Prof Jörg Vogel
About
Prof. Jörg Vogel is the founding director of the Helmholtz Institute for RNA-based Infection Research (HIRI) as well as the director of the Institute of Molecular Infection Biology (IMIB) at the University of Würzburg, Germany. As world-leading scientist in the field of RNA biology, Jörg Vogel is considered a pioneer in the application and development of high-throughput sequencing methods for the analysis of individual infected cells as well as interactions between pathogenic bacteria and their hosts.
Prof. Jörg Vogel studied biochemistry at Humboldt University, Berlin, Germany, and at Imperial College, London, UK. In 1999, he received his PhD from Humboldt University with a thesis on Group II intron splicing. He spent his postdoctoral years at Uppsala University, Sweden (2000-2001) and as an EMBO fellow at the Hebrew University, Jerusalem, Israel (2002-2003) before he started an Independent Junior Research Group at the Max Planck Institute for Infection Biology in Berlin, Germany (2004-2010). He became Full Professor and Director of the Institute for Molecular Infection Biology at the University of Würzburg in 2009. As of 2017, he is the Director of the Helmholtz Institute for RNA-based Infection Research (HIRI) in Würzburg.
Jörg Vogel is an elected member of EMBO, the German National Academy of Sciences, as well as the European and American Academies of Microbiology. In 2017, he received a Leibniz Prize, Germany’s most prestigious research award, for his ground-breaking contributions to the understanding of regulatory RNA molecules in infection biology.
Prof. Vogel’s group seek to understand the full (noncoding) RNA world of bacterial pathogens and use RNA-centric approaches to targeting pathogens and manipulating microbiota. A major innovative goal is the comprehensive simultaneous RNA-based profiling of the pathogen and the infected host in real time and at single-cell resolution; where applicable, this should also include co-colonizing microbiota. Researchers at the Vogel lab focus on the mode of action of those noncoding RNA molecules that are crucial for the virulence of the pathogen, differentially expressed upon exposure to the host, or impact gene expression in interacting members of the microbiota. The knowledge obtained will be exploited for therapeutic intervention with clinically relevant bacterial pathogens.
2024
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 side-by-side comparison of peptide-delivered antisense antibiotics employing different 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
2023
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
2022
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
2021
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
2020
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
2019
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
2018
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
2017
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
2016
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
2015
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
2014
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
2013
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
2012
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
2011
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
2010
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
2009
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
2008
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
2007
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
2006
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
2005
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
2004
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
2003
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
2002
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
2001
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