• 2025
  , Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems, Science, 388, 6747, (2025)..
• 2025
  Darracq B, Littner E, Brunie M, Bos J, Kaminski PA, Depardieu F, Slesak W, Debatisse K, Touchon M, Bernheim A, Bikard D, Le Roux F, Mazel D, Rocha EPC, Loot C, Sedentary chromosomal integrons as biobanks of bacterial antiphage defense systems., Science, 2025 May; 388(6747): eads0768.
• 2025
  Vendrell-Fernández S, Beamud B, Abou Haydar Y, Am de Sousa J, Burlaud-Gaillard J, Kornobis E, Raynal B, Vinh J, Bikard D, Ghigo JM, Incomplete lytic cycle of a widespread Bacteroides bacteriophage leads to the formation of defective viral particles., PLoS Biol 2025 Mar; 23(3): e3002787.
• 2024
  Guzmán-Herrador DL, Fernández-Gómez A, Depardieu F, Bikard D, Llosa M, Delivery of functional Cas:DNA nucleoprotein complexes into recipient bacteria through a type IV secretion system., Proc Natl Acad Sci U S A 2024 Oct; 121(43): e2408509121.
• 2024
  Nathaniel Burman, Svetlana Belukhina, Florence Depardieu, Royce Wilkinson, Mikhail Skutel, Andrew Santiago-Frangos, Ava Graham, Alexei Livenskyi, Anna Chechenina, Natalia Morozova, Trevor Zahl, William Henriques, Murat Buyukyoruk, Christophe Rouillon, Baptiste Saudemont, Lena Shyrokova, Tatsuaki Kurata, Vasili Hauryliuk, Konstantin Severinov, Justine Groseille, Agnès Thierry, Romain Koszul, Florian Tesson, Aude Bernheim, David Bikard, Blake Wiedenheft, Artem Isaev, A virally encoded tRNA neutralizes the PARIS antiviral defence system, Nature, 2024, 634 (8033), pp.424-431. ⟨10.1038/s41586-024-07874-3⟩.
• 2024
  Brödel AK, Charpenay LH, Galtier M, Fuche FJ, Terrasse R, Poquet C, Havránek J, Pignotti S, Krawczyk A, Arraou M, Prevot G, Spadoni D, Yarnall MTN, Hessel EM, Fernandez-Rodriguez J, Duportet X, Bikard D, In situ targeted base editing of bacteria in the mouse gut., Nature 2024 Aug; 632(8026): 877-884.
• 2024
  Benz F, Camara-Wilpert S, Russel J, Wandera KG, Čepaitė R, Ares-Arroyo M, Gomes-Filho JV, Englert F, Kuehn JA, Gloor S, Mestre MR, Cuénod A, Aguilà-Sans M, Maccario L, Egli A, Randau L, Pausch P, Rocha EPC, Beisel CL, Madsen JS, Bikard D, Hall AR, Sørensen SJ, Pinilla-Redondo R, Type IV-A3 CRISPR-Cas systems drive inter-plasmid conflicts by acquiring spacers in trans., Cell Host Microbe 2024 May; (): .
• 2024
  Vialetto E, Miele S, Goren MG, Yu J, Yu Y, Collias D, Beamud B, Osbelt L, Lourenço M, Strowig T, Brisse S, Barquist L, Qimron U, Bikard D, Beisel CL, Systematic interrogation of CRISPR antimicrobials in Klebsiella pneumoniae reveals nuclease-, guide- and strain-dependent features influencing antimicrobial activity., Nucleic Acids Res 2024 Jun; 52(10): 6079-6091.
• 2024
  Egill Richard, Baptiste Darracq, Eloi Littner, Claire Vit, Clémence Whiteway, Julia Bos, Florian Fournes, Geneviève Garriss, Valentin Conte, Delphine Lapaillerie, Vincent Parissi, François Rousset, Ole Skovgaard, David Bikard, Eduardo P. C. Rocha, Didier Mazel, Céline Loot, Cassette recombination dynamics within chromosomal integrons are regulated by toxin-antitoxin systems., Science Advances , 2024, 10 (2), pp.eadj3498. ⟨10.1126/sciadv.adj3498⟩.
• 2023
  Malbranke C, Rostain W, Depardieu F, Cocco S, Monasson R, Bikard D, Computational design of novel Cas9 PAM-interacting domains using evolution-based modelling and structural quality assessment., PLoS Comput Biol 2023 Nov; 19(11): e1011621.
• 2023
  Malbranke C, Bikard D, Cocco S, Monasson R, Tubiana J, Machine learning for evolutionary-based and physics-inspired protein design: Current and future synergies., Curr Opin Struct Biol 2023 Jun; 80(): 102571.
• 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
  François Rousset, Florence Depardieu, Solange Miele, Julien Dowding, Anne-Laure Laval, Erica Lieberman, Daniel Garry, Eduardo P. C. Rocha, Aude Bernheim, David Bikard, Phages and their satellites encode hotspots of antiviral systems, Cell Host & Microbe, 2022, 30 (5), pp.740 - 753.e5. ⟨10.1016/j.chom.2022.02.018⟩.
• 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
  Aleksandra Nivina, Maj Svea Grieb, Céline Loot, David Bikard, Jean Cury, Laila Shehata, Juliana Bernardes, Didier Mazel, Structure-specific DNA recombination sites: Design, validation, and machine learning–based refinement, Science Advances , 2020, 6 (30), pp.eaay2922. ⟨10.1126/sciadv.aay2922⟩.
• 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
  Aude Bernheim, David Bikard, Marie Touchon, Eduardo Rocha, Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements, Nucleic Acids Research, 2020, 48, pp.748 - 760. ⟨10.1093/nar/gkz1091⟩.
• 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
  Aude Bernheim, David Bikard, Marie Touchon, Eduardo P C Rocha, A matter of background: DNA repair pathways as a possible cause for the sparse distribution of CRISPR-Cas systems in bacteria, Philosophical Transactions of the Royal Society B: Biological Sciences, 2019, 374 (1772), pp.20180088. ⟨10.1098/rstb.2018.0088⟩.
• 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
  Céline Loot, Aleksandra Nivina, Jean Cury, José Antonio Escudero, Magaly Ducos-Galand, David Bikard, Eduardo P C Rocha, Didier Mazel, Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance., mBio, 2017, 8 (2), pp.e02296-16. ⟨10.1128/mBio.02296-16⟩.
• 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.
• 2014
  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
  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.
• 2008
  Bikard D, Képès F, , [First French team success during iGEM synthetic biology competition], Med Sci (Paris) 2008 May;24(5):541-4.