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.
Transversal Projects
Projects
Software
Tools
CV
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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2019Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility, PLoS Biol. 2019 Jul;17(7):e3000390.
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2019A 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.
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2019Ultrafast search of all deposited bacterial and viral genomic data, Nat. Biotechnol. 2019 Feb;37(2):152-159.
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2018Genetic exchanges are more frequent in bacteria encoding capsules, PLoS Genet. 2018 12;14(12):e1007862.
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2018CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins, Nucleic Acids Res. 2018 Jul;46(W1):W246-W251.
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2018Host range and genetic plasticity explain the co-existence of integrative and extrachromosomal mobile genetic elements, Mol. Biol. Evol. 2018 Jun;.
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2018Parallels between experimental and natural evolution of legume symbionts, Nat Commun 2018 06;9(1):2264.
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2018Neutral Theory, Microbial Practice: Challenges in Bacterial Population Genetics, Mol. Biol. Evol. 2018 Jun;35(6):1338-1347.
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2018Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement, Microb Biotechnol 2018 01;11(1):3-17.
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2017Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria, Nature Communications 8, 2094..
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