Publications chronological (pdf)

Publications sorted (pdf)


Dischinger U, Kötzner L, Kovatcheva-Datchary P, Kleinschmidt H, Haas C, Perez J, Presek C, Koschker AC, Miras AD, Hankir MK, Vogel J, Germer CT, Fassnacht M, Herrmann MJ, Seyfried F (2023)
Hypothalamic integrity is necessary for sustained weight loss after bariatric surgery: A prospective, cross-sectional study
Metabolism 138:155341 (Epub 2022)

Chihara K, Gerovac M, Hör J, Vogel J (2022)
Global profiling of the RNA and protein complexes of Escherichia coli by size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq)
RNA rna.079439.122

Gomez-Raya-Vilanova MV, Leskinen K, Bhattacharjee A, Virta P, Rosenqvist P, Smith JLR, Bayfield OW, Homberger C, Kerrinnes T, Vogel J, Pajunen MI, Skurnik M (2022)
The DNA polymerase of bacteriophage YerA41 replicates its T-modified DNA in a primer-independent manner
Nucleic Acids Research 50(7):3985-3997

Halloy F, Biscans A, Bujold KE, Debacker A, Hill AC, Lacroix A, Luige O, Strömberg R, Sundstrom L, Vogel J, Ghidini A (2022)
Innovative developments and emerging technologies in RNA therapeutics
RNA Biology 19(1):313-332

Hör J, Jung J, Ðurica-Mitić S, Barquist L, Vogel J (2022)
INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors
Nucleic Acids Research 50(22):e128

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)

Matera G, Altuvia Y, Gerovac M, El Mouali Y, Margalit H, Vogel J (2022)
Global RNA interactome of Salmonella discovers a 5' UTR sponge for the MicF small RNA that connects membrane permeability to transport capacity
Molecular Cell 82(3):629-644.e4

Popella L, Jung J, Do PT, Hayward RJ, Barquist L, Vogel J (2022)
Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenic Escherichia coli
Nucleic Acids Research 50(11):6435–52

Schneider C, Erhard F, Binotti B, Buchberger A, Vogel J#, Fischer U# (2022)
An unusual mode of baseline translation adjusts cellular protein synthesis capacity to metabolic needs
Cell Reports 41(2):111467

Schuster EV, Epple MW, Glaser K, Mihlan M, Lucht K, Zimmermann JA, Bremser A,  Polyzou A, Obier N, Cabezas-Wallscheid N, Trompouki E, Ballabio A, Vogel J, Buescher JM, Lämmermann T, Westermann AJ, Rambold AS (2022)
TFEB induces mitochondrial itaconate synthesis to suppress bacterial growth in macrophages
Nature Metabolism in press

Solar Venero EC, Matera G, Vogel J, López NI#, Tribelli PM# (2022)
Small RNAs in the Antarctic bacterium Pseudomonas extremaustralis responsive to oxygen availability and oxidative stress
Environmental Microbiology Reports Online ahead of print

Yair Y , Michaux C , Biran D, Bernhard J, Vogel J, Barquist L, Ron EZ (2022)
Cellular RNA Targets of Cold Shock Proteins CspC and CspE and Their Importance for Serum Resistance in Septicemic Escherichia coli
mSystems e0008622

El Mouali Y, Ponath F, Scharrer V, Wenner N, Hinton JCD, Vogel J (2021)
Scanning mutagenesis of RNA-binding protein ProQ reveals a quality control role for the Lon protease
RNA (online ahead of print)

Fulde M*, van Vorst K*, Zhang K, Westermann AJ, Busche T, Huei YC, Welitschanski K, Froh I, Pägelow D, Johanna Plend, Pfarrer C, Kalinowski J, Vogel J, Weigand PV, Hensel M, Tedin K, Repnik U, Hornef MW (2021)
SPI2 T3SS effectors facilitate enterocyte apical to basolateral transmigration of Salmonella containing vacuoles in vivo
Gut Microbes 13(1):1973836

Islam MS, Bandyra KJ, Chao Y, Vogel J, Luisi BF (2021)
Impact of pseudo-uridylation, substrate fold and degradosome organization on the endonuclease activity of RNase E
RNA (online ahead of print)

Wicke L, Ponath F, Coppens L, Gerovac M, Lavigne R, Vogel J (2021)
Introducing differential RNA-seq mapping to track the early infection phase for Pseudomonas phage ɸKZ
RNA Biology 18(8):1099-1110

Ponath F, Tawk C, Zhu Y, Barquist L, Faber F, Vogel J (2021)
RNA landscape of the emerging cancer-associated microbe Fusobacterium nucleatum
Nature Microbiology doi: 10.1038/s41564-021-00927-7)

Popella L, Jung J, Popova K, Ðurica-Mitić S, Barquist L, Vogel J (2021)
Global RNA profiles show target selectivity and physiological effects of peptide-delivered antisense antibiotics
Nucleics Acids Research 49(8):4705-4724

Westermann AJ*, Vogel J* (2021)
Cross-species RNA-seq deciphers host-microbe interactions
Nature Reviews Genetics 22(6):361-378 Review

El Mouali Y, Gerovac M, Mineikaitė R, Vogel J (2021)
In vivo targets of Salmonella FinO include a FinP-like small RNA controlling copy number of a cohabitating plasmid
Nucleic Acids Research 49(9):5319-5335

Gerovac M, Vogel J, Smirnov A (2021)
The world of stable ribonucleoproteins and its mapping with Grad-seq and related approaches
Frontiers in Molecular Biosciences in press

Hör J, Vogel J (2021)
Analysis of the RNA and Protein Complexome by Grad-seq
Methods in Molecular Biology in press 

Lamm-Schmidt V, Fuchs M, Sulzer J, Gerovac M, Hör J, Dersch P, Vogel J, Faber F (2021)
Grad-seq identifies KhpB as a global RNA-binding protein in Clostridioides difficile that regulates toxin production
microLife 2:uqab004

Fuchs M, Lamm-Schmidt V, Sulzer J, Ponath F, Jenniches L, Kirk JA, Fagan RP, Barquist L, Vogel J, Faber F (2021)
An RNA-centric global view of Clostridioides difficile reveals broad activity of Hfq in a clinically important gram-positive bacterium
PNAS 22;118(25):e2103579118

Bernhardt L, Dittrich M, ElMerahbi R, Saliba AE, Müller T, Sumara G, Vogel J, NicholsBurns S, Mitchell, Haaf T, El Hajj N (2021)
A genome
wide transcriptomic analysis of embryos fathered by obese males in a murine model of dietinduced obesity
Scientific Reports (in press)

Santos SC, Bischler T, Westermann AJ*, Vogel J* (2021)
MAPS integrates overlooked regulation of actin-targeting effector SteC into the virulence control network of Salmonella small RNA PinT
Cell Reports (in press)

Schmidt N, Lareau C, Keshishian H, Ganskih S, Schneider C, Hennig T, Melanson R, Werner S, Wei Y, Zimmer M, Ade J, Kirschner L, Zielinski S, Dölken L, Lander ES, Caliskan N, Fischer U, Vogel J, Carr S, Bodem J, Munschauer M (2021)
The SARS-CoV-2 RNA-protein interactome in infected human cells
Nature Microbiology (in press)

Gerovac M, Wicke L, Chihara K, Schneider C, Lavigne R, Vogel J (2021)
A Grad-seq view of RNA and protein complexes in Pseudomonas aeruginosa under standard and bacteriophage predation conditions
mBio (in press)

Hör J, Garriss G, Di Giorgio S, Hack LM, Vanselow JT, Förstner KU, Schlosser A, Henriques-Normark B, Vogel J (2020)
Grad-seq in a Gram-positive bacterium reveals exonucleolytic sRNA activation in competence control

Wang C, Chao Y, Matera G, Gao Q, Vogel J (2020)
The conserved 3’ UTR-derived small RNA NarS mediates mRNA crossregulation during nitrate respiration
Nucleic Acids Research 48(4):2126–2143

Bauriedl S, Gerovac M, Heidrich N, Bischler T, Barquist L, Vogel J, Schoen C(2020)
The minimal ProQ protein of Neisseria meningitidis reveals an intrinsic capacity for structure-based global RNA recognition by the FinO domain
Nature Communications accepted

Schulte LN, Schweinlin M, Westermann AJ, Janga H, Santos SC, Appenzeller S, Walles H, Vogel J, Metzger M (2020)
An advanced human intestinal co-culture model reveals compartmentalized host and pathogen strategies during Salmonella infection
mBio 11(1) e03348-19

Hollenhorst MI, Jurastow I, Nandigama R, Appenzeller S, Li L, Vogel J, Wiederhold S, Althaus M, Empting M, Altmüller J, Hirsch AKH, Flockerzi V, Canning BJ, Saliba AE, Krasteva-Christ G (2020)
Tracheal brush cells release acetylcholine in response to bitter tastants for paracrine and autocrine signaling

FASEB Journal 34:316–332

Vogel J (2020)
An RNA biology perspective on species-specific programmable RNA antibiotics
Molecular Microbiology in press

Hör J, Matera G, Vogel J, Gottesman S, Storz G (2020)
Trans-acting small RNAs and their effects on gene expression in Escherichia coli and Salmonella enterica
EcoSal in press

Gerovac M, Vogel J (2019)
An RNA Surprise in Bacterial Effector Mechanisms
Cell Host Microbes 11;26(6):709-711

Chihara K, Bischler T, Barquist L, Monzon VA, Noda N, Vogel J, Tsuneda S (2019)
Conditional Hfq Association with Small Noncoding RNAs in Pseudomonas aeruginosa Revealed through Comparative UV Cross-Linking Immunoprecipitation Followed by High-Throughput Sequencing
mSystems 3;4(6). pii: e00590-19. doi:10.1128

Westermann AJ, Venturini E, Sellin ME, Förstner KU, Hardt WD, Vogel J (2019)
The Major RNA-Binding Protein ProQ Impacts Virulence Gene Expression in Salmonella
enterica Serovar Typhimurium

MBio 2;10(1). pii: e02504-18

Miyakoshi M, Matera G, Maki K, Sone Y, Vogel J (2019)
Functional expansion of a TCA cycle operon mRNA by a 3' end-derived small RNA
Nucleic Acids Research 12 doi: 10.1093/nar/gky1243

Heidrich N, Hagmann A, Bauriedl S, Vogel J, Schoen C (2019)
The CRISPR/Cas system in Neisseria meningitidis affects bacterial adhesion to human nasopharyngeal
epithelial cells

RNA Biolology 16(4):390-396

Stapels DAC, Hill PWS, Westermann AJ, Fisher RA, Thurston TL, Saliba AE,
Blommestein I, Vogel J, Helaine S (2018)
Salmonella persisters undermine host immune defenses during antibiotic treatment
Science 7;362(6419):1156-1160

Tawk C, Nigro G, Rodrigues Lopes I, Aguilar C, Lisowski C, Mano M, Sansonetti
P, Vogel J, Eulalio A (2018)
Stress-induced host membrane remodeling protects from infection by non-motile bacterial pathogens
EMBO Journal 3;37(23). pii:e98529

Müller LSM, Cosentino RO, Förstner KU, Guizetti J, Wedel C, Kaplan N, Janzen CJ, Arampatzi P, Vogel J, Steinbiss S, Otto TD, Saliba AE, Sebra RP, Siegel TN (2018)
Genome organization and DNA accessibility control antigenic variation in trypanosomes

Yu SH, Vogel J, Förstner KU (2018)
ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes
Gigascience 1;7(9) doi: 10.1093/gigascience/giy096

Munschauer M, Vogel J (2018)
Nuclear lncRNA stabilization in the host response to bacterial infection
EMBO Journal 2;37 doi:10.15252/embj.201899875

Holmqvist E, Vogel J (2018)
RNA-binding proteins in bacteria
Nature Reviews Microbiology 16(10):601-615

Holmqvist E, Li L, Bischler T, Barquist L, Vogel J (2018)
Global maps of ProQ binding in vivo reveal target recognition via RNA structure and stability control at mRNA 3' ends
Molecular Cell 7;70(5):971-982

Hör J, Gorski SA, Vogel J (2018)
Bacterial RNA Biology on a Genome Scale

Molecular Cell
7;70(5):785-799 Review

Munschauer M, Vogel J (2018)
Nuclear lncRNA stabilization in the host response to bacterial infection
EMBO Journal 2;37(13). pii: e99875

El Mouali Y, Gaviria-Cantin T, Sánchez-Romero MA, Gibert M, Westermann AJ, Vogel J, Balsalobre C (2018)
CRP-cAMP mediates silencing of Salmonella virulence at the post-transcriptional level
PLoS Genetics 7;14(6):e1007401

Westermann AJ, Vogel J (2018)
Host-pathogen transcriptomics by Dual RNA-seq
Methods in Molecular Biology 1737:59-75

Smirnov A, Schneider C, Hör J, Vogel J (2017)
Discovery of new RNA classes and global RNA-binding proteins
Current Opinion Microbiology 39:152-160 Review

Michaux C, Holmqvist E, Vasicek E, Sharan M, Barquist L, Westermann AJ, Gunn JS, Vogel J (2017)
RNA target profiles direct the discovery of virulence functions for thecold shock proteins CspC and CspE PNAS 114(26):6824-6829

Chao Y, Li L, Girodat D, Förstner KU, Said N, Corcoran C, Śmiga M, Papenfort K, Reinhardt R, Wieden HJ, Luisi BF, Vogel J (2017)
In vivo cleavage map illuminates the central role of RNase E in coding and noncoding RNA pathways
Molecular Cell 65(1):39-51

Smirnov A, Wang C, Drewry LL, Vogel J (2017)
Molecular mechanism of mRNA repression in trans by a ProQ-dependent small RNA
EMBO Journal in press

Heidrich N, Bauriedl S, Barquist L, Li L, Schoen S, Vogel J (2017)
The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq
Nucleic Acids Research in press

Sharan M, Förstner KU, Eulalio A, Vogel J (2017)
APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins
Nucleic Acids Research in press

Gonzalez GM, Hardwick SW, Maslen SL, Skehel JM, Holmqvist E, Vogel J, Bateman A, Luisi BF, Broadhurst RW (2017)
Structure of the Escherichia 1 coli ProQ RNA binding protein
RNA in press

r J, Vogel J (2017)
Global snapshots of bacterial RNA networks
EMBO Journal 36(3):245-247

Gorski SA, Vogel J, Doudna JA (2017)
RNA-based Recognition and targeting: Sowing the seeds of specificity
Nature Reviews Molecular Cell Biology in press

Westermann AJ, Barquist L, Vogel J (2017)
Resolving host-pathogen interactions by Dual RNA-seq
PLoS Pathogens in press

Saliba AE, Santos SC, Vogel J (2017)
New RNA-seq approaches for the study of bacterial pathogens
Current Opinion in Microbiology in press

Westermann AJ, Förstner KU, Amman F, Barquist L, Chao Y, Schulte LN, Müller L, Reinhardt R, Stadler PF, Vogel J (2016)
Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions
Nature 529:496-501

Smirnov A, Förstner KU, Holmqvist E, Otto A, Günster R, Becher D, Reinhardt R, Vogel J (2016)
Grad-seq guides the discovery of ProQ as a major small RNA binding protein
PNAS 113(41):11591-6

Saliba AE, Lei Li, Westermann AJ, Appenzeller S, Stapels DAC, Schulte LN, Helaine S, Vogel J (2016)
Single cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella
Nature Microbiology 2:16206

Holmqvist E, Wright PR, Li L, Bischler T, Barquist L, Reinhardt R, Backofen R, Vogel J (2016)
Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo
EMBO Journal 35(9):991-1011

Chao Y, Vogel J (2016)
A 3' UTR-Derived Small RNA Provides the Regulatory Noncoding Arm of the Inner Membrane Stress Response
Molecular Cell 61:352-363

Fröhlich KS, Haneke K, Papenfort K, Vogel J (2016)
The target spectrum of SdsR small RNA in Salmonella
Nucleic Acids Research 44(21): 10406-22

Das S, Lindemann C, Young BC, Muller J, Österreich B, Ternette N, Winkler AC, Paprotka K, Reinhardt R, Förstner KU, Allen E, Flaxman A, Yamaguchi Y, Rollier CS, van Diemen P, Blättner S, Remmele CW, Selle M, Dittrich M, Mueller T, Vogel J, Ohlsen K, Crook DW, Massey R, Wilson DJ, Rudel R, Wyllie DH, Fraunholz MJ (2016)
Natural mutations in a S. aureus virulence regulator attenuate cytotoxicity but permit bacteremia and abscess formation
PNAS 113(22):E3101–E3110

Hershko-Shalev T, Odenheimer-Bergman A, Elgrably-Weiss M, Ben-Zvi T, Govindarajan S, Seri H, Papenfort K, Vogel J, Altuvia S (2016)
Gifsy-1 prophage IsrK with dual function as small and messenger RNA modulates vital bacterial machineries
PLoS Genetics 12(4):e1005975

Müller AA, Dolowschiak T, Sellin ME, Felmy B, Verbree C, Gadient S, Westermann AJ, Vogel J, LeibundGut-Landmann S,
Hardt WD (2016)
An NK cell perforin response elicited via IL-18 controls mucosal inflammation kinetics during Salmonella gut infection
PLoS Pathogens 12(6):e1005723

Cao Y, Förstner KU, Vogel J, Smith J (2016)
Cis-encoded sRNAs, a conserved mechanism for repression of polysaccharide utilization in the Bacteroides
Journal of Bacteriology in press

Barquist L, Westermann AJ, Vogel J (2016)
Molecular phenotyping of infection-associated small noncoding RNAs
Philosophical Transactions B in press

Marbaniang CM, Vogel J (2016)
Emerging roles of RNA modifications in bacteria
Current Opinion Microbiology 30:50-57




Papenfort K, Espinosa E, Casadesús J, Vogel J (2015)
Small RNA-based feed-forward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella
PNAS 112(34):E4772-81

Miyakoshi M, Chao Y, Vogel J (2015)
Crosstalk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA
EMBO Journal 34(11):1478-92

Heidrich N, Dugar G, Vogel J, Sharma CM (2014)
Investigating CRISPR RNA biogenesis and function using RNA-seq
Methods in Molecular Biology 1311:1-21

Sass A, Van Acker H, Förstner KU, Van Nieuwerburgh F, Deforce D, Vogel J, Coenye T (2015)
Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315
BMC Genomics 16(1):775

Afonso-Grunz F, Hoffmeier K, Müller S, Westermann AJ, Rotter B, Vogel J, Winter P, Kahl G (2015)
Dual 3´Seq using deepSuperSAGE uncovers transcriptomes of interacting Salmonella enterica Typhimurium and human host cells
BMC Genomics 16(1):323

Fan B, Li L, Chao Y, Jiang CL, Förstner KU, Vogel J, Borriss B, Wu XQ (2015)
dRNA-seq reveals genomewide TSSs and noncoding RNAs of plant beneficial rhizobacterium Bacillus amyloliquefaciens FZB42
PLoS One 10(11):e0142002

Ziebuhr W, Vogel J (2015)
The end is not the end: remnants of tRNA precursors live on to sponge up small regulatory RNAs
Molecular Cell 58(3):389-90

Barquist L, Vogel J (2015)
Accelerating discovery and functional analysis of small RNAs with new technologies
Annual Review of Genetics 49:367-94

Miyakoshi M, Chao Y, Vogel J (2015)
Regulatory small RNAs from the 3’ regions of bacterial mRNAs
Current Opinion in Microbiology 24:132-139



Dimastrogiovanni D, Fröhlich KS, Bandyra KJ, Bruce HA, Hohensee S, Vogel J, Luisi BF (2014)
Recognition of the small regulatory RNA RydC by the bacterial Hfq protein
eLife 3:e05375

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

Vogel J (2014)
A bacterial seek-and-destroy system for foreign DNA
Science 344(6187):972-3

Saliba AE, Westermann AJ, Gorski SA, Vogel J (2014)
Single-cell RNA-seq: advances and future challenges
Nucleic Acids Research 42(14):8845-60

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

Papenfort K, Vogel J (2014)
Small RNA functions in carbon metabolism and virulence of enteric pathogens
Frontiers in Cellular and Infection Microbiology 4:91

Vogel J, Gottesman S, Belasco JG, Narberhaus F (2014)
Meeting report: Regulating with RNA in Bacteria 2013
RNA Biology 11(5):403-12


Papenfort K, Sun Y, Miyakoshi M, Vanderpool CK, Vogel J (2013)
Small RNA-mediated activation of sugar phosphatase mRNA regulates glucose homeostasis
Cell 153:426–437

Fröhlich KS, Papenfort K, Fekete A, Vogel J (2013)
A small RNA activates CFA synthase by isoform-specific mRNA stabilization
EMBO Journal 13;32(22):2963-79

Heidrich N, Vogel J (2013)
Same same but different: new structural insight into CRISPR-Cas complexes
Molecular Cell 10;52(1):4-7

Zhang Y, Heidrich N, Ampattu BJ, Gunderson CW, Seifert HS, Schoen C, Vogel J, Sontheimer EJ (2013)
Processing-Independent CRISPR RNAs Limit Natural Transformation in Neisseria meningitides
Molecular Cell 23;50(4):488-503

Holmqvist E, Vogel J (2013)
A small RNA serving both the Hfq and CsrA regulons
Genes & Development 27:1073-1078

Göpel Y, Papenfort K, Reichenbach B, Vogel J, Görke B (2013)
Targeted decay of a regulatory small RNA by an adaptor protein for RNase E and counteraction by an anti-adaptor RNA
Genes & Development

Wright PR, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J (2013)
Comparative genomics boosts target prediction for bacterial small RNAs
PNAS 110(37):E3487-96

Heidrich N, Vogel J (2013)
CRISPRs extending their reach: Prokaryotic RNAi protein Cas9 recruited for gene regulation
EMBO Journal 3;32(13):1802-4

Gutierrez A, Laureti L, Crussard S, Abida H, Rodríguez-Rojas A, Blázquez J, Baharoglu Z, Mazel D, Darfeuille F, Vogel J, Matic I (2013)
beta-lactam antibiotics promote bacterial mutagenesis via an RpoS-mediated reduction in replication fidelity
Nature Communications 19;4:1610

Schulte LN, Westerman AJ, Vogel J (2013)Differential activiation and functional specialisation of miR-146 and miR-155 in innate immune sensing
Nucleic Acids Research 41(1):542-53

Vogel J, Bassler BL (2013)
Bacterial Regulatory Mechanisms: The gene and beyond
Current Opinion in Microbiology 16(2):109-11

Caldelari I, Chao Y, Romby P, Vogel J (2013)
RNA-mediated regulation in pathogenic bacteria. 
In: Bacterial Pathogens and Pathogenesis (eds. Cossart P, Maloy S), CSH Press, Sep 1;3(9). doi:pii: a010298

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

Podkaminski D, Bouvier M, Vogel J (2013)
Identification and characterization of small noncoding RNAs in bacteria
In: Handbook of RNA Biochemistry (eds. Hartmann RK, Bindereif A, Schön A, Westhof E), Wiley-VCH, in press


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 Journal 31(29):4005-19

Westermann AJ, Gorski SA, Vogel J (2012)
Dual RNA-seq of pathogen and host
Nature Reviews Microbiology 14;10(9):618-30

Bandyra K, Said N, Pfeiffer V, Górna MW, Vogel J#, Luisi BF# (2012)
The seed region of a small RNA drives the controlled destruction of target mRNA by the endoribonuclease RNase E
Molecular Cell 28;47(6):943-53

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

Eulalio A, Schulte L, Vogel J (2012)
The mammalian microRNA response to bacterial infections
RNA Biology 9(6):742-750

Corcoran CP, Rieder R, Podkaminski D, Hofmann B, Vogel J (2012)
Use of Aptamer Tagging to Identify In Vivo Protein Binding Partners of Small Regulatory RNAs
Methods Mol Biol 2012;905:177-200

Papenfort K, Podkaminski D, Hinton JC, Vogel J (2012)
The ancestral SgrS RNA discriminates horizontally acquired Salmonella mRNAs through a single G-U wobble pair

Argaman L, Elgrably-Weiss M, Hershko T, Vogel J, Altuvia S (2012)
RelA protein stimulates the activity of RyhB small RNA by acting on RNA-binding protein Hfq
PNAS 109(12):4621-6

Kröger C, Dillon SC, Cameron AD, Papenfort K, Sivasankaran SK, Hokamp K, Chao Y, Sittka A, Hébrard M, Händler K, Colgan A, Leekitcharoenphon P, Langridge GC, Lohan AJ, Loftus B, Lucchini S, Ussery DW, Dorman CJ, Thomson NR, Vogel J, Hinton JC (2012)
The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium

Corcoran CP, Podkaminski D, Papenfort K, Urban JH, Hinton JC, Vogel J (2012)
Superfolder GFP reporters validate diverse new mRNA targets of the classic porin regulator, MicF RNA
Molecular Microbiology

Boehm A, Vogel J (2012)
The csgD mRNA as a hub for signal integration via multiplesmall RNAs
Molecular Microbiology 84(1):1-5

Fröhlich KS, Papenfort K, Berger AA, Vogel J (2012)
A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD
Nucleic Acids Research 40(8):3623-40

Rieder R, Reinhardt R, Sharma C, Vogel J (2012)
Experimental tools to identify RNA-protein interactions in Helicobacter pylori
RNA Biology

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 function
Nucleic Acids Research 40(5):2020-31

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

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



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

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

Storz G, Vogel J, Wassarman KM (2011)
Regulation by small RNAs in bacteria: expanding frontiers
Molecular Cell 43(6):880-91

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-dependent GcvB small RNA
Molecular Microbiology 81(5):1144-65

Vogel J, Luisi B (2011)
Hfq and its constellation of RNA
Nature Reviews Microbiology 9(8):578-89

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

Schulte LN, Eulalio A, Mollenkopf HJ, Reinhardt R, Vogel J (2011)
Analysis of the host microRNA response to Salmonella uncovers the control of major cytokines by the let-7 family
EMBO J 30(10):1977-89

Gogol EB, Rhodius VA, Papenfort K, Vogel J#, Gross CA# (2011)
Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon
PNAS 108(31):12875-80

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. PCC 6803
PNAS 108(5):2124-9

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-dependent GcvB small RNA
Molecular Microbiology 81(5):1144-65

Berghoff B, 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 Microbiology 80(6):1479-95

Papenfort K, Vogel J (2011)
Sweet business: Spot42 RNA networks with CRP to modulate catabolite repression
Molecular Cell 41(3):245-6

Eulalio A, Fröhlich KS, Mano M, Giacca M, Vogel J (2011)
A candidate approach implicates the secreted Salmonella effector protein SpvB in P-body disassembly

Böhm A, Papenfort K, Lopez D, Vogel J (2011)
Microbes at their best: First Mol Micro Meeting Würzburg
Molecular Microbiology 82(4):797-806

Corcoran CP, Rieder R, Podkaminski D, Hofmann B, Vogel J (2011)
Use of aptamer tagging to identify in vivo protein binding partners of small regulatory RNAs
Methods in Molecular Biology in press

Corcoran C, Papenfort K, Vogel J (2011)
Hfq-associated regulatory small RNAs
In: Regulatory RNAs in Prokaryotes, Eds. A. Marchfelder, W.R. Hess, Springer Germany

Podkaminski D, Bouvier M, Vogel J (2011)
Identification and characterization of small noncoding RNAs in bacteria
In: Handbook of RNA Biochemistry (eds. Hartmann RK, Bindereif A, Schön A, Westhof E), Wiley-VCH

Borries A, Vogel J, Sharma CM (2011)
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



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

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

Heale BS, Eulalio A, Schulte LN, Vogel J, O’Connell MA (2010)
Analysis of A to I editing of miRNA in Macrophages exposed to Salmonella
RNA Biology 7(5):116-22

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

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

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

Papenfort K, Vogel J (2010)
Regulatory RNA in bacterial pathogens
Cell Host & Microbe 8(1):116-27

Podkaminski D, Vogel J (2010)
Small RNAs promote mRNA stability to activate the synthesis of virulence factors
Molecular Microbiology 78(6):1327-31

Chao Y, Vogel J (2010)
The role of Hfq in bacterial pathogens
Current Opinion in Microbiology 13(1):24-33

Javayel S, Papenfort K, Vogel J (2010)
The small RNAs of Salmonella
Salmonella: From Genome to Function (Edited by S. Prowollik), Caister Academic Press; ISBN: 978-1-904455-73-8


Pfeiffer V, Papenfort K, Lucchini S, Hinton JC, Vogel J (2009)
Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation
Nature Structural and Molecular Biology 16(8):840-46 [pdf] [comment]

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 [pdf]

Papenfort K, Said N, Welsink T, Lucchini S, Hinton JC, Vogel J (2009)
Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA
Molecular Microbiology 74(1):139-58 [pdf]

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

Said N, Rieder R, Hurwitz R, Deckert J, Urlaub H, Vogel J (2009)
In vivo expression and purification of aptamer-tagged small RNA regulators
Nucleic Acids Research 37(20):e133 [pdf] [suppl]

Albrecht M, Sharma CM, Reinhardt R, Vogel J, Rudel T (2009)
Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome

Nucleic Acids Research 38(3):868-77 [pdf]

Fröhlich K, Vogel J (2009)
Activation of gene expression by small RNA
Current Opinion in Microbiology 12(6):674-82 [pdf]

Narberhaus F, Vogel J (2009)
Regulatory RNAs in prokaryotes: Here, there and everywhere
Molecular Microbiology 74(2):261-69 [pdf]

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

Vogel J (2009)
An RNA trap helps bacteria get the most of out of chitobiose
Molecular Microbiology 73(5):737–41 [pdf]

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 [pdf]

Papenfort K, Vogel J (2009)
Multiple target regulation by small noncoding RNAs rewires gene expression at the post-transcriptional level
Research in Microbiology 160:278-87 [pdf]

Urban JH, Vogel J (2009)
A green fluorescent protein (GFP) based plasmid system to study post-transcriptional control of gene expression in vivo
Methods in Molecular Biology 540:301-19

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 [pdf] [suppl]

Muller C, Bang IS, Velayudhan J, Karlinsey J, Papenfort K, Vogel J, Fang FC (2009)
Acid Stress Activation of the σE Stress Response in Salmonella enterica serovar Typhimurium
Molecular Microbiology 71(5):1228-38

Vogel J (2009)
A rough guide to the noncoding RNA world of Salmonella
Molecular Microbiology 71(1):1-11 [pdf]


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 [pdf] [suppl] [preview]

Urban JH, Vogel J (2008)
Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation
PLoS Biology  6(3):e64 [pdf] [suppl]

Sittka A, Lucchini S, Papenfort K, Sharma C, 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 [pdf] [suppl]

Görke B, Vogel J
Noncoding RNA functions in the making and breaking of sugars
Genes & Development 22(21):2914-25 [pdf]

Papenfort K , Pfeiffer V , Lucchini S, Sonawane A, Hinton JC, Vogel J (2008)
Systematic deletion of Salmonella small RNA genes identifies CyaR, a conserved CRP-dependent riboregulator of OmpX synthesis
Molecular Microbiology 68(4); 890-906 [pdf] [suppl]

Sittka A, Vogel J (2008)
A glimpse at the evolution of virulence control
Cell Host & Microbe 4:310-12 [pdf]

Song T, Mika F, Lindmark B, Liu Z, Schild S, Bishop A, Zhu J, Camilli A, Johansson J, Vogel J, Wai SN (2008)
A new Vibrio cholerae sRNA modulates colonization and affects release of outer membrane vesicles
Molecular Microbiology 70(1):100-11[pdf]

Dienst D, Dühring U, Mollenkopf HJ, Vogel J, Golecki J, Hess WR, Wilde A (2008)
The cyanobacterial homologue of the RNA chaperone Hfq is essential for motility of Synechocystis sp PCC 6803
Microbiology 154(10):3134-43


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):2804-17 [pdf] [suppl]

Darfeuille F, Unoson C, Vogel J, Wagner EGH (2007)
An antisense RNA inhibits translation by competing with 'standby' ribosomes
Molecular Cell 26(3):381-92 [pdf] [suppl]

Sittka A, Pfeiffer V, Tedin K, Vogel J (2007)
The RNA chaperone Hfq is essential for the virulence of Salmonella typhimurium
Molecular Microbiology 63(1):193-217 [pdf] [suppl]

Pfeiffer V, Sittka A, Tomer R, Tedin K, Brinkmann V, Vogel J (2007)
A small noncoding RNA of the invasion gene island (SPI-1) represses outer membrane protein synthesis from the Salmonella core genome
Molecular Microbiology 66(5):1174-91 [pdf] [suppl]

Urban JH, Vogel J (2007)
Translational control and target recognition by Escherichia coli small RNAs in vivo
Nucleic Acids Research 35(3):1018-37 [pdf] [suppl]

Wilson JW, Ott CM, Höner zu Bentrup K, Ramamurthy R, Quick L, Porwollik S, Cheng P, McClelland M, Tsaprailis G, Radabaugh T, Hunt A, Fernandez D, Richter E, Shah M, Kilcoyne M, Joshi L, Nelman-Gonzalez M, Hing S, Parra M, Dumars P, Norwood K, Bober R, Devich J, Ruggles A, Goulart C, Rupert M, Stodieck L, Stafford P, Catella L, Schurr MJ, Buchanan K, Morici L, McCracken J, Allen P, Baker-Coleman C, Hammond T, Vogel J, Nelson R, Pierson DL, Stefanyshyn-Piper HM, Nickerson CA (2007)
Space flight alters bacterial gene expression and virulence and reveals roles for global regulator Hfq
PNAS 104(41):16299–304 [pdf]

Narberhaus F, Vogel J (2007)
Sensory and regulatory RNAs in prokaryotes: A new German research focus
RNA Biology 4(3):160-4 [pdf]

Viegas S, Pfeiffer V, Sittka A, Silva IJ, Vogel J, Arraiano CM (2007)
Characterization of the role of Ribonucleases in Salmonella small RNA decay
Nucleic Acids Research 35(22):7651-64 [pdf]

Arraiano CM, Bamford J, Brüssow H, Carpousis AJ, Pelicic V, Pflüger K, Polard P, Vogel J (2007)
Recent Advances on the Expression, Evolution and Dynamics of Prokaryotic Genomes
Journal of Bacteriology 189(17):6093-100 [pdf]

Urban JH, Papenfort K, Thompsen J, Schmitz RA, Vogel J (2007)
 A conserved small RNA promotes discoordinate expression of the glmUS operon mRNA to activate GlmS synthesis
Journal of Molecular Biology 373(3): 521–28 [pdf]

Vogel J, Wagner EGH (2007)
Target identification of small non-coding RNAs in bacteria
Current Opinion in Microbiology 10:262–70 [pdf]


Papenfort K, Pfeiffer V, Mika F, Lucchini S, Hinton JC, Vogel J (2006)
SigmaE-dependent small RNAs of Salmonella respond to membrane stress by accelerating global omp mRNA decay
Molecular Microbiology 62(6):1674–88 [pdf] [suppl]

Vogel J, Papenfort K (2006)
Small non-coding RNAs and the bacterial outer membrane
Current Opinion in Microbiology 9(6):605-11 [pdf]

Henry AA, Vogel J (2006)
Non-coding RNAs
In: Wiley Encyclopedia of Chemical Biology (WECB)

Hüttenhofer A, Vogel J (2006)
Experimental approaches to identify non-coding RNAs
Nucleic Acids Research 34(2):635-46 [pdf]


Udekwu KI, Darfeuille F, Vogel J, Reimegård J, Holmqvist E, Wagner EGH (2005)
Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA
Genes & Development 19:2355-66 [pdf] [suppl]

Axmann IM, Kensche P, Vogel J, Kohl S, Herzel H, Hess WR (2005)
Identification of cyanobacterial non-coding RNAs by comparative genome analysis
Genome Biology 6:R73 [pdf]

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

Vogel J, Wagner EGH (2005)
RNA mining
In: Handbook of RNA Biochemistry (eds. Hartmann RK, Bindereif A, Schön A, Westhof E), Wiley-VCH Vol 2: 595-613 [pdf]

Wagner EGH, Vogel J (2005)
Functional analysis of identified non-mRNAs
In: Handbook of RNA Biochemistry (eds. Hartmann RK, Bindereif A, Schön A, Westhof E), Wiley-VCH, Vol 2: 614-42 [pdf]


Vogel J, Argaman L, Wagner EGH, Altuvia S (2004)
The small RNA IstR inhibits synthesis of an SOS-induced toxic peptide
Current Biology 11(12):941-50 [pdf] [suppl]

Vogel J, Bartel V, Tang TH, Churakov G, Slagter-Jäger, Hüttenhofer A, Wagner EGH (2003)
RNomics in Escherichia coli: New sRNA genes and distinct small RNA species derived from untranslated regions of mRNAs
Nucleic Acids Research 31(22):6435-43 [pdf] [suppl]

Wagner EGH, Vogel J (2003)
Noncoding RNAs encoded by bacterial chromosomes
In: Noncoding RNAs (eds. Barciszewski J, Erdmann V), Landes Bioscience, 243-59 [pdf]

Vogel J, Axmann IM, Herzel H, Hess WR (2003)
Experimental and computational analysis of transcriptional start sites in the cyanobacterium Prochlorococcus MED4
Nucleic Acids Research 31(11):2890-99 [pdf]

Vogel J, Börner T (2002)
Lariat formation and a hydrolytic pathway in plant chloroplast group II intron splicing
EMBO J 21(14):3794-3803 [pdf] [suppl]

Argaman L, Hershberg R , Vogel J, Bejerano G, Wagner EGH, Margalit H, Altuvia S (2001)
Novel small RNA-encoding genes in the intergenic regions of Escherichia coli
Current Biology 11(12):941–50 [pdf]

Bonen L, Vogel J (2001)
The ins and outs of group II introns
Trends Genet 17(6):322-31 [pdf]

Vogel J, Hess WR (2001)
Complete 5' and 3' end maturation of group II intron containing tRNA precursors
RNA 7(2):285-92 [pdf]

Vogel J, Börner T, Hess WR (1999)
Comparative analysis of splicing of the complete set of chloroplast group II introns in three higher plant mutants
Nucleic Acids Research 27(19): 3866-74 [pdf]

Vogel J, Börner T, Hess WR (1998)
Barley plastid genes encoding trnI-GAU and trnA-UGC are disrupted by group II introns
Plant Physiol 118:331

Vogel J, Hess WR, Börner T (1997)
Precise branch point mapping and quantification of splicing intermediates

Nucleic Acids Research 25(10):2030-31 [pdf]

Vogel J, Hübschmann T, Börner T, Hess WR (1997)
Splicing and intron-internal RNA editing of trnK-matK transcripts in barley plastids: support for MatK as an essential splice factor
J Mol Biol 270(2):179-87 [pdf]