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Publications

Our mission is to pursue scientific research without boundaries. We want the research we produce to be accessible and reproducible. The main outputs of our research are new ideas, knowledge and techniques, which we publish as peer-reviewed research publications. Maximising the sharing of our research is the best way of ensuring that people can access, read and develop upon it.

Publication Highlights

Have a look at our latest discoveries.

2019

Barriers to genome editing with CRISPR in bacteria

Vento J, Crook N, Beisel C (2019)

J Ind Microbiol Biotechnol, 46 (9-10): 1327-1341DOI: 10.1007/s10295-019-02195-1

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

Ondari E, Klemm E, Msefula C, El Ghany M, Heath J, Pickard D, Barquist L, Dougan G, Kingsley R, MacLennan C (2019)

Wellcome Open Res, 4: 74DOI: 10.12688/wellcomeopenres.15059.1

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

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

Liao C, Ttofali F, Slotkowski R, Denny S, Cecil T, Leenay R, Keung A, Beisel C (2019)

Nat Commun, 10 (1): 2948DOI: 10.1038/s41467-019-10747-3

Thermodynamic control of -1 programmed ribosomal frameshifting

Bock L, Caliskan N, Korniy N, Peske F, Rodnina M, Grubmüller H (2019)

Nat Commun, 10 (1): 4598DOI: 10.1038/s41467-019-12648-x

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

Pickar-Oliver A, Black J, Lewis M, Mutchnick K, Klann T, Gilcrest K, Sitton M, Nelson C, Barrera A, Bartelt L, …, Barrangou R, Gersbach C (2019)

Nat BiotechnolDOI: 10.1038/s41587-019-0235-7

Transcriptional noise and exaptation as sources for bacterial sRNAs

Jose B, Gardner P, Barquist L (2019)

Biochem Soc Trans, 47 (2): 527-539DOI: 10.1042/BST20180171

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

Garenne D, Beisel C, Noireaux V (2019)

Rapid Commun Mass Spectrom, 33 (11): 1036-1048DOI: 10.1002/rcm.8438

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

Erhard F, Baptista M, Krammer T, Hennig T, Lange M, Arampatzi P, Jürges C, Theis F, Saliba A, Dölken L (2019)

Nature, 571 (7765): 419-423DOI: 10.1038/s41586-019-1369-y

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

Westermann A, Venturini E, Sellin M, Förstner K, Hardt W, Vogel J (2019)

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

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

Martins Gomes S, Westermann A, Sauerwein T, Hertlein T, Förstner K, Ohlsen K, Metzger M, Shusta E, Kim B, Appelt-Menzel A, Schubert-Unkmeir A (2019)

Front Microbiol, 10: 1181DOI: 10.3389/fmicb.2019.01181

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

Westbrook A, Tang X, Marshall R, Maxwell C, Chappell J, Agrawal D, Dunlop M, Noireaux V, Beisel C, Lucks J, Franco E (2019)

Biotechnol Bioeng, 116 (5): 1139-1151DOI: 10.1002/bit.26918

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

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

Wandera K, Collins S, Wimmer F, Marshall R, Noireaux V, Beisel C (2019)

Methods (San Diego, Calif.) (19): 1046-2023DOI: 10.1016/j.ymeth.2019.05.014

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

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

Wiley Interdiscip Rev RNA, 10 (2): 1518DOI: 10.1002/wrna.1518

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

Liao C, Slotkowski R, Beisel C (2019)

Methods Enzymol, 629: 493-511DOI: 10.1016/bs.mie.2019.04.011

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

Jacobsen T, Liao C, Beisel C (2019)

FEMS Microbiol Lett, 366 (8): 085DOI: 10.1093/femsle/fnz085

2018

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

Smyth R, Negroni M, Lever A, Mak J, Kenyon J (2018)

Front Immunol, 9: 2097DOI: 10.3389/fimmu.2018.02097

Toward Cell Type-Specific In Vivo Dual RNA-Seq

Frönicke L, Bronner D, Byndloss M, McLaughlin B, Bäumler A, Westermann A (2018)

Meth Enzymol, 612: 505-522DOI: 10.1016/bs.mie.2018.08.013

Advances in CRISPR Technologies for Microbial Strain Engineering

Alper H, Beisel C (2018)

Biotechnol J, 13 (9): 18004DOI: 10.1002/biot.201800460

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

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

Nat Commun, 9 (1): 3903DOI: 10.1038/s41467-018-06423-7

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

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

Cell Host Microbe, 24 (1): 109-119DOI: 10.1016/j.chom.2018.06.001

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 Y, Lei A, Parker B, …, Choi H, Vogel C (2018)

Elife, 7: 39054DOI: 10.7554/eLife.39054

Functional analysis of Salmonella Typhi adaptation to survival in water

Kingsley R, Langridge G, Smith S, Makendi C, Fookes M, Wileman T, El Ghany M, Keith Turner A, Dyson Z, Sridhar S, …, Barquist L, Dougan G (2018)

Environ Microbiol, 20 (11): 4079-4090DOI: 10.1111/1462-2920.14458

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 A, Zernecke A (2018)

Circ Res, 122 (12): 1661-1674DOI: 10.1161/CIRCRESAHA.117.312509

Bacterial RNA Biology on a Genome Scale

Hör J, Gorski S, Vogel J (2018)

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

Host-Pathogen Transcriptomics by Dual RNA-Seq

Westermann A, Vogel J (2018)

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

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

Liao C, Slotkowski R, Achmedov T, Beisel C (2018)

RNA Biol, 16 (4): 404-412DOI: 10.1080/15476286.2018.1526537

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

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

Methods (San Diego, Calif.), 143: 48-57DOI: 10.1016/j.ymeth.2018.02.016

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

Simon L, Karg S, Westermann A, Engel M, Elbehery A, Hense B, Heinig M, Deng L, Theis F (2018)

Gigascience, 7 (6): 070DOI: 10.1093/gigascience/giy070

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

Wheeler N, Gardner P, Barquist L (2018)

Plos Genet, 14 (5): 10073DOI: 10.1371/journal.pgen.1007333

CRISPR tool puts RNA on the record

Beisel C (2018)

Nature, 562 (7727): 347-349DOI: 10.1038/d41586-018-06869-1

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

Leenay R, Vento J, Shah M, Martino M, Leulier F, Beisel C (2018)

Biotechnol J, 14 (3): 17005DOI: 10.1002/biot.201700583

RNA-binding proteins in bacteria

Holmqvist E, Vogel J (2018)

Nat Rev Microbiol, 16 (10): 601-615DOI: 10.1038/s41579-018-0049-5

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)

EMBO J, 37 (23): 98529DOI: 10.15252/embj.201798529

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

Bober J, Beisel C, Nair N (2018)

Annu Rev Biomed Eng, 20: 277-300DOI: 10.1146/annurev-bioeng-062117-121019

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

Marshall R, Maxwell C, Collins S, Jacobsen T, Luo M, Begemann M, Gray B, January E, Singer A, He Y, Beisel C, Noireaux V (2018)

Mol Cell, 69 (1): 146-157DOI: 10.1016/j.molcel.2017.12.007

The NORAD lncRNA assembles a topoisomerase complex critical for genome stability

Munschauer M, Nguyen C, Sirokman K, Hartigan C, Hogstrom L, Engreitz J, Ulirsch J, Fulco C, Subramanian V, Chen J, …, Carr S, Lander E (2018)

Nature, 561 (7721): 132-136DOI: 10.1038/s41586-018-0453-z

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)

Mol Cell, 70 (5): 971-982DOI: 10.1016/j.molcel.2018.04.017

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

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

Plos Genet, 14 (6): 10074DOI: 10.1371/journal.pgen.1007401

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 H, Kobiyama K, Hamers A, Cochain C, Vafadarnejad E, Saliba A, …, Ley K, Wolf D (2018)

Circ Res, 122 (12): 1675-1688DOI: 10.1161/CIRCRESAHA.117.312513

Structural and Functional Motifs in Influenza Virus RNAs

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

Front Microbiol, 9: 559DOI: 10.3389/fmicb.2018.00559

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

Agrawal D, Tang X, Westbrook A, Marshall R, Maxwell C, Lucks J, Noireaux V, Beisel C, Dunlop M, Franco E (2018)

ACS Synth Biol, 7 (5): 1219-1228DOI: 10.1021/acssynbio.8b00040

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

Nolan L, Whitchurch C, Barquist L, Katrib M, Boinett C, Mayho M, Goulding D, Charles I, Filloux A, Parkhill J, Cain A (2018)

Microb Genom, 4 (11): 00022DOI: 10.1099/mgen.0.000229

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

Cain A, Boinett C, Barquist L, Dordel J, Fookes M, Mayho M, Ellington M, Goulding D, Pickard D, Wick R, …, Parkhill J, Thomson N (2018)

Sci Rep, 8 (1): 9868DOI: 10.1038/s41598-018-28199-y

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

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

Nucleic Acids Res, 46 (16): 8079-8089DOI: 10.1093/nar/gky689

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

Dugar G, Leenay R, Eisenbart S, Bischler T, Aul B, Beisel C, Sharma C (2018)

Mol Cell, 69 (5): 893-905DOI: 10.1016/j.molcel.2018.01.032

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

Yu S, Vogel J, Förstner K (2018)

Gigascience, 7 (9): 096DOI: 10.1093/gigascience/giy096

Salmonella persisters undermine host immune defenses during antibiotic treatment

Stapels D, Hill P, Westermann A, Fisher R, Thurston T, Saliba A, Blommestein I, Vogel J, Helaine S (2018)

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

Nuclear lncRNA stabilization in the host response to bacterial infection

Munschauer M, Vogel J (2018)

EMBO J, 37 (13): 99875DOI: 10.15252/embj.201899875

Ribosome Levels Selectively Regulate Translation and Lineage Commitment in Human Hematopoiesis

Khajuria R, Munschauer M, Ulirsch J, Fiorini C, Ludwig L, McFarland S, Abdulhay N, Specht H, Keshishian H, Mani D, …, Carr S, Sankaran V (2018)

Cell, 173 (1): 90-103DOI: 10.1016/j.cell.2018.02.036

Genome organization and DNA accessibility control antigenic variation in trypanosomes

Müller L, Cosentino R, Förstner K, Guizetti J, Wedel C, Kaplan N, Janzen C, Arampatzi P, Vogel J, Steinbiss S, …, Sebra R, Siegel T (2018)

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

Regulatory RNAs in Virulence and Host-Microbe Interactions

Westermann A (2018)

Microbiol Spectr, 6 (4): 305-337DOI: 10.1128/microbiolspec.RWR-0002-2017

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

Nucleic Acids Res, 46 (9): 57DOI: 10.1093/nar/gky152

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