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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): 9301-9319

A positive, growth-based PAM screen identifies noncanonical motifs recognized by the S. pyogenes Cas9

Collias D, Leenay RT, Slotkowski RA, Zuo Z, Collins SP, McGirr BA, Liu J, Beisel CL (2020)

Science Advances, 6 (29): 4054

LifeTime and improving European healthcare through cell-based interceptive medicine

Rajewsky N, Almouzni G, Gorski SA, Aerts S, Amit I, Bertero MG, Bock C, Bredenoord AL, Cavalli G, Chiocca S, …, Vidal M, Voet T (2020)

Nature, Preprint

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: 1202

A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron

Ryan D, Jenniches L, Reichardt S, Barquist L, Westermann AJ (2020)

Nature Communications, 11 (1): 3557

Severe COVID-19 is marked by a dysregulated myeloid cell compartment

Schulte-Schrepping J, Reusch N, Paclik D, Baßler K, Schlickeiser S, Zhang B, Krämer B, Krammer T, Brumhard S, Bonaguro L, …, Saliba AE, Sander LE (2020)

Cell, 182 (6): 1419-1440

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 (1): 3363

An amphipathic peptide with antibiotic activity against multidrug-resistant Gram-negative bacteria

Elliott AG, Huang JX, Neve S, Zuegg J, Edwards IA, Cain AK, Boinett CJ, Barquist L, Lundberg CV, Steen J, …, Strandh M, Cooper MA (2020)

Nature Communications, 11 (1): 3184

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 (1): 3259

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 (1): 2823

Characterization of Cas12a nucleases reveals diverse PAM profiles between closely-related orthologs

Jacobsen T, Ttofali F, Liao C, Manchalu S, Gray BN, Beisel CL (2020)

Nucleic Acids Research, 48 (10): 5624-5638

Integrative functional genomics decodes herpes simplex virus 1

Whisnant AW, Jürges CS, Hennig T, Wyler E, Prusty B, Rutkowski AJ, L'hernault A, Djakovic L, Göbel M, Döring K, …, Erhard F, Dölken L (2020)

Nature Communications, 11 (1): 2038

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

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

The EMBO Journal: 10385

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): 2126-2143

Eleven grand challenges in single-cell data science

Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, …, Shah SP, Schönhuth A (2020)

Genome Biology, 21 (1): 31

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): 1448-1463

Dynamics of Cardiac Neutrophil Diversity in Murine Myocardial Infarction

Vafadarnejad E, Rizzo G, Krampert L, Arampatzi P, Arias-Loza A, Nazzal Y, Rizakou A, Knochenhauer T, Bandi SR, Nugroho VA, …, Saliba AE, Cochain C (2020)

Circulation Research, 127 (9): 232-

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): 1-19

Whole genome sequencing of Thametopoea pityocampa revealed putative pesticide targets

Shahraki A, Yu Y, Gul ZM, Liang C, Iyison NB (2020)

Genomics, 112 (6): 4203-4207

Reprogramming of host glutamine metabolism during Chlamydia trachomatis infection and its key role in peptidoglycan synthesis

Rajeeve K, Vollmuth N, Janaki-Raman S, Wulff TF, Baluapuri A, Dejure FR, Huber C, Fink J, Schmalhofer M, Schmitz W, …, Seibel J, Rudel T (2020)

Nature Microbiology, Preprint

Growth-uncoupled isoprenoid synthesis in Rhodobacter sphaeroides

Orsi E, Mougiakos I, Post W, Beekwilder J, Dompè M, Eggink G, van der Oost J, Kengen SW, Weusthuis RA (2020)

Biotechnology for Biofuels, 13: 123

Mass-Encoded Reporters Reporting Proteolytic Activity from within the Extracellular Matrix

Dodt K, Lamer S, Drießen M, Bölch S, Schlosser A, Lühmann T, Meinel L (2020)

ACS Biomaterials Science & Engineering

A direct RNA-protein interaction atlas of the SARS-CoV-2 RNA in infected human cells

Schmidt N, Lareau CA, Keshishian H, Melanson R, Zimmer M, Kirschner L, Ade J, Werner S, Caliskan N, Lander ES, …, Bodem J, Munschauer M (2020)

Book, 382

Targeting interleukin-4 to the arthritic joint

Spieler V, Ludwig M, Dawson J, Tigani B, Littlewood-Evans A, Safina C, Ebersbach H, Seuwen K, Raschig M, Ter Mors B, …, Meinel L, Lühmann T (2020)

Journal of Controlled Release, 326: 172-180

Antibacterial Anacardic Acid Derivatives

Saedtler M, Förtig N, Ohlsen K, Faber F, Masota N, Kowalick K, Holzgrabe U, Meinel L (2020)

ACS Infectious Diseases, 6 (7): 1674-1685

A decade of advances in transposon-insertion sequencing

Cain AK, Barquist L, Goodman AL, Paulsen IT, Parkhill J, van Opijnen T (2020)

Nature Reviews Genetics, 21: 526-540

Increasing storage stability of freeze-dried plasma using trehalose

Brogna R, Oldenhof H, Sieme H, Figueiredo C, Kerrinnes T, Wolkers WF (2020)

PLOS One, 15 (6): 02345

Plugging Small RNAs into the Network

Barquist L (2020)

mSystems, 5 (3): 00422-20

Tunable self-cleaving ribozymes for modulating gene expression in eukaryotic systems

Jacobsen T, Yi G, Al Asafen H, Jermusyk AA, Beisel CL, Reeves GT (2020)

PLOS One, 15 (4): 02320

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)


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)

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): 316-332

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): 03348-19

Herpes simplex virus blocks host transcription termination via the bimodal activities of ICP27

Wang X, Hennig T, Whisnant AW, Erhard F, Prusty BK, Friedel CC, Forouzmand E, Hu W, Erber L, Chen Y, …, Dölken L, Shi Y (2020)

Nature Communications, 11 (1): 293

Competitive exclusion is a major bioprotective mechanism of lactobacilli against fungal spoilage in fermented milk products

Siedler S, Rau MH, Bidstrup S, Vento JM, Aunsbjerg SD, Bosma EF, McNair LM, Beisel CL, Neves AR (2020)

Applied and Environmental Microbiology, 86 (7): 02312-19

CRISPR-Cas Systems and the Paradox of Self-Targeting Spacers

Wimmer F, Beisel CL (2020)

Frontiers in Microbiology, 10: 3078


An RNA Surprise in Bacterial Effector Mechanisms

Gerovac M, Vogel J (2019)

Cell Host & Microbe, 26 (6): 709-711

Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells

Pickar-Oliver A, Black JB, Lewis MM, Mutchnick KJ, Klann TS, Gilcrest KA, Sitton MJ, Nelson CE, Barrera A, Bartelt LC, …, Barrangou R, Gersbach CA (2019)

Nature Biotechnology, 37 (12): 1493-1501

Thermodynamic control of -1 programmed ribosomal frameshifting

Bock LV, Caliskan N, Korniy N, Peske F, Rodnina MV, Grubmüller H (2019)

Nature Communications, 10 (1): 4598

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): 2075-2088

scSLAM-seq reveals core features of transcription dynamics in single cells

Erhard F, Baptista MA, Krammer T, Hennig T, Lange M, Arampatzi P, Jürges CS, Theis FJ, Saliba AE, Dölken L (2019)

Nature, 571 (7765): 419-423

Modular one-pot assembly of CRISPR arrays enables library generation and reveals factors influencing crRNA biogenesis

Liao C, Ttofali F, Slotkowski RA, Denny SR, Cecil TD, Leenay RT, Keung AJ, Beisel CL (2019)

Nature Communications, 10 (1): 2948

An educational module to explore CRISPR technologies with a cell-free transcription-translation system

Collias D, Marshall R, Collins SP, Beisel CL, Noireaux V (2019)

Synthetic Biology, 4 (1): 156

Rapid Testing of CRISPR Nucleases and Guide RNAs in an E. coli Cell-Free Transcription-Translation System

Marshal R, Beisel CL, Noireaux V (2019)

STAR Protocols

CRATES: A one-step assembly method for Class 2 CRISPR arrays

Liao C, Slotkowski RA, Beisel CL (2019)

Methods In Enzymology, 629: 493-511

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): 390-396

Induced Pluripotent Stem Cell-Derived Brain Endothelial Cells as a Cellular Model to Study Neisseria meningitidis Infection

Martins Gomes SF, Westermann AJ, Sauerwein T, Hertlein T, Förstner KU, Ohlsen K, Metzger M, Shusta EV, Kim BJ, Appelt-Menzel A, Schubert-Unkmeir A (2019)

Frontiers in Microbiology, 10: 1181

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): 02504-18

Rapid transcriptional responses to serum exposure are associated with sensitivity and resistance to antibody-mediated complement killing in invasive Salmonella Typhimurium ST313

Ondari EM, Klemm EJ, Msefula CL, El Ghany MA, Heath JN, Pickard DJ, Barquist L, Dougan G, Kingsley RA, MacLennan CA (2019)

Wellcome Open Research, 4: 74

Transcriptional noise and exaptation as sources for bacterial sRNAs

Jose BR, Gardner PP, Barquist L (2019)

Biochemical Society Transactions, 47 (2): 527-539

Distinct timescales of RNA regulators enable the construction of a genetic pulse generator

Westbrook A, Tang X, Marshall R, Maxwell CS, Chappell J, Agrawal DK, Dunlop MJ, Noireaux V, Beisel CL, Lucks J, Franco E (2019)

Biotechnology and Bioengineering, 116 (5): 1139-1151

Characterization of the all-E. coli transcription-translation system myTXTL by mass spectrometry

Garenne D, Beisel CL, Noireaux V (2019)

Rapid Communications In Mass Spectrometry, 33 (11): 1036-1048

An enhanced assay to characterize anti-CRISPR proteins using a cell-free transcription-translation system

Wandera KG, Collins SP, Wimmer F, Marshall R, Noireaux V, Beisel CL (2019)

Methods, 172: 42-50

The Acidaminococcus sp. Cas12a nuclease recognizes GTTV and GCTV as non-canonical PAMs

Jacobsen T, Liao C, Beisel CL (2019)

FEMS Microbiology Letters, 366 (8): 085

Barriers to genome editing with CRISPR in bacteria

Vento JM, Crook N, Beisel CL (2019)

Journal of Industrial Microbiology & Biotechnology, 46 (9-10): 1327-1341

The evolution of RNA structural probing methods: From gels to next-generation sequencing

Mailler E, Paillart J, Marquet R, Smyth RP, Vivet-Boudou V (2019)

Wiley Interdisciplinary Reviews: RNA, 10 (2): 1518


Bacterial Adaptation to the Host's Diet Is a Key Evolutionary Force Shaping Drosophila-Lactobacillus Symbiosis

Martino ME, Joncour P, Leenay R, Gervais H, Shah M, Hughes S, Gillet B, Beisel CL, Leulier F (2018)

Cell Host & Microbe, 24 (1): 109-119

CRISPR tool puts RNA on the record

Beisel CL (2018)

Nature, 562 (7727): 347-349

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): 1156-1160

Neonatally imprinted stromal cell subsets induce tolerogenic dendritic cells in mesenteric lymph nodes

Pezoldt J, Pasztoi M, Zou M, Wiechers C, Beckstette M, Thierry GR, Vafadarnejad E, Floess S, Arampatzi P, Buettner M, …, Saliba AE, Huehn J (2018)

Nature Communications, 9 (1): 3903

Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis

Cochain C, Vafadarnejad E, Arampatzi P, Pelisek J, Winkels H, Ley K, Wolf D, Saliba AE, Zernecke A (2018)

Circulation Research, 122 (12): 1661-1674

Atlas of the Immune Cell Repertoire in Mouse Atherosclerosis Defined by Single-Cell RNA-Sequencing and Mass Cytometry

Winkels H, Ehinger E, Vassallo M, Buscher K, Dinh HQ, Kobiyama K, Hamers AA, Cochain C, Vafadarnejad E, Saliba AE, …, Ley K, Wolf D (2018)

Circulation Research, 122 (12): 1675-1688

Ribosome Levels Selectively Regulate Translation and Lineage Commitment in Human Hematopoiesis

Khajuria RK, Munschauer M, Ulirsch JC, Fiorini C, Ludwig LS, McFarland SK, Abdulhay NJ, Specht H, Keshishian H, Mani DR, …, Carr SA, Sankaran VG (2018)

Cell, 173 (1): 90-103

The NORAD lncRNA assembles a topoisomerase complex critical for genome stability

Munschauer M, Nguyen CT, Sirokman K, Hartigan CR, Hogstrom L, Engreitz JM, Ulirsch JC, Fulco CP, Subramanian V, Chen J, …, Carr SA, Lander ES (2018)

Nature, 561 (7721): 132-136

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): 121-125

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): 98529

RNA-binding proteins in bacteria

Holmqvist E, Vogel J (2018)

Nature Reviews Microbiology, 16 (10): 601-615

Bacterial RNA Biology on a Genome Scale

Hör J, Gorski SA, Vogel J (2018)

Molecular Cell, 70 (5): 785-799

Nuclear lncRNA stabilization in the host response to bacterial infection

Munschauer M, Vogel J (2018)

The EMBO Journal, 37 (13): 99875

Small synthetic molecule-stabilized RNA pseudoknot as an activator for -1 ribosomal frameshifting

Matsumoto S, Caliskan N, Rodnina MV, Murata A, Nakatani K (2018)

Nucleic Acids Research, 46 (16): 8079-8089

In cell mutational interference mapping experiment (in cell MIME) identifies the 5' polyadenylation signal as a dual regulator of HIV-1 genomic RNA production and packaging

Smyth RP, Smith MR, Jousset A, Despons L, Laumond G, Decoville T, Cattenoz P, Moog C, Jossinet F, Mougel M, …, Kleist M, Marquet R (2018)

Nucleic Acids Research, 46 (9): 57

Rapid and Scalable Characterization of CRISPR Technologies Using an E. coli Cell-Free Transcription-Translation System

Marshall R, Maxwell CS, Collins SP, Jacobsen T, Luo ML, Begemann MB, Gray BN, January E, Singer A, He Y, Beisel CL, Noireaux V (2018)

Molecular Cell, 69 (1): 146-157

CRISPR RNA-Dependent Binding and Cleavage of Endogenous RNAs by the Campylobacter jejuni Cas9

Dugar G, Leenay RT, Eisenbart SK, Bischler T, Aul BU, Beisel CL, Sharma CM (2018)

Molecular Cell, 69 (5): 893-905

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

Toward Cell Type-Specific In Vivo Dual RNA-Seq

Frönicke L, Bronner DN, Byndloss MX, McLaughlin B, Bäumler AJ, Westermann AJ (2018)

Methods In Enzymology, 612: 505-522

Regulatory RNAs in Virulence and Host-Microbe Interactions

Westermann AJ (2018)

Microbiology Spectrum, 6 (4): 305-337

MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data

Simon LM, Karg S, Westermann AJ, Engel M, Elbehery AH, Hense B, Heinig M, Deng L, Theis FJ (2018)

GigaScience, 7 (6): 070

A global genomic approach uncovers novel components for twitching motility-mediated biofilm expansion in Pseudomonas aeruginosa

Nolan LM, Whitchurch CB, Barquist L, Katrib M, Boinett CJ, Mayho M, Goulding D, Charles IG, Filloux A, Parkhill J, Cain AK (2018)

Microbial Genomics, 4 (11): 00022

Functional analysis of Salmonella Typhi adaptation to survival in water

Kingsley RA, Langridge G, Smith SE, Makendi C, Fookes M, Wileman TM, El Ghany MA, Keith Turner A, Dyson ZA, Sridhar S, …, Barquist L, Dougan G (2018)

Environmental Microbiology, 20 (11): 4079-4090

New insights into the cellular temporal response to proteostatic stress

Rendleman J, Cheng Z, Maity S, Kastelic N, Munschauer M, Allgoewer K, Teo G, Zhang YB, Lei A, Parker B, …, Choi H, Vogel C (2018)

eLife, 7: 39054

Advances in CRISPR Technologies for Microbial Strain Engineering

Alper HS, Beisel CL (2018)

Biotechnology Journal, 13 (9): 18004

Synthetic Biology Approaches to Engineer Probiotics and Members of the Human Microbiota for Biomedical Applications

Bober JR, Beisel CL, Nair NU (2018)

Annual Review of Biomedical Engineering, 20: 277-300

Mathematical Modeling of RNA-Based Architectures for Closed Loop Control of Gene Expression

Agrawal DK, Tang X, Westbrook A, Marshall R, Maxwell CS, Lucks J, Noireaux V, Beisel CL, Dunlop MJ, Franco E (2018)

ACS Synthetic Biology, 7 (5): 1219-1228

A detailed cell-free transcription-translation-based assay to decipher CRISPR protospacer-adjacent motifs

Maxwell CS, Jacobsen T, Marshall R, Noireaux V, Beisel CL (2018)

Methods, 143: 48-57

Genome Editing with CRISPR-Cas9 in Lactobacillus plantarum Revealed That Editing Outcomes Can Vary Across Strains and Between Methods

Leenay RT, Vento JM, Shah M, Martino ME, Leulier F, Beisel CL (2018)

Biotechnology Journal, 14 (3): 17005

The Francisella novicida Cas12a is sensitive to the structure downstream of the terminal repeat in CRISPR arrays

Liao C, Slotkowski RA, Achmedov T, Beisel CL (2018)

RNA Biology, 16 (4): 404-412

RNA Structure - A Neglected Puppet Master for the Evolution of Virus and Host Immunity

Smyth RP, Negroni M, Lever AM, Mak J, Kenyon JC (2018)

Frontiers in Immunology, 9: 2097

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): 10074

Structural and Functional Motifs in Influenza Virus RNAs

Ferhadian D, Contrant M, Printz-Schweigert A, Smyth RP, Paillart J, Marquet R (2018)

Frontiers in Microbiology, 9: 559

Host-Pathogen Transcriptomics by Dual RNA-Seq

Westermann AJ, Vogel J (2018)

In: Arluison V., Valverde C. (eds) Bacterial Regulatory RNA, Methods Mol Biol (Methods in Molecular Biology), 1737: 59-75

Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin

Cain AK, Boinett CJ, Barquist L, Dordel J, Fookes M, Mayho M, Ellington MJ, Goulding D, Pickard D, Wick RR, …, Parkhill J, Thomson NR (2018)

Scientific Reports, 8 (1): 9868

Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica

Wheeler NE, Gardner PP, Barquist L (2018)

PLOS Genetics, 14 (5): 10073


Global snapshots of bacterial RNA networks

Hör J, Vogel J (2017)

The EMBO Journal, 36 (3): 245-247

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

Gorski SA, Vogel J, Doudna JA (2017)

Nature Reviews Molecular Cell Biology, 18 (4): 215-228

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): 96

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): 39-51

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): 1029-45

Conditional Switch between Frameshifting Regimes upon Translation of dnaX mRNA

Caliskan N, Wohlgemuth I, Korniy N, Pearson M, Peske F, Rodnina MV (2017)

Molecular Cell, 66 (4): 558-567

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): 6147-6167

Developmentally-faithful and effective human erythropoiesis in immunodeficient and Kit mutant mice

Fiorini C, Abdulhay NJ, McFarland SK, Munschauer M, Ulirsch JC, Chiarle R, Sankaran VG (2017)

American Journal of Hematology, 92 (9): 513-

Deciphering, Communicating, and Engineering the CRISPR PAM

Leenay RT, Beisel CL (2017)

Journal of Molecular Biology, 429 (2): 177-191

Toward a genetic tool development pipeline for host-associated bacteria

Waller MC, Bober JR, Nair NU, Beisel CL (2017)

Current Opinion in Microbiology, 38: 156-164

Short DNA containing χ sites enhances DNA stability and gene expression in E. coli cell-free transcription-translation systems

Marshall R, Maxwell CS, Collins SP, Beisel CL, Noireaux V (2017)

Biotechnology and Bioengineering, 114 (9): 2137-41

Advancing the design and delivery of CRISPR antimicrobials

Fagen JR, Collias D, Singh AK, Beisel CL (2017)

Current Opinion in Biomedical Engineering, 4: 57-64

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): 9328

Einzelzell-RNA-Sequenzierung beleuchtet den Infektionsprozess

Saliba AE, Westermann AJ, Vogel J (2017)

BIOspektrum, 23 (5): 525-528

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): 696-711

New RNA-seq approaches for the study of bacterial pathogens

Saliba AE, Santos SC, Vogel J (2017)

Current Opinion in Microbiology, 35: 78-87

Discovery of new RNA classes and global RNA-binding proteins

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

Current Opinion in Microbiology, 39: 152-160

HIV-1 Pr55Gag binds genomic and spliced RNAs with different affinity and stoichiometry

Bernacchi S, Abd El-Wahab EW, Dubois N, Hijnen M, Smyth RP, Mak J, Marquet R, Paillart J (2017)

RNA Biology, 14 (1): 90-103

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)

Proceedings of the National Academy of Sciences of the United States of America, 114 (26): 6824-6829

Role of sapA and yfgA in Susceptibility to Antibody-Mediated Complement-Dependent Killing and Virulence of Salmonella enterica Serovar Typhimurium

Ondari EM, Heath JN, Klemm EJ, Langridge G, Barquist L, Goulding DA, Clare S, Dougan G, Kingsley RA, MacLennan CA (2017)

Infection and Immunity, 85 (9): 00419-17

Resolving host-pathogen interactions by dual RNA-seq

Westermann AJ, Barquist L, Vogel J (2017)

PLOS Pathogens, 13 (2): 10060

Resolving host-pathogen interactions by dual RNA-seq

Westermann AJ, Barquist L, Vogel J (2017)

PLOS Pathogens, 13 (2): 10060

Resolving host-pathogen interactions by dual RNA-seq

Westermann AJ, Barquist L, Vogel J (2017)

PLOS Pathogens, 13 (2): 10060


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): 184

A protocol for the systematic and quantitative measurement of protein-lipid interactions using the liposome-microarray-based assay

Saliba AE, Vonkova I, Deghou S, Ceschia S, Tischer C, Kugler KG, Bork P, Ellenberg J, Gavin A (2016)

Nature Protocols, 11 (6): 1021-38

Systematic mapping of functional enhancer-promoter connections with CRISPR interference

Fulco CP, Munschauer M, Anyoha R, Munson G, Grossman SR, Perez EM, Kane M, Cleary B, Lander ES, Engreitz JM (2016)

Science, 354 (6313): 769-773

The CRISPR RNA-guided surveillance complex in Escherichia coli accommodates extended RNA spacers

Luo ML, Jackson RN, Denny SR, Tokmina-Lukaszewska M, Maksimchuk KR, Lin W, Bothner B, Wiedenheft B, Beisel CL (2016)

Nucleic Acids Research, 44 (15): 7385-94

The target spectrum of SdsR small RNA in Salmonella

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

Nucleic Acids Research, 44 (21): 10406-22

Choreography of molecular movements during ribosome progression along mRNA

Belardinelli R, Sharma H, Caliskan N, Cunha CE, Peske F, Wintermeyer W, Rodnina MV (2016)

Nature Structural & Molecular Biology, 23 (4): 342-8

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: 16206

Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems

Leenay RT, Maksimchuk KR, Slotkowski RA, Agrawal RN, Gomaa AA, Briner AE, Barrangou R, Beisel CL (2016)

Molecular Cell, 62 (1): 137-47

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): 496-501

Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings

Feasey NA, Hadfield J, Keddy KH, Dallman TJ, Jacobs J, Deng X, Wigley P, Barquist L, Langridge GC, Feltwell T, …, Gordon MA, Thomson NR (2016)

Nature Genetics, 48 (10): 1211-1217

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): 2410-8

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: 35307

Synthetic Biology - Engineering Genes with CRISPR-Cas9

Luo ML, Beisel CL (2016)

CEP Magazine, September

Rethinking the Hierarchy of Sugar Utilization in Bacteria

Beisel CL, Afroz T (2016)

Journal of Bacteriology, 198 (3): 374-376

Current and future prospects for CRISPR-based tools in bacteria

Luo ML, Leenay RT, Beisel CL (2016)

Biotechnology and Bioengineering, 113 (5): 930-43

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)

Proceedings of the National Academy of Sciences of the United States of America, 113 (22): 3101-10

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): 10057

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): 10059

Emerging roles of RNA modifications in bacteria

Marbaniang CN, Vogel J (2016)

Current Opinion in Microbiology, 30: 50-57

HIV-1 Mutation and Recombination Rates Are Different in Macrophages and T-cells

Cromer D, Schlub TE, Smyth RP, Grimm AJ, Chopra A, Mallal S, Davenport MP, Mak J (2016)

Viruses, 8 (4): 118

A step forward understanding HIV-1 diversity

Smyth RP, Negroni M (2016)

Retrovirology, 13: 27

The Life-Cycle of the HIV-1 Gag-RNA Complex

Mailler E, Bernacchi S, Marquet R, Paillart J, Vivet-Boudou V, Smyth RP (2016)

Viruses, 8 (9): 248

MIMEAnTo: profiling functional RNA in mutational interference mapping experiments

Smith MR, Smyth RP, Marquet R, Kleist M (2016)

Bioinformatics, 32 (21): 3369-3370

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)

Proceedings of the National Academy of Sciences of the United States of America, 113 (41): 11591-11596

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): 20160

Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families

Barquist L, Burge SW, Gardner PP (2016)

Current Protocols in Bioinformatics, 54: 1-12

The in vitro and in vivo effects of constitutive light expression on a bioluminescent strain of the mouse enteropathogen Citrobacter rodentium

Read HM, Mills G, Johnson S, Tsai P, Dalton J, Barquist L, Print CG, Patrick WM, Wiles S (2016)

PeerJ, 4: 2130

A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes

Wheeler NE, Barquist L, Kingsley RA, Gardner PP (2016)

Bioinformatics, 32 (23): 3566-3574

The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries

Barquist L, Mayho M, Cummins C, Cain AK, Boinett CJ, Page AJ, Langridge GC, Quail MA, Keane JA, Parkhill J (2016)

Bioinformatics, 32 (7): 1109-11

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): 991-1011


Changed in translation: mRNA recoding by -1 programmed ribosomal frameshifting

Caliskan N, Peske F, Rodnina MV (2015)

Trends in Biochemical Sciences, 40 (5): 265-74

Efficient Delivery of CRISPR-Cas9 for Genome Editing via Self-Assembled DNA Nanoclews**

Sun W, Ji W, Hall JM, Hu Q, Wang C, Beisel CL, Gu Z (2015)

Angewandte Chemie International Edition, 54 (41): 12029-33

Mutational interference mapping experiment (MIME) for studying RNA structure and function

Smyth RP, Despons L, Huili G, Bernacchi S, Hijnen M, Mak J, Jossinet F, Weixi L, Paillart J, Kleist M, Marquet R (2015)

Nature Methods, 12 (9): 866-72

The systematic analysis of protein-lipid interactions comes of age

Saliba AE, Vonkova I, Gavin A (2015)

Nature Reviews Molecular Cell Biology, 16 (12): 753-61

Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies

Barquist L, Vogel J (2015)

Annual Review of Genetics, 49: 367-94

Lipid Cooperativity as a General Membrane-Recruitment Principle for PH Domains

Vonkova I, Saliba AE, Deghou S, Anand K, Ceschia S, Doerks T, Galih A, Kugler KG, Maeda K, Rybin V, …, Bork P, Gavin A (2015)

Cell Reports, 12 (9): 1519-30

Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins

Bish R, Cuevas-Polo N, Cheng Z, Hambardzumyan D, Munschauer M, Landthaler M, Vogel C (2015)

Biomolecules, 5 (3): 1441-66

Trade-offs in engineering sugar utilization pathways for titratable control

Afroz T, Biliouris K, Boykin KE, Kaznessis Y, Beisel CL (2015)

ACS Synthetic Biology, 4 (2): 141-9

Impact of Residual Inducer on Titratable Expression Systems

Afroz T, Luo ML, Beisel CL (2015)

PLOS One, 10 (9): 01374

High-throughput analysis of gene essentiality and sporulation in Clostridium difficile

Dembek M, Barquist L, Boinett CJ, Cain AK, Mayho M, Lawley TD, Fairweather NF, Fagan RP (2015)

mBio, 6 (2): 02383

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

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

Proceedings of the National Academy of Sciences of the United States of America, 112 (34): 4772-81

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): 01420

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): 1478-92

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: 1-21

Regulatory small RNAs from the 3' regions of bacterial mRNAs

Miyakoshi M, Chao Y, Vogel J (2015)

Current Opinion in Microbiology, 24: 132-9

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: 775

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: 323

Evaluation of anti-HIV-1 mutagenic nucleoside analogues

Vivet-Boudou V, Isel C, El Safadi Y, Smyth RP, Laumond G, Moog C, Paillart J, Marquet R (2015)

The Journal of Biological Chemistry, 290 (1): 371-83

Properties of HIV-1 associated cholesterol in addition to raft formation are important for virus infection

Hawkes D, Jones KL, Smyth RP, Pereira CF, Bittman R, Jaworowski A, Mak J (2015)

Virus Research, 210: 18-21

Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression

Luo ML, Mullis AS, Leenay RT, Beisel CL (2015)

Nucleic Acids Research, 43 (1): 674-81

Signatures of adaptation in human invasive Salmonella Typhimurium ST313 populations from sub-Saharan Africa

Okoro CK, Barquist L, Connor TR, Harris SR, Clare S, Stevens MP, Arends MJ, Hale C, Kane L, Pickard DJ, …, Dougan G, Kingsley RA (2015)

PLOS Neglected Tropical Diseases, 9 (3): 00036

Patterns of genome evolution that have accompanied host adaptation in Salmonella

Langridge GC, Fookes M, Connor TR, Feltwell T, Feasey N, Parsons BN, Seth-Smith HM, Barquist L, Stedman A, Humphrey T, …, Dougan G, Thomson NR (2015)

Proceedings of the National Academy of Sciences of the United States of America, 112 (3): 863-8


MOV10 Is a 5' to 3' RNA helicase contributing to UPF1 mRNA target degradation by translocation along 3' UTRs

Gregersen LH, Schueler M, Munschauer M, Mastrobuoni G, Chen W, Kempa S, Dieterich C, Landthaler M (2014)

Molecular Cell, 54 (4): 573-85

Differential protein occupancy profiling of the mRNA transcriptome

Schueler M, Munschauer M, Gregersen LH, Finzel A, Loewer A, Chen W, Landthaler M, Dieterich C (2014)

Genome Biology, 15 (1): 15

A CRISPR design for next-generation antimicrobials

Beisel CL, Gomaa AA, Barrangou R (2014)

Genome Biology, 15 (11): 516

Guide RNA functional modules direct Cas9 activity and orthogonality

Briner AE, Donohoue PD, Gomaa AA, Selle K, Slorach EM, Nye CH, Haurwitz RE, Beisel CL, May AP, Barrangou R (2014)

Molecular Cell, 56 (2): 333-339

A bacterial seek-and-destroy system for foreign DNA

Vogel J (2014)

Science, 344 (6187): 972-3

Programmed -1 frameshifting by kinetic partitioning during impeded translocation

Caliskan N, Katunin VI, Belardinelli R, Peske F, Rodnina MV (2014)

Cell, 157 (7): 1619-31

Specific recognition of the HIV-1 genomic RNA by the Gag precursor

Abd El-Wahab EW, Smyth RP, Mailler E, Bernacchi S, Vivet-Boudou V, Hijnen M, Jossinet F, Mak J, Paillart J, Marquet R (2014)

Nature Communications, 5: 4304

A quantitative liposome microarray to systematically characterize protein-lipid interactions

Saliba AE, Vonkova I, Ceschia S, Findlay GM, Maeda K, Tischer C, Deghou S, van Noort V, Bork P, Pawson T, Ellenberg J, Gavin A (2014)

Nature Methods, 11 (1): 47-50

Construction of ligand-responsive microRNAs that operate through inhibition of Drosha processing

Beisel CL, Bloom RJ, Smolke CD (2014)

In: Artificial Riboswitches (ed Ogawa A), Methods Mol Biol, 1111: 259-67

Identification and Characterization of Small Non-coding RNAs in Bacteria

Podkaminski D, Bouvier M, Vogel J (2014)

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

Förstner KU, Vogel J, Sharma CM (2014)

Bioinformatics, 30 (23): 3421-3

High-resolution profiling of protein occupancy on polyadenylated RNA transcripts

Munschauer M, Schueler M, Dieterich C, Landthaler M (2014)

Methods, 65 (3): 302-9

Bacterial sugar utilization gives rise to distinct single-cell behaviours

Afroz T, Biliouris K, Kaznessis Y, Beisel CL (2014)

Molecular Microbiology, 93 (6): 1093-1103

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: 91

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: 05375

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

Sharma CM, Vogel J (2014)

Current Opinion in Microbiology, 19: 97-105

Identifying recombination hot spots in the HIV-1 genome

Smyth RP, Schlub TE, Grimm AJ, Waugh C, Ellenberg P, Chopra A, Mallal S, Cromer D, Mak J, Davenport MP (2014)

Journal of Virology, 88 (5): 2891-902

Fifteen to twenty percent of HIV substitution mutations are associated with recombination

Schlub TE, Grimm AJ, Smyth RP, Cromer D, Chopra A, Mallal S, Venturi V, Waugh C, Mak J, Davenport MP (2014)

Journal of Virology, 88 (7): 3837-49

Single-cell RNA-seq: advances and future challenges

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

Nucleic Acids Research, 42 (14): 8845-60

Programmable removal of bacterial strains by use of genome-targeting CRISPR-Cas systems

Gomaa AA, Klumpe HE, Luo ML, Selle K, Barrangou R, Beisel CL (2014)

mBio, 5 (1): 00928-13

Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling

Lindgreen S, Umu SU, Lai AS, Eldai H, Liu W, McGimpsey S, Wheeler NE, Biggs PJ, Thomson NR, Barquist L, Poole AM, Gardner PP (2014)

PLOS Computational Biology, 10 (10): 10039

Functional genomics reveals that Clostridium difficile Spo0A coordinates sporulation, virulence and metabolism

Pettit LJ, Browne HP, Yu L, Smits WK, Fagan RP, Barquist L, Martin MJ, Goulding D, Duncan SH, Flint HJ, …, Choudhary JS, Lawley TD (2014)

BMC Genomics, 15: 160

Parallel independent evolution of pathogenicity within the genus Yersinia

Reuter S, Connor TR, Barquist L, Walker D, Feltwell T, Harris SR, Fookes M, Hall ME, Petty NK, Fuchs TM, …, McNally A, Thomson NR (2014)

Proceedings of the National Academy of Sciences of the United States of America, 111 (18): 6768-73

An introduction to RNA databases

Hoeppner MP, Barquist L, Gardner PP (2014)

In: RNA Sequence, Structure, and Function: Computational and Bioinformatic Methods (eds Gorodkin J, Ruzzo W), Methods Mol Biol, 1097: 107-23


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

Heidrich N, Vogel J (2013)

Molecular Cell, 52 (1): 4-7

Circular RNAs are a large class of animal RNAs with regulatory potency

Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M, …, Le Noble F, Rajewsky N (2013)

Nature, 495 (7441): 333-8

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: 1610

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): 488-503

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): 552-64

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): 2963-79

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

Heidrich N, Vogel J (2013)

The EMBO Journal, 32 (13): 1802-4

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): 426-437

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): 493-527

RNA-mediated regulation in pathogenic bacteria

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

Cold Spring Harbor Perspectives In Medicine, 3 (9): 01029

Bacterial regulatory mechanisms: the gene and beyond

Bassler B, Vogel J (2013)

Current Opinion in Microbiology, 16 (2): 109-11

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)

Proceedings of the National Academy of Sciences of the United States of America, 110 (37): 3487-96

Identification of LIN28B-bound mRNAs reveals features of target recognition and regulation

Graf R, Munschauer M, Mastrobuoni G, Mayr F, Heinemann U, Kempa S, Rajewsky N, Landthaler M (2013)

RNA Biology, 10 (7): 1146-59

Understanding and exploiting feedback in synthetic biology

Afroz T, Beisel CL (2013)

Chemical Engineering Science, 103: 79-90

Alexander Böhm (1971-2012)

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

Molecular Microbiology, 88 (2): 219-21

Improved quantification of HIV-1-infected CD4+ T cells using an optimised method of intracellular HIV-1 gag p24 antigen detection

Yang H, Yorke E, Hancock G, Clutton G, Sande N, Angus B, Smyth RP, Mak J, Dorrell L (2013)

Journal of Immunological Methods, 391 (1-2): 174-8

Intracellular Dynamics of HIV Infection

Petravic J, Ellenberg P, Chan M, Paukovics G, Smyth RP, Mak J, Davenport MP (2013)

Journal of Virology, 88 (2): 1113-24

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): 542-53

A functional sequence-specific interaction between influenza A virus genomic RNA segments

Gavazzi C, Yver M, Isel C, Smyth RP, Rosa-Calatrava M, Lina B, Moulès V, Marquet R (2013)

Proceedings of the National Academy of Sciences of the United States of America, 110 (41): 16604-9

Rfam 11.0: 10 years of RNA families

Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A (2013)

Nucleic Acids Research, 41 (Database issue): 226-32

Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium

Wong VK, Pickard DJ, Barquist L, Sivaraman K, Page AJ, Hart PJ, Arends MJ, Holt KE, Kane L, Mottram LF, …, Kingsley RA, Dougan G (2013)

PLOS One, 8 (12): 84567

Approaches to querying bacterial genomes with transposon-insertion sequencing

Barquist L, Boinett CJ, Cain AK (2013)

RNA Biology, 10 (7): 1161-9

Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar

Kingsley RA, Kay S, Connor T, Barquist L, Sait L, Holt KE, Sivaraman K, Wileman TM, Goulding D, Clare S, …, Parkhill J, Dougan G (2013)

mBio, 4 (5): 00565-13

A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium

Barquist L, Langridge GC, Turner DJ, Phan M, Turner AK, Bateman A, Parkhill J, Wain J, Gardner PP (2013)

Nucleic Acids Research, 41 (8): 4549-64

RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006

Wilf NM, Reid AJ, Ramsay JP, Williamson NR, Croucher NJ, Gatto L, Hester SS, Goulding D, Barquist L, Lilley KS, …, Dougan G, Salmond GP (2013)

BMC Genomics, 14: 822

Dominant role of nucleotide substitution in the diversification of serotype 3 pneumococci over decades and during a single infection

Croucher NJ, Mitchell AM, Gould KA, Inverarity D, Barquist L, Feltwell T, Fookes MC, Harris SR, Dordel J, Salter SJ, …, Mitchell TJ, Bentley SD (2013)

PLOS Genetics, 9 (10): 10038

The agr locus regulates virulence and colonization genes in Clostridium difficile 027

Martin MJ, Clare S, Goulding D, Faulds-Pain A, Barquist L, Browne HP, Pettit LJ, Dougan G, Lawley TD, Wren BW (2013)

Journal of Bacteriology, 195 (16): 3672-81


FMRP targets distinct mRNA sequence elements to regulate protein expression

Ascano M, Mukherjee N, Bandaru P, Miller JB, Nusbaum JD, Corcoran DL, Langlois C, Munschauer M, Dewell S, Hafner M, …, Ohler U, Tuschl T (2012)

Nature, 492 (7429): 382-6

The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts

Baltz AG, Munschauer M, Schwanhäusser B, Vasile A, Murakawa Y, Schueler M, Youngs N, Penfold-Brown D, Drew K, Milek M, …, Dieterich C, Landthaler M (2012)

Molecular Cell, 46 (5): 674-90

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): 943-53

Dual RNA-seq of pathogen and host

Westermann AJ, Gorski SA, Vogel J (2012)

Nature Reviews Microbiology, 10 (9): 618-30

Multiple factors dictate target selection by Hfq-binding small RNAs

Beisel CL, Updegrove TB, Janson BJ, Storz G (2012)

The EMBO Journal, 31 (8): 1961-74

The mammalian microRNA response to bacterial infections

Eulalio A, Schulte LN, Vogel J (2012)

RNA Biology, 9 (6): 742-50

Experimental tools to identify RNA-protein interactions in Helicobacter pylori

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

RNA Biology, 9 (4): 520-31

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): 47-58

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)

Proceedings of the National Academy of Sciences of the United States of America, 109 (13): 757-64

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)

Proceedings of the National Academy of Sciences of the United States of America, 109 (20): 1277-86

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)

Proceedings of the National Academy of Sciences of the United States of America, 109 (12): 4621-6

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 Genetics, 8 (6): 10027

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

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

The Plant Cell, 24 (1): 123-36

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): 428-45

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

Boehm A, Vogel J (2012)

Molecular Microbiology, 84 (1): 1-5

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): 4005-19

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: 177-200

Hfq-associated Regulatory Small RNAs

Corcoran CP, Papenfort K, Vogel J (2012)

In: Regulatory RNAs in Prokaryotes (eds Marchfelder A, Hess WR): 15-50

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: 109-121

The Origin of Genetic Diversity in HIV-1

Smyth RP, Davenport MP, Mak J (2012)

Virus Research, 169 (2): 415-29

A high-resolution view of genome-wide pneumococcal transformation

Croucher NJ, Harris SR, Barquist L, Parkhill J, Bentley SD (2012)

PLOS Pathogens, 8 (6): 10027

HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction

Westesson O, Barquist L, Holmes I (2012)

Bioinformatics, 28 (8): 1170-1


Hfq and its constellation of RNA

Vogel J, Luisi BF (2011)

Nature Reviews Microbiology, 9 (8): 578-89

Regulation by small RNAs in bacteria: expanding frontiers

Storz G, Vogel J, Wassarman KM (2011)

Molecular Cell, 43 (6): 880-91

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

Papenfort K, Vogel J (2011)

Molecular Cell, 41 (3): 245-6

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): 602-7

Design of small molecule-responsive microRNAs based on structural requirements for Drosha processing

Beisel CL, Chen YY, Culler SJ, Hoff KG, Smolke CD (2011)

Nucleic Acids Research, 39 (7): 2981-94

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): 3623-40

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): 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)

Proceedings of the National Academy of Sciences of the United States of America, 108 (31): 12875-80

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)

Proceedings of the National Academy of Sciences of the United States of America, 108 (5): 2124-9

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): 17296

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): 2020-31

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): 1144-65

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): 1479-95

Microbes at their best: first Mol Micro Meeting Würzburg

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

Molecular Microbiology, 82 (4): 797-806

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): 98

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): 1977-89

8-Modified-2'-deoxyadenosine analogues induce delayed polymerization arrest during HIV-1 reverse transcription

Vivet-Boudou V, Isel C, Sleiman M, Smyth RP, Ben Gaied N, Barhoum P, Laumond G, Bec G, Götte M, Mak J, …, Burger A, Marquet R (2011)

PLOS One, 6 (11): 27456

Early events of HIV-1 infection: can signaling be the next therapeutic target?

Jones KL, Smyth RP, Pereira CF, Cameron PU, Lewin SR, Jaworowski A, Mak J (2011)

Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology, 6 (2): 269-83

Labeling of multiple HIV-1 proteins with the biarsenical-tetracysteine system

Pereira CF, Ellenberg PC, Jones KL, Fernandez TL, Smyth RP, Hawkes DJ, Hijnen M, Vivet-Boudou V, Marquet R, Johnson I, Mak J (2011)

PLOS One, 6 (2): 17016

RNIE: genome-wide prediction of bacterial intrinsic terminators

Gardner PP, Barquist L, Bateman A, Nawrocki EP, Weinberg Z (2011)

Nucleic Acids Research, 39 (14): 5845-52


Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP

Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp A, Munschauer M, …, Zavolan M, Tuschl T (2010)

Cell, 141 (1): 129-41

Base pairing small RNAs and their roles in global regulatory networks

Beisel CL, Storz G (2010)

FEMS Microbiology Reviews, 34 (5): 866-82

Regulatory RNA in bacterial pathogens

Papenfort K, Vogel J (2010)

Cell Host & Microbe, 8 (1): 116-27

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): 250-5

The small RNAs of Salmonella

Javayel S, Papenfort K, Vogel J (2010)

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

PAR-CliP--a method to identify transcriptome-wide the binding sites of RNA binding proteins

Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp A, Munschauer M, …, Zavolan M, Tuschl T (2010)

Journal of Visualized Experiments (41): 2034

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): 621-7

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)

Proceedings of the National Academy of Sciences of the United States of America, 107 (47): 20435-40

Identification of regulatory RNAs in Bacillus subtilis

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

Nucleic Acids Research, 38 (19): 6637-51

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): 868-77

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): 6620-36

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

Podkaminski D, Vogel J (2010)

Molecular Microbiology, 78 (6): 1327-31

The role of Hfq in bacterial pathogens

Chao Y, Vogel J (2010)

Current Opinion in Microbiology, 13 (1): 24-33

Accurately measuring recombination between closely related HIV-1 genomes

Schlub TE, Smyth RP, Grimm AJ, Mak J, Davenport MP (2010)

PLOS Computational Biology, 6 (4): 10007

Reducing chimera formation during PCR amplification to ensure accurate genotyping

Smyth RP, Schlub TE, Grimm A, Venturi V, Chopra A, Mallal S, Davenport MP, Mak J (2010)

Gene, 469 (1-2): 45-51

Microfluidic sorting and multimodal typing of cancer cells in self-assembled magnetic arrays

Saliba AE, Saias L, Psychari E, Minc N, Simon D, Bidard F, Mathiot C, Pierga J, Fraisier V, Salamero J, …, Malaquin L, Viovy J (2010)

Proceedings of the National Academy of Sciences of the United States of America, 107 (33): 14524-9


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): 840-6

A small RNA cascade regulates aminosugar synthesis

Vogel J (2009)

In: Nova Acta Leopoldina, 378: 41-50

Cellules tumorales circulantes et cancer du sein : méthodes de détection et résultats cliniques

Bidard F, Saliba AE, Saias L, Degeorges A, Cremoux Pd, Viovy J, Vincent-Salomon A, Mathiot C, Pierga J, Gramont A (2009)

Bulletin du Cancer, 96 (1): 73-86

Synthetic control of a fitness tradeoff in yeast nitrogen metabolism

Bayer TS, Hoff KG, Beisel CL, Lee JJ, Smolke CD (2009)

Journal of Biological Engineering, 3: 1

Design Principles for Riboswitch Function

Beisel CL, Smolke CD (2009)

PLOS Computational Biology, 5 (4): 10003

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: 301-19

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): 278-87

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)

Proceedings of the National Academy of Sciences of the United States of America, 106 (51): 21878-82

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): 133-

An RNA trap helps bacteria get the most out of chitosugars

Vogel J (2009)

Molecular Microbiology, 73 (5): 737-41

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

Vogel J (2009)

Molecular Microbiology, 71 (1): 1-11

Regulatory RNAs in prokaryotes: here, there and everywhere

Narberhaus F, Vogel J (2009)

Molecular Microbiology, 74 (2): 261-9

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): 1497-512

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): 139-158

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): 1228-38

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): 10005

Experimental approaches for the discovery and characterization of regulatory small RNA

Sharma CM, Vogel J (2009)

Current Opinion in Microbiology, 12 (5): 536-46

Activation of gene expression by small RNA

Fröhlich KS, Vogel J (2009)

Current Opinion in Microbiology, 12 (6): 674-82

The A-rich RNA sequences of HIV-1 pol are important for the synthesis of viral cDNA

Keating CP, Hill MK, Hawkes DJ, Smyth RP, Isel C, Le S, Palmenberg AC, Marshall JA, Marquet R, Nabel GJ, Mak J (2009)

Nucleic Acids Research, 37 (3): 945-56

Evolutionary modeling and prediction of non-coding RNAs in Drosophila

Bradley RK, Uzilov AV, Skinner ME, Bendana YR, Barquist L, Holmes I (2009)

PLOS One, 4 (8): 6478


Model-guided design of ligand-regulated RNAi for programmable control of gene expression

Beisel CL, Bayer TS, Hoff KG, Smolke CD (2008)

Molecular Systems Biology, 4: 224

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): 827-837

Noncoding RNA control of the making and breaking of sugars

Görke B, Vogel J (2008)

Genes & Development, 22 (21): 2914-25

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): 3134-3143

RNA: Noncoding

Henry AA, Vogel J (2008)

In: Wiley Encyclopedia of Chemical Biology (ed Begley TP), 22: 2183

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): 10001

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): 100-111

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): 890-906

A Glimpse at the Evolution of Virulence Control

Sittka A, Vogel J (2008)

Cell Host & Microbe, 4 (4): 310-312

xREI: a phylo-grammar visualization webserver

Barquist L, Holmes I (2008)

Nucleic Acids Research, 36 (Web Server issue): 65-


An antisense RNA inhibits translation by competing with standby ribosomes

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

Molecular Cell, 26 (3): 381-92

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): 2804-17

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): 6093-100

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

Narberhaus F, Vogel J (2007)

RNA Biology, 4 (3): 160-4

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): 193-217

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

Urban JH, Vogel J (2007)

Journal of Molecular Biology, 35 (3): 1018-37

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): 521-8

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): 7651-64

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)

Proceedings of the National Academy of Sciences of the United States of America, 104 (41): 16299-304

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): 1174-91

Target identification of small noncoding RNAs in bacteria

Vogel J, Wagner EG (2007)

Current Opinion in Microbiology, 10 (3): 262-70


Small non-coding RNAs and the bacterial outer membrane

Vogel J, Papenfort K (2006)

Current Opinion in Microbiology, 9 (6): 605-11

Experimental approaches to identify non-coding RNAs

Hüttenhofer A, Vogel J (2006)

Nucleic Acids Research, 34 (2): 635-46

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): 1674-1688


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): 2355-66

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: 614-642

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: 595-613

Conformational analysis of gossypol and its derivatives by molecular mechanics

Beisel CL, Dowd MK, Reilly PJ (2005)

Journal Of Molecular Structure: Computational and Theoretical Chemistry, 730 (1-3): 51-58

How to find small non-coding RNAs in bacteria

Vogel J, Sharma CM (2005)

Biological Chemistry, 386 (12): 1219-38

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): 73


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): 2271-6

Nanotechnology serving biochips – The Toulouse example

Vieu C, Malaquin L, Thibault C, Saliba AE, Daran E, Dildan M, Carcenac F, Leberre V, Trevisiol E, François JM (2004)

Biofutur (250): 41-45


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): 3794-803

Cochlear whole mount in situ hybridization: identification of longitudinal and radial gradients

Judice TN, Nelson NC, Beisel CL, Delimont DC, Fritzsch B, Beisel KW (2002)

Brain Research Protocols, 9 (1): 65-76


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

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