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.
The microbial communities that live with us, the microbiota, are now understood to be a key component of our being, playing roles in metabolism, immunity and behavior. More than a decade has elapsed since […]
INCEPTION – Institut Convergence for the study of Emergence of Pathology Through Individuals and Populations
IINCEPTION Goal The Inception aims to develop a core structure to mobilize data resources, numerical sciences, and fundamental experimental biology in various health issues (Official website here: https://www.inception-program.fr/en). The inception program uses Integrative Biology, […]
LabEx IBEID – Integrative Biology of Emerging Infectious Diseases
Presentation The aim of the Integrative Biology of Emerging Infectious Diseases (IBEID) project, coordinated by Professors Philippe Sansonetti and Pascale Cossart and currently coordinated by Carla Saleh and Philippe Bastin, is to develop a […]
ANR SHAPE: Shaping new rhizobia by experimental evolution
Towards the design of new nitrogen fixing symbionts Elucidate how the capacity to establish a nitrogen fixing symbiosis with legumes has been acquired by new bacterial taxons via a lab-evolution experiment should allow developping […]
ANR Magisbac : Genesis and Maintenance of Bacterial Secondary Chromosomes
Bacterial genomes are mainly composed of two types of replicons: chromosomes and plasmids. Plasmids are accessory mobile genetic elements acquired by horizontal transfer between strains or species. Their domestication by new hosts is of […]
Prokaryotes evolve rapidly new functionalities by horizontal gene transfer delivered by mobile genetic elements (MGE). MGE increase relatedness between individuals and thereby might also promote the establishment of microbial social networks. Many studies have […]
The imprint of growth
Replication-associated gene dosage effects Maximal growth rates are central to microbial life-history strategies because there is a trade-off between fast growth in copiotrophs and scavenging potential in slow-growing oligotrophs. When E. coli’s generation time […]
Bacteriophage–bacteria interactions are affected by phage satellites, elements that exploit phages for transfer between bacteria. Satellites can encode defense systems, antibiotic resistance genes, and virulence factors, but their number and diversity are unknown. We […]
The CRISPRCasFinder program enables the easy detection of CRISPRs and cas genes in user-submitted sequence data (allows sequences up to 50 Mo otherwise download standalone program). This is an update of the CRISPRFinder program […]
PanACoTA: A modular tool for massive microbial comparative genomics
The study of the gene repertoires of microbial species, their pangenomes, has become a key part of microbial evolution and functional genomics. Yet, the increasing number of genomes available complicates the establishment of the […]
IntegronFinder is a program that detects integrons in DNA sequences. The program is available on a webserver (Galaxy), or by command line (IntegronFinder on github). It is now in its second version. Integrons are […]
Scans a set of protein sequences for type IV secretion systems and relaxases using HMM profiles. See Guglielmini et al. (2011) for our criteria to class loci on the basis of this output. Except […]
While there were efficient methods for detecting strict repeats or detecting already characterised repeats, there was no software available for detecting approximate repeats in large DNA sequences allowing for weighted substitutions and indels in […]
Intragenic duplications of genetic material have important biological roles because of their consequences in terms of protein sequence and structure. We developed Swelfe to find internal repeats at three levels. Swelfe quickly identifies statistically […]
Growthpred predicts bacterial minimal doubling times by analysing codon usage bias in genomes and metagenomes. The program takes a set of DNA protein coding sequences, searches for ribosomal protein coding genes and translates all […]
MacSyFinder & MacSyView
Macromolecular System Finder (MacSyFinder) provides a flexible framework to model the properties of molecular systems (cellular machinery or pathway) including their components, evolutionary associations with other systems and genetic architecture. Modelled features also include […]
CapsuleFinder is a program that detects capsule systems with high accuracy in proteic sequences. It is based on the use of HMM profiles for the detection of the essential proteins of capsule biogenesis and requires computational models describing […]
TXSSdb, a database of protein secretion systems
The database TXSSdb includes all results from our works on the detection of protein secretion systems in 1,528 complete genomes of bacteria with diderm-LPS cellular enveloppes. It is by far the most complete database […]
TXSScan – models and profiles for protein secretion systems
Protein secretion systems are key virulence factors of all major bacterial pathogens with an LPS-containing outer membrane: Shigella, Escherichia coli, Yersinia pestis, Salmonella, Pseudomonas aeruginosa, Helicobacter pylori, Vibrio cholerae, etc. Protein secretion systems are […]
Secreton – Non-Flagellar Type III Secretion Systems in sequenced genomes
Warning: This data is old and the site will be discontinued soon. We are working on an alternative. Non-Flagellar Type III Secretion Systems (NF-T3SS, or injectisomes) are bacterial machineries partially homologous to the bacterial […]
ConjDB – a database of conjugative & mobilization systems and T4SS
Warning: This data is old and the site will be discontinued soon. We are working on an alternative. This website allows to query a dataset of 947 conjugative systems, 646 non-conjugative T4SS and 1,180 […]
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).
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⟩.
2023Competition between lysogenic and sensitive bacteria is determined by the fitness costs of the different emerging phage-resistance strategies., Elife 2023 Mar; 12(): .
2023Identification and characterization of thousands of bacteriophage satellites across bacteria., Nucleic Acids Res 2023 Mar; (): .
2022Origins of transfer establish networks of functional dependencies for plasmid transfer by conjugation., Nucleic Acids Res 2022 Nov; (): .
2022Structural and Genomic Evolution of RRNPPA Systems and Their Pheromone Signaling., mBio 2022 Oct; (): e0251422.
2022Phage-Plasmids Spread Antibiotic Resistance Genes through Infection and Lysogenic Conversion., mBio 2022 Sep; (): e0185122.
2022Adaptation to novel spatially-structured environments is driven by the capsule and alters virulence-associated traits., Nat Commun 2022 Aug; 13(1): 4751.
2022Evolution of Plasmid Mobility: Origin and Fate of Conjugative and Nonconjugative Plasmids., Mol Biol Evol 2022 Jun; 39(6): .
2022Phages and their satellites encode hotspots of antiviral systems., Cell Host Microbe 2022 May; 30(5): 740-753.e5.
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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