• 2023
  Rostain W, Grebert T, Vyhovskyi D, Pizarro PT, Tshinsele-Van Bellingen G, Cui L, Bikard D, Cas9 off-target binding to the promoter of bacterial genes leads to silencing and toxicity., Nucleic Acids Res 2023 Mar; (): .
• 2022
  Rousset F, Depardieu F, Miele S, Dowding J, Laval AL, Lieberman E, Garry D, Rocha EPC, Bernheim A, Bikard D, , Phages and their satellites encode hotspots of antiviral systems., Cell Host Microbe 2022 May; 30(5): 740-753.e5.
• 2021
  Julian R. Garneau, Véronique Legrand, Martial Marbouty, Maximilian O. Press, Dean R. Vik, Louis-Charles Fortier, Matthew B. Sullivan, David Bikard , Marc Monot, High‑throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome, Sci Rep 11, 18319 (2021)..
• 2021
  Malbranke C, Bikard D, Cocco S, Monasson R, Improving sequence-based modeling of protein families using secondary structure quality assessment., Bioinformatics 2021 Jun; (): .
• 2021
  Ranava D, Yang Y, Orenday-Tapia L, Rousset F, Turlan C, Morales V, Cui L, Moulin C, Froment C, Munoz G, Rech J, Marcoux J, Caumont-Sarcos A, Albenne C, Bikard D, Ieva R, , Lipoprotein DolP supports proper folding of BamA in the bacterial outer membrane, promoting fitness upon envelope stress., Elife 2021 Apr; 10(): .
• 2021
  Rousset F, Cabezas-Caballero J, Piastra-Facon F, Fernández-Rodríguez J, Clermont O, Denamur E, Rocha EPC, Bikard D, , The impact of genetic diversity on gene essentiality within the Escherichia coli species., Nat Microbiol 2021 03; 6(3): 301-312.
• 2021
  Hawkins-Hooker A, Depardieu F, Baur S, Couairon G, Chen A, Bikard D, , Generating functional protein variants with variational autoencoders., PLoS Comput Biol 2021 Feb; 17(2): e1008736.
• 2020
  Nivina A, Grieb MS, Loot C, Bikard D, Cury J, Shehata L, Bernardes J, Mazel D, , Structure-specific DNA recombination sites: Design, validation, and machine learning-based refinement., Sci Adv 2020 Jul; 6(30): eaay2922.
• 2020
  Calvo-Villamañán A, Ng JW, Planel R, Ménager H, Chen A, Cui L, Bikard D, On-target activity predictions enable improved CRISPR-dCas9 screens in bacteria, Nucleic Acids Res. 2020 Apr;.
• 2020
  Bernheim A, Bikard D, Touchon M, Rocha EPC, Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements, Nucleic Acids Res. 2020 Jan;48(2):748-760.
• 2020
  A. Vigouroux, Cordier B., Aristov A., Alvarez L., Özbaykal G., Chaze T., Oldewurtel E.R., Matondo M., Cava F., Bikard D., van Teeffelen S., Class-A penicillin binding proteins do not contribute to cell shape but repair cell-wall defects, eLife 2020;9:e51998.
• 2019
  Depardieu F, Bikard D, Gene silencing with CRISPRi in bacteria and optimization of dCas9 expression levels, Methods 2019 Aug;.
• 2019
  Ramachandran G, Bikard D, Editing the microbiome the CRISPR way, Philos. Trans. R. Soc. Lond., B, Biol. Sci. 2019 May;374(1772):20180103.
• 2019
  Bernheim A, Bikard D, Touchon M, Rocha EPC, A matter of background: DNA repair pathways as a possible cause for the sparse distribution of CRISPR-Cas systems in bacteria, Philos. Trans. R. Soc. Lond., B, Biol. Sci. 2019 May;374(1772):20180088.
• 2018
  François Rousset, Lun Cui, Elise Siouve, Christophe Becavin, Florence Depardieu, David Bikard, Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors, PLOS Genetics 14(11): e1007749..
• 2018
  Cui L, Vigouroux A, Rousset F, Varet H, Khanna V, Bikard D, A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9, Nat Commun. 2018 May 15;9(1):1912. doi: 10.1038/s41467-018-04209-5.
• 2018
  Vigouroux A, Oldewurtel ER, Cui L, Bikard D and van Teeffelen S, Tuning dCas9’s ability to block transcription enables robust, noiseless knockdown of bacterial genes, Molecular Systems Biology (2018) 14, e7899.
• 2017
  Aude Bernheim, Alicia Calvo Villamanan, Clovis Basier, Lun Cui, Eduardo P. C. Rocha, Marie Touchon, David Bikard, Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria, Nature Communications 8, 2094..
• 2017
  Garneau JR, Depardieu F, Fortier LC, Bikard D, Monot M, PhageTerm: a tool for fast and accurate determination of phage termini and packaging mechanism using next-generation sequencing data, Sci Rep 2017 Aug;7(1):8292.
• 2017
  David Bikard, Rodolphe Barrangou, Using CRISPR-Cas systems as antimicrobials, Current Opinion in Microbiology 2017, 37:155–160.
• 2017
  Loot C, Nivina A, Cury J, Escudero JA, Ducos-Galand M, Bikard D, Rocha EP, Mazel D, Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance, MBio 2017 Mar;8(2).
• 2017
  R Heler, AV Wright, M Vucelja, D Bikard, JA Doudna, LA Marraffini, Mutations in Cas9 Enhance the Rate of Acquisition of Viral Spacer Sequences during the CRISPR-Cas Immune Response, Molecular Cell 65 (1), 168-175.
• 2016
  Depardieu F, Didier JP, Bernheim A, Sherlock A, Molina H, Duclos B, Bikard D, A Eukaryotic-like Serine/Threonine Kinase Protects Staphylococci against Phages, Cell Host Microbe 2016 Sep;.
• 2016
  Cui L, Bikard D, Consequences of Cas9 cleavage in the chromosome of Escherichia coli, Nucleic Acids Res. 2016 Apr;.
• 2015
  Heler R, Marraffini LA, Bikard D, Adapting to new threats: the generation of memory by CRISPR-Cas immune systems, Mol. Microbiol. 2014 Jul;93(1):1-9.
• 2015
  Heler R, Samai P, Modell JW, Weiner C, Goldberg GW, Bikard D, Marraffini LA, Cas9 specifies functional viral targets during CRISPR-Cas adaptation, Nature 2015 Mar;519(7542):199-202.
• 2014
  Bikard D, Euler CW, Jiang W, Nussenzweig PM, Goldberg GW, Duportet X, Fischetti VA, Marraffini LA, Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials, Nat. Biotechnol. 2014 Nov;32(11):1146-50.
• 2014
  Goldberg GW, Jiang W, Bikard D, Marraffini LA, Conditional tolerance of temperate phages via transcription-dependent CRISPR-Cas targeting, Nature 2014 Oct;514(7524):633-7.
• 2013
  Loot C, Parissi V, Escudero JA, Amarir-Bouhram J, Bikard D, Mazel D, The integron integrase efficiently prevents the melting effect of Escherichia coli single-stranded DNA-binding protein on folded attC sites, J. Bacteriol. 2014 Feb;196(4):762-71.
• 2013
  Bikard D, Marraffini LA, Control of gene expression by CRISPR-Cas systems, F1000Prime Rep 2013;5:47.
• 2013
  Bikard D, Jiang W, Samai P, Hochschild A, Zhang F, Marraffini LA, Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system, Nucleic Acids Res. 2013 Aug;41(15):7429-37.
• 2013
  Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA, RNA-guided editing of bacterial genomes using CRISPR-Cas systems, Nat. Biotechnol. 2013 Mar;31(3):233-9.
• 2013
  Bikard D, Mazel D, Shuffling of DNA cassettes in a synthetic integron, Methods Mol. Biol. 2013;1073:169-74.
• 2012
  Bikard D, Hatoum-Aslan A, Mucida D, Marraffini LA, CRISPR interference can prevent natural transformation and virulence acquisition during in vivo bacterial infection, Cell Host Microbe 2012 Aug;12(2):177-86.
• 2011
  Bikard D, Marraffini LA, Innate and adaptive immunity in bacteria: mechanisms of programmed genetic variation to fight bacteriophages, Curr. Opin. Immunol. 2012 Feb;24(1):15-20.
• 2010
  Loot C, Bikard D, Rachlin A, Mazel D, Cellular pathways controlling integron cassette site folding, EMBO J. 2010 Aug;29(15):2623-34.
• 2010
  Bikard D, Julié-Galau S, Cambray G, Mazel D, The synthetic integron: an in vivo genetic shuffling device, Nucleic Acids Res. 2010 Aug;38(15):e153.
• 2009
  Bouvier M, Ducos-Galand M, Loot C, Bikard D, Mazel D, Structural features of single-stranded integron cassette attC sites and their role in strand selection, PLoS Genet. 2009 Sep;5(9):e1000632.
• 2008
  Bikard D, Képès F, , [First French team success during iGEM synthetic biology competition], Med Sci (Paris) 2008 May;24(5):541-4.