular phenotyping of infection-associated small non-coding RNAs

Barquist L, Westermann A, Vogel J (2016)

Philos Trans R Soc Lond B Biol Sci, 371 (1707)DOI: 10.1098/rstb.2016.0081

cis-Encoded Small RNAs, a Conserved Mechanism for Repression of Polysaccharide Utilization in Bacteroides

Cao Y, Förstner K, Vogel J, Smith C (2016)

J Bacteriol, 198 (18): 2410-8DOI: 10.1128/JB.00381-16

Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions

Westermann A, Forstner K, Amman F, Barquist L, Chao Y, Schulte L, Muller L, Reinhardt R, Stadler P, Vogel J (2016)

Nature, 529 (7587): 496-501DOI: 10.1038/nature16547

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

Berger P, Knödler M, Förstner K, Berger M, Bertling C, Sharma C, Vogel J, Karch H, Dobrindt U, Mellmann A (2016)

Sci Rep, 6DOI: 10.1038/srep35307

Emerging roles of RNA modifications in bacteria

Marbaniang C, Vogel J (2016)

Curr Opin Microbiol, 30: 50-57DOI: 10.1016/j.mib.2016.01.001

Gifsy-1 Prophage IsrK with Dual Function as Small and Messenger RNA Modulates Vital Bacterial Machineries

Hershko-Shalev T, Odenheimer-Bergman A, Elgrably-Weiss M, Ben-Zvi T, Govindarajan S, Seri H, Papenfort K, Vogel J, Altuvia S (2016)

Plos Genet, 12 (4)DOI: 10.1371/journal.pgen.1005975


Dual 3'Seq using deepSuperSAGE uncovers transcriptomes of interacting Salmonella enterica Typhimurium and human host cells

Afonso-Grunz F, Hoffmeier K, Müller S, Westermann A, Rotter B, Vogel J, Winter P, Kahl G (2015)

BMC Genomics, 16DOI: 10.1186/s12864-015-1489-1

Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella

Papenfort K, Espinosa E, Casadesús J, Vogel J (2015)

Proc Natl Acad Sci U S A, 112 (34): 4772-81DOI: 10.1073/pnas.1507825112

Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies

Barquist L, Vogel J (2015)

Annu Rev Genet, 49: 367-94DOI: 10.1146/annurev-genet-112414-054804

dRNA-Seq Reveals Genomewide TSSs and Noncoding RNAs of Plant Beneficial Rhizobacterium Bacillus amyloliquefaciens FZB42

Fan B, Li L, Chao Y, Förstner K, Vogel J, Borriss R, Wu X (2015)

Plos One, 10 (11)DOI: 10.1371/journal.pone.0142002

Regulatory small RNAs from the 3' regions of bacterial mRNAs

Miyakoshi M, Chao Y, Vogel J (2015)

Curr Opin Microbiol, 24: 132-9DOI: 10.1016/j.mib.2015.01.013

Investigating CRISPR RNA Biogenesis and Function Using RNA-seq

Heidrich N, Dugar G, Vogel J, Sharma C (2015)

In: CRISPR: Methods and protocols (eds Lundgren M, Charpentier E, Fineran PC), Methods Mol Biol (Methods in Molecular Biology), 1311: 1-21DOI: 10.1007/978-1-4939-2687-9_1

Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA

Miyakoshi M, Chao Y, Vogel J (2015)

EMBO J, 34 (11): 1478-92DOI: 10.15252/embj.201490546

The end is not the end: remnants of tRNA precursors live on to sponge up small regulatory RNAs

Ziebuhr W, Vogel J (2015)

Mol Cell, 58 (3): 389-90DOI: 10.1016/j.molcel.2015.04.032

Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

Sass A, van Acker H, Förstner K, van Nieuwerburgh F, Deforce D, Vogel J, Coenye T (2015)

BMC Genomics, 16DOI: 10.1186/s12864-015-1993-3


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

Sharma C, Vogel J (2014)

Curr Opin Microbiol, 19: 97-105DOI: 10.1016/j.mib.2014.06.010

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

Förstner K, Vogel J, Sharma C (2014)

Bioinformatics, 30 (23): 3421-3DOI: 10.1093/bioinformatics/btu533

Recognition of the small regulatory RNA RydC by the bacterial Hfq protein

Dimastrogiovanni D, Fröhlich K, Bandyra K, Bruce H, Hohensee S, Vogel J, Luisi B (2014)

Elife, 3DOI: 10.7554/eLife.05375

A bacterial seek-and-destroy system for foreign DNA

Vogel J (2014)

Science, 344 (6187): 972-3DOI: 10.1126/science.1252962

Small RNA functions in carbon metabolism and virulence of enteric pathogens

Papenfort K, Vogel J (2014)

Front Cell Infect Microbiol, 4DOI: 10.3389/fcimb.2014.00091

Single-cell RNA-seq: advances and future challenges

Saliba A, Westermann A, Gorski S, Vogel J (2014)

Nucleic Acids Res, 42 (14): 8845-60DOI: 10.1093/nar/gku555

Identification and Characterization of Small Non-coding RNAs in Bacteria

Podkaminski D, Bouvier M, Vogel J (2014)

, 136: 719-786DOI: 10.1002/9783527647064.ch33


β-Lactam antibiotics promote bacterial mutagenesis via an RpoS-mediated reduction in replication fidelity

Gutierrez A, Laureti L, Crussard S, Abida H, Rodríguez-Rojas A, Blázquez J, Baharoglu Z, Mazel D, Darfeuille F, Vogel J, Matic I (2013)

Nat Commun, 4DOI: 10.1038/ncomms2607

Targeted decay of a regulatory small RNA by an adaptor protein for RNase E and counteraction by an anti-adaptor RNA

Göpel Y, Papenfort K, Reichenbach B, Vogel J, Görke B (2013)

Gene Dev, 27 (5): 552-64DOI: 10.1101/gad.210112.112

Processing-Independent CRISPR RNAs Limit Natural Transformation in Neisseria meningitidis

Zhang Y, Heidrich N, Ampattu B, Gunderson C, Seifert H, Schoen C, Vogel J, Sontheimer E (2013)

Mol Cell, 50 (4): 488-503DOI: 10.1016/j.molcel.2013.05.001

Same same but different: new structural insight into CRISPR-Cas complexes

Heidrich N, Vogel J (2013)

Mol Cell, 52 (1): 4-7DOI: 10.1016/j.molcel.2013.09.023.

Comparative genomics boosts target prediction for bacterial small RNAs

Wright P, Richter A, Papenfort K, Mann M, Vogel J, Hess W, Backofen R, Georg J (2013)

Proc Natl Acad Sci U S A, 110 (37): 3487-96DOI: 10.1073/pnas.1303248110

Alexander Böhm (1971-2012)

Boos W, Parkinson J, Jenal U, Vogel J, Søgaard-Andersen L (2013)

Mol Microbiol, 88 (2): 219-21DOI: 10.1111/mmi.12198

Differential activation and functional specialization of miR-146 and miR-155 in innate immune sensing

Schulte L, Westermann A, Vogel J (2013)

Nucleic Acids Res, 41 (1): 542-53DOI: 10.1093/nar/gks1030

Bacterial regulatory mechanisms: the gene and beyond

Bassler B, Vogel J (2013)

Curr Opin Microbiol, 16 (2): 109-11DOI: 10.1016/j.mib.2013.04.001

CRISPRs extending their reach: prokaryotic RNAi protein Cas9 recruited for gene regulation

Heidrich N, Vogel J (2013)

EMBO J, 32 (13): 1802-4DOI: 10.1038/emboj.2013.141

Small RNA-Mediated Activation of Sugar Phosphatase mRNA Regulates Glucose Homeostasis

Papenfort K, Sun Y, Miyakoshi M, Vanderpool C, Vogel J (2013)

Cell, 153 (2): 426-437DOI: 10.1016/j.cell.2013.03.003

RNA-mediated regulation in pathogenic bacteria

Caldelari I, Chao Y, Romby P, Vogel J (2013)

Cold Spring Harb Perspect Med, 3 (9)DOI: 10.1101/cshperspect.a010298

A small RNA activates CFA synthase by isoform-specific mRNA stabilization

Fröhlich K, Papenfort K, Fekete A, Vogel J (2013)

EMBO J, 32 (22): 2963-79DOI: 10.1038/emboj.2013.222

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

Papenfort K, Corcoran C, Gupta S, Miyakoshi M, Heidrich N, Chao Y, Fröhlich K, Ziebuhr W, Böhm A, Vogel J, Sharma C (2013)

In: Regulation of Bacterial Virulence (eds Darwin AJ, Vasil ML): 493-527DOI: 10.1128/9781555818524.ch25


Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their analysis

Madhugiri R, Pessi G, Voss B, Hahn J, Sharma C, Reinhardt R, Vogel J, Hess W, Fischer H, Evguenieva-Hackenberg E (2012)

RNA Biol, 9 (1): 47-58DOI: 10.4161/rna.9.1.18008

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

Lioliou E, Sharma C, Caldelari I, Helfer A, Fechter P, Vandenesch F, Vogel J, Romby P (2012)

Plos Genet, 8 (6)DOI: 10.1371/journal.pgen.1002782

The csgD mRNA as a hub for signal integration via multiple small RNAs

Boehm A, Vogel J (2012)

Mol Microbiol, 84 (1): 1-5DOI: 10.1111/j.1365-2958.2012.08033.x

Use of aptamer tagging to identify in vivo protein binding partners of small regulatory RNAs

Corcoran C, Rieder R, Podkaminski D, Hofmann B, Vogel J (2012)

In: Bacterial Regulatory RNA: Methods and protocols (ed Keiler KC), 905: 177-200DOI: 10.1007/978-1-61779-949-5_11

The mammalian microRNA response to bacterial infections

Eulalio A, Schulte L, Vogel J (2012)

RNA Biol, 9 (6): 742-50DOI: 10.4161/rna.20018

The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium

Kröger C, Dillon S, Cameron A, Papenfort K, Sivasankaran S, Hokamp K, Chao Y, Sittka A, Hébrard M, Händler K, …, Vogel J, Hinton J (2012)

Proc Natl Acad Sci U S A, 109 (20): 1277-86DOI: 10.1073/pnas.1201061109

Experimental tools to identify RNA-protein interactions in Helicobacter pylori

Rieder R, Reinhardt R, Sharma C, Vogel J (2012)

RNA Biol, 9 (4): 520-31DOI: 10.4161/rna.20331

Superfolder GFP reporters validate diverse new mRNA targets of the classic porin regulator, MicF RNA

Corcoran C, Podkaminski D, Papenfort K, Urban J, Hinton J, Vogel J (2012)

Mol Microbiol, 84 (3): 428-45DOI: 10.1111/j.1365-2958.2012.08031.x

Dual RNA-seq of pathogen and host

Westermann A, Gorski S, Vogel J (2012)

Nat Rev Microbiol, 10 (9): 618-30DOI: 10.1038/nrmicro2852

Hfq-associated Regulatory Small RNAs

Corcoran C, Papenfort K, Vogel J (2012)

In: Regulatory RNAs in Prokaryotes (eds Marchfelder A, Hess WR): 15-50DOI: 10.1007/978-3-7091-0218-3_2

The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase E

Bandyra K, Said N, Pfeiffer V, Górna M, Vogel J, Luisi B (2012)

Mol Cell, 47 (6): 943-53DOI: 10.1016/j.molcel.2012.07.015

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

Borries A, Vogel J, Sharma C (2012)

In: Tag-based next generation sequencing (eds Kahl G, Harbers M ), 316: 109-121DOI: 10.1002/9783527644582.ch7

The Primary Transcriptome of Barley Chloroplasts: Numerous Noncoding RNAs and the Dominating Role of the Plastid-Encoded RNA PolymeraseCWOA

Zhelyazkova P, Sharma C, Förstner K, Liere K, Vogel J, Börner T (2012)

Plant Cell, 24 (1): 123-36DOI: 10.1105/tpc.111.089441

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

Chao Y, Papenfort K, Reinhardt R, Sharma C, Vogel J (2012)

EMBO J, 31 (20): 4005-19DOI: 10.1038/emboj.2012.229

RelA protein stimulates the activity of RyhB small RNA by acting on RNA-binding protein Hfq

Argaman L, Elgrably-Weiss M, Hershko T, Vogel J, Altuvia S (2012)

Proc Natl Acad Sci U S A, 109 (12): 4621-6DOI: 10.1073/pnas.1113113109

The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair

Papenfort K, Podkaminski D, Hinton J, Vogel J (2012)

Proc Natl Acad Sci U S A, 109 (13): 757-64DOI: 10.1073/pnas.1119414109


The transcriptional landscape of Chlamydia pneumoniae

Albrecht M, Sharma C, Dittrich M, Müller T, Reinhardt R, Vogel J, Rudel T (2011)

Genome Biol, 12 (10)DOI: 10.1186/gb-2011-12-10-r98

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

Sharma C, Papenfort K, Pernitzsch S, Mollenkopf H, Hinton J, Vogel J (2011)

Mol Microbiol, 81 (5): 1144-65DOI: 10.1111/j.1365-2958.2011.07751.x

Sweet Business: Spot42 RNA networks with CRP to Modulate Catabolite Repression

Papenfort K, Vogel J (2011)

Mol Cell, 41 (3): 245-6DOI: 10.1016/j.molcel.2011.01.011

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

Schmidtke C, Findeiß S, Sharma C, Kuhfuß J, Hoffmann S, Vogel J, Stadler P, Bonas U (2011)

Nucleic Acids Res, 40 (5): 2020-31DOI: 10.1093/nar/gkr904

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

Deltcheva E, Chylinski K, Sharma C, Gonzales K, Chao Y, Pirzada Z, Eckert M, Vogel J, Charpentier E (2011)

Nature, 471 (7340): 602-7DOI: 10.1038/nature09886

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

Berghoff B, Glaeser J, Sharma C, Zobawa M, Lottspeich F, Vogel J, Klug G (2011)

Mol Microbiol, 80 (6): 1479-95DOI: 10.1111/j.1365-2958.2011.07658.x

Microbes at their best: first Mol Micro Meeting Würzburg

Böhm A, Papenfort K, Lopez D, Vogel J (2011)

Mol Microbiol, 82 (4): 797-806DOI: 10.1111/j.1365-2958.2011.07852.x

Regulation by small RNAs in bacteria: expanding frontiers

Storz G, Vogel J, Wassarman K (2011)

Mol Cell, 43 (6): 880-91DOI: 10.1016/j.molcel.2011.08.022

A candidate approach implicates the secreted Salmonella effector protein SpvB in P-body disassembly

Eulalio A, Fröhlich K, Mano M, Giacca M, Vogel J (2011)

Plos One, 6 (3)DOI: 10.1371/journal.pone.0017296

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

Belair C, Baud J, Chabas S, Sharma C, Vogel J, Staedel C, Darfeuille F (2011)

Silence, 2 (1)DOI: 10.1186/1758-907X-2-7

Hfq and its constellation of RNA

Vogel J, Luisi B (2011)

Nat Rev Microbiol, 9 (8): 578-89DOI: 10.1038/nrmicro2615

A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD

Fröhlich K, Papenfort K, Berger A, Vogel J (2011)

Nucleic Acids Res, 40 (8): 3623-40DOI: 10.1093/nar/gkr1156

Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon

Gogol E, Rhodius V, Papenfort K, Vogel J, Gross C (2011)

Proc Natl Acad Sci U S A, 108 (31): 12875-80DOI: 10.1073/pnas.1109379108

Analysis of the host microRNA response to Salmonella uncovers the control of major cytokines by the let-7 family

Schulte L, Eulalio A, Mollenkopf H, Reinhardt R, Vogel J (2011)

EMBO J, 30 (10): 1977-89DOI: 10.1038/emboj.2011.94

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

Mitschke J, Georg J, Scholz I, Sharma C, Dienst D, Bantscheff J, Voss B, Steglich C, Wilde A, Vogel J, Hess W (2011)

Proc Natl Acad Sci U S A, 108 (5): 2124-9DOI: 10.1073/pnas.1015154108


The primary transcriptome of the major human pathogen Helicobacter pylori

Sharma C, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler P, Vogel J (2010)

Nature, 464 (7286): 250-5DOI: 10.1038/nature08756

The role of Hfq in bacterial pathogens

Chao Y, Vogel J (2010)

Curr Opin Microbiol, 13 (1): 24-33DOI: 10.1016/j.mib.2010.01.001

Analysis of A to I editing of miRNA in macrophages exposed to salmonella

Heale B, Eulalio A, Schulte L, Vogel J, O'Connell M (2010)

RNA Biol, 7 (5): 621-7DOI: 10.4161/rna.7.5.13269

Small RNAs promote mRNA stability to activate the synthesis of virulence factors

Podkaminski D, Vogel J (2010)

Mol Microbiol, 78 (6): 1327-31DOI: 10.1111/j.1365-2958.2010.07428.x

Identification of regulatory RNAs in Bacillus subtilis

Irnov I, Sharma C, Vogel J, Winkler W (2010)

Nucleic Acids Res, 38 (19): 6637-51DOI: 10.1093/nar/gkq454

Regulatory RNA in bacterial pathogens

Papenfort K, Vogel J (2010)

Cell Host Microbe, 8 (1): 116-27DOI: 10.1016/j.chom.2010.06.008

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

Papenfort K, Bouvier M, Mika F, Sharma C, Vogel J (2010)

Proc Natl Acad Sci U S A, 107 (47): 20435-40DOI: 10.1073/pnas.1009784107

Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome

Albrecht M, Sharma C, Reinhardt R, Vogel J, Rudel T (2010)

Nucleic Acids Res, 38 (3): 868-77DOI: 10.1093/nar/gkp1032

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

Bohn C, Rigoulay C, Chabelskaya S, Sharma C, Marchais A, Skorski P, Borezée-Durant E, Barbet R, Jacquet E, Jacq A, …, Vogel J, Bouloc P (2010)

Nucleic Acids Res, 38 (19): 6620-36DOI: 10.1093/nar/gkq462


Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation

Pfeiffer V, Papenfort K, Lucchini S, Hinton J, Vogel J (2009)

Nat Struct Mol Biol, 16 (8): 840-6DOI: 10.1038/nsmb.1631

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

Hoffmann S, Otto C, Kurtz S, Sharma C, Khaitovich P, Vogel J, Stadler P, Hackermüller J (2009)

PLos Comput Biol, 5 (9)DOI: 10.1371/journal.pcbi.1000502

In vivo expression and purification of aptamer-tagged small RNA regulators

Said N, Rieder R, Hurwitz R, Deckert J, Urlaub H, Vogel J (2009)

Nucleic Acids Res, 37 (20): 133-DOI: 10.1093/nar/gkp719

A green fluorescent protein (GFP)-based plasmid system to study post-transcriptional control of gene expression in vivo

Urban J, Vogel J (2009)

In: Riboswitches: Methods and protocols (ed Serganov A), Methods Mol Biol, 540: 301-19DOI: 10.1007/978-1-59745-558-9_22

Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA

Papenfort K, Said N, Welsink T, Lucchini S, Hinton J, Vogel J (2009)

Mol Microbiol, 74 (1): 139-158DOI: 10.1111/j.1365-2958.2009.06857.x

An RNA trap helps bacteria get the most out of chitosugars

Vogel J (2009)

Mol Microbiol, 73 (5): 737-41DOI: 10.1111/j.1365-2958.2009.06806.x

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

Jäger D, Sharma C, Thomsen J, Ehlers C, Vogel J, Schmitz R (2009)

Proc Natl Acad Sci U S A, 106 (51): 21878-82DOI: 10.1073/pnas.0909051106

Multiple target regulation by small noncoding RNAs rewires gene expression at the post-transcriptional level

Papenfort K, Vogel J (2009)

Res Microbiol, 160 (4): 278-87DOI: 10.1016/j.resmic.2009.03.004

Photooxidative stress-induced and abundant small RNAs in Rhodobacter sphaeroides

Berghoff B, Glaeser J, Sharma C, Vogel J, Klug G (2009)

Mol Microbiol, 74 (6): 1497-512DOI: 10.1111/j.1365-2958.2009.06949.x

Experimental approaches for the discovery and characterization of regulatory small RNA

Sharma C, Vogel J (2009)

Curr Opin Microbiol, 12 (5): 536-46DOI: 10.1016/j.mib.2009.07.006

A rough guide to the non-coding RNA world of Salmonella

Vogel J (2009)

Mol Microbiol, 71 (1): 1-11DOI: 10.1111/j.1365-2958.2008.06505.x

Activation of gene expression by small RNA

Fröhlich K, Vogel J (2009)

Curr Opin Microbiol, 12 (6): 674-82DOI: 10.1016/j.mib.2009.09.009

Acid stress activation of the sigma(E) stress response in Salmonella enterica serovar Typhimurium

Muller C, Bang I, Velayudhan J, Karlinsey J, Papenfort K, Vogel J, Fang F (2009)

Mol Microbiol, 71 (5): 1228-38DOI: 10.1111/j.1365-2958.2009.06597.x

Regulatory RNAs in prokaryotes: here, there and everywhere

Narberhaus F, Vogel J (2009)

Mol Microbiol, 74 (2): 261-9DOI: 10.1111/j.1365-2958.2009.06869.x


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

Sittka A, Lucchini S, Papenfort K, Sharma C, Rolle K, Binnewies T, Hinton J, Vogel J (2008)

Plos Genet, 4 (8)DOI: 10.1371/journal.pgen.1000163

Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation

Urban J, Vogel J (2008)

PLos Biol, 6 (3)DOI: 10.1371/journal.pbio.0060064

A Glimpse at the Evolution of Virulence Control

Sittka A, Vogel J (2008)

Cell Host Microbe, 4 (4): 310-2DOI: 10.1016/j.chom.2008.09.006

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

Bouvier M, Sharma C, Mika F, Nierhaus K, Vogel J (2008)

Mol Cell, 32 (6): 827-37DOI: 10.1016/j.molcel.2008.10.027

A new Vibrio cholerae sRNA modulates colonization and affects release of outer membrane vesicles

Song T, Mika F, Lindmark B, Liu Z, Schild S, Bishop A, Zhu J, Camilli A, Johansson J, Vogel J, Wai S (2008)

Mol Microbiol, 70 (1): 100-11DOI: 10.1111/j.1365-2958.2008.06392.x

Systematic deletion of Salmonella small RNA genes identifies CyaR, a conserved CRP-dependent riboregulator of OmpX synthesis

Papenfort K, Pfeiffer V, Lucchini S, Sonawane A, Hinton J, Vogel J (2008)

Mol Microbiol, 68 (4): 890-906DOI: 10.1111/j.1365-2958.2008.06189.x

RNA: Noncoding

Henry A, Vogel J (2008)

In: Wiley Encyclopedia of Chemical Biology (ed Begley TP), 22DOI: 10.1002/9780470048672.wecb522

Noncoding RNA control of the making and breaking of sugars

Görke B, Vogel J (2008)

Gene Dev, 22 (21): 2914-25DOI: 10.1101/gad.1717808

The cyanobacterial homologue of the RNA chaperone Hfq is essential for motility of Synechocystis sp. PCC 6803

Dienst D, Dühring U, Mollenkopf H, Vogel J, Golecki J, Hess W, Wilde A (2008)

Microbiology, 154 (Pt 10): 3134-3143DOI: 10.1099/mic.0.2008/020222-0.


Translational control and target recognition by Escherichia coli small RNAs in vivo

Urban J, Vogel J (2007)

Nucleic Acids Res, 35 (3): 1018-37DOI: 10.1093/nar/gkl1040

Sensory and regulatory RNAs in prokaryotes: a new German research focus

Narberhaus F, Vogel J (2007)

RNA Biol, 4 (3): 160-4DOI: 10.4161/rna.4.3.5308

An antisense RNA inhibits translation by competing with standby ribosomes

Darfeuille F, Unoson C, Vogel J, Wagner E (2007)

Mol Cell, 26 (3): 381-92DOI: 10.1016/j.molcel.2007.04.003

A conserved small RNA promotes discoordinate expression of the glmUS operon mRNA to activate GlmS synthesis

Urban J, Papenfort K, Thomsen J, Schmitz R, Vogel J (2007)

J Mol Biol, 373 (3): 521-8DOI: 10.1016/j.jmb.2007.07.035

The RNA chaperone Hfq is essential for the virulence of Salmonella typhimurium

Sittka A, Pfeiffer V, Tedin K, Vogel J (2007)

Mol Microbiol, 63 (1): 193-217DOI: 10.1111/j.1365-2958.2006.05489.x

A small non-coding RNA of the invasion gene island (SPI-1) represses outer membrane protein synthesis from the Salmonella core genome

Pfeiffer V, Sittka A, Tomer R, Tedin K, Brinkmann V, Vogel J (2007)

Mol Microbiol, 66 (5): 1174-91DOI: 10.1111/j.1365-2958.2007.05991.x

Space flight alters bacterial gene expression and virulence and reveals a role for global regulator Hfq

Wilson J, Ott C, Höner zu Bentrup K, Ramamurthy R, Quick L, Porwollik S, Cheng P, McClelland M, Tsaprailis G, Radabaugh T, …, Stefanyshyn-Piper H, Nickerson C (2007)

Proc Natl Acad Sci U.S.A., 104 (41): 16299-304DOI: 10.1073/pnas.0707155104

Characterization of the role of ribonucleases in Salmonella small RNA decay

Viegas S, Pfeiffer V, Sittka A, Silva I, Vogel J, Arraiano C (2007)

Nucleic Acids Res, 35 (22): 7651-64DOI: 10.1093/nar/gkm916

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

Sharma C, Darfeuille F, Plantinga T, Vogel J (2007)

Gene Dev, 21 (21): 2804-17DOI: 10.1101/gad.447207

Recent advances in the expression, evolution, and dynamics of prokaryotic genomes

Arraiano C, Bamford J, Brüssow H, Carpousis A, Pelicic V, Pflüger K, Polard P, Vogel J (2007)

J Bacteriol, 189 (17): 6093-100DOI: 10.1128/JB.00612-07

Target identification of small noncoding RNAs in bacteria

Vogel J, Wagner E (2007)

Curr Opin Microbiol, 10 (3): 262-70DOI: 10.1016/j.mib.2007.06.001


Experimental approaches to identify non-coding RNAs

Hüttenhofer A, Vogel J (2006)

Nucleic Acids Res, 34 (2): 635-46DOI: 10.1093/nar/gkj469

σE-dependent small RNAs of Salmonella respond to membrane stress by accelerating global omp mRNA decay

Papenfort K, Pfeiffer V, Mika F, Lucchini S, Hinton J, Vogel J (2006)

Mol Microbiol, 62 (6): 1674-1688DOI: 10.1111/j.1365-2958.2006.05524.x

Small non-coding RNAs and the bacterial outer membrane

Vogel J, Papenfort K (2006)

Curr Opin Microbiol, 9 (6): 605-11DOI: 10.1016/j.mib.2006.10.006


Approaches to Identify Novel Non-messenger RNAs in Bacteria and to Investigate their Biological Functions: Functional Analysis of Identified Non-mRNAs

Gerhart E, Wagner H, Vogel J (2005)

In: Handbook of RNA Biochemistry (eds Hartmann RK, Bindereif A, Schön A, Westhof E), 2: 614-642DOI: 10.1002/9783527619504.ch37

Approaches to Identify Novel Non-messenger RNAs in Bacteria and to Investigate their Biological Functions: RNA Mining

Vogel J, Gerhart E, Wagner H (2005)

In: Handbook of RNA Biochemistry (eds Hartmann RK, Bindereif A, Schön A, Westhof E), 2: 595-613DOI: 10.1002/9783527619504.ch36

How to find small non-coding RNAs in bacteria

Vogel J, Sharma C (2005)

Biol Chem, 386 (12): 1219-38DOI: 10.1515/BC.2005.140

Identification of cyanobacterial non-coding RNAs by comparative genome analysis

Axmann I, Kensche P, Vogel J, Kohl S, Herzel H, Hess W (2005)

Genome Biol, 6 (9)DOI: 10.1186/gb-2005-6-9-r73

Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA

Udekwu K, Darfeuille F, Vogel J, Reimegård J, Holmqvist E, Wagner E (2005)

Gene Dev, 19 (19): 2355-66DOI: 10.1101/gad.354405


The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide

Vogel J, Argaman L, Wagner E, Altuvia S (2004)

Curr Biol, 14 (24): 2271-6DOI: 10.1016/j.cub.2004.12.003


Lariat formation and a hydrolytic pathway in plant chloroplast group II intron splicing

Vogel J, Börner T (2002)

EMBO J, 21 (14): 3794-803DOI: 10.1093/emboj/cdf359


Novel small RNA-encoding genes in the intergenic regions of Escherichia coli

Argaman L, Hershberg R, Vogel J, Bejerano G, Wagner E, Margalit H, Altuvia S (2001)

Curr Biol, 11 (12): 941-50

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