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Consequences of Cas9 cleavage in the chromosome of Escherichia coli

 Lun Cui , David Bikard
Nucleic Acids Research, 2016, 44 (9), pp.4243-4251. ⟨10.1093/nar/gkw223⟩
Article dans une revue pasteur-01967442v1
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The impact of genetic diversity on gene essentiality within the E. coli species

 François Rousset , José Cabezas Caballero , Florence Piastra-Facon , Jesús Fernández-Rodríguez , Olivier Clermont , et al.
Nature Microbiology, 2021, 6 (3), pp.301-312. ⟨10.1038/s41564-020-00839-y⟩
Article dans une revue pasteur-03264663v1
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Cas9 off-target binding to the promoter of bacterial genes leads to silencing and toxicity

 William Rostain , Theophile Grebert , Danylo Vyhovskyi , Paula Thiel Pizarro , Gatwa Tshinsele-van Bellingen , et al.
Nucleic Acids Research, 2023, 51 (7), pp.3485-3496. ⟨10.1093/nar/gkad170⟩
Article dans une revue pasteur-04130634v1

Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials

 David Bikard , Chad Euler , Wenyan Jiang , Nussenzweig Philip , Gregory Goldberg , et al.
Nature Biotechnology, 2014, 32 (11), pp.5. ⟨10.1038/nbt.3043⟩
Article dans une revue hal-01103559v1
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A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9

 Lun Cui , Antoine Vigouroux , François Rousset , Hugo Varet , Varun Khanna , et al.
Nature Communications, 2018, 9 (1), pp.1912. ⟨10.1038/s41467-018-04209-5⟩
Article dans une revue pasteur-01819630v1
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Phages and their satellites encode hotspots of antiviral systems

 François Rousset , Florence Depardieu , Solange Miele , Julien Dowding , Anne-Laure Laval , et al.
Cell Host & Microbe, 2022, 30 (5), pp.740 - 753.e5. ⟨10.1016/j.chom.2022.02.018⟩
Article dans une revue pasteur-04075930v1
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Genome-wide CRISPR-Cas9 screen in E. coli identifies design rules for efficient targeting

 Belen Gutierrez , Jérôme Wong Ng , Lun Cui , Christophe Becavin , David Bikard
2020
Pré-publication, Document de travail pasteur-02486815v1
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Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance

 Céline Loot , Aleksandra Nivina , Jean Cury , José Antonio Escudero , Magaly Ducos-Galand , et al.
mBio, 2017, 8 (2), pp.e02296-16. ⟨10.1128/mBio.02296-16⟩
Article dans une revue pasteur-01689524v1
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A Eukaryotic-like Serine/Threonine Kinase Protects Staphylococci against Phages

 Florence Depardieu , Jean-Philippe Didier , Aude Bernheim , Andrew Sherlock , Henrik Molina , et al.
Cell Host and Microbe, 2016, 20 (4), pp.471 - 481. ⟨10.1016/j.chom.2016.08.010⟩
Article dans une revue pasteur-01402430v1
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Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria

 Aude Bernheim , Alicia Calvo-Villamañán , Clovis Basier , Lun Cui , Eduardo P C Rocha , et al.
Nature Communications, 2017, 8, pp.2094. ⟨10.1038/s41467-017-02350-1⟩
Article dans une revue pasteur-01967501v1
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Microbial-derived products as potential new antimicrobials

 Bruce S. Seal , Djamel Drider , Brian B. Oakley , Harald Brüssow , David Bikard , et al.
Veterinary Research, 2018, 49 (1), pp.66. ⟨10.1186/s13567-018-0563-5⟩
Article dans une revue hal-02973515v1
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The synthetic integron: an in vivo genetic shuffling device

 David Bikard , Stéphane Julié-Galau , Guillaume Cambray , Didier Mazel
Nucleic Acids Research, 2010, 38 (15), ⟨10.1093/nar/gkq511⟩
Article dans une revue hal-01876815v1

Divergent evolution of duplicate genes leads to genetic incompatibilities within A. thaliana

 David Bikard , Dhaval Patel , Claire Le Mette , Veronica Giorgi , Christine Camilleri , et al.
Science, 2009, 323, pp.623-626. ⟨10.1126/science.1165917⟩
Article dans une revue hal-01203956v1
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Shuffling of DNA cassettes in a synthetic integron

 David Bikard , Didier Mazel
Karen M. Polizzi; Cleo Kontoravdi. Synthetic Biology, 1073, Humana Press, pp.169-174, 2013, Methods in Molecular Biology (MIMB), 978-1-62703-624-5 (Hardcover), 978-1-4939-6286-0 (Softcover), 978-1-62703-625-2 (eBook). ⟨10.1007/978-1-62703-625-2_14⟩
Chapitre d'ouvrage pasteur-01698800v1
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Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors

 Francois Rousset , Lun Cui , Elise Siouve , Christophe Bécavin , Florence Depardieu , et al.
PLoS Genetics, 2018, 14 (11), pp.e1007749. ⟨10.1371/journal.pgen.1007749⟩
Article dans une revue pasteur-01975438v1
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Lipoprotein DolP supports proper folding of BamA in the bacterial outer membrane promoting fitness upon envelope stress

 David Ranava , Yiying Yang , Luis Orenday-Tapia , François Rousset , Catherine Turlan , et al.
eLife, 2021, 10, pp.e67817. ⟨10.7554/eLife.67817⟩
Article dans une revue hal-03396730v1
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Outer membrane lipoprotein DolP interacts with the BAM complex and promotes fitness during envelope stress response

 David Ranava , Yiying Yang , Luis Orenday-Tapia , François Rousset , Catherine Turlan , et al.
2020
Pré-publication, Document de travail hal-03039259v1
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A matter of background: DNA repair pathways as a possible cause for the sparse distribution of CRISPR-Cas systems in bacteria

 Aude Bernheim , David Bikard , Marie Touchon , Eduardo P C Rocha
Philosophical Transactions of the Royal Society B: Biological Sciences, 2019, 374 (1772), pp.20180088. ⟨10.1098/rstb.2018.0088⟩
Article dans une revue hal-02329742v1
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Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements

 Aude Bernheim , David Bikard , Marie Touchon , Eduardo Rocha
Nucleic Acids Research, 2020, 48, pp.748 - 760. ⟨10.1093/nar/gkz1091⟩
Article dans une revue pasteur-02626502v1
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The integron integrase efficiently prevents the melting effect of Escherichia coli single-stranded DNA-binding protein on folded attC sites.

 Céline Loot , Vincent Parissi , José Antonio Escudero , Jihane Amarir-Bouhram , David Bikard , et al.
Journal of Bacteriology, 2014, 196 (4), pp.762-771. ⟨10.1128/JB.01109-13⟩
Article dans une revue hal-01101080v1
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Cellular pathways controlling integron cassette site folding

 Céline Loot , David Bikard , Anna Rachlin , Didier Mazel
EMBO Journal, 2010, 29 (15), pp.2623-2634. ⟨10.1038/emboj.2010.151⟩
Article dans une revue pasteur-02477658v1

Cas9 specifies functional viral targets during CRISPR–Cas adaptation

 Robert Heler , Poulami Samai , Joshua W. Modell , Catherine Weiner , Gregory W. Goldberg , et al.
Nature, 2015, 519 (7542), pp.199-202. ⟨10.1038/nature14245⟩
Article dans une revue pasteur-02505374v1
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CRISPR screens in the era of microbiomes

 François Rousset , David Bikard
Current Opinion in Microbiology, 2020, 57, pp.70-77. ⟨10.1016/j.mib.2020.07.009⟩
Article dans une revue pasteur-02978339v1
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Tuning dCas9's ability to block transcription enables robust, noiseless knockdown of bacterial genes

 Antoine Vigouroux , Enno Oldewurtel , Lun Cui , Sven van Teeffelen , David Bikard
Molecular Systems Biology, 2018, 14 (3), pp.e7899. ⟨10.15252/msb.20177899⟩
Article dans une revue pasteur-01967521v1
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Generating functional protein variants with variational autoencoders

 Alex Hawkins-Hooker , Florence Depardieu , Sebastien Baur , Guillaume Couairon , Arthur Chen , et al.
PLoS Computational Biology, 2021, 17 (2), pp.e1008736. ⟨10.1371/journal.pcbi.1008736⟩
Article dans une revue pasteur-03263932v1
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PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data

 Julian Garneau , Florence Depardieu , Louis-Charles Fortier , David Bikard , Marc Monot
Scientific Reports, 2017, 7 (1), pp.8292. ⟨10.1038/s41598-017-07910-5⟩
Article dans une revue pasteur-01613364v1
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Conjugative DNA transfer induces the bacterial SOS response and promotes antibiotic resistance development through integron activation

 Zeynep Baharoglu , David Bikard , Didier Mazel
PLoS Genetics, 2010, 6 (10), pp.e1001165. ⟨10.1371/journal.pgen.1001165⟩
Article dans une revue pasteur-02477623v1
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Gene silencing with CRISPRi in bacteria and optimization of dCas9 expression levels

 Florence Depardieu , David Bikard
Methods, 2020, 172, pp.61-75. ⟨10.1016/j.ymeth.2019.07.024⟩
Article dans une revue pasteur-02476079v1
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Folded DNA in Action: Hairpin Formation and Biological Functions in Prokaryotes

 David Bikard , Céline Loot , Zeynep Baharoglu , Didier Mazel
Microbiology and Molecular Biology Reviews, 2010, 74 (4), pp.570-588. ⟨10.1128/MMBR.00026-10⟩
Article dans une revue pasteur-02505407v1
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Editing the microbiome the CRISPR way

 Gayetri Ramachandran , David Bikard
Philosophical Transactions of the Royal Society B: Biological Sciences, 2019, 374 (1772), pp.20180103. ⟨10.1098/rstb.2018.0103⟩
Article dans une revue hal-02470706v1
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