Reasearch with a purpose

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 what we have recently discovered.

Publications in chronological order

Agrawal, Deepak K.; Tang, Xun; Westbrook, Alexandra; Marshall, Ryan; Maxwell, Colin S.; Lucks, Julius et al. (2018): Mathematical Modeling of RNA-Based Architectures for Closed Loop Control of Gene Expression. In: ACS Synthetic Biology 7 (5), S. 1219–1228. DOI: 10.1021/acssynbio.8b00040.

Alper, Hal S.; Beisel, Chase L. (2018): Advances in CRISPR Technologies for Microbial Strain Engineering. In: Biotechnology Journal 13 (9), e1800460. DOI: 10.1002/biot.201800460.

Beisel, Chase L. (2018): CRISPR tool puts RNA on the record. In: Nature 34, S. 933. DOI: 10.1038/d41586-018-06869-1.

Bober, Josef R.; Beisel, Chase L.; Nair, Nikhil U. (2018): Synthetic Biology Approaches to Engineer Probiotics and Members of the Human Microbiota for Biomedical Applications. In: Annual Review of Biomedical Engineering 20, S. 277–300. DOI: 10.1146/annurev-bioeng-062117-121019.

Cain, Amy K.; Boinett, Christine J.; Barquist, Lars; Dordel, Janina; Fookes, Maria; Mayho, Matthew et al. (2018): Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin. In: Scientific Reports 8 (1), S. 9868. DOI: 10.1038/s41598-018-28199-y.

Dugar, Gaurav; Leenay, Ryan T.; Eisenbart, Sara K.; Bischler, Thorsten; Aul, Belinda U.; Beisel, Chase L.; Sharma, Cynthia M. (2018): CRISPR RNA-Dependent Binding and Cleavage of Endogenous RNAs by the Campylobacter jejuni Cas9. In: Molecular Cell 69 (5), 893-905.e7. DOI: 10.1016/j.molcel.2018.01.032.

El Mouali, Youssef; Gaviria-Cantin, Tania; Sánchez-Romero, María Antonia; Gibert, Marta; Westermann, Alexander J.; Vogel, Jörg; Balsalobre, Carlos (2018): CRP-cAMP mediates silencing of Salmonella virulence at the post-transcriptional level. In: PLoS Genetics 14 (6), e1007401. DOI: 10.1371/journal.pgen.1007401.

Ferhadian, Damien; Contrant, Maud; Printz-Schweigert, Anne; Smyth, Redmond P.; Paillart, Jean-Christophe; Marquet, Roland (2018): Structural and Functional Motifs in Influenza Virus RNAs. In: Frontiers in Microbiology 9, S. 559. DOI: 10.3389/fmicb.2018.00559.

Holmqvist, Erik; Li, Lei; Bischler, Thorsten; Barquist, Lars; Vogel, Jorg (2018): Global Maps of ProQ Binding In Vivo Reveal Target Recognition via RNA Structure and Stability Control at mRNA 3' Ends. In: Molecular Cell 70 (5), 971-982.e6. DOI: 10.1016/j.molcel.2018.04.017.

Holmqvist, Erik; Vogel, Jörg (2018): RNA-binding proteins in bacteria. In: Nature Reviews Microbiology. DOI: 10.1038/s41579-018-0049-5.

Hör, Jens; Gorski, Stanislaw A.; Vogel, Jörg (2018): Bacterial RNA Biology on a Genome Scale. In: Molecular Cell 70 (5), S. 785–799. DOI: 10.1016/j.molcel.2017.12.023.

Kingsley, Robert A.; Langridge, Gemma; Smith, Sarah; Makendi, Carine; Fookes, Maria; Wileman, Tom et al. (2018): Functional analysis of Salmonella Typhi adaptation to survival in water. In: Environmental Microbiology.

Leenay, Ryan T.; Vento, Justin M.; Shah, Malay; Martino, Maria Elena; Leulier, François; Beisel, Chase L. (2018): Genome Editing with CRISPR-Cas9 in Lactobacillus plantarum Revealed That Editing Outcomes Can Vary Across Strains and Between Methods. In: Biotechnology Journal, e1700583. DOI: 10.1002/biot.201700583.

Liao, Chunyu; Slotkowski, Rebecca A.; Achmedov, Tatjana; Beisel, Chase L. (2018): The Francisella novicida Cas12a is sensitive to the structure downstream of the terminal repeat in CRISPR arrays. In: RNA Biology. DOI: 10.1080/15476286.2018.1526537.

Marshall, Ryan; Maxwell, Colin S.; Collins, Scott P.; Jacobsen, Thomas; Luo, Michelle L.; Begemann, Matthew B. et al. (2018): Rapid and Scalable Characterization of CRISPR Technologies Using an E. coli Cell-Free Transcription-Translation System. In: Molecular Cell 69 (1), 146-157.e3. DOI: 10.1016/j.molcel.2017.12.007.

Matsumoto, Saki; Caliskan, Neva; Rodnina, Marina V.; Murata, Asako; Nakatani, Kazuhiko (2018): Small synthetic molecule-stabilized RNA pseudoknot as an activator for -1 ribosomal frameshifting. In: Nucleic Acids Research. DOI: 10.1093/nar/gky689.

Maxwell, Colin S.; Jacobsen, Thomas; Marshall, Ryan; Noireaux, Vincent; Beisel, Chase L. (2018): A detailed cell-free transcription-translation-based assay to decipher CRISPR protospacer-adjacent motifs. In: Methods (San Diego, Calif.) 143, S. 48–57. DOI: 10.1016/j.ymeth.2018.02.016.

Munschauer, Mathias; Vogel, Jörg (2018): Nuclear lncRNA stabilization in the host response to bacterial infection. In: The EMBO Journal 37 (13). DOI: 10.15252/embj.201899875.

Nolan, Laura M.; Whitchurch, Cynthia B.; Barquist, Lars; Katrib, Marilyn; Boinett, Christine J.; Mayho, Matthew et al. (2018): A global genomic approach uncovers novel components for twitching motility-mediated biofilm expansion in Pseudomonas aeruginosa. Online available  https://www.biorxiv.org/content/biorxiv/early/2018/07/19/372805.full.pdf.

Smyth, Redmond P.; Negroni, Matteo; Lever, Andrew M.; Mak, Johnson; Kenyon, Julia C. (2018): RNA Structure - A Neglected Puppet Master for the Evolution of Virus and Host Immunity. In: Front. Immunol. 9, S. 4433. DOI: 10.3389/fimmu.2018.02097.

Smyth, Redmond P.; Smith, Maureen R.; Jousset, Anne-Caroline; Despons, Laurence; Laumond, Geraldine; Decoville, Thomas et al. (2018): 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. In: Nucleic Acids Research 46 (9), e57. DOI: 10.1093/nar/gky152.

Tawk, Caroline; Nigro, Giulia; Rodrigues Lopes, Ines; Aguilar, Carmen; Lisowski, Clivia; Mano, Miguel et al. (2018): Stress-induced host membrane remodeling protects from infection by non-motile bacterial pathogens. In: The EMBO Journal. DOI: 10.15252/embj.201798529.

Westermann, Alexander J.; Vogel, Jörg (2018): Host-Pathogen Transcriptomics by Dual RNA-Seq. In: Methods in Molecular Biology (Clifton, N.J.) 1737, S. 59–75. DOI: 10.1007/978-1-4939-7634-8_4.

Wheeler, Nicole E.; Gardner, Paul P.; Barquist, Lars (2018): Machine learning identifies signatures of host adaptation in the bacterial pathogen Salmonella enterica. In: PLoS Genetics 14 (5), e1007333. DOI: 10.1371/journal.pgen.1007333.

Beisel, Chase (2017): What Is the Role of Circuit Design in the Advancement of Synthetic Biology? Part 1. In: Cell Systems 4 (4), S. 370–372. DOI: 10.1016/j.cels.2017.04.003.

Bernacchi, Serena; Abd El-Wahab, Ekram W.; Dubois, Noé; Hijnen, Marcel; Smyth, Redmond P.; Mak, Johnson et al. (2017): HIV-1 Pr55Gag binds genomic and spliced RNAs with different affinity and stoichiometry. In: RNA Biology 14 (1), S. 90–103. DOI: 10.1080/15476286.2016.1256533.

Caliskan, Neva; Wohlgemuth, Ingo; Korniy, Natalia; Pearson, Michael; Peske, Frank; Rodnina, Marina V. (2017): Conditional Switch between Frameshifting Regimes upon Translation of dnaX mRNA. In: Molecular Cell 66 (4), 558-567.e4. DOI: 10.1016/j.molcel.2017.04.023.

Chao, Yanjie; Li, Lei; Girodat, Dylan; Förstner, Konrad U.; Said, Nelly; Corcoran, Colin et al. (2017): In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways. In: Molecular Cell 65 (1), S. 39–51. DOI: 10.1016/j.molcel.2016.11.002.

Fagen, Jennie R.; Collias, Daphne; Singh, Atul K.; Beisel, Chase L. (2017): Advancing the design and delivery of CRISPR antimicrobials. In: Current Opinion in Biomedical Engineering 4, S. 57–64. DOI: 10.1016/j.cobme.2017.10.001.

Feasey, Nicholas A.; Hadfield, James; Keddy, Karen H.; Dallman, Timothy J.; Jacobs, Jan; Deng, Xiangyu et al. (2017): Erratum: Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings. In: Nature Genetics 49 (4), S. 651. DOI: 10.1038/ng0417-651c.

García-López, Jesús; Larriba, Eduardo; Del Mazo, Jesús (2017): Detection and Characterization of Small Noncoding RNAs in Mouse Gametes and Embryos Prior to Zygotic Genome Activation. In: Methods in Molecular Biology (Clifton, N.J.) 1605, S. 105–120. DOI: 10.1007/978-1-4939-6988-3_7.

Gonzalez, Grecia M.; Hardwick, Steven W.; Maslen, Sarah L.; Skehel, J. Mark; Holmqvist, Erik; Vogel, Jörg et al. (2017): Structure of the Escherichia coli ProQ RNA-binding protein. In: RNA (New York, N.Y.) 23 (5), S. 696–711. DOI: 10.1261/rna.060343.116.

Gorski, Stanislaw A.; Vogel, Jörg; Doudna, Jennifer A. (2017): RNA-based recognition and targeting: sowing the seeds of specificity. In: Nature Reviews Molecular Cell Biology 18 (4), S. 215–228. DOI: 10.1038/nrm.2016.174.

Heidrich, Nadja; Bauriedl, Saskia; Barquist, Lars; Li, Lei; Schoen, Christoph; Vogel, Jorg (2017): The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq. In: Nucleic Acids Research 45 (10), S. 6147–6167. DOI: 10.1093/nar/gkx168.

Leenay, Ryan T.; Beisel, Chase L. (2017): Deciphering, Communicating, and Engineering the CRISPR PAM. In: Journal of Molecular Biology 429 (2), S. 177–191. DOI: 10.1016/j.jmb.2016.11.024.

Marshall, Ryan; Maxwell, Colin S.; Collins, Scott P.; Beisel, Chase L.; Noireaux, Vincent (2017): Short DNA containing ? sites enhances DNA stability and gene expression in E. coli cell-free transcription-translation systems. In: Biotechnology and Bioengineering 114 (9), S. 2137–2141. DOI: 10.1002/bit.26333.

Martino, Maria Elena; Joncour, Pauline; Leenay, Ryan; Gervais, Hugo; Shah, Malay; Hughes, Sandrine et al. (2017): Bacterial adaptation to diet is a key evolutionary force shaping Drosophila-Lactobacillus symbiosis. Online available https://www.biorxiv.org/content/biorxiv/early/2018/02/02/222364.full.pdf.

Michaux, Charlotte; Holmqvist, Erik; Vasicek, Erin; Sharan, Malvika; Barquist, Lars; Westermann, Alexander J. et al. (2017): RNA target profiles direct the discovery of virulence functions for the cold-shock proteins CspC and CspE. In: Proceedings of the National Academy of Sciences of the United States of America 114 (26), S. 6824–6829. DOI: 10.1073/pnas.1620772114.

Ondari, Edna M.; Heath, Jennifer N.; Klemm, Elizabeth J.; Langridge, Gemma; Barquist, Lars; Goulding, David A. et al. (2017): Role of sapA and yfgA in Susceptibility to Antibody-Mediated Complement-Dependent Killing and Virulence of Salmonella enterica Serovar Typhimurium. In: Infection and Immunity 85 (9). DOI: 10.1128/IAI.00419-17.

Saliba, Antoine-Emmanuel; C Santos, Sara; Vogel, Jörg (2017): New RNA-seq approaches for the study of bacterial pathogens. In: Current Opinion in Microbiology 35, S. 78–87. DOI: 10.1016/j.mib.2017.01.001.

Saliba, Antoine-Emmanuel; Westermann, Alexander J.; Vogel, Jörg (2017): Einzelzell-RNA-Sequenzierung beleuchtet den Infektionsprozess. In: Biospektrum 23 (5), S. 525–528. DOI: 10.1007/s12268-017-0836-y.

Sharan, Malvika; Förstner, Konrad U.; Eulalio, Ana; Vogel, Jörg (2017): APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins. In: Nucleic Acids Research 45 (11), e96. DOI: 10.1093/nar/gkx137.

Smirnov, Alexandre; Schneider, Cornelius; Hör, Jens; Vogel, Jörg (2017): Discovery of new RNA classes and global RNA-binding proteins. In: Current Opinion in Microbiology 39, S. 152–160. DOI: 10.1016/j.mib.2017.11.016.

Smirnov, Alexandre; Wang, Chuan; Drewry, Lisa L.; Vogel, Jörg (2017): Molecular mechanism of mRNA repression in trans by a ProQ-dependent small RNA. In: The EMBO Journal 36 (8), S. 1029–1045. DOI: 10.15252/embj.201696127.

Tawk, Caroline; Sharan, Malvika; Eulalio, Ana; Vogel, Jörg (2017): A systematic analysis of the RNA-targeting potential of secreted bacterial effector proteins. In: Scientific Reports 7 (1), S. 9328. DOI: 10.1038/s41598-017-09527-0.

Waller, Matthew C.; Bober, Josef R.; Nair, Nikhil U.; Beisel, Chase L. (2017): Toward a genetic tool development pipeline for host-associated bacteria. In: Current Opinion in Microbiology 38, S. 156–164. DOI: 10.1016/j.mib.2017.05.006.

Westermann, Alexander J.; Barquist, Lars; Vogel, Jörg (2017): Resolving host-pathogen interactions by dual RNA-seq. In: PLoS Pathogens 13 (2), e1006033. DOI: 10.1371/journal.ppat.1006033.

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