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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Since 2019 – 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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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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2021Interplay between the cell envelope and mobile genetic elements shapes gene flow in populations of the nosocomial pathogen Klebsiella pneumoniae., PLoS Biol 2021 Jul; 19(7): e3001276.
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2021Bacteria have numerous distinctive groups of phage-plasmids with conserved phage and variable plasmid gene repertoires., Nucleic Acids Res 2021 03; 49(5): 2655-2673.
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2021Nutrient conditions are primary drivers of bacterial capsule maintenance in Klebsiella, Proc. R. Soc. B.288:20202876.
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2021The impact of genetic diversity on gene essentiality within the Escherichia coli species., Nat Microbiol 2021 03; 6(3): 301-312.
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2021Causes and consequences of bacteriophage diversification via genetic exchanges across lifestyles and bacterial taxa., Mol Biol Evol 2021 Feb; (): .
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2020Modular prophage interactions driven by capsule serotype select for capsule loss under phage predation, ISME J (2020). https://doi.org/10.1038/s41396-020-0726-z.
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2020Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids., Nat Commun 2020 07; 11(1): 3602.
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2020A synthesis of bacterial and archaeal phenotypic trait data., Sci Data 2020 06; 7(1): 170.
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2020Phylogenetic background and habitat drive the genetic diversification of Escherichia coli., PLoS Genet. 2020 Jun; 16(6): e1008866.
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