My work focuses on the interplay between the organisation of genomes arising by the chromosomal interactions of cellular processes and the recombination processes generating adaptive genetic variation. Genetic elements tend to be organized in genomes by natural selection in order to optimize this highly complex structure. Yet, they are also constantly faced with genomic variations including mutations, amplifications, rearrangements and horizontal gene transfer. I study the conflict between organisational features and the adaptive plasticity of genomes and how it determines genome evolution and ecological adaptation.
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About
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Since 2023 – Head of the UMR3525 CNRS/Institut Pasteur
2019-2023 – Head of the Genomes & Genetics department at Pasteur Institute.
Since 2013 – Head of the unit Microbial Evolutionary Genomics at Pasteur Institute.
Since 2009 – Senior researcher (DR2 then DR1) at the UMR3525 CNRS in Pasteur Institute.
2016-2017 – Member of the COMESP (president SC5)
2015-17 – Associate director for research of the C3BI (Pasteur Institute).
2012-16– President of the CID51 of the National Research Committee (CoNRS).
2010-2015 – Associate director of the GdR BIM.
2008 to 2012– Head junior team Microbial Evolutionary Genomics in URA2171 and UMR3525.
2005– Habilitation in Biology (U Pierre et Marie Curie, Paris).
2000 to 2009– Junior researcher (CR) at the URA2171 CNRS in the Atelier de BioInformatique at UPMC and at Pasteur Institute.
2000– PhD in BioInformatics (U Versailles Saint–Quentin en Yvelines, France).
1997– MSc in Applied Mathematics (Lisbon Technical U, Portugal).
1995– BSc and MSc in Chemical Engineering/Biotechnology (Lisbon Technical U, Portugal).
Publications
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2023Latent evolution of biofilm formation depends on life-history and genetic background, npj Biofilms and Microbiomes, 2023, 9 (1), pp.53. ⟨10.1038/s41522-023-00422-3⟩.
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2023Competition between lysogenic and sensitive bacteria is determined by the fitness costs of the different emerging phage-resistance strategies., Elife 2023 Mar; 12(): .
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2023Identification and characterization of thousands of bacteriophage satellites across bacteria., Nucleic Acids Res 2023 Mar; (): .
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2022Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation., Nucleic Acids Res 2022 Nov; (): .
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2022Structural and Genomic Evolution of RRNPPA Systems and Their Pheromone Signaling., mBio 2022 Oct; (): e0251422.
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2022Phage-Plasmids Spread Antibiotic Resistance Genes through Infection and Lysogenic Conversion., mBio 2022 Sep; (): e0185122.
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2022Adaptation to novel spatially-structured environments is driven by the capsule and alters virulence-associated traits., Nat Commun 2022 Aug; 13(1): 4751.
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2022Evolution of Plasmid Mobility: Origin and Fate of Conjugative and Nonconjugative Plasmids., Mol Biol Evol 2022 Jun; 39(6): .
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2022Phages and their satellites encode hotspots of antiviral systems., Cell Host Microbe 2022 May; 30(5): 740-753.e5.
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2022To catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites., Philos Trans R Soc Lond B Biol Sci 2022 Jan; 377(1842): 20200475.
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