Prof. Jörg Vogel


Prof. Jörg Vogel ist seit 2017 Direktor des Helmholtz-Instituts für RNA-basierte Infektionsforschung (HIRI) in Würzburg, wo er schon seit 2009 als Professor und Direktor des Instituts für Molekulare Infektionsbiologie (IMIB) tätig war. Als weltweit anerkannter Wissenschaftler auf dem Gebiet der RNA-Biologie, 2017 mit dem Leibniz-Preis ausgezeichnet, gilt er als Pionier in der Anwendung und Entwicklung von Hochdurchsatz-Sequenziermethoden für die Analyse einzelner infizierter Zellen sowie von Interaktionen zwischen krankheitserregenden Bakterien und ihren Wirten. Er studierte Biochemie an der Humboldt-Universität zu Berlin und am Imperial College, London (GB). 1999 promovierte er an der Humboldt-Universität mit einer Dissertation über
Gruppe II-Intronspleißen . Er forschte 2000/2001 an der Universität Uppsala (Schweden) und 2002/2003 als EMBO-Fellow an der Hebrew University, Jerusalem (Israel), bevor er 2004 eine unabhängige Nachwuchsgruppe am Max-Planck-Institut für Infektionsbiologie in Berlin gründete. 


Transcriptome fine-mapping in Fusobacterium nucleatum reveals FoxJ, a new σE-dependent small RNA with unusual mRNA activation activity

Ponath F, Zhu Y, Vogel J (2024)

mBio 15 (4): e0353623DOI: 10.1128/mbio.03536-23

Phage proteins target and co-opt host ribosomes immediately upon infection

Gerovac M, Chihara K, Wicke L, Böttcher B, Lavigne R, Vogel J (2024)

Nature Microbiology 9 (3): 787-800DOI: 10.1038/s41564-024-01616-x

Improved RNA stability estimation through Bayesian modeling reveals most Salmonella transcripts have subminute half-lives

Jenniches L, Michaux C, Popella L, Reichardt S, Vogel J, Westermann AJ, Barquist L (2024)

Proceedings of the National Academy of Sciences of the United States of America 121 (14): e2308814121DOI: 10.1073/pnas.2308814121

A comparative analysis of peptide-delivered antisense antibiotics employing diverse nucleotide mimics

Ghosh C, Popella L, Dhamodharan V, Jung J, Dietzsch J, Barquist L, Höbartner C, Vogel J (2024)

RNA (Online ahead of print)DOI: 10.1261/rna.079969.124

Exploring the transcriptional landscape of phage-host interactions using novel high-throughput approaches

Putzeys L, Wicke L, Brandão A, Boon M, Pires DP, Azeredo J, Vogel J, Lavigne R, Gerovac M (2024)

Current Opinion in Microbiology 77: 102419DOI: 10.1016/j.mib.2023.102419

A global survey of small RNA interactors identifies KhpA and KhpB as major RNA-binding proteins in Fusobacterium nucleatum

Zhu Y, Ponath F, Cosi V, Vogel J (2024)

Nucleic Acids Research (Online ahead of print)DOI: 10.1093/nar/gkae010

Global Hfq-mediated RNA interactome of nitrogen starved Escherichia coli uncovers a conserved post-transcriptional regulatory axis required for optimal growth recovery

McQuail J, Matera G, Gräfenhan T, Bischler T, Haberkant P, Stein F, Vogel J, Wigneshweraraj S (2024)

Nucleic Acids Research 52 (5): 2323-2339DOI: 10.1093/nar/gkad1211


Brain-to-gut trafficking of alpha-synuclein by CD11c+ cells in a mouse model of Parkinson's disease

McFleder RL, Makhotkina A, Groh J, Keber U, Imdahl F, Peña Mosca J, Peteranderl A, Wu J, Tabuchi S, Hoffmann J, …, Volkmann J, Ip CW (2023)

Nature Communications 14 (1): 7529DOI: 10.1038/s41467-023-43224-z

A SAM analogue-utilizing ribozyme for site-specific RNA alkylation in living cells

Okuda T, Lenz AK, Seitz F, Vogel J, Höbartner C (2023)

Nature Chemistry 15 (11): 1523-1531DOI: 10.1038/s41557-023-01320-z

RNA-based medicine: from molecular mechanisms to therapy

Sparmann A, Vogel J (2023)

The EMBO Journal 42 (21): e114760DOI: 10.15252/embj.2023114760

Grad-seq analysis of Enterococcus faecalis and Enterococcus faecium provides a global view of RNA and protein complexes in these two opportunistic pathogens

Michaux C, Gerovac M, Hansen EE, Barquist L, Vogel J (2023)

microLife 4: uqac027DOI: 10.1093/femsml/uqac027

Gut Microbiota Contribution to Weight-Independent Glycemic Improvements after Gastric Bypass Surgery

Hankir MK, Kovatcheva-Datchary P, Springer R, Hoffmann A, Vogel J, Seyfried F, Arora T (2023)

Microbiology Spectrum 11 (3): e0510922DOI: 10.1128/spectrum.05109-22

Improved Bacterial Single-Cell RNA-Seq through Automated MATQ-Seq and Cas9-Based Removal of rRNA Reads

Homberger C, Hayward RJ, Barquist L, Vogel J (2023)

mBio 14 (2): e0355722DOI: 10.1128/mbio.03557-22

A primary cell-based in vitro model of the human small intestine reveals host olfactomedin 4 induction in response to Salmonella Typhimurium infection

Däullary T, Imdahl F, Dietrich O, Hepp L, Krammer T, Fey C, Neuhaus W, Metzger M, Vogel J, Westermann AJ, Saliba AE, Zdzieblo D (2023)

Gut Microbes 15 (1): 2186109DOI: 10.1080/19490976.2023.2186109

Design and off-target prediction for antisense oligomers targeting bacterial mRNAs with the MASON webserver

Jung JJ, Popella L, Do PT, Pfau P, Vogel J, Barquist L (2023)

RNA 299 (5): 570-583DOI: 10.1261/rna.079263.122

RNA recording in single bacterial cells using reprogrammed tracrRNAs

Jiao C, Reckstadt C, König F, Homberger C, Yu J, Vogel J, Westermann AJ, Sharma CM, Beisel CL (2023)

Nature Biotechnology 41 (8): 1107-1116DOI: 10.1038/s41587-022-01604-8

A MATQ-seq-Based Protocol for Single-Cell RNA-seq in Bacteria

Homberger C, Saliba AE, Vogel J (2023)

Methods in Molecular Biology 2584: 105-121DOI: 10.1007/978-1-0716-2756-3_4


Ushering in a new era of single-cell transcriptomics in bacteria

Homberger C, Barquist L, Vogel J (2022)

microLife 3: uqac020DOI: 10.1093/femsml/uqac020

Hypothalamic integrity is necessary for sustained weight loss after bariatric surgery: A prospective, cross-sectional study

Dischinger U, Kötzner L, Kovatcheva-Datchary P, Kleinschmidt H, Haas C, Perez J, Presek C, Koschker AC, Miras AD, Hankir MK, …, Herrmann MJ, Seyfried F (2022)

Metabolism: Clinical and Experimental 138: 155341DOI: 10.1016/j.metabol.2022.155341

Global profiling of the RNA and protein complexes of Escherichia coli by size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq)

Chihara K, Gerovac M, Hör J, Vogel J (2022)

RNA 29 (1): 123-39DOI: 10.1261/rna.079439.122

An unusual mode of baseline translation adjusts cellular protein synthesis capacity to metabolic needs

Schneider C, Erhard F, Binotti B, Buchberger A, Vogel J, Fischer U (2022)

Cell Reports 41 (2): 111467DOI: 10.1016/j.celrep.2022.111467

INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors

Hör J, Jung J, Ðurica-Mitic S, Barquist L, Vogel J (2022)

Nucleic Acids Research 50 (22): e128DOI: 10.1093/nar/gkac838

Expanding the genetic toolkit helps dissect a global stress response in the early-branching species Fusobacterium nucleatum

Ponath F, Zhu Y, Cosi V, Vogel J (2022)

PNAS 119 (40): e2201460119DOI: 10.1073/pnas.2201460119

TFEB induces mitochondrial itaconate synthesis to suppress bacterial growth in macrophages

Schuster EM, Epple MW, Glaser KM, Mihlan M, Lucht K, Zimmermann JA, Bremser A, Polyzou A, Obier N, Cabezas-Wallscheid N, …, Westermann AJ, Rambold AS (2022)

Nature Metabolism 4 (7): 856-866DOI: 10.1038/s42255-022-00605-w

Comprehensive analysis of PNA-based antisense antibiotics targeting various essential genes in uropathogenic Escherichia coli

Popella L, Jung J, Do PT, Hayward RJ, Barquist L, Vogel J (2022)

Nucleic Acids Research 50 (11): 6435–6452DOI: 10.1093/nar/gkac362

Cellular RNA Targets of Cold Shock Proteins CspC and CspE and Their Importance for Serum Resistance in Septicemic Escherichia coli

Yair Y, Michaux C, Biran D, Bernhard J, Vogel J, Barquist L, Ron EZ (2022)

mSystems 7 (4): e0008622DOI: 10.1128/msystems.00086-22

An overview of gene regulation in bacteria by small RNAs derived from mRNA 3' ends

Ponath F, Hör J, Vogel J (2022)

FEMS Microbiology Reviews 46 (5): fuac017DOI: 10.1093/femsre/fuac017

Global RNA interactome of Salmonella discovers a 5' UTR sponge for the MicF small RNA that connects membrane permeability to transport capacity

Matera G, Altuvia Y, Gerovac M, El Mouali Y, Margalit H, Vogel J (2022)

Molecular Cell 82 (3): 629-644.e4DOI: 10.1016/j.molcel.2021.12.030

The DNA polymerase of bacteriophage YerA41 replicates its T-modified DNA in a primer-independent manner

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)

Nucleic Acids Research 50 (7): 3985-3997DOI: 10.1093/nar/gkac203

Innovative developments and emerging technologies in RNA therapeutics

Halloy F, Biscans A, Bujold KE, Debacker A, Hill AC, Lacroix A, Luige O, Strömberg R, Sundstrom L, Vogel J, Ghidini A (2022)

RNA Biology 19 (1): 313-332DOI: 10.1080/15476286.2022.2027150


Grad-seq identifies KhpB as a global RNA-binding protein in Clostridioides difficile that regulates toxin production

Lamm-Schmidt V, Fuchs M, Sulzer J, Gerovac M, Hör J, Dersch P, Vogel J, Faber F (2021)

microLife 2: uqab004DOI: 10.1093/femsml/uqab004

Impact of pseudouridylation, substrate fold, and degradosome organization on the endonuclease activity of RNase E

Islam MS, Bandyra KJ, Chao Y, Vogel J, Luisi BF (2021)

RNA 27 (11): 1339-1352DOI: 10.1261/rna.078840.121

SPI2 T3SS effectors facilitate enterocyte apical to basolateral transmigration of Salmonella-containing vacuoles in vivo

Fulde M, van Vorst K, Zhang K, Westermann AJ, Busche T, Huei YC, Welitschanski K, Froh I, Pägelow D, Plendl J, …, Repnik U, Hornef MW (2021)

Gut Microbes 13 (1): 1973836DOI: 10.1080/19490976.2021.1973836

Scanning mutagenesis of RNA-binding protein ProQ reveals a quality control role for the Lon protease

El Mouali Y, Ponath F, Scharrer V, Wenner N, Hinton JCD, Vogel J (2021)

RNA 27 (12): 1512-1527DOI: 10.1261/rna.078954.121

An RNA-centric global view of Clostridioides difficile reveals broad activity of Hfq in a clinically important gram-positive bacterium

Fuchs M, Lamm-Schmidt V, Sulzer J, Ponath F, Jenniches L, Kirk JA, Fagan RP, Barquist L, Vogel J, Faber F (2021)

PNAS 118 (25): e2103579118DOI: 10.1073/pnas.2103579118

RNA landscape of the emerging cancer-associated microbe Fusobacterium nucleatum

Ponath F, Tawk C, Zhu Y, Barquist L, Faber F, Vogel J (2021)

Nature Microbiology 6 (8): 1007-1020DOI: 10.1038/s41564-021-00927-7

The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches

Gerovac M, Vogel J, Smirnov A (2021)

Frontiers in Molecular Biosciences 8: 661448DOI: 10.3389/fmolb.2021.661448

In vivo targets of Salmonella FinO include a FinP-like small RNA controlling copy number of a cohabitating plasmid

El Mouali Y, Gerovac M, Mineikaite R, Vogel J (2021)

Nucleic Acids Research 49 (9): 5319-5335DOI: 10.1093/nar/gkab281

Analysis of the RNA and Protein Complexome by Grad-seq

Hör J, Vogel J (2021)

Methods in Molecular Biology 2300: 183-201DOI: 10.1007/978-1-0716-1386-3_16

Global RNA profiles show target selectivity and physiological effects of peptide-delivered antisense antibiotics

Popella L, Jung J, Popova K, Ðurica-Mitic S, Barquist L, Vogel J (2021)

Nucleic Acids Research 49 (8): 4705-4724DOI: 10.1093/nar/gkab242

A Grad-seq View of RNA and Protein Complexes in Pseudomonas aeruginosa under Standard and Bacteriophage Predation Conditions

Gerovac M, Wicke L, Chihara K, Schneider C, Lavigne R, Vogel J (2021)

mBio 12 (1): e03454-20DOI: 10.1128/mBio.03454-20

MAPS integrates regulation of actin-targeting effector SteC into the virulence control network of Salmonella small RNA PinT

Correia Santos S, Bischler T, Westermann AJ, Vogel J (2021)

Cell Reports 34 (5): 108722DOI: 10.1016/j.celrep.2021.108722

Cross-species RNA-seq for deciphering host–microbe interactions

Westermann AJ, Vogel J (2021)

Nature Reviews Genetics 22 (6): 361–378DOI: 10.1038/s41576-021-00326-y

A genome-wide transcriptomic analysis of embryos fathered by obese males in a murine model of diet-induced obesity

Bernhardt L, Dittrich M, El-Merahbi R, Saliba AE, Müller T, Sumara G, Vogel J, Nichols-Burns S, Mitchell M, Haaf T, El Hajj N (2021)

Scientific Reports 11: 1979DOI: 10.1038/s41598-021-81226-3

Opposing Wnt signals regulate cervical squamocolumnar homeostasis and emergence of metaplasia

Chumduri C, Gurumurthy RK, Berger H, Dietrich O, Kumar N, Koster S, Brinkmann V, Hoffmann K, Drabkina M, Arampatzi P, …, Saliba AE, Meyer TF (2021)

Nature Cell Biology 23 (2): 184–197DOI: 10.1038/s41556-020-00619-0

Introducing differential RNA-seq mapping to track the early infection phase for Pseudomonas phage ɸKZ

Wicke L, Ponath F, Coppens L, Gerovac M, Lavigne R, Vogel J (2021)

RNA Biology 18 (8): 1099-1110DOI: 10.1080/15476286.2020.1827785


An RNA biology perspective on species-specific programmable RNA antibiotics

Vogel J (2020)

Molecular Microbiology 113 (3): 550-559DOI: 10.1111/mmi.14476

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

Venturini E, Svensson SL, Maaß S, Gelhausen R, Eggenhofer F, Li L, Cain AK, Parkhill J, Becher D, Backofen R, …, Westermann AJ, Vogel J (2020)

microLife 1 (1): 597DOI: 10.1093/femsml/uqaa002

Single-Nucleotide RNA Maps for the Two Major Nosocomial Pathogens Enterococcus faecalis and Enterococcus faecium

Michaux C, Hansen EE, Jenniches L, Gerovac M, Barquist L, Vogel J (2020)

Frontiers in Cellular and Infection Microbiology 10: 600325DOI: 10.3389/fcimb.2020.600325

The SARS-CoV-2 RNA-protein interactome in infected human cells

Schmidt N, Lareau CA, Keshishian H, Ganskih S, Schneider C, Hennig T, Melanson R, Werner S, Wei Y, Zimmer M, …, Bodem J, Munschauer M (2020)

Nature Microbiology 6 (3): 339-353DOI: 10.1038/s41564-020-00846-z

Triple RNA-Seq Reveals Synergy in a Human Virus-Fungus Co-infection Model

Seelbinder B, Wallstabe J, Marischen L, Weiss E, Wurster S, Page L, Löffler C, Bussemer L, Schmitt A, Wolf T, …, Schäuble S, Loeffler J (2020)

Cell Reports 33 (7): 108389DOI: 10.1016/j.celrep.2020.108389

Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein

Gerovac M, El Mouali Y, Kuper J, Kisker C, Barquist L, Vogel J (2020)

RNA 26 (10): 1448-1463DOI: 10.1261/rna.076992.120

Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli

Hör J, Di Giorgio S, Gerovac M, Venturini E, Förstner KU, Vogel J (2020)

Nucleic Acids Research 48 (16): 9301-9319DOI: 10.1093/nar/gkaa676

Amidochelocardin Overcomes Resistance Mechanisms Exerted on Tetracyclines and Natural Chelocardin

Hennessen F, Miethke M, Zaburannyi N, Loose M, Lukežic T, Bernecker S, Hüttel S, Jansen R, Schmiedel J, Fritzenwanker M, …, Herrmann J, Müller R (2020)

Antibiotics 9 (9): 619DOI: 10.3390/antibiotics9090619

Single-cell RNA-sequencing reports growth-condition-specific global transcriptomes of individual bacteria

Imdahl F, Vafadarnejad E, Homberger C, Saliba AE, Vogel J (2020)

Nature Microbiology 5 (10): 1202–1206DOI: 10.1038/s41564-020-0774-1

Dual RNA-seq of Orientia tsutsugamushi informs on host-pathogen interactions for this neglected intracellular human pathogen

Mika-Gospodorz B, Giengkam S, Westermann AJ, Wongsantichon J, Kion-Crosby W, Chuenklin S, Wang LC, Sunyakumthorn P, Sobota RM, Subbian S, …, Barquist L, Salje J (2020)

Nature Communications 11: 3363DOI: 10.1038/s41467-020-17094-8

Breast cancer colonization by Fusobacterium nucleatum accelerates tumor growth and metastatic progression

Parhi L, Alon-Maimon T, Sol A, Nejman D, Shhadeh A, Fainsod-Levi T, Yajuk O, Isaacson B, Abed J, Maalouf N, …, Straussman R, Bachrach G (2020)

Nature Communications 11: 3259DOI: 10.1038/s41467-020-16967-2

The minimal meningococcal ProQ protein has an intrinsic capacity for structure-based global RNA recognition

Bauriedl S, Gerovac M, Heidrich N, Bischler T, Barquist L, Vogel J, Schoen C (2020)

Nature Communications 11: 2823DOI: 10.1038/s41467-020-16650-6

Improved bacterial RNA-seq by Cas9-based depletion of ribosomal RNA reads

Prezza G, Heckel T, Dietrich S, Homberger C, Westermann AJ, Vogel J (2020)

RNA 26 (8): 1069-1078DOI: 10.1261/rna.075945.120

Grad-seq in a Gram-positive bacterium reveals exonucleolytic sRNA activation in competence control

Hör J, Garriss G, Di Giorgio S, Hack LM, Vanselow JT, Förstner KU, Schlosser A, Henriques-Normark B, Vogel J (2020)

The EMBO Journal 39 (9): e103852DOI: 10.15252/embj.2019103852

Trans-Acting Small RNAs and Their Effects on Gene Expression in Escherichia coli and Salmonella enterica

Hör J, Matera G, Vogel J, Gottesman S, Storz G (2020)

EcoSal Plus 9 (1): 10.1128/ecosalplus.ESP-0030-2019DOI: 10.1128/ecosalplus.ESP-0030-2019

Tracheal brush cells release acetylcholine in response to bitter tastants for paracrine and autocrine signaling

Hollenhorst MI, Jurastow I, Nandigama R, Appenzeller S, Li L, Vogel J, Wiederhold S, Althaus M, Empting M, Altmüller J, …, Saliba AE, Krasteva-Christ G (2020)

The FASEB Journal 34 (1): 316-332DOI: 10.1096/fj.201901314RR

An Advanced Human Intestinal Coculture Model Reveals Compartmentalized Host and Pathogen Strategies during Salmonella Infection

Schulte LN, Schweinlin M, Westermann AJ, Janga H, Santos SC, Appenzeller S, Walles H, Vogel J, Metzger M (2020)

mBio 11 (1): e03348-19DOI: 10.1128/mBio.03348-19

The conserved 3' UTR-derived small RNA NarS mediates mRNA crossregulation during nitrate respiration

Wang C, Chao Y, Matera G, Gao Q, Vogel J (2020)

Nucleic Acids Research 48 (4): 2126-2143DOI: 10.1093/nar/gkz1168


Conditional Hfq Association with Small Noncoding RNAs in Pseudomonas aeruginosa Revealed through Comparative UV Cross-Linking Immunoprecipitation Followed by High-Throughput Sequencing

Chihara K, Bischler T, Barquist L, Monzon VA, Noda N, Vogel J, Tsuneda S (2019)

mSystems 4 (6): e00590-19DOI: 10.1128/mSystems.00590-19

An RNA Surprise in Bacterial Effector Mechanisms

Gerovac M, Vogel J (2019)

Cell Host & Microbe 26 (6): 709-711DOI: 10.1016/j.chom.2019.11.005

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 Biology 16 (4): 390-396DOI: 10.1080/15476286.2018.1486660

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 Research 47 (4): 2075-2088DOI: 10.1093/nar/gky1243

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

Westermann AJ, Venturini E, Sellin ME, Förstner KU, Hardt W, Vogel J (2019)

mBio 10 (1): e02504-18DOI: 10.1128/mBio.02504-18


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

Yu S, Vogel J, Förstner KU (2018)

GigaScience 7 (9): giy096DOI: 10.1093/gigascience/giy096

Salmonella persisters undermine host immune defenses during antibiotic treatment

Stapels DA, Hill PW, Westermann AJ, Fisher RA, Thurston TL, Saliba AE, Blommestein I, Vogel J, Helaine S (2018)

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

Genome organization and DNA accessibility control antigenic variation in trypanosomes

Müller LS, Cosentino RO, Förstner KU, Guizetti J, Wedel C, Kaplan N, Janzen CJ, Arampatzi P, Vogel J, Steinbiss S, …, Sebra RP, Siegel TN (2018)

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

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)

The EMBO Journal 37 (23): pii: e98529DOI: 10.15252/embj.201798529

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

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

PLOS Genetics 14 (6): e1007401DOI: 10.1371/journal.pgen.1007401

RNA-binding proteins in bacteria

Holmqvist E, Vogel J (2018)

Nature Reviews Microbiology 16 (10): 601-615DOI: 10.1038/s41579-018-0049-5

Bacterial RNA Biology on a Genome Scale

Hör J, Gorski SA, Vogel J (2018)

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

Nuclear lncRNA stabilization in the host response to bacterial infection

Munschauer M, Vogel J (2018)

The EMBO Journal 37 (13): e99875DOI: 10.15252/embj.201899875

Host-Pathogen Transcriptomics by Dual RNA-Seq

Westermann AJ, Vogel J (2018)

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

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)

Molecular Cell 70 (5): 971-982.e6DOI: 10.1016/j.molcel.2018.04.017


Global snapshots of bacterial RNA networks

Hör J, Vogel J (2017)

The EMBO Journal 36 (3): 245-247DOI: 10.15252/embj.201696072

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

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

Scientific Reports 7 (1): 9328DOI: 10.1038/s41598-017-09527-0

Einzelzell-RNA-Sequenzierung beleuchtet den Infektionsprozess

Saliba AE, Westermann AJ, Vogel J (2017)

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

Structure of the Escherichia coli ProQ RNA-binding protein

Gonzalez GM, Hardwick SW, Maslen SL, Skehel JM, Holmqvist E, Vogel J, Bateman A, Luisi BF, Broadhurst RW (2017)

RNA 23 (5): 696-711DOI: 10.1261/rna.060343.116

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

Gorski SA, Vogel J, Doudna JA (2017)

Nature Reviews Molecular Cell Biology 18 (4): 215-228DOI: 10.1038/nrm.2016.174

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

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

Nucleic Acids Research 45 (11): e96DOI: 10.1093/nar/gkx137

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 KU, Said N, Corcoran C, Smiga M, Papenfort K, Reinhardt R, Wieden H, Luisi BF, Vogel J (2017)

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

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

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

The EMBO Journal 36 (8): 1029-45DOI: 10.15252/embj.201696127

New RNA-seq approaches for the study of bacterial pathogens

Saliba AE, Santos SC, Vogel J (2017)

Current Opinion in Microbiology 35: 78-87DOI: 10.1016/j.mib.2017.01.001

Discovery of new RNA classes and global RNA-binding proteins

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

Current Opinion in Microbiology 39: 152-160DOI: 10.1016/j.mib.2017.11.016

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 Research 45 (10): 6147-6167DOI: 10.1093/nar/gkx168

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 AJ, Gunn JS, Vogel J (2017)

PNAS 114 (26): 6824-6829DOI: 10.1073/pnas.1620772114

Resolving host-pathogen interactions by dual RNA-seq

Westermann AJ, Barquist L, Vogel J (2017)

PLOS Pathogens 13 (2): e1006033DOI: 10.1371/journal.ppat.1006033


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

Cao Y, Förstner KU, Vogel J, Smith CJ (2016)

Journal of Bacteriology 198 (18): 2410-8DOI: 10.1128/JB.00381-16

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 KU, Berger M, Bertling C, Sharma CM, Vogel J, Karch H, Dobrindt U, Mellmann A (2016)

Scientific Reports 6: 35307DOI: 10.1038/srep35307

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

Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, …, Friedberg I, Radivojac P (2016)

Genome Biology 17 (1): 184DOI: 10.1186/s13059-016-1037-6

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

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

PNAS 113 (22): E3101-10DOI: 10.1073/pnas.1520255113

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

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

PLOS Pathogens 12 (6): e1005723DOI: 10.1371/journal.ppat.1005723

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 Genetics 12 (4): e1005975DOI: 10.1371/journal.pgen.1005975

The target spectrum of SdsR small RNA in Salmonella

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

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

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

Chao Y, Vogel J (2016)

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

Emerging roles of RNA modifications in bacteria

Marbaniang CN, Vogel J (2016)

Current Opinion in Microbiology 30: 50-57DOI: 10.1016/j.mib.2016.01.001

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

Saliba AE, Li L, Westermann AJ, Appenzeller S, Stapels DA, Schulte LN, Helaine S, Vogel J (2016)

Nature Microbiology 2: 16206DOI: 10.1038/nmicrobiol.2016.206

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

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

PNAS 113 (41): 11591-11596DOI: 10.1073/pnas.1609981113

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

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

The EMBO Journal 35 (9): 991-1011DOI: 10.15252/embj.201593360

Molecular phenotyping of infection-associated small non-coding RNAs

Barquist L, Westermann AJ, Vogel J (2016)

Philosophical Transactions of the Royal Society of London B: Biological Sciences 371 (1707): 20160081DOI: 10.1098/rstb.2016.0081

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

Westermann AJ, Forstner KU, Amman F, Barquist L, Chao Y, Schulte LN, Muller L, Reinhardt R, Stadler PF, Vogel J (2016)

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


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

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

PNAS 112 (34): E4772-81DOI: 10.1073/pnas.1507825112

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): e0142002DOI: 10.1371/journal.pone.0142002

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

Ziebuhr W, Vogel J (2015)

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

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

Miyakoshi M, Chao Y, Vogel J (2015)

The EMBO Journal 34 (11): 1478-92DOI: 10.15252/embj.201490546

Investigating CRISPR RNA Biogenesis and Function Using RNA-seq

Heidrich N, Dugar G, Vogel J, Sharma CM (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

Regulatory small RNAs from the 3' regions of bacterial mRNAs

Miyakoshi M, Chao Y, Vogel J (2015)

Current Opinion in Microbiology 24: 132-9DOI: 10.1016/j.mib.2015.01.013

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

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

BMC Genomics 16: 775DOI: 10.1186/s12864-015-1993-3

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

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

BMC Genomics 16: 323DOI: 10.1186/s12864-015-1489-1

Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies

Barquist L, Vogel J (2015)

Annual Review of Genetics 49: 367-94DOI: 10.1146/annurev-genet-112414-054804


Identification and Characterization of Small Non-coding RNAs in Bacteria

Podkaminski D, Bouvier M, Vogel J (2014)

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

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

Förstner KU, Vogel J, Sharma CM (2014)

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

A bacterial seek-and-destroy system for foreign DNA

Vogel J (2014)

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

Meeting report: Regulating with RNA in Bacteria 2013

Vogel J, Gottesman S, Belasco J, Narberhaus F (2014)

RNA Biology 11 (5): 403-12

Small RNA functions in carbon metabolism and virulence of enteric pathogens

Papenfort K, Vogel J (2014)

Frontiers in Cellular and Infection Microbiology 4: 91DOI: 10.3389/fcimb.2014.00091

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

Dimastrogiovanni D, Fröhlich KS, Bandyra KJ, Bruce HA, Hohensee S, Vogel J, Luisi BF (2014)

eLife 3: e05375DOI: 10.7554/eLife.05375

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

Sharma CM, Vogel J (2014)

Current Opinion in Microbiology 19: 97-105DOI: 10.1016/j.mib.2014.06.010

Single-cell RNA-seq: advances and future challenges

Saliba AE, Westermann AJ, Gorski SA, Vogel J (2014)

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


A small RNA serving both the Hfq and CsrA regulons

Holmqvist E, Vogel J (2013)

Genes & Development 27 (10): 1073-8DOI: 10.1101/gad.220178.113

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

Papenfort K, Corcoran CP, Gupta SK, Miyakoshi M, Heidrich N, Chao Y, Fröhlich KS, Ziebuhr W, Böhm A, Vogel J, Sharma CM (2013)

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

RNA-mediated regulation in pathogenic bacteria

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

Cold Spring Harbor Perspectives In Medicine 3 (9): a010298DOI: 10.1101/cshperspect.a010298

Bacterial regulatory mechanisms: the gene and beyond

Bassler B, Vogel J (2013)

Current Opinion in Microbiology 16 (2): 109-11DOI: 10.1016/j.mib.2013.04.001

Comparative genomics boosts target prediction for bacterial small RNAs

Wright PR, Richter AS, Papenfort K, Mann M, Vogel J, Hess WR, Backofen R, Georg J (2013)

PNAS 110 (37): E3487-96DOI: 10.1073/pnas.1303248110

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

Heidrich N, Vogel J (2013)

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

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)

Nature Communications 4: 1610DOI: 10.1038/ncomms2607

Alexander Böhm (1971-2012)

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

Molecular Microbiology 88 (2): 219-21DOI: 10.1111/mmi.12198

Processing-Independent CRISPR RNAs Limit Natural Transformation in Neisseria meningitidis

Zhang Y, Heidrich N, Ampattu BJ, Gunderson CW, Seifert HS, Schoen C, Vogel J, Sontheimer EJ (2013)

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

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)

Genes & Development 27 (5): 552-64DOI: 10.1101/gad.210112.112

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

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

The EMBO Journal 32 (22): 2963-79DOI: 10.1038/emboj.2013.222

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

Heidrich N, Vogel J (2013)

The EMBO Journal 32 (13): 1802-4DOI: 10.1038/emboj.2013.141

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

Schulte LN, Westermann AJ, Vogel J (2013)

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

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

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

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


The mammalian microRNA response to bacterial infections

Eulalio A, Schulte LN, Vogel J (2012)

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

Experimental tools to identify RNA-protein interactions in Helicobacter pylori

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

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

Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their analysis

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

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

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

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

PNAS 109 (13): E757-64DOI: 10.1073/pnas.1119414109

The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium

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

PNAS 109 (20): E1277-86DOI: 10.1073/pnas.1201061109

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)

PNAS 109 (12): 4621-6DOI: 10.1073/pnas.1113113109

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

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

PLOS Biology 8 (6): e1002782DOI: 10.1371/journal.pgen.1002782

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

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

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

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

Corcoran CP, Podkaminski D, Papenfort K, Urban JH, Hinton JC, Vogel J (2012)

Molecular Microbiology 84 (3): 428-45DOI: 10.1111/j.1365-2958.2012.08031.x

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

Boehm A, Vogel J (2012)

Molecular Microbiology 84 (1): 1-5DOI: 10.1111/j.1365-2958.2012.08033.x

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

Bandyra KJ, Said N, Pfeiffer V, Górna MW, Vogel J, Luisi BF (2012)

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

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

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

The EMBO Journal 31 (20): 4005-19DOI: 10.1038/emboj.2012.229

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

Corcoran CP, 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

Hfq-associated Regulatory Small RNAs

Corcoran CP, 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

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

Borries A, Vogel J, Sharma CM (2012)

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

Dual RNA-seq of pathogen and host

Westermann AJ, Gorski SA, Vogel J (2012)

Nature Reviews Microbiology 10 (9): 618-30DOI: 10.1038/nrmicro2852


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

Fröhlich KS, Papenfort K, Berger AA, Vogel J (2011)

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

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

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

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

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

Gogol EB, Rhodius VA, Papenfort K, Vogel J, Gross CA (2011)

PNAS 108 (31): 12875-80DOI: 10.1073/pnas.1109379108

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

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

PNAS 108 (5): 2124-9DOI: 10.1073/pnas.1015154108

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

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

PLOS One 6 (3): e17296DOI: 10.1371/journal.pone.0017296

Hfq and its constellation of RNA

Vogel J, Luisi BF (2011)

Nature Reviews Microbiology 9 (8): 578-89DOI: 10.1038/nrmicro2615

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

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

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

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

Sharma CM, Papenfort K, Pernitzsch SR, Mollenkopf H, Hinton JC, Vogel J (2011)

Molecular Microbiology 81 (5): 1144-65DOI: 10.1111/j.1365-2958.2011.07751.x

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

Berghoff BA, Glaeser J, Sharma CM, Zobawa M, Lottspeich F, Vogel J, Klug G (2011)

Molecular Microbiology 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)

Molecular Microbiology 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 KM (2011)

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

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

Papenfort K, Vogel J (2011)

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

The transcriptional landscape of Chlamydia pneumoniae

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

Genome Biology 12 (10): R98DOI: 10.1186/gb-2011-12-10-r98

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

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

The EMBO Journal 30 (10): 1977-89DOI: 10.1038/emboj.2011.94

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

Deltcheva E, Chylinski K, Sharma CM, Gonzales K, Chao Y, Pirzada ZA, Eckert MR, Vogel J, Charpentier E (2011)

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


The small RNAs of Salmonella

Javayel S, Papenfort K, Vogel J (2010)

In: Salmonella: From Genome to Function (ed Prowollik S)

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

Heale BS, Eulalio A, Schulte LN, Vogel J, O'Connell MA (2010)

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

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

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

PNAS 107 (47): 20435-40DOI: 10.1073/pnas.1009784107

Identification of regulatory RNAs in Bacillus subtilis

Irnov I, Sharma CM, Vogel J, Winkler WC (2010)

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

Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome

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

Nucleic Acids Research 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 CM, Marchais A, Skorski P, Borezée-Durant E, Barbet R, Jacquet E, Jacq A, …, Vogel J, Bouloc P (2010)

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

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

Podkaminski D, Vogel J (2010)

Molecular Microbiology 78 (6): 1327-31DOI: 10.1111/j.1365-2958.2010.07428.x

The role of Hfq in bacterial pathogens

Chao Y, Vogel J (2010)

Current Opinion in Microbiology 13 (1): 24-33DOI: 10.1016/j.mib.2010.01.001

Regulatory RNA in bacterial pathogens

Papenfort K, Vogel J (2010)

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

The primary transcriptome of the major human pathogen Helicobacter pylori

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)

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


A small RNA cascade regulates aminosugar synthesis

Vogel J (2009)

In: Nova Acta Leopoldina 378: 41-50

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

Urban JH, 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

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

Sittka A, Sharma CM, Rolle K, Vogel J (2009)

RNA Biology 6 (3): 266-75

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

Papenfort K, Vogel J (2009)

Research in Microbiology 160 (4): 278-87DOI: 10.1016/j.resmic.2009.03.004

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

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

PNAS 106 (51): 21878-82DOI: 10.1073/pnas.0909051106

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

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

Nature Structural & Molecular Biology 16 (8): 840-6DOI: 10.1038/nsmb.1631

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 Research 37 (20): e133-e133DOI: 10.1093/nar/gkp719

An RNA trap helps bacteria get the most out of chitosugars

Vogel J (2009)

Molecular Microbiology 73 (5): 737-41DOI: 10.1111/j.1365-2958.2009.06806.x

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

Vogel J (2009)

Molecular Microbiology 71 (1): 1-11DOI: 10.1111/j.1365-2958.2008.06505.x

Regulatory RNAs in prokaryotes: here, there and everywhere

Narberhaus F, Vogel J (2009)

Molecular Microbiology 74 (2): 261-9DOI: 10.1111/j.1365-2958.2009.06869.x

Photooxidative stress-induced and abundant small RNAs in Rhodobacter sphaeroides

Berghoff BA, Glaeser J, Sharma CM, Vogel J, Klug G (2009)

Molecular Microbiology 74 (6): 1497-512DOI: 10.1111/j.1365-2958.2009.06949.x

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

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

Molecular Microbiology 74 (1): 139-158DOI: 10.1111/j.1365-2958.2009.06857.x

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 FC (2009)

Molecular Microbiology 71 (5): 1228-38DOI: 10.1111/j.1365-2958.2009.06597.x

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

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

PLOS Computational Biology 5 (9): e1000502DOI: 10.1371/journal.pcbi.1000502

Experimental approaches for the discovery and characterization of regulatory small RNA

Sharma CM, Vogel J (2009)

Current Opinion in Microbiology 12 (5): 536-46DOI: 10.1016/j.mib.2009.07.006

Activation of gene expression by small RNA

Fröhlich KS, Vogel J (2009)

Current Opinion in Microbiology 12 (6): 674-82DOI: 10.1016/j.mib.2009.09.009


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 WR, Wilde A (2008)

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

RNA: Noncoding

Henry AA, Vogel J (2008)

In: Wiley Encyclopedia of Chemical Biology (ed Begley TP) 22: 2183DOI: 10.1002/9780470048672.wecb522

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

Sittka A, Lucchini S, Papenfort K, Sharma CM, Rolle K, Binnewies TT, Hinton JC, Vogel J (2008)

PLOS Genetics 4 (8): e1000163DOI: 10.1371/journal.pgen.1000163

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

Urban JH, Vogel J (2008)

PLOS Biology 6 (3): e64DOI: 10.1371/journal.pbio.0060064

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 SN (2008)

Molecular Microbiology 70 (1): 100-111DOI: 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 JC, Vogel J (2008)

Molecular Microbiology 68 (4): 890-906DOI: 10.1111/j.1365-2958.2008.06189.x

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

Bouvier M, Sharma CM, Mika F, Nierhaus KH, Vogel J (2008)

Molecular Cell 32 (6): 827-837DOI: 10.1016/j.molcel.2008.10.027

Noncoding RNA control of the making and breaking of sugars

Görke B, Vogel J (2008)

Genes & Development 22 (21): 2914-25DOI: 10.1101/gad.1717808

A Glimpse at the Evolution of Virulence Control

Sittka A, Vogel J (2008)

Cell Host & Microbe 4 (4): 310-312DOI: 10.1016/j.chom.2008.09.006


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

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

Journal of Bacteriology 189 (17): 6093-100DOI: 10.1128/JB.00612-07

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

Narberhaus F, Vogel J (2007)

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

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

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

Molecular Microbiology 63 (1): 193-217DOI: 10.1111/j.1365-2958.2006.05489.x

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

Urban JH, Vogel J (2007)

Journal of Molecular Biology 35 (3): 1018-37DOI: 10.1093/nar/gkl1040

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

Urban JH, Papenfort K, Thomsen J, Schmitz RA, Vogel J (2007)

Journal of Molecular Biology 373 (3): 521-8DOI: 10.1016/j.jmb.2007.07.035

Characterization of the role of ribonucleases in Salmonella small RNA decay

Viegas SC, Pfeiffer V, Sittka A, Silva IJ, Vogel J, Arraiano CM (2007)

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

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

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

PNAS 104 (41): 16299-304DOI: 10.1073/pnas.0707155104

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)

Molecular Microbiology 66 (5): 1174-91DOI: 10.1111/j.1365-2958.2007.05991.x

An antisense RNA inhibits translation by competing with standby ribosomes

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

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

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

Sharma CM, Darfeuille F, Plantinga TH, Vogel J (2007)

Genes & Development 21 (21): 2804-17DOI: 10.1101/gad.447207

Target identification of small noncoding RNAs in bacteria

Vogel J, Wagner EG (2007)

Current Opinion in Microbiology 10 (3): 262-70DOI: 10.1016/j.mib.2007.06.001


Small non-coding RNAs and the bacterial outer membrane

Vogel J, Papenfort K (2006)

Current Opinion in Microbiology 9 (6): 605-11DOI: 10.1016/j.mib.2006.10.006

Experimental approaches to identify non-coding RNAs

Hüttenhofer A, Vogel J (2006)

Nucleic Acids Research 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 JC, Vogel J (2006)

Molecular Microbiology 62 (6): 1674-1688DOI: 10.1111/j.1365-2958.2006.05524.x


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

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

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

Genes & Development 19 (19): 2355-66DOI: 10.1101/gad.354405

How to find small non-coding RNAs in bacteria

Vogel J, Sharma CM (2005)

Biological Chemistry 386 (12): 1219-38DOI: 10.1515/BC.2005.140

Identification of cyanobacterial non-coding RNAs by comparative genome analysis

Axmann IM, Kensche P, Vogel J, Kohl S, Herzel H, Hess WR (2005)

Genome Biology 6 (9): R73DOI: 10.1186/gb-2005-6-9-r73


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

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

Current Biology 14 (24): 2271-6DOI: 10.1016/j.cub.2004.12.003


Noncoding RNAs encoded by bacterial chromosomes

Wagner EG, Vogel J (2003)

In: Noncoding RNAs (eds Barciszewski J, Erdmann V): 243-259

Experimental and computational analysis of transcriptional start sites in the cyanobacterium Prochlorococcus MED4

Vogel J, Axmann IM, Herzel H, Hess WR (2003)

Nucleic Acids Research 31 (11): 2890-9

RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria

Vogel J, Bartels V, Tang TH, Churakov G, Slagter-Jäger JG, Hüttenhofer A, Wagner EG (2003)

Nucleic Acids Research 31 (22): 6435-43


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

Vogel J, Börner T (2002)

The EMBO Journal 21 (14): 3794-803DOI: 10.1093/emboj/cdf359


Complete 5' and 3' end maturation of group II intron-containing tRNA precursors

Vogel J, Hess WR (2001)

RNA 7 (2): 285-92

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

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

Current Biology 11 (12): 941-50

The ins and outs of group II introns

Bonen L, Vogel J (2001)

Trends In Genetics 17 (6): 322-31