Publications of HIRI

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

Advanced fluorescence microscopy in respiratory virus cell biology

Xie E, Ahmad S, Smyth RP, Sieben C (2023)

Advances in Virus Research 116: 123-172

Genetic inhibition of CARD9 accelerates the development of atherosclerosis in mice through CD36 dependent-defective autophagy

Zhang Y, Vandestienne M, Lavillegrand JR, Joffre J, Santos-Zas I, Lavelle A, Zhong X, Le Goff W, Guérin M, Al-Rifai R, …, Sokol H, Ait-Oufella H (2023)

Nature Communications 14 (1): 4622

Harnessing Bile for Drug Absorption through Rational Excipient Selection

Schlauersbach J, Werthmüller D, Harlacher C, Galli B, Hanio S, Lenz B, Endres S, Pöppler AC, Scherf-Clavel O, Meinel L (2023)

Molecular Pharmaceutics 20 (8): 3864-3875

Short-range interactions between fibrocytes and CD8+ T cells in COPD bronchial inflammatory response

Eyraud E, Maurat E, Sac-Epée JM, Henrot P, Zysman M, Esteves P, Trian T, Dupuy JW, Leipold A, Saliba AE, …, Berger P, Dupin I (2023)

eLife 12: RP85875

An RNA modification enzyme directly senses reactive oxygen species for translational regulation in Enterococcus faecalis

Lee WL, Sinha A, Lam LN, Loo HL, Liang J, Ho P, Cui L, Chan CSC, Begley T, Kline KA, Dedon P (2023)

Nature Communications 14 (1): 4093

Lymph node medulla regulates the spatiotemporal unfolding of resident dendritic cell networks

Ugur M, Labios RJ, Fenton C, Knöpper K, Jobin K, Imdahl F, Golda G, Hoh K, Grafen A, Kaisho T, …, Bajénoff M, Kastenmüller W (2023)

Immunity 58 (8): 1778-1793.e10

VarID2 quantifies gene expression noise dynamics and unveils functional heterogeneity of ageing hematopoietic stem cells

Rosales-Alvarez RE, Rettkowski J, Herman JS, Dumbovic G, Cabezas-Wallscheid N, Grün D (2023)

Genome Biology 24 (1): 148

DOT1L activity affects neural stem cell division mode and reduces differentiation and ASNS expression

Appiah B, Fullio CL, Ossola C, Bertani I, Restelli E, Cheffer A, Polenghi M, Haffner C, Garcia-Miralles M, Zeis P, …, Taverna E, Vogel T (2023)

EMBO Reports 24 (8): e56233

Mouse Liver-Expressed Shiftless Is an Evolutionarily Conserved Antiviral Effector Restricting Human and Murine Hepaciviruses

Zhang Y, Kinast V, Sheldon J, Frericks N, Todt D, Zimmer M, Caliskan N, Brown RJP, Steinmann E, Pietschmann T (2023)

Microbiology Spectrum 11 (4): e0128423

CD4+ T cells are the major predictor of HCMV control in allogeneic stem cell transplant recipients on letermovir prophylaxis

Lauruschkat CD, Muchsin I, Rein A, Erhard F, Grathwohl D, Dölken L, Köchel C, Falk CS, Einsele H, Wurster S, Grigoleit GU, Kraus S (2023)

Frontiers in Immunology 14: 1148841

Decoding murine cytomegalovirus

Lodha M, Muchsin I, Jürges C, Juranic Lisnic V, L'Hernault A, Rutkowski AJ, Prusty BK, Grothey A, Milic A, Hennig T, …, Erhard F, Dölken L (2023)

PLOS Pathogens 19 (5): e1010992

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

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

microLife 4: uqac027

DksA is a conserved master regulator of stress response in Acinetobacter baumannii

Maharjan RP, Sullivan GJ, Adams FG, Shah BS, Hawkey J, Delgado N, Semenec L, Dinh H, Li L, Short FL, …, Eijkelkamp BA, Cain AK (2023)

Nucleic Acids Research 51 (12): 6101-6119

Cytotoxic CNS-associated T cells drive axon degeneration by targeting perturbed oligodendrocytes in PLP1 mutant mice

Abdelwahab T, Stadler D, Knöpper K, Arampatzi P, Saliba AE, Kastenmüller W, Martini R, Groh J (2023)

iScience 26 (5): 106698

An interferon gamma response signature links myocardial aging and immunosenescence

Ashour D, Rebs S, Arampatzi P, Saliba AE, Dudek J, Schulz R, Hofmann U, Frantz S, Cochain C, Streckfuß-Bömeke K, Ramos GC (2023)

Cardiovascular Research 119 (14): 2458-2468

Optimized metrics for orthogonal combinatorial CRISPR screens

Cetin R, Wegner M, Luwisch L, Saud S, Achmedov T, Süsser S, Vera-Guapi A, Müller K, Matthess Y, Quandt E, …, Beisel CL, Kaulich M (2023)

Scientific Reports 13 (1): 7405

Lab-scale siRNA and mRNA LNP manufacturing by various microfluidic mixing techniques – an evaluation of particle properties and efficiency

Jürgens DC, Deßloch L, Porras-Gonzalez D, Winkeljann J, Zielinski S, Munschauer M, Hörner AL, Burgstaller G, Winkeljann B, Merkel OM (2023)

OpenNano 12 (1): 100161

Sequential disruption of SPLASH-identified vRNA-vRNA interactions challenges their role in influenza A virus genome packaging

Jakob C, Lovate GL, Desirò D, Gießler L, Smyth RP, Marquet R, Lamkiewicz K, Marz M, Schwemmle M, Bolte H (2023)

Nucleic Acids Research 51 (12): 6479-6494

Insight COMPASS – the physics behind

Günther J, Kampf T, Rückert MA, Friedrich B, Tietze R, Lyer S, Hennig T, Dölken L, Alexiou C, Behr VC, Vogel P (2023)

International Journal on Magnetic Particle Imaging 9 (1)

Fast detection of Sars-CoV2 Antibodies by the use of critical off-set magnetic particle spectroscopy (COMPASS)

Friedrich B, Tietze R, Rückert MA, Kampf T, Hennig T, Dölken L, Behr VC, Alexiou C, Vogel P, Lyer S (2023)

International Journal on Magnetic Particle Imaging 9 (1)

Slow integrin-dependent migration organizes networks of tissue-resident mast cells

Kaltenbach L, Martzloff P, Bambach SK, Aizarani N, Mihlan M, Gavrilov A, Glaser KM, Stecher M, Thünauer R, Thiriot A, …, Grün D, Lämmermann T (2023)

Nature Immunology 24 (6): 915-924

HSV-1 Infection Induces a Downstream Shift of Promoter-Proximal Pausing for Host Genes

Weiß E, Hennig T, Graßl P, Djakovic L, Whisnant AW, Jürges CS, Koller F, Kluge M, Erhard F, Dölken L, Friedel CC (2023)

Journal of Virology 97 (5): e0038123

Bioresponsive Cytokine Delivery Responding to Matrix Metalloproteinases

Ter Mors B, Spieler V, Merino Asumendi E, Gantert B, Lühmann T, Meinel L (2023)

ACS Biomaterials Science and Engineering 10 (1): 29-37

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

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

Microbiology Spectrum 11 (3): e0510922

Nano-DMS-MaP allows isoform-specific RNA structure determination

Bohn P, Gribling-Burrer AS, Ambi UB, Smyth RP (2023)

Nature Methods 20 (6): 849-859

Durchfallerreger und die Homöostase der Mikrobiota

Winter S, Faber F, Bäumler A (2023)

BIOspektrum 29 (2): 127-129

A network of small RNAs regulates sporulation initiation in C difficile

Fuchs M, Lamm-Schmidt V, Lence T, Sulzer J, Bublitz A, Wackenreuter J, Gerovac M, Strowig T, Faber F (2023)

EMBO Journal 42 (12): e112858

Transdermal carbon monoxide delivery

Ruopp M, Reiländer S, Haas D, Caruana I, Kronenberg D, Schmehl W, Stange R, Meinel L (2023)

Journal of Controlled Release 357: 299-308

Amber Light Control of Peptide Secondary Structure by a Perfluoroaromatic Azobenzene Photoswitch

Cataldi E, Raschig M, Gutmann M, Geppert PT, Ruopp M, Schock M, Gerwe H, Bertermann R, Meinel L, Finze M, …, Decker M, Lühmann T (2023)

ChemBioChem 24 (5): e202200570

Solid microemulsion preconcentrates on pH responsive metal-organic framework for tableting

Scheller L, Bachmann S, Zorn T, Hanio S, Gbureck U, Fatouros D, Pöppler AC, Meinel L (2023)

European Journal of Pharmaceutics and Biopharmaceutics 186: 105-111

Advancing massive transcriptional profiling of single bacteria

Saliba AE (2023)

Cell Reports Methods 3 (2): 100416

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

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

mBio 14 (2): e0355722

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

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

Gut Microbes 15 (1): 2186109

Seroprevalence of Hepatitis E virus in children and adolescents living in urban Bogotá: An explorative cross-sectional study

Fernández Villalobos NV, Kessel B, Torres Páez JC, Strömpl J, Kerrinnes T, de la Hoz Restrepo FP, Strengert M, Krause G (2023)

Frontiers in Public Health 11: 981172

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

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

RNA 299 (5): 570-583

Central Role of Sibling Small RNAs NgncR_162 and NgncR_163 in Main Metabolic Pathways of Neisseria gonorrhoeae

Steiner T, Zachary M, Bauer S, Müller MJ, Krischke M, Radziej S, Klepsch M, Huettel B, Eisenreich W, Rudel T, Beier D (2023)

mBio 14 (1)

Altered and allele-specific open chromatin landscape reveals epigenetic and genetic regulators of innate immunity in COVID-19

Zhang B, Zhang Z, Koeken VACM, Kumar S, Aillaud M, Tsay HC, Liu Z, Kraft ARM, Soon CF, Odak I, …, Schulte LN, Li Y (2023)

Cell Genomics 3 (2): 100232

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

Homberger C, Saliba AE, Vogel J (2023)

Methods in Molecular Biology 2584: 105-121

Oral Use of Therapeutic Carbon Monoxide for Anyone, Anywhere, and Anytime

Reiländer S, Schmehl W, Popp K, Nuss K, Kronen P, Verdino D, Wiezorek C, Gutmann M, Hahn L, Däubler C, …, Scherf-Clavel O, Meinel L (2023)

ACS Biomaterials Science & Engineering 9 (6): 2937-2948

Azobenzene derivatives with activity against drug-resistant Candida albicans and Candida auris

Raschig M, Ramírez-Zavala B, Wiest J, Saedtler M, Gutmann M, Holzgrabe U, Morschhäuser J, Meinel L (2023)

Archiv der Pharmazie 356 (2): e2200463

2022

Network community detection and clustering with random walks

Ballal A, Kion-Crosby W, Morozov A (2022)

Physical Review Research 4 (4): 583

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

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

Metabolism: Clinical and Experimental 138: 155341

JAK2V617F mutation drives vascular resident macrophages toward a pathogenic phenotype and promotes dissecting aortic aneurysm

Al-Rifai R, Vandestienne M, Lavillegrand JR, Mirault T, Cornebise J, Poisson J, Laurans L, Esposito B, James C, Mansier O, …, Rautou PE, Ait-Oufella H (2022)

Nature Communications 13 (1): 6592

The miniature CRISPR-Cas12m effector binds DNA to block transcription

Wu WY, Mohanraju P, Liao C, Adiego-Pérez B, Creutzburg SCA, Makarova KS, Keessen K, Lindeboom TA, Khan TS, Prinsen S, …, Beisel CL, van der Oost J (2022)

Molecular Cell 82 (23): 4487-4502.e7

Postnatal expansion of mesenteric lymph node stromal cells towards reticular and CD34+ stromal cell subsets

Pezoldt J, Wiechers C, Zou M, Litovchenko M, Biocanin M, Beckstette M, Sitnik K, Palatella M, van Mierlo G, Chen W, …, Deplancke B, Huehn J (2022)

Nature Communications 13 (1): 7227

Helicobacter pylori shows tropism to gastric differentiated pit cells dependent on urea chemotaxis

Aguilar C, Pauzuolis M, Pompaiah M, Vafadarnejad E, Arampatzi P, Fischer M, Narres D, Neyazi M, Kayisoglu Ö, Sell T, …, Saliba AE, Bartfeld S (2022)

Nature Communications 13 (1): 5878

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

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

Cell Reports 41 (2): 111467

Fibroblastic reticular cells mitigate acute graft-versus-host disease via MHCII-dependent maintenance of regulatory T cells

Shaikh H, Pezoldt J, Mokhtari Z, Gamboa Vargas J, Le DD, Peña Mosca J, Arellano-Viera E, Kern MA, Graf C, Beyersdorf N, …, Huehn J, Beilhack A (2022)

JCI Insight 7 (22): e154250

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

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

Nucleic Acids Research 50 (22): e128

Landscape and age dynamics of immune cells in the Egyptian rousette bat

Friedrichs V, Toussaint C, Schäfer A, Rissmann M, Dietrich O, Mettenleiter TC, Pei G, Balkema-Buschmann A, Saliba AE, Dorhoi A (2022)

Cell Reports 40 (10): 111305

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

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

PNAS 119 (40): e2201460119

TFEB induces mitochondrial itaconate synthesis to suppress bacterial growth in macrophages

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

Nature Metabolism 4 (7): 856-866

Nonproductive exposure of PBMCs to SARS-CoV-2 induces cell-intrinsic innate immune responses

Kazmierski J, Friedmann K, Postmus D, Emanuel J, Fischer C, Jansen J, Richter A, Bosquillon de Jarcy L, Schüler C, Sohn M, …, Niemeyer D, Goffinet C (2022)

Molecular Systems Biology 18 (8): e10961

Lymphatic migration of unconventional T cells promotes site-specific immunity in distinct lymph nodes

Ataide MA, Knöpper K, Cruz de Casas P, Ugur M, Eickhoff S, Zou M, Shaikh H, Trivedi A, Grafen A, Yang T, …, Gasteiger G, Kastenmüller W (2022)

Immunity 55 (10): 1813–1828.e9

Anti-CRISPR prediction using deep learning reveals an inhibitor of Cas13b nucleases

Wandera KG, Alkhnbashi OS, Bassett HVI, Mitrofanov A, Hauns S, Migur A, Backofen R, Beisel CL (2022)

Molecular Cell 82 (14): 2714-2726.e4

A target expression threshold dictates invader defense and prevents autoimmunity by CRISPR-Cas13

Vialetto E, Yu Y, Collins SP, Wandera KG, Barquist L, Beisel CL (2022)

Cell Host & Microbe 3128 (22): 00273-6

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

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

Nucleic Acids Research 50 (11): 6435–6452

CRISPR memories in single cells

Sparmann A BC (2022)

Molecular Systems Biology 18 (4): e11011

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

Ponath F, Hör J, Vogel J (2022)

FEMS Microbiology Reviews 46 (5): fuac017

Congenital anemia reveals distinct targeting mechanisms for master transcription factor GATA1

Ludwig LS, Lareau CA, Bao EL, Liu N, Utsugisawa T, Tseng AM, Myers SA, Verboon JM, Ulirsch JC, Luo W, …, Kanno H, Sankaran VG (2022)

Blood 139 (16): 2534-2546

The ambivalent role of Bacteroides in enteric infections

Bornet E, Westermann AJ (2022)

Trends in Microbiology 30 (2): 104-108

Complement activation induces excessive T cell cytotoxicity in severe COVID-19

Georg P, Astaburuaga-García R, Bonaguro L, Brumhard S, Michalick L, Lippert LJ, Kostevc T, Gäbel C, Schneider M, Streitz M, …, Sawitzki B, PA-COVID-19 Study Group (2022)

Cell 185 (3): 493-512.e25

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

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

Molecular Cell 82 (3): 629-644.e4

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

Gomez-Raya-Vilanova MV, Leskinen K, Bhattacharjee A, Virta P, Rosenqvist P, Smith JLR, Bayfield OW, Homberger C, Kerrinnes T, Vogel J, Pajunen MI, Skurnik M (2022)

Nucleic Acids Research 50 (7): 3985-3997

Interleukin-23 receptor expressing γδ T cells locally promote early atherosclerotic lesion formation and plaque necrosis in mice

Gil-Pulido J, Amézaga N, Jorgacevic I, Manthey HD, Rösch M, Brand T, Cidlinsky P, Schäfer S, Beilhack A, Saliba AE, …, Cochain C, Zernecke A (2022)

Cardiovascular Research 118 (14): 2932-2945

Rapid cell-free characterization of multi-subunit CRISPR effectors and transposons

Wimmer F, Mougiakos I, Englert F, Beisel CL (2022)

Molecular Cell 82 (6): 1210-1224.e6

Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection

Pekayvaz K, Leunig A, Kaiser R, Joppich M, Brambs S, Janjic A, Popp O, Nixdorf D, Fumagalli V, Schmidt N, …, Stark K, Nicolai L (2022)

Nature Communications 13 (1): 1018

Short- and long-range interactions in the HIV-1 5' UTR regulate genome dimerization and packaging

Ye L, Gribling-Burrer AS, Bohn P, Kibe A, Börtlein C, Ambi UB, Ahmad S, Olguin-Nava M, Smith M, Caliskan N, von Kleist M, Smyth RP (2022)

Nature Structural & Molecular Biology 29 (4): 306-319

Spacer prioritization in CRISPR-Cas9 immunity is enabled by the leader RNA

Liao C, Sharma S, Svensson SL, Kibe A, Weinberg Z, Alkhnbashi OS, Bischler T, Backofen R, Caliskan N, Sharma CM, Beisel CL (2022)

Nature Microbiology 7 (4): 530-541

An expanded arsenal of immune systems that protect bacteria from phages

Millman A, Melamed S, Leavitt A, Doron S, Bernheim A, Hör J, Garb J, Bechon N, Brandis A, Lopatina A, …, Amitai G, Sorek R (2022)

Cell Host & Microbe 30 (11): 1556-1569.e5

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

Homberger C, Barquist L, Vogel J (2022)

microLife 3: uqac020

Stage-specific and cell type-specific requirements of ikzf1 during haematopoietic differentiation in zebrafish

Hess I, Sagar, O Meara C, Grün D, Schorpp M, Boehm T (2022)

Scientific Reports 12 (1): 21401

Two murine cytomegalovirus microRNAs target the major viral immediate early 3 gene

Herb S, Zeleznjak J, Hennig T, L'Hernault A, Lodha M, Jürges C, Trsan T, Juranic Lisnic V, Jonjic S, Erhard F, Krmpotic A, Dölken L (2022)

The Journal of General Virology 103 (11)

Leveraging Dissolution by Autoinjector Designs

Spangardt C, Keßler C, Dobrzewski R, Tepler A, Hanio S, Klaubert B, Meinel L (2022)

Pharmaceutics 14 (11): 2544

Critical Offset Magnetic PArticle SpectroScopy for rapid and highly sensitive medical point-of-care diagnostics

Vogel P, Rückert MA, Friedrich B, Tietze R, Lyer S, Kampf T, Hennig T, Dölken L, Alexiou C, Behr VC (2022)

Nature Communications 13 (1): 7230

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

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

RNA 29 (1): 123-39

Seroepidemiology of Borrelia burgdorferi s.l. among German National Cohort (NAKO) Participants, Hanover

Hassenstein MJ, Janzen I, Krause G, Harries M, Melhorn V, Kerrinnes T, Kemmling Y, Castell S (2022)

Microorganisms 10 (11): 2286

Chemo-Enzymatic PEGylation/POxylation of Murine Interleukin-4

Haas D, Hauptstein N, Dirauf M, Driessen MD, Ruopp M, Schubert US, Lühmann T, Meinel L (2022)

Bioconjugate Chemistry 33 (1): 97-104

A generic protocol for the affinity-purification of native macromolecular complexes from poxvirus-infected cells

Bartuli J, Lorenzi I, Backes S, Grimm C, Fischer U (2022)

STAR Protocols 3 (1): 101116

Time-resolved single-cell RNA-seq using metabolic RNA labelling

Erhard F, Saliba AE, Lusser A (2022)

Nature Reviews Methods Primers 2 (1): 331

Eine Einzelzell-RNA-Sequenzierung identifiziert Metabolismus und CD52 als neue Angriffspunkte in Ibrutinib-persistenten Mantelzelllymphomzellen

Fuhr V, Vafadarnejad E, Dietrich O, Arampatzi P, Riedel A, Saliba AE, Rosenwald A, Rauert-Wunderlich H (2022)

Die Pathologie 43 (1): 31–35

Resident TH2 cells orchestrate adipose tissue remodeling at a site adjacent to infection

Kabat AM, Hackl A, Sanin DE, Zeis P, Grzes KM, Baixauli F, Kyle R, Caputa G, Edwards-Hicks J, Villa M, …, Pearce EL, Pearce EJ (2022)

Science Immunology 7 (76): eadd3263

Concentration and composition dependent aggregation of Pluronic- and Poly-(2-oxazolin)-Efavirenz formulations in biorelevant media

Endres S, Karaev E, Hanio S, Schlauersbach J, Kraft C, Rasmussen T, Luxenhofer R, Böttcher B, Meinel L, Pöppler AC (2022)

Journal of Colloid and Interface Science 606 (Pt 2): 1179-1192

Linear Polyglycerol for N-terminal-selective Modification of Interleukin-4

Tully M, Hauptstein N, Licha K, Meinel L, Lühmann T, Haag R (2022)

Journal of Pharmaceutical Sciences 111 (6): 1642-1651

Bioconjugation strategies and clinical implications of Interferon-bioconjugates

Hauptstein N, Meinel L, Lühmann T (2022)

European Journal of Pharmaceutics and Biopharmaceutics 172: 157-167

Proteogenomic analysis of cancer aneuploidy and normal tissues reveals divergent modes of gene regulation across cellular pathways

Cheng P, Zhao X, Katsnelson L, Camacho-Hernandez EM, Mermerian A, Mays JC, Lippman SM, Rosales-Alvarez RE, Moya R, Shwetar J, …, Fenyo D, Davoli T (2022)

eLife 11: e75227

Editorial: mRNA Translational Control as a Mechanism of Post-transcriptional Gene Regulation

Kiss DL, Vasudevan D, Ho CK, Caliskan N (2022)

Frontiers in Molecular Biosciences 9: 947516

POTATO: Automated pipeline for batch analysis of optical tweezers data

Buck S, Pekarek L, Caliskan N (2022)

Biophysical Journal 121 (15): 2830-2839

Predicting Bile and Lipid Interaction for Drug Substances

Schlauersbach J, Kehrein J, Hanio S, Galli B, Harlacher C, Heidenreich C, Lenz B, Sotriffer C, Meinel L (2022)

Molecular Pharmaceutics 19 (8): 2868-2876

Regional seropositivity for Borrelia burgdorferi and associated risk factors: findings from the Rhineland Study, Germany

Coors A, Hassenstein MJ, Krause G, Kerrinnes T, Harries M, Breteler MMB, Castell S (2022)

Parasites & Vectors 15 (1): 241

PEtOxylated Interferon-α2a Bioconjugates Addressing H1N1 Influenza A Virus Infection

Hauptstein N, Dirauf M, Wittwer K, Cinar G, Siering O, Raschig M, Lühmann T, Scherf-Clavel O, Sawatsky B, Nischang I, …, Pfaller CK, Meinel L (2022)

Biomacromolecules 23 (9): 3593–3601

Bile and excipient interactions directing drug pharmacokinetics in rats

Schlauersbach J, Hanio S, Raschig M, Lenz B, Scherf-Clavel O, Meinel L (2022)

European Journal of Pharmaceutics and Biopharmaceutics 178: 65-68

Cell-Free Protein Synthesis from Exonuclease-Deficient Cellular Extracts Utilizing Linear DNA Templates

Sabeti Azad M, Cardoso Batista A, Faulon JL, Beisel CL, Bonnet J, Kushwaha M (2022)

Journal of Visualized Experiments (186): e64236

Reprogramming TracrRNAs for Multiplexed RNA Detection

Jiao C, Beisel CL (2022)

Methods in Molecular Biology 2518: 217-235

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

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

mSystems 7 (4): e0008622

Hyaluronic acid-GPRC5C signalling promotes dormancy in haematopoietic stem cells

Zhang YW, Mess J, Aizarani N, Mishra P, Johnson C, Romero-Mulero MC, Rettkowski J, Schönberger K, Obier N, Jäcklein K, …, Grün D, Cabezas-Wallscheid N (2022)

Nature Cell Biology 24: 1038–1048

Polymer selection impacts the pharmaceutical profile of site-specifically conjugated Interferon-α2a

Hauptstein N, Pouyan P, Wittwer K, Cinar G, Scherf-Clavel O, Raschig M, Licha K, Lühmann T, Nischang I, Schubert US, …, Haag R, Meinel L (2022)

Journal of Controlled Release 348: 881-892

Selective inhibition of miRNA processing by a herpesvirus-encoded miRNA

Hennig T, Prusty AB, Kaufer BB, Whisnant AW, Lodha M, Enders A, Thomas J, Kasimir F, Grothey A, Klein T, …, Dölken L, Prusty BK (2022)

Nature 605 (7910): 539-544

Merging bioresponsive release of insulin-like growth factor I with 3D printable thermogelling hydrogels

Beudert M, Hahn L, Horn AH, Hauptstein N, Sticht H, Meinel L, Luxenhofer R, Gutmann M, Lühmann T (2022)

Journal of Controlled Release 347: 115-126

Cytoplasmic gene expression: lessons from poxviruses

Grimm C, Bartuli J, Fischer U (2022)

Trends in Biochemical Sciences 47 (10): 892-902

Fibrin Sealants: Challenges and Solutions

Beudert M, Gutmann M, Lühmann T, Meinel L (2022)

ACS Biomaterials Science & Engineering 8 (6): 2220–2231

Developmental dynamics of two bipotent thymic epithelial progenitor types

Nusser A, Sagar, Swann JB, Krauth B, Diekhoff D, Calderon L, Happe C, Grün D, Boehm T (2022)

Nature 606 (7912): 165-171

Beneficial commensal bacteria promote Drosophila growth by downregulating the expression of peptidoglycan recognition proteins

Gallo M, Vento JM, Joncour P, Quagliariello A, Maritan E, Silva-Soares NF, Battistolli M, Beisel CL, Martino ME (2022)

iScience 25 (6): 104357

Genome Editing with Cas9 in Lactobacilli

Vento JM BC (2022)

Methods in Molecular Biology 2479: 245-261

Rapidly Characterizing CRISPR-Cas13 Nucleases Using Cell-Free Transcription-Translation Systems

Wandera KG, Beisel CL (2022)

Methods in Molecular Biology 2404: 135-153

Differentially Optimized Cell-Free Buffer Enables Robust Expression from Unprotected Linear DNA in Exonuclease-Deficient Extracts

Batista AC, Levrier A, Soudier P, Voyvodic PL, Achmedov T, Reif-Trauttmansdorff T, DeVisch A, Cohen-Gonsaud M, Faulon JL, Beisel CL, Bonnet J, Kushwaha M (2022)

ACS Synthetic Biology 11 (2): 732-746

A TXTL-Based Assay to Rapidly Identify PAMs for CRISPR-Cas Systems with Multi-Protein Effector Complexes

Wimmer F, Englert F, Beisel CL (2022)

Methods in Molecular Biology 2433: 391-411

Insights from structural studies of the cardiovirus 2A protein

Caliskan N, Hill CH (2022)

Bioscience Reports 42 (1): BSR20210406

Type 1 conventional dendritic cells maintain and guide the differentiation of precursors of exhausted T cells in distinct cellular niches

Dähling S, Mansilla AM, Knöpper K, Grafen A, Utzschneider DT, Ugur M, Whitney PG, Bachem A, Arampatzi P, Imdahl F, …, Bedoui S, Kastenmüller W (2022)

Immunity 55 (4): 656-670.e8

Comparative genomics provides structural and functional insights into Bacteroides RNA biology

Prezza G, Ryan D, Mädler G, Reichardt S, Barquist L, Westermann AJ (2022)

Molecular Microbiology 117 (1): 67-85

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Pekarek L, Buck S, Caliskan N (2022)

Journal of Visualized Experiments (180)

Comparative Magnitude and Persistence of Humoral SARS-CoV-2 Vaccination Responses in the Adult Population in Germany

Dulovic A, Kessel B, Harries M, Becker M, Ortmann J, Griesbaum J, Jüngling J, Junker D, Hernandez P, Gornyk D, …, Schneiderhan-Marra N, Strengert M (2022)

Frontiers in Immunology 13: 828053

Thinking Outside the Frame: Impacting Genomes Capacity by Programmed Ribosomal Frameshifting

Riegger RJ, Caliskan N (2022)

Frontiers in Molecular Biosciences 9: 842261

Innovative developments and emerging technologies in RNA therapeutics

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

RNA Biology 19 (1): 313-332

2021

Effector differentiation downstream of lineage commitment in ILC1s is driven by Hobit across tissues

Friedrich C, Taggenbrock RLRE, Doucet-Ladevèze R, Golda G, Moenius R, Arampatzi P, Kragten NAM, Kreymborg K, Gomez de Agüero M, Kastenmüller W, …, van Gisbergen KPJM, Gasteiger G (2021)

Nature Immunology 22 (10): 1256-1267

SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis

Wendisch D, Dietrich O, Mari T, von Stillfried S, Ibarra IL, Mittermaier M, Mache C, Chua RL, Knoll R, Timm S, …, Saliba AE, Sander LE (2021)

Cell 184 (26): 6243-6261.e27

Structural and molecular basis for Cardiovirus 2A protein as a viral gene expression switch

Hill CH, Pekarek L, Napthine S, Kibe A, Firth AE, Graham SC, Caliskan N, Brierley I (2021)

Nature Communications 12 (1): 7166

Investigating molecular mechanisms of 2A-stimulated ribosomal pausing and frameshifting in Theilovirus

Hill CH, Cook GM, Napthine S, Kibe A, Brown K, Caliskan N, Firth AE, Graham SC, Brierley I (2021)

Nucleic Acids Research 49 (20): 11938-11958

Illuminating the path to DNA repair

Gupta D, Beisel CL (2021)

Cell 184 (22): 5503-5505

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

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

Gut Microbes 13 (1): 1973836

The tracrRNA in CRISPR Biology and Technologies

Liao C, Beisel CL (2021)

Annual Review of Genetics 55: 161-181

The short isoform of the host antiviral protein ZAP acts as an inhibitor of SARS-CoV-2 programmed ribosomal frameshifting

Zimmer MM, Kibe A, Rand U, Pekarek L, Ye L, Buck S, Smyth RP, Cicin-Sain L, Caliskan N (2021)

Nature Communications 12 (1): 7193

A genetically encoded anti-CRISPR protein constrains gene drive spread and prevents population suppression

Taxiarchi C, Beaghton A, Don NI, Kyrou K, Gribble M, Shittu D, Collins SP, Beisel CL, Galizi R, Crisanti A (2021)

Nature Communications 12 (1): 3977

RNA landscape of the emerging cancer-associated microbe Fusobacterium nucleatum

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

Nature Microbiology 6 (8): 1007-1020

CRISPR transposons on the move

Mougiakos I, Beisel CL (2021)

Cell Host & Microbe 29 (5): 675-677

Noncanonical crRNAs derived from host transcripts enable multiplexable RNA detection by Cas9

Jiao C, Sharma S, Dugar G, Peeck NL, Bischler T, Wimmer F, Yu Y, Barquist L, Schoen C, Kurzai O, Sharma CM, Beisel CL (2021)

Science 372 (6545): 941-948

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

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

Nucleic Acids Research 49 (9): 5319-5335

Analysis of the RNA and Protein Complexome by Grad-seq

Hör J, Vogel J (2021)

Methods in Molecular Biology 2300: 183-201

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

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

Nucleic Acids Research 49 (8): 4705-4724

Homozygous BCMA gene deletion in response to anti-BCMA CAR T cells in a patient with multiple myeloma

Da Vià MC, Dietrich O, Truger M, Arampatzi P, Duell J, Heidemeier A, Zhou X, Danhof S, Kraus S, Chatterjee M, …, Saliba AE, Rasche L (2021)

Nature Medicine 27 (4): 616-619

Sequence-independent RNA sensing and DNA targeting by a split domain CRISPR-Cas12a gRNA switch

Collins SP, Rostain W, Liao C, Beisel CL (2021)

Nucleic Acids Research 49 (5): 2985-2999

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

Westermann AJ, Vogel J (2021)

Nature Reviews Genetics 22 (6): 361–378

CRISPR technologies and the search for the PAM-free nuclease

Collias D, Beisel CL (2021)

Nature Communications 12 (1): 555

Opposing Wnt signals regulate cervical squamocolumnar homeostasis and emergence of metaplasia

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

Nature Cell Biology 23 (2): 184–197

Structure and function of the poxvirus transcription machinery

Fischer U, Bartuli J, Grimm C (2021)

The Enzymes 50: 1-20

Structural basis of the complete poxvirus transcription initiation process

Grimm C, Bartuli J, Boettcher B, Szalay AA, Fischer U (2021)

Nature Structural & Molecular Biology 28 (10): 779-788

A Review of the Multipronged Attack of Herpes Simplex Virus 1 on the Host Transcriptional Machinery

Hennig T, Djakovic L, Dölken L, Whisnant AW (2021)

Viruses 13 (9): 1836

Molecular Insights into Site-Specific Interferon-α2a Bioconjugates Originated from PEG, LPG, and PEtOx

Hauptstein N, Pouyan P, Kehrein J, Dirauf M, Driessen MD, Raschig M, Licha K, Gottschaldt M, Schubert US, Haag R, …, Sotriffer C, Lühmann T (2021)

Biomacromolecules 22 (11): 4521-4534

Concatemeric Broccoli reduces mRNA stability and induces aggregates

Rink MR, Baptista MA, Flomm FJ, Hennig T, Whisnant AW, Wolf N, Seibel J, Dölken L, Bosse JB (2021)

PLOS One 16 (8): e0244166

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

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

microLife 2: uqab004

Malaria parasite infection compromises colonization resistance to an enteric pathogen by reducing gastric acidity

Walker GT, Yang G, Tsai JY, Rodriguez JL, English BC, Faber F, Souvannaseng L, Butler BP, Tsolis RM (2021)

Science Advances 7 (27): eabd6232

The metabolic footprint of Clostridia and Erysipelotrichia reveals their role in depleting sugar alcohols in the cecum

Tiffany CR, Lee JY, Rogers AWL, Olsan EE, Morales P, Faber F, Bäumler AJ (2021)

Microbiome 9 (1): 174

Coupling smartphone and CRISPR–Cas12a for digital and multiplexed nucleic acid detection

Yu T, Zhang S, Matei R, Marx W, Beisel CL, Wei Q (2021)

American Institute of Chemical Engineers Journal 67 (12): 17399‐17405

BRD9 is a druggable component of interferon-stimulated gene expression and antiviral activity

Börold J, Eletto D, Busnadiego I, Mair NK, Moritz E, Schiefer S, Schmidt N, Petric PP, Wong WW, Schwemmle M, Hale BG (2021)

EMBO Reports 22 (10): e52823

RNA Structures and Their Role in Selective Genome Packaging

Ye L, Ambi UB, Olguin-Nava M, Gribling-Burrer AS, Ahmad S, Bohn P, Weber MM, Smyth RP (2021)

Viruses 13 (9): 1788

Dysregulated Immunometabolism Is Associated with the Generation of Myeloid-Derived Suppressor Cells in Staphylococcus aureus Chronic Infection

Dietrich O, Heinz A, Goldmann O, Geffers R, Beineke A, Hiller K, Saliba AE, Medina E (2021)

Journal of Innate Immunity: 1-18

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

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

RNA 27 (11): 1339-1352

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

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

RNA 27 (12): 1512-1527

A Hyperthermoactive-Cas9 Editing Tool Reveals the Role of a Unique Arsenite Methyltransferase in the Arsenic Resistance System of Thermus thermophilus HB27

Gallo G, Mougiakos I, Bianco M, Carbonaro M, Carpentieri A, Illiano A, Pucci P, Bartolucci S, van der Oost J, Fiorentino G (2021)

mBio 12 (6): e0281321

Common Features in lncRNA Annotation and Classification: A Survey

Klapproth C, Sen R, Stadler PF, Findeiß S, Fallmann J (2021)

Non-Coding RNA 7 (4): 77

SARS-CoV-2 Seroprevalence in Germany

Gornyk D, Harries M, Glöckner S, Strengert M, Kerrinnes T, Heise JK, Maaß H, Ortmann J, Kessel B, Kemmling Y, Lange B, Krause G (2021)

Deutsches Ärzteblatt international 118 (48): 824-831

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

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

PNAS 118 (25): e2103579118

Atlas der SARS-CoV-2-RNA-Protein-Interaktionen in infizierten Zellen

Schmidt N, Munschauer M (2021)

BIOspektrum 27 (4): 376-379

Viral infection of the ovaries compromises pregnancy and reveals innate immune mechanisms protecting fertility

Tomac J, Mazor M, Lisnic B, Golemac M, Kveštak D, Bralic M, Bilic Zulle L, Brinkmann MM, Dölken L, Reinert LS, …, Jonjic S, Juranic Lisnic V (2021)

Immunity 54 (7): 1478-1493.e6

Remdesivir for Early COVID-19 Treatment of High-Risk Individuals Prior to or at Early Disease Onset-Lessons Learned

Dölken L, Stich A, Spinner CD (2021)

Viruses 13 (6): 963

The healing myocardium mobilises a distinct B-cell subset through a CXCL13-CXCR5-dependent mechanism

Heinrichs M, Ashour D, Siegel J, Büchner L, Wedekind G, Heinze KG, Arampatzi P, Saliba AE, Cochain C, Hofmann U, Frantz S, Campos Ramos G (2021)

Cardiovascular Research 117 (13): 2664-2676

Functional analysis of colonization factor antigen I positive enterotoxigenic Escherichia coli identifies genes implicated in survival in water and host colonization

Abd El Ghany M, Barquist L, Clare S, Brandt C, Mayho M, Joffre E, Sjöling Å, Turner AK, Klena JD, Kingsley RA, …, Dougan G, Pickard D (2021)

Microbial Genomics 7 (6): 000554

Amelioration of Cognitive and Behavioral Deficits after Traumatic Brain Injury in Coagulation Factor XII Deficient Mice

Stetter C, Lopez-Caperuchipi S, Hopp-Krämer S, Bieber M, Kleinschnitz C, Sirén A, Albert-Weißenberger C (2021)

International Journal of Molecular Sciences 22 (9): 4855

The Zinc Finger Antiviral Protein ZAP Restricts Human Cytomegalovirus and Selectively Binds and Destabilizes Viral UL4/UL5 Transcripts

Gonzalez-Perez AC, Stempel M, Wyler E, Urban C, Piras A, Hennig T, Ganskih S, Wei Y, Heim A, Landthaler M, …, Erhard F, Brinkmann MM (2021)

mBio 12 (3): e02683-20

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

Gerovac M, Vogel J, Smirnov A (2021)

Frontiers in Molecular Biosciences 8: 661448

Posttraumatic learning deficits correlate with initial trauma severity and chronic cellular reactions after closed head injury in male mice

Lopez-Caperuchipi S, Kürzinger L, Hopp-Krämer S, Albert-Weißenberger C, Paul MM, Sirén A, Stetter C (2021)

Experimental Neurology 341: 113721

In Situ Biomanufacturing of Small Molecules in the Mammalian Gut by Probiotic Saccharomyces boulardii

Durmusoglu D, Al'Abri IS, Collins SP, Cheng J, Eroglu A, Beisel CL, Crook N (2021)

ACS Synthetic Biology 10 (5): 1039-1052

Global identification of RsmA/N binding sites in Pseudomonas aeruginosa by in vivo UV CLIP-seq

Chihara K, Barquist L, Takasugi K, Noda N, Tsuneda S (2021)

RNA Biology 18 (12): 2401-2416

Mechanism and consequences of herpes simplex virus 1-mediated regulation of host mRNA alternative polyadenylation

Wang X, Liu L, Whisnant AW, Hennig T, Djakovic L, Haque N, Bach C, Sandri-Goldin RM, Erhard F, Friedel CC, Dölken L, Shi Y (2021)

PLOS Genetics 17 (3): e1009263

Time-Resolved scRNA-Seq Tracks the Adaptation of a Sensitive MCL Cell Line to Ibrutinib Treatment

Fuhr V, Vafadarnejad E, Dietrich O, Arampatzi P, Riedel A, Saliba AE, Rosenwald A, Rauert-Wunderlich H (2021)

International Journal of Molecular Sciences 22 (5): 2276

Bioactive Electrospun Fibers: Fabrication Strategies and a Critical Review of Surface-Sensitive Characterization and Quantification

Taskin MB, Ahmad T, Wistlich L, Meinel L, Schmitz M, Rossi A, Groll J (2021)

Chemical Reviews 121 (18): 11194-11237

Initial HCV infection of adult hepatocytes triggers a temporally structured transcriptional program containing diverse pro- and anti-viral elements

Tegtmeyer B, Vieyres G, Todt D, Lauber C, Ginkel C, Engelmann M, Herrmann M, Pfaller CK, Vondran FW, Broering R, …, Pietschmann T, Brown RJ (2021)

Journal of Virology 95 (10)

Author Correction: 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 (2021)

Nature Microbiology 6 (4): 533

A Code of Ethics for Gene Drive Research

Annas GJ, Beisel CL, Clement K, Crisanti A, Francis S, Galardini M, Galizi R, Grünewald J, Immobile G, Khalil AS, …, Taxiarchi C, Joung JK (2021)

The CRISPR Journal 4 (1): 19-24

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

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

mBio 12 (1): e03454-20

Drug-Induced Dynamics of Bile Colloids

Hanio S, Schlauersbach J, Lenz B, Spiegel F, Böckmann RA, Schweins R, Nischang I, Schubert US, Endres S, Pöppler A, …, Kolter K, Meinel L (2021)

Langmuir 37 (8): 2543-2551

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

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

Cell Reports 34 (5): 108722

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

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

Scientific Reports 11: 1979

Global identification of RsmA/N binding sites in Pseudomonas aeruginosa by in vivo UV CLIP-seq

Chihara K, Barquist L, Takasugi K, Noda N, Tsuneda S (2021)

RNA Biology 18 (12): 2401-2416

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

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

RNA Biology 18 (8): 1099-1110

2020

Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19

Bernardes JP, Mishra N, Tran F, Bahmer T, Best L, Blase JI, Bordoni D, Franzenburg J, Geisen U, Josephs-Spaulding J, …, Schultze JL, Rosenstiel P (2020)

Immunity 53 (6): 1296-1314.e9

Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation

Basak A, Munschauer M, Lareau CA, Montbleau KE, Ulirsch JC, Hartigan CR, Schenone M, Lian J, Wang Y, Huang Y, …, Lander ES, Sankaran VG (2020)

Nature Genetics 52 (2): 138-145

The lncRNA lincNMR regulates nucleotide metabolism via a YBX1 - RRM2 axis in cancer

Gandhi M, Groß M, Holler JM, Coggins SA, Patil N, Leupold JH, Munschauer M, Schenone M, Hartigan CR, Allgayer H, Kim B, Diederichs S (2020)

Nature Communications 11: 3214

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): e232-249

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): eabb4054

Your Base Editor Might Be Flirting with Single (Stranded) DNA: Faithful On-Target CRISPR Base Editing without Promiscuous Deamination

Collins SP, Beisel CL (2020)

Molecular Cell 79 (5): 703-704

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 587 (7834): 377-386

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

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

Nature Microbiology 5 (10): 1202–1206

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: 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: 3184

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 (9): 526-540

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: 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: 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

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

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

The EMBO Journal 39 (9): e103852

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: 31

Frugal Innovation for Point-of-Care Diagnostics Controlling Outbreaks and Epidemics

Miesler T, Wimschneider C, Brem A, Meinel L (2020)

ACS Biomaterials Science & Engineering 6 (5): 2709-2725

An RNA biology perspective on species-specific programmable RNA antibiotics

Vogel J (2020)

Molecular Microbiology 113 (3): 550-559

An RNA-centric view on gut Bacteroidetes

Ryan D, Prezza G, Westermann AJ (2020)

Biological Chemistry 402 (1): 55-72

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

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

microLife 1 (1): 597

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

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

Frontiers in Cellular and Infection Microbiology 10: 600325

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

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

Nature Microbiology 6 (3): 339-353

Intracellular Staphylococcus aureus Perturbs the Host Cell Ca2+ Homeostasis To Promote Cell Death

Stelzner K, Winkler A, Liang C, Boyny A, Ade CP, Dandekar T, Fraunholz MJ, Rudel T (2020)

mBio 11 (6): e02250-20

Leveraging bile solubilization of poorly water-soluble drugs by rational polymer selection

Schlauersbach J, Hanio S, Lenz B, Vemulapalli SP, Griesinger C, Pöppler A, Harlacher C, Galli B, Meinel L (2020)

Journal of Controlled Release 330: 36-48

Biodistribution and serologic response in SARS-CoV-2 induced ARDS: A cohort study

Schlesinger T, Weißbrich B, Wedekink F, Notz Q, Herrmann J, Krone M, Sitter M, Schmid B, Kredel M, Stumpner J, …, Meybohm P, Lotz C (2020)

PLOS One 15 (11): e0242917

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

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

Cell Reports 33 (7): 108389

Dissecting Herpes Simplex Virus 1-Induced Host Shutoff at the RNA Level

Friedel CC, Whisnant AW, Djakovic L, Rutkowski AJ, Friedl M, Kluge M, Williamson JC, Sai S, Vidal RO, Sauer S, …, Erhard F, Dölken L (2020)

Journal of Virology 95 (3): e01399-20

Advances and challenges in single-cell RNA-seq of microbial communities

Imdahl F, Saliba A (2020)

Current Opinion in Microbiology 57: 102-110

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

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

Marshall R, Beisel CL, Noireaux V (2020)

STAR Protocols 1 (1): 100003

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

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): 619

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 5 (11): 1390-1402

Identification of a Novel LysR-Type Transcriptional Regulator in Staphylococcus aureus That Is Crucial for Secondary Tissue Colonization during Metastatic Bloodstream Infection

Groma M, Horst SA, Das S, Huettel B, Klepsch M, Rudel T, Medina E, Fraunholz M (2020)

mBio 11 (4): e01646-20

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 6 (9): 5240–5253

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

Seropositivity for pathogens associated with chronic infections is a risk factor for all-cause mortality in the elderly: findings from the Memory and Morbidity in Augsburg Elderly (MEMO) Study

Zeeb M, Kerrinnes T, Cicin-Sain L, Guzman CA, Puppe W, Schulz TF, Peters A, Berger K, Castell S, Karch A (2020)

Geroscience 42: 1365-1376

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

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): e0234502

Plugging Small RNAs into the Network

Barquist L (2020)

mSystems 5 (3): e00422-20

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: 2038

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): e0232046

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

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

RNA 26 (8): 1069-1078

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

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

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

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

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

The FASEB Journal 34 (1): 316-332

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): e03348-19

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: 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): e02312-19

Methods for characterizing, applying, and teaching CRISPR-Cas systems

Beisel CL (2020)

Methods 172: 1-2

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

Wimmer F, Beisel CL (2020)

Frontiers in Microbiology 10: 3078

2019

Commensal Enterobacteriaceae Protect against Salmonella Colonization through Oxygen Competition

Litvak Y, Mon KKZ, Nguyen H, Chanthavixay G, Liou M, Velazquez EM, Kutter L, Alcantara MA, Byndloss MX, Tiffany CR, …, Zhou H, Bäumler AJ (2019)

Cell Host & Microbe 25 (1): 128-139.e5

Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection

Velazquez EM, Nguyen H, Heasley KT, Saechao CH, Gil LM, Rogers AWL, Miller BM, Rolston MR, Lopez CA, Litvak Y, …, Byndloss AJ, Bäumler AJ (2019)

Nature Microbiology 4 (6): 1057-1064

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: 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: 2948

Social behaviour and making attachments: a report from the fifth 'Young Microbiologists Symposium on Microbe Signalling, Organisation and Pathogenesis'

An SQ, Ding YC, Faber F, Hobley L, Sá-Pessoa J (2019)

Microbiology 165 (2): 138-145

Context-specific regulation of cell survival by a miRNA-controlled BIM rheostat

Labi V, Peng S, Klironomos F, Munschauer M, Kastelic N, Chakraborty T, Schoeler K, Derudder E, Martella M, Mastrobuoni G, …, Rajewsky N, Rajewsky K (2019)

Genes & Development 33 (23-24): 1673-1687

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

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

mSystems 4 (6): e00590-19

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

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): e02504-18

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

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

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

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

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): pii: fnz085

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): e1518

2018

Genetic Ablation of Butyrate Utilization Attenuates Gastrointestinal Salmonella Disease

Bronner DN, Faber F, Olsan EE, Byndloss MX, Sayed NA, Xu G, Yoo W, Kim D, Ryu S, Lebrilla CB, Bäumler AJ (2018)

Cell Host & Microbe 23 (2): 266-273.e4

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.e6

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: 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.e19

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): pii: e98529

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): e99875

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): e57

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.e3

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.e7

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.e6

Tolerogenic Transcriptional Signatures of Steady-State and Pathogen-Induced Dendritic Cells

Vendelova E, Ashour D, Blank P, Erhard F, Saliba AE, Kalinke U, Lutz MB (2018)

Frontiers in Immunology 9: 333

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

Yu S, Vogel J, Förstner KU (2018)

GigaScience 7 (9): giy096

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): giy070

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): e000229

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: e39054

Advances in CRISPR Technologies for Microbial Strain Engineering

Alper HS, Beisel CL (2018)

Biotechnology Journal 13 (9): e1800460

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): e1700583

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): e1007401

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 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): e1007333

2017

Microbiota-activated PPAR-γ signaling inhibits dysbiotic Enterobacteriaceae expansion

Byndloss MX, Olsan EE, Rivera-Chávez F, Tiffany CR, Cevallos SA, Lokken KL, Torres TP, Byndloss AJ, Faber F, Gao Y, …, Lebrilla CB, Bäumler AJ (2017)

Science 357 (6351): 570-575

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): e96

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.e4

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

A Small Number of Low-abundance Bacteria Dominate Plant Species-specific Responses during Rhizosphere Colonization

Dawson W, Hör J, Egert M, van Kleunen M, Pester M (2017)

Frontiers in Microbiology 8: 975

Colonization resistance: The deconvolution of a complex trait

Olsan EE, Byndloss MX, Faber F, Rivera-Chávez F, Tsolis RM, Bäumler AJ (2017)

The Journal of Biological Chemistry 292 (21): 8577-8581

A Salmonella Regulator Modulates Intestinal Colonization and Use of Phosphonoacetic Acid

Elfenbein JR, Knodler LA, Schaeffer AR, Faber F, Bäumler AJ, Andrews-Polymenis HL (2017)

Frontiers in Cellular and Infection Microbiology 7: 69

Respiration of Microbiota-Derived 1,2-propanediol Drives Salmonella Expansion during Colitis

Faber F, Thiennimitr P, Spiga L, Byndloss MX, Litvak Y, Lawhon S, Andrews-Polymenis HL, Winter SE, Bäumler AJ (2017)

PLOS Pathogens 13 (1): e1006129

P5SM suicide exon for regulating gene expression

Hammond MC, Westermann AJ, Qin Q (2017)

Patent (US9637750B2)

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): E513-E519

What Is the Role of Circuit Design in the Advancement of Synthetic Biology? Part 1

Beisel CL (2017)

Cell Systems 4 (4): 370-372

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)

PNAS 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): pii: e00419-17

Resolving host-pathogen interactions by dual RNA-seq

Westermann AJ, Barquist L, Vogel J (2017)

PLOS Pathogens 13 (2): e1006033

2016

Depletion of Butyrate-Producing Clostridia from the Gut Microbiota Drives an Aerobic Luminal Expansion of Salmonella

Rivera-Chávez F, Zhang LF, Faber F, Lopez CA, Byndloss MX, Olsan EE, Xu G, Velazquez EM, Lebrilla CB, Winter SE, Bäumler AJ (2016)

Cell Host & Microbe 19 (4): 443-54

Host-mediated sugar oxidation promotes post-antibiotic pathogen expansion

Faber F, Tran L, Byndloss MX, Lopez CA, Velazquez EM, Kerrinnes T, Nuccio SP, Wangdi T, Fiehn O, Tsolis RM, Bäumler AJ (2016)

Nature 534 (7609): 697-9

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

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

Chao Y, Vogel J (2016)

Molecular Cell 61 (3): 352-363

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

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

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

SBE Supplement: Synthetic Biology – Engineering Genes with CRISPR-Cas9

Luo ML, Beisel CL (2016)

American Institute of Chemical Engineers

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)

PNAS 113 (22): E3101-10

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): e1005723

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): e1005975

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): E248

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)

PNAS 113 (41): 11591-11596

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

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

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: 12.13.1-12.13.25

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): 20160081

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: e2130

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

2015

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

Self‐Assembled DNA Nanoclews for the Efficient Delivery of CRISPR–Cas9 for Genome Editing

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

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

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

Ziebuhr W, Vogel J (2015)

Molecular Cell 58 (3): 389-90

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

Inflammation-associated alterations to the intestinal microbiota reduce colonization resistance against non-typhoidal Salmonella during concurrent malaria parasite infection

Mooney JP, Lokken KL, Byndloss MX, George MD, Velazquez EM, Faber F, Butler BP, Walker GT, Ali MM, Potts R, …, Luckhart S, Tsolis RM (2015)

Scientific Reports 5: 14603

Integrative, ligand-responsive microRNAs

Smolke CD, Beisel CL (2015)

Patent (US9145555B2)

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): e0137421

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): e02383

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

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

PNAS 112 (34): E4772-81

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): e0142002

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

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)

PNAS 112 (3): 863-8

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): e0003611

2014

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): R15

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

The impact of intestinal inflammation on the nutritional environment of the gut microbiota

Faber F, Bäumler AJ (2014)

Immunology Letters 162 (2 Pt A): 48-53

Salmonella enterica Serovar Typhi conceals the invasion-associated type three secretion system from the innate immune system by gene regulation

Winter SE, Winter MG, Poon V, Keestra AM, Sterzenbach T, Faber F, Costa LF, Cassou F, Costa EA, Alves GE, …, Santos RL, Bäumler AJ (2014)

PLOS Pathogens 10 (7): e1004207

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)

136: 719-786

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: e05375

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): e00928-13

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

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): e1003907

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)

PNAS 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

2013

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

Modular polynucleotides for ligand-controlled regulatory systems

Smolke CD, Win MN, Beisel CL (2013)

Patent (US8367815B2)

A small RNA serving both the Hfq and CsrA regulons

Holmqvist E, Vogel J (2013)

Genes & Development 27 (10): 1073-8

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): a010298

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)

PNAS 110 (37): E3487-96

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)

PNAS 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): 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

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

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

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): e1003868

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

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): e00565-13

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): e84567

2012

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

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 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

Surface-associated motility, a common trait of clinical isolates of Acinetobacter baumannii, depends on 1,3-diaminopropane

Skiebe E, de Berardinis V, Morczinek P, Kerrinnes T, Faber F, Lepka D, Hammer B, Zimmermann O, Ziesing S, Wichelhaus TA, …, Pfeifer Y, Wilharm G (2012)

International Journal of Medical Microbiology 302 (3): 117-28

Transgene regulation in plants by alternative splicing of a suicide exon

Hickey SF, Sridhar M, Westermann AJ, Qin Q, Vijayendra P, Liou G, Hammond MC (2012)

Nucleic Acids Research 40 (10): 4701-10

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)

PNAS 109 (13): E757-64

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)

PNAS 109 (20): E1277-86

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)

PNAS 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 Biology 8 (6): e1002782

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

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

The Plant Cell 24 (1): 123-36

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): 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

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

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

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

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

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

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

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