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2024
The RNA landscape of the human commensal Segatella copri reveals a small RNA essential for gut colonization
El Mouali Y, Tawk C, Huang KD, Amend L, Lesker TR, Ponath F, Vogel J, Strowig T (2024)
Cell Host & Microbe (Online ahead of print)
A resurrected ancestor of Cas12a expands target access and substrate recognition for nucleic acid editing and detection
Jabalera Y, Tascón I, Samperio S, López-Alonso JP, Gonzalez-Lopez M, Aransay AM, Abascal-Palacios G, Beisel CL, Ubarretxena-Belandia I, Perez-Jimenez R (2024)
Nature Biotechnology (Online ahead of print)
Formation of the pyruvoyl-dependent proline reductase Prd from Clostridioides difficile requires the maturation enzyme PrdH
Behlendorf C, Diwo M, Neumann-Schaal M, Fuchs M, Körner D, Jänsch L, Faber F, Blankenfeldt W (2024)
PNAS nexus 3 (7): pgae249
Global analysis of the RNA-RNA interactome in Acinetobacter baumannii AB5075 uncovers a small regulatory RNA repressing the virulence-related outer membrane protein CarO
Hamrock FJ, Ryan D, Shaibah A, Ershova AS, Mogre A, Sulimani MM, Ben Taarit S, Reichardt S, Hokamp K, Westermann AJ, Kröger C (2024)
Nucleic Acids Research 52 (18): 11283–11300
Bacteria conjugate ubiquitin-like proteins to interfere with phage assembly
Hör J, Wolf SG, Sorek R (2024)
Nature 631 (8022): 850-856
The life-saving benefit of dexamethasone in severe COVID-19 is linked to a reversal of monocyte dysregulation
Knoll R, Helbig ET, Dahm K, Bolaji O, Hamm F, Dietrich O, van Uelft M, Müller S, Bonaguro L, Schulte-Schrepping J, …, Aschenbrenner AC, Kurth F (2024)
Cell 187 (16): 4318-4335.e20
Phage anti-CRISPR control by an RNA- and DNA-binding helix-turn-helix protein
Birkholz N, Kamata K, Feussner M, Wilkinson ME, Cuba Samaniego C, Migur A, Kimanius D, Ceelen M, Went SC, Usher B, …, Jackson SA, Fineran PC (2024)
Nature 631 (8021): 670-677
L-Wnk1 Deletion in Smooth Muscle Cells Causes Aortitis and Inflammatory Shift
Quelquejay H, Al-Rifai R, Silvestro M, Vandestienne M, Ferreira I, Mirault T, Henrion D, Zhong X, Santos-Zas I, Goudot G, …, Jeunemaitre X, Ait-Oufella H (2024)
Circulation Research 135 (4): 488-502
TracrRNA reprogramming enables direct PAM-independent detection of RNA with diverse DNA-targeting Cas12 nucleases
Jiao C, Peeck NL, Yu J, Ghaem Maghami M, Kono S, Collias D, Martinez Diaz SL, Larose R, Beisel CL (2024)
Nature Communications 15 (1): 5909
sCIRCLE-An interactive visual exploration tool for single cell RNA-Seq data
Seeger M, Schöls E, Barquist L (2024)
NAR Genomics and Bioinformatics 6 (3): lqae084
Cooperation of regulatory RNA and the RNA degradosome in transcript surveillance
Bandyra KJ, Fröhlich KS, Vogel J, Rodnina M, Goyal A, Luisi BF (2024)
Nucleic Acids Research 52 (15): 9161-9173
A cell-free transcription-translation pipeline for recreating methylation patterns boosts DNA transformation in bacteria
Vento JM, Durmusoglu D, Li T, Patinios C, Sullivan S, Ttofali F, van Schaik J, Yu Y, Wang Y, Barquist L, Crook N, Beisel CL (2024)
Molecular Cell 84 (14): 2785-2796.e4
Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans
Benz F, Camara-Wilpert S, Russel J, Wandera KG, Cepaite R, Ares-Arroyo M, Gomes-Filho JV, Englert F, Kuehn JA, Gloor S, …, Sørensen SJ, Pinilla-Redondo R (2024)
Cell Host & Microbe 32 (6): 875-886.e9
Decoding spatiotemporal transcriptional dynamics and epithelial fibroblast crosstalk during gastroesophageal junction development through single cell analysis
Kumar N, Prakash PG, Wentland C, Kurian SM, Jethva G, Brinkmann V, Mollenkopf HJ, Krammer T, Toussaint C, Saliba AE, …, Gurumurthy RK, Chumduri C (2024)
Nature Communications 15 (1): 3064
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): 787-800
Expanding the flexibility of base editing for high-throughput genetic screens in bacteria
Gawlitt S, Collins SP, Yu Y, Blackman SA, Barquist L, Beisel CL (2024)
Nucleic Acids Research 52 (7): 4079-4097
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): e2308814121
An expanded transcriptome atlas for Bacteroides thetaiotaomicron reveals a small RNA that modulates tetracycline sensitivity
Ryan D, Bornet E, Prezza G, Alampalli SV, Franco de Carvalho T, Felchle H, Ebbecke T, Hayward RJ, Deutschbauer AM, Barquist L, Westermann AJ (2024)
Nature Microbiology 9 (4): 1130-1144
CRISPR-based screening of small RNA modulators of bile susceptibility in Bacteroides thetaiotaomicron
Prezza G, Liao C, Reichardt S, Beisel CL, Westermann AJ (2024)
Proceedings of the National Academy of Sciences of the United States of America 121 (6): 1096
Non-professional efferocytosis of Salmonella-infected intestinal epithelial cells in the neonatal host
Zhang K, Repnik U, Diab N, Friske D, Pütz A, Bachmann AZ, Gubbi NMKP, Hensel M, Förstner KU, Westermann AJ, Dupont A, Hornef MW (2024)
The Journal of Experimental Medicine 221 (3)
Isoform-specific RNA structure determination using Nano-DMS-MaP
Gribling-Burrer AS, Bohn P, Smyth RP (2024)
Nature Protocols 19 (6): 1835-1865
Human cytomegalovirus exploits STING signaling and counteracts IFN/ISG induction to facilitate infection of dendritic cells
Costa B, Becker J, Krammer T, Mulenge F, Durán V, Pavlou A, Gern OL, Chu X, Li Y, Cicin-Šain L, …, Erhard F, Kalinke U (2024)
Nature Communications 15 (1): 1745
Improved prediction of bacterial CRISPRi guide efficiency from depletion screens through mixed-effect machine learning and data integration
Yu Y, Gawlitt S, de Andrade E Sousa LB, Merdivan E, Piraud M, Beisel CL, Barquist L (2024)
Genome Biology 25 (1): 13
Nucleolar detention of NONO shields DNA double-strand breaks from aberrant transcripts
Trifault B, Mamontova V, Cossa G, Ganskih S, Wei Y, Hofstetter J, Bhandare P, Baluapuri A, Nieto B, Solvie D, …, Munschauer M, Burger K (2024)
Nucleic Acids Research 52 (6): 3050-3068
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 52 (7): 3950-3970
SHIFTR enables the unbiased identification of proteins bound to specific RNA regions in live cells
Aydin J, Gabel A, Zielinski S, Ganskih S, Schmidt N, Hartigan CR, Schenone M, Carr SA, Munschauer M (2024)
Nucleic Acids Research 52 (5): e26
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): 2323-2339
Circulating NK cells establish tissue residency upon acute infection of skin and mediate accelerated effector responses to secondary infection
Torcellan T, Friedrich C, Doucet-Ladevèze R, Ossner T, Solé VV, Riedmann S, Ugur M, Imdahl F, Rosshart SP, Arnold SJ, …, Kastenmüller W, Gasteiger G (2024)
Immunity 57 (1): 124-140.e7
Sequential Antigen-loss and Branching Evolution in Lymphoma after CD19- and CD20-Targeted T-cell Redirecting Therapy
Duell J, Leipold AM, Appenzeller S, Fuhr V, Rauert-Wunderlich H, Da Vià MC, Dietrich O, Toussaint C, Imdahl F, Eisele F, …, Saliba AE, Rasche L (2024)
Blood 143 (8): 685-696
Streptococcus agalactiae strain COH1 transcriptome in association with stem cell-derived brain-like endothelial cells
Vollmuth N, Sauerwein T, Foerstner KU, Westermann AJ, Schubert-Unkmeir A, Lam DW, Kim BJ (2024)
Microbiology Resource Announcements (Online ahead of print)
NEAT1 promotes genome stability via m6A methylation-dependent regulation of CHD4
Mamontova V, Trifault B, Gribling-Burrer AS, Bohn P, Boten L, Preckwinkel P, Gallant P, Solvie D, Ade CP, Papadopoulos D, …, Smyth RP, Burger K (2024)
Genes & Development 38 (17-20): 915-930
SARS-CoV-2 antigen rapid detection tests: test performance during the COVID-19 pandemic and the impact of COVID-19 vaccination
Wagenhäuser I, Knies K, Pscheidl T, Eisenmann M, Flemming S, Petri N, McDonogh M, Scherzad A, Zeller D, Gesierich A, …, Gabel A, Krone M (2024)
EBioMedicine (Online ahead of print)
Alternating high-fat diet enhances atherosclerosis by neutrophil reprogramming
Lavillegrand JR, Al-Rifai R, Thietart S, Guyon T, Vandestienne M, Cohen R, Duval V, Zhong X, Yen D, Ozturk M, …, Riksen NP, Ait-Oufella H (2024)
Nature 634 (8033): 447-456
A novel in vitro tubular model to recapitulate features of distal airways: The bronchioid
Maurat E, Raasch K, Leipold AM, Henrot P, Zysman M, Prevel R, Trian T, Krammer T, Bergeron V, Thumerel M, …, Recher G, Dupin I (2024)
The European Respiratory journal 64 (4)
Getting to the root of root-microbe interactions
King WL, Hayward RJ, Goebel M, Fleishman SM, Bauerle TL, Bell TH (2024)
Science Progress 107 (3)
Phages to the rescue: in situ editing of the gut microbiota
Kamm C, Beisel CL (2024)
Trends in Microbiology 32 (10): 934-935
Ten Years of the Synthetic Biology Summer Course at Cold Spring Harbor Laboratory
Haynes KA, Andrews LB, Beisel CL, Chappell J, Cuba Samaniego CE, Dueber JE, Dunlop MJ, Franco E, Lucks JB, Noireaux V, …, Smanski M, Young E (2024)
ACS Synthetic Biology 13 (9): 2635-2642
Neural network-assisted humanisation of COVID-19 hamster transcriptomic data reveals matching severity states in human disease
Friedrich VD, Pennitz P, Wyler E, Adler JM, Postmus D, Müller K, Teixeira Alves LG, Prigann J, Pott F, Vladimirova D, …, Kirsten H, Nouailles G (2024)
EBioMedicine 108: 105312
Transglutaminase-catalyzed covalent
Hamm P, Beckmann D, Worschech R, Braun A, Gutmann M, Korb-Pap A, Lühmann T, Pap T, Meinel L (2024)
European Journal of Pharmaceutics and Biopharmaceutics 203: 114462
Cell-free expression with a quartz crystal microbalance enables rapid, dynamic, and label-free characterization of membrane-interacting proteins
Khakimzhan A, Izri Z, Thompson S, Dmytrenko O, Fischer P, Beisel C, Noireaux V (2024)
Communications Biology 7 (1): 1005
SOX2 interacts with hnRNPK to modulate alternative splicing in mouse embryonic stem cells
Huang Y, Liu Y, Pu M, Zhang Y, Cao Q, Li S, Wei Y, Hou L (2024)
Cell & Bioscience 14 (1): 102
MprF-mediated immune evasion is necessary for Lactiplantibacillus plantarum resilience in the Drosophila gut during inflammation
Arias-Rojas A, Arifah AQ, Angelidou G, Alshaar B, Schombel U, Forest E, Frahm D, Brinkmann V, Paczia N, Beisel CL, Gisch N, Iatsenko I (2024)
PLOS Pathogens 20 (8): e1012462
Characterization and implementation of the MarathonRT template-switching reaction to expand the capabilities of RNA-Seq
Guo LT, Grinko A, Olson S, Leipold A, Graveley B, Saliba AE, Pyle AM (2024)
RNA 30 (11): 1495–1512
Spatial transcriptomics reveals profound subclonal heterogeneity and T-cell dysfunction in extramedullary myeloma
John M, Helal M, Duell J, Mattavelli G, Stanojkovska E, Afrin N, Leipold AM, Steinhardt MJ, Zhou X, Žihala D, …, Riedel A, Rasche L (2024)
Blood (Online ahead of print)
High-throughput transposon mutagenesis in the family Enterobacteriaceae reveals core essential genes and rapid turnover of essentiality
A Ghomi F, Jung JJ, Langridge GC, Cain AK, Boinett CJ, Abd El Ghany M, Pickard DJ, Kingsley RA, Thomson NR, Parkhill J, Gardner PP, Barquist L (2024)
mBio: e0179824
Visually distinguishing between tumor tissue and healthy tissue within ten minutes using proteolytic probes
Reinhardt D, Ter Mors B, Driessen MD, Gutmann M, Faber J, Haug L, Faber AM, Herrmann A, Hamm P, Lühmann T, Linz C, Meinel L (2024)
Sensors & Diagnostics 68 (6): 394
Translation Inhibition Mediated by Interferon-Stimulated Genes during Viral Infections
Smart A, Gilmer O, Caliskan N (2024)
Viruses 16 (7)
Impaired T cells and "memory-like" NK-cell reconstitution is linked to late-onset HCMV reactivation after letermovir cessation
Lauruschkat CD, Muchsin I, Rein AF, Erhard F, Grathwohl D, Dölken L, Köchel C, Nehmer A, Falk CS, Grigoleit GU, …, Wurster S, Kraus S (2024)
Blood advances 8 (11): 2967-2979
Refining the transcriptional landscapes for distinct clades of virulent phages infecting Pseudomonas aeruginosa
Putzeys L, Wicke L, Boon M, van Noort V, Vogel J, Lavigne R (2024)
microLife 5: uqae002
CD8+ T Cells Drive Plaque Smooth Muscle Cell Dedifferentiation in Experimental Atherosclerosis
Schäfer S, Gogiraju R, Rösch M, Kerstan Y, Beck L, Garbisch J, Saliba AE, Gisterå A, Hermanns HM, Boon L, …, Cochain C, Zernecke A (2024)
Arteriosclerosis Thrombosis, and Vascular biology 44 (8): 1852-1872
PEGylated Recombinant Aplysia punctata Ink Toxin Depletes Arginine and Lysine and Inhibits the Growth of Tumor Xenografts
Wolkersdorfer AM, Bergmann B, Adelmann J, Ebbinghaus M, Günther E, Gutmann M, Hahn L, Hurwitz R, Krähmer R, Leenders F, …, Meinel L, Rudel T (2024)
ACS Biomaterials Science & Engineering 10 (6): 3825-3832
An Introductory Guide to Protease Sensitive Linker Design Using Matrix Metalloproteinase 13 as an Example
Hamm P, Meinel L, Driessen MD (2024)
ACS Biomaterials Science & Engineering 10 (6): 3693-3706
Network depth affects inference of gene sets from bacterial transcriptomes using denoising autoencoders
Kion-Crosby W, Barquist L (2024)
Bioinformatics Advances 4 (1): 181
Recruitment of multi-segment genomic RNAs by Bluetongue virus requires a preformed RNA network
Sung PY, Phelan JE, Luo D, Kulasegaran-Shylini R, Bohn P, Smyth RP, Roy P (2024)P., Roy P (2024)
Nucleic Acids Research 52 (14): 8500-8514
Group B Streptococcus transcriptome when interacting with brain endothelial cells
Vollmuth N, Bridgers BE, Armstrong ML, Wood JF, Gildea AR, Espinal ER, Hooven TA, Barbieri G, Westermann AJ, Sauerwein T, …, Schubert-Unkmeir A, Kim BJ (2024)
Journal of Bacteriology 206 (6): e0008724
Characterization of a Human Respiratory Mucosa Model to Study Odorant Metabolism
Mérignac-Lacombe J, Kornbausch N, Sivarajan R, Boichot V, Berg K, Oberwinkler H, Saliba AE, Loos HM, Ehret Kasemo T, Scherzad A, …, Heydel JM, Steinke M (2024)
Journal of Agricultural and Food Chemistry 72 (22): 12696-12706
Sequencing accuracy and systematic errors of nanopore direct RNA sequencing
Liu-Wei W, van der Toorn W, Bohn P, Hölzer M, Smyth RP, von Kleist M (2024)
BMC Genomics 25 (1): 528
TREM2 protects from atherosclerosis by limiting necrotic core formation
Piollet M, Porsch F, Rizzo G, Kapser F, Schulz DJ, Kiss MG, Schlepckow K, Morenas-Rodriguez E, Sen MO, Gropper J, …, Binder CJ, Cochain C (2024)
Nature Cardiovascular Research 3 (3): 269-282
Meeting report 'Microbiology 2023: from single cell to microbiome and host', an international interacademy conference in Würzburg
Cossart P, Hacker J, Holden DH, Normark S, Vogel J (2024)
microLife 5: uqae008
Activated rate-response is associated with increased mortality risk in cardiac device carriers with acute heart failure
Huttelmaier MT, Münsterer S, Morbach C, Sahiti F, Scholz N, Albert J, Gabel A, Angermann C, Ertl G, Frantz S, Störk S, Fischer TH (2024)
PLOS One 19 (4): e0302321
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): e0353623
A method to correct for local alterations in DNA copy number that bias functional genomics assays applied to antibiotic-treated bacteria
Sullivan GJ, Barquist L, Cain AK (2024)
mSystems 12: e0066523
RNA helicase IGHMBP2 regulates THO complex to ensure cellular mRNA homeostasis
Prusty AB, Hirmer A, Sierra-Delgado JA, Huber H, Guenther UP, Schlosser A, Dybkov O, Yildirim E, Urlaub H, Meyer KC, …, Erhard F, Fischer U (2024)
Cell Reports 43 (2): 113802
A Hitchhiker's guide to CRISPR editing tools in bacteria : CRISPR can help unlock the bacterial world, but technical and regulatory barriers persist
Krink N, Nikel PI, Beisel CL (2024)
EMBO Reports 25 (4): 1694-1699
An adapted method for Cas9-mediated editing reveals the species-specific role of β-glucoside utilization driving competition between Klebsiella species
Almási ÉdH, Knischewski N, Osbelt L, Muthukumarasamy U, El Mouali Y, Vialetto E, Beisel CL, Strowig T (2024)
Journal of Bacteriology 206 (3): e0031723
A comparative analysis of peptide-delivered antisense antibiotics employing diverse nucleotide mimics
Ghosh C, Popella L, Dhamodharan V, Jung J, Dietzsch J, Barquist L, Höbartner C, Vogel J (2024)
RNA 30 (6): 624-643
CRISPR Interference-Based Functional Small RNA Genomics
Prezza G, Westermann AJ (2024)
Methods in Molecular Biology 2741: 101-116
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: 102419
PEGylation of Human Vascular Endothelial Growth Factor
Wolkersdorfer AM, Jugovic I, Scheller L, Gutmann M, Hahn L, Diessner J, Lühmann T, Meinel L (2024)
ACS Biomaterials Science and Engineering 10 (1): 149-155
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): 7529
Vector-borne Trypanosoma brucei parasites develop in artificial human skin and persist as skin tissue forms
Reuter C, Hauf L, Imdahl F, Sen R, Vafadarnejad E, Fey P, Finger T, Jones NG, Walles H, Barquist L, …, Groeber-Becker F, Engstler M (2023)
Nature Communications 14 (1): 7660
Interrogating two extensively self-targeting Type I CRISPR-Cas systems in Xanthomonas albilineans reveals distinct anti-CRISPR proteins that block DNA degradation
Wimmer F, Englert F, Wandera KG, Alkhnbashi OS, Collins SP, Backofen R, Beisel CL (2023)
Nucleic Acids Research 52 (2): 769-783
Microglia-mediated demyelination protects against CD8+ T cell-driven axon degeneration in mice carrying PLP defects
Groh J, Abdelwahab T, Kattimani Y, Hörner M, Loserth S, Gudi V, Adalbert R, Imdahl F, Saliba AE, Coleman M, …, Simons M, Martini R (2023)
Nature Communications 14 (1): 6911
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): 1523-1531
RNA-based medicine: from molecular mechanisms to therapy
Sparmann A, Vogel J (2023)
The EMBO Journal 42 (21): e114760
Cytosolic Ptbp2 modulates axon growth in motoneurons through axonal localization and translation of Hnrnpr
Salehi S, Zare A, Prezza G, Bader J, Schneider C, Fischer U, Meissner F, Mann M, Briese M, Sendtner M (2023)
Nature Communications 14 (1): 4158
A predicted CRISPR-mediated symbiosis between uncultivated archaea
Esser SP, Rahlff J, Zhao W, Predl M, Plewka J, Sures K, Wimmer F, Lee J, Adam PS, McGonigle J, …, Zhang Y, Probst AJ (2023)
Nature Microbiology 8 (9): 1619-1633
Th17.1 cell driven sarcoidosis-like inflammation after anti-BCMA CAR T cells in multiple myeloma
Leipold AM, Werner RA, Düll J, Jung P, John M, Stanojkovska E, Zhou X, Hornburger H, Ruckdeschel A, Dietrich O, …, Saliba AE, Rasche L (2023)
Leukemia 37 (3): 650-658
Myocardial Milieu Favors Local Differentiation of Regulatory T Cells
Delgobo M, Weiß E, ElDin Ashour D, Richter L, Popiolkowski L, Arampatzi P, Stangl V, Arias-Loza P, Mariotti-Ferrandiz E, Rainer PP, …, Frantz S, Campos Ramos G (2023)
Circulation Research 132 (5): 565-582
Systematically attenuating DNA targeting enables CRISPR-driven editing in bacteria
Collias D, Vialetto E, Yu J, Co K, Almási ÉDH, Rüttiger AS, Achmedov T, Strowig T, Beisel CL (2023)
Nature Communications 14 (1): 680
RNA targeting unleashes indiscriminate nuclease activity of CRISPR-Cas12a2
Bravo JPK, Hallmark T, Naegle B, Beisel CL, Jackson RN, Taylor DW (2023)
Nature 613 (7944): 582-587
Cas12a2 elicits abortive infection through RNA-triggered destruction of dsDNA
Dmytrenko O, Neumann GC, Hallmark T, Keiser DJ, Crowley VM, Vialetto E, Mougiakos I, Wandera KG, Domgaard H, Weber J, …, Jackson RN, Beisel CL (2023)
Nature 613 (7944): 588-594
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): 1107-1116
Cis-mediated interactions of the SARS-CoV-2 frameshift RNA alter its conformations and affect function
Pekarek L, Zimmer MM, Gribling-Burrer AS, Buck S, Smyth RP, Caliskan N (2023)
Nucleic Acids Research 51 (2): 728–743
Integrated single-cell analysis based classification of vascular mononuclear phagocytes in mouse and human atherosclerosis
Zernecke A, Erhard F, Weinberger T, Schulz C, Ley K, Saliba AE, Cochain C (2023)
Cardiovascular Research 119 (8): 1676-1689
Dynamics of monocyte-derived macrophage diversity in experimental myocardial infarction
Rizzo G, Gropper J, Piollet M, Vafadarnejad E, Rizakou A, Bandi SR, Arampatzi P, Krammer T, DiFabion N, Dietrich O, …, Saliba AE, Cochain C (2023)
Cardiovascular Research 119 (3): 772-785
Rapid neutrophil mobilisation by VCAM-1+ endothelial extracellular vesicles
Akbar N, Braithwaite AT, Corr EM, Koelwyn GJ, van Solingen C, Cochain C, Saliba AE, Corbin A, Pezzolla D, Møller Jørgensen M, …, Melling GE, Shanmuganathan M (2023)
Cardiovascular Research 119 (1): 236-251
EAM highlights in FEMS 2023: from the Petri dish to planet Earth
Vogel J, de Lorenzo V (2023)
microLife 4: uqad045
Discovery of phage determinants that confer sensitivity to bacterial immune systems
Stokar-Avihail A, Fedorenko T, Hör J, Garb J, Leavitt A, Millman A, Shulman G, Wojtania N, Melamed S, Amitai G, Sorek R (2023)
Cell 186 (9): 1863-1876.e16
Bile Is a Selective Elevator for Mucosal Mechanics and Transport
Hanio S, Möllmert S, Möckel C, Choudhury S, Höpfel AI, Zorn T, Endres S, Schlauersbach J, Scheller L, Keßler C, …, Guck J, Meinel L (2023)
Molecular Pharmaceutics 20 (12): 6151-6161
Matrix Metalloproteinase-Responsive Delivery of PEGylated Fibroblast Growth Factor 2
Gutmann M, Reinhardt D, Seidensticker C, Raschig M, Hahn L, Moscaroli A, Behe M, Meinel L, Lühmann T (2023)
ACS Biomaterials Science & Engineering 10 (1): 156-165
Ribosome profiling reveals the fine-tuned response of Escherichia coli to mild and severe acid stress
Schumacher K, Gelhausen R, Kion-Crosby W, Barquist L, Backofen R, Jung K (2023)
mSystems 8 (6): e0103723
Seropositivity of Borrelia burgdorferi s.l. in Germany-an analysis across four German National Cohort (NAKO) study sites
Hassenstein MJ, Pischon T, Karch A, Peters A, Kerrinnes T, Teismann H, Schneider A, Thierry S, Moreno Velásquez I, Janke J, Kemmling Y, Castell S (2023)
Scientific Reports 13 (1): 21087
SND1 binds SARS-CoV-2 negative-sense RNA and promotes viral RNA synthesis through NSP9
Schmidt N, Ganskih S, Wei Y, Gabel A, Zielinski S, Keshishian H, Lareau CA, Zimmermann L, Makroczyova J, Pearce C, …, Erhard F, Munschauer M (2023)
Cell 186 (22): 4834-4850.e23
The development of matrix-metalloproteinase responsive sensors for the machine-independent detection of oral inflammation
Ter Mors B, Driessen M. D., Seher A, Haubitz I. R., Raschig M, Nowak M, Jockel-Schneider Y, Linz C, Meinel L (2023)
Sensors & Diagnostics 2 (4): 867-877
Shortened CRISPR-Cas9 arrays enable multiplexed gene targeting in bacteria from a smaller DNA footprint
Gawlitt S, Liao C, Achmedov T, Beisel CL (2023)
RNA Biology 20 (1): 666-680
For the CRISPR Fan(zor)atics: RNA-guided DNA endonucleases discovered in eukaryotes
Patinios C, Beisel CL (2023)
Molecular Cell 83 (17): 3046-3048
Bioconjugation of a Fibroblast Activation Protein Targeted Interleukin-4
Ruopp M, Zhu S, Worschech R, Haas D, Maschauer S, Prante O, Meinel L, Lühmann T (2023)
ACS Biomaterials Science & Engineering 9 (10): 5580-5588
The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes
Djakovic L, Hennig T, Reinisch K, Milic A, Whisnant AW, Wolf K, Weiß E, Haas T, Grothey A, Jürges CS, …, Friedel CC, Dölken L (2023)
Nature Communications 14 (1): 4591
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Identifying and Visualizing Functional PAM Diversity across CRISPR-Cas Systems
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SBE Supplement: Synthetic Biology – Engineering Genes with CRISPR-Cas9
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American Institute of Chemical Engineers
cis-Encoded Small RNAs, a Conserved Mechanism for Repression of Polysaccharide Utilization in Bacteroides
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The primary transcriptome of the Escherichia coli O104:H4 pAA plasmid and novel insights into its virulence gene expression and regulation
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Rethinking the Hierarchy of Sugar Utilization in Bacteria
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Gifsy-1 Prophage IsrK with Dual Function as Small and Messenger RNA Modulates Vital Bacterial Machineries
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Current Opinion in Microbiology 30: 50-57
HIV-1 Mutation and Recombination Rates Are Different in Macrophages and T-cells
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The Life-Cycle of the HIV-1 Gag-RNA Complex
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MIMEAnTo: profiling functional RNA in mutational interference mapping experiments
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Grad-seq guides the discovery of ProQ as a major small RNA-binding protein
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Studying RNA Homology and Conservation with Infernal: From Single Sequences to RNA Families
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Molecular phenotyping of infection-associated small non-coding RNAs
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Philosophical Transactions of the Royal Society of London B: Biological Sciences 371 (1707): 20160081
The in vitro and in vivo effects of constitutive light expression on a bioluminescent strain of the mouse enteropathogen Citrobacter rodentium
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Changed in translation: mRNA recoding by -1 programmed ribosomal frameshifting
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Mutational interference mapping experiment (MIME) for studying RNA structure and function
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Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies
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Annual Review of Genetics 49: 367-94
Inflammation-associated alterations to the intestinal microbiota reduce colonization resistance against non-typhoidal Salmonella during concurrent malaria parasite infection
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Comprehensive Protein Interactome Analysis of a Key RNA Helicase: Detection of Novel Stress Granule Proteins
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mBio 6 (2): e02383
Small RNA-based feedforward loop with AND-gate logic regulates extrachromosomal DNA transfer in Salmonella
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dRNA-Seq Reveals Genomewide TSSs and Noncoding RNAs of Plant Beneficial Rhizobacterium Bacillus amyloliquefaciens FZB42
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Investigating CRISPR RNA Biogenesis and Function Using RNA-seq
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Regulatory small RNAs from the 3' regions of bacterial mRNAs
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Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315
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BMC Genomics 16: 775
Dual 3'Seq using deepSuperSAGE uncovers transcriptomes of interacting Salmonella enterica Typhimurium and human host cells
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Evaluation of anti-HIV-1 mutagenic nucleoside analogues
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Properties of HIV-1 associated cholesterol in addition to raft formation are important for virus infection
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Repurposing endogenous type I CRISPR-Cas systems for programmable gene repression
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PLOS Neglected Tropical Diseases 9 (3): e0003611
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MOV10 Is a 5' to 3' RNA helicase contributing to UPF1 mRNA target degradation by translocation along 3' UTRs
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A CRISPR design for next-generation antimicrobials
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Specific recognition of the HIV-1 genomic RNA by the Gag precursor
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Nature Communications 5: 4304
A quantitative liposome microarray to systematically characterize protein-lipid interactions
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READemption-a tool for the computational analysis of deep-sequencing-based transcriptome data
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Bioinformatics 30 (23): 3421-3
High-resolution profiling of protein occupancy on polyadenylated RNA transcripts
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Bacterial sugar utilization gives rise to distinct single-cell behaviours
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RNA Biology 11 (5): 403-12
Small RNA functions in carbon metabolism and virulence of enteric pathogens
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Frontiers in Cellular and Infection Microbiology 4: 91
Recognition of the small regulatory RNA RydC by the bacterial Hfq protein
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eLife 3: e05375
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Identifying recombination hot spots in the HIV-1 genome
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Fifteen to twenty percent of HIV substitution mutations are associated with recombination
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Programmable removal of bacterial strains by use of genome-targeting CRISPR-Cas systems
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PNAS 111 (18): 6768-73
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Same same but different: new structural insight into CRISPR-Cas complexes
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Molecular Cell 52 (1): 4-7
Circular RNAs are a large class of animal RNAs with regulatory potency
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Nature Communications 4: 1610
Processing-Independent CRISPR RNAs Limit Natural Transformation in Neisseria meningitidis
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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
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A small RNA activates CFA synthase by isoform-specific mRNA stabilization
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The EMBO Journal 32 (22): 2963-79
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Small RNA-Mediated Activation of Sugar Phosphatase mRNA Regulates Glucose Homeostasis
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Cold Spring Harbor Perspectives In Medicine 3 (9): a010298
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Understanding and exploiting feedback in synthetic biology
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Improved quantification of HIV-1-infected CD4+ T cells using an optimised method of intracellular HIV-1 gag p24 antigen detection
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Intracellular Dynamics of HIV Infection
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Differential activation and functional specialization of miR-146 and miR-155 in innate immune sensing
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A functional sequence-specific interaction between influenza A virus genomic RNA segments
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PNAS 110 (41): 16604-9
Rfam 11.0: 10 years of RNA families
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Nucleic Acids Research 41 (Database issue): D226-32
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
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A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium
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Dominant role of nucleotide substitution in the diversification of serotype 3 pneumococci over decades and during a single infection
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The agr locus regulates virulence and colonization genes in Clostridium difficile 027
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Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar
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Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium
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Nature Reviews Microbiology 10 (9): 618-30
Surface-associated motility, a common trait of clinical isolates of Acinetobacter baumannii, depends on 1,3-diaminopropane
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The mammalian microRNA response to bacterial infections
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RNA Biology 9 (6): 742-50
Experimental tools to identify RNA-protein interactions in Helicobacter pylori
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RNA Biology 9 (4): 520-31
Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their analysis
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Global regulatory functions of the Staphylococcus aureus endoribonuclease III in gene expression
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The Primary Transcriptome of Barley Chloroplasts: Numerous Noncoding RNAs and the Dominating Role of the Plastid-Encoded RNA Polymerase
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Superfolder GFP reporters validate diverse new mRNA targets of the classic porin regulator, MicF RNA
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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): e1002745
HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction
Westesson O, Barquist L, Holmes I (2012)
Bioinformatics 28 (8): 1170-1
2011
The base pairing RNA Spot 42 participates in a multi-output feedforward loop to help enact catabolite repression in Escherichia coli
Beisel CL, Storz G (2011)
Molecular Cell 41 (3): 286-97
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
Discriminating tastes: physiological contributions of the Hfq-binding small RNA Spot 42 to catabolite repression
Beisel CL, Storz G (2011)
RNA Biology 8 (5): 766-70
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)
PNAS 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)
PNAS 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): e17296
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): 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): 1977-89
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): e27456
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): e17016
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
2010
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
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
A simple and rapid method of bacterial transformation
Wilharm G, Lepka D, Faber F, Hofmann J, Kerrinnes T, Skiebe E (2010)
Journal of Microbiological Methods 80 (2): 215-6
Orbus hercynius gen. nov., sp. nov., isolated from faeces of wild boar, is most closely related to members of the orders 'Enterobacteriales' and Pasteurellales
Volkmann M, Skiebe E, Kerrinnes T, Faber F, Lepka D, Pfeifer Y, Holland G, Bannert N, Wilharm G (2010)
International Journal of Systematic and Evolutionary Microbiology 60 (Pt 11): 2601-2605
Polypyrimidine tract-binding protein homologues from Arabidopsis underlie regulatory circuits based on alternative splicing and downstream control
Stauffer E, Westermann A, Wagner G, Wachter A (2010)
The Plant journal : for cell and molecular biology 64 (2): 243-55
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): pii: 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)
PNAS 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): e1000766
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)
PNAS 107 (33): 14524-9
2009
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
CsrA and CsrB are required for the post-transcriptional control of the virulence-associated effector protein AvrA of Salmonella enterica
Kerrinnes T, Zelas ZB, Streckel W, Faber F, Tietze E, Tschäpe H, Yaron S (2009)
International Journal of Medical Microbiology 299 (5): 333-41
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): e1000363
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)
PNAS 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): e133-e133
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): e1000502
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): e6478
2008
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
Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation
Urban JH, Vogel J (2008)
PLOS Biology 6 (3): e64
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): e1000163
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): W65-W69
2007
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
Influence of poly(L-lysine) on the structure of dipalmitoylphosphatidylglycerol/water dispersions studied by X-ray scattering
Förster G, Schwieger C, Faber F, Weber T, Blume A (2007)
European Biophysics Journal 36 (4-5): 425-35
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)
PNAS 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
2006
Lack of angiotensin II conversion to angiotensin III increases water but not alcohol consumption in aminopeptidase A-deficient mice
Faber F, Gembardt F, Sun X, Mizutani S, Siems WE, Walther T (2006)
Regulatory Peptides 136 (1-3): 130-7
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
2005
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): 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): 2271-6
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
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): 3794-803
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
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