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.
INCEPTION – Institut Convergence for the study of Emergence of Pathology Through Individuals and Populations
IINCEPTION Goal The Inception’s goal is to develop a core structure to mobilize data resources, numerical sciences, and fundamental experimental biology in a range of health issues. Inception program uses Integrative Biology, Social Science […]
SPARK: Transmission of multidrug resistant Klebsiella clones and genes – a One Health approach
The SPARK (Spread of Population-wide Antibiotic Resistance in Klebsiella) project, funded by the JPIAMR instrument of the European Union H2020 programme, seeks to address the complex issue of transmission of antimicrobial resistance genes and […]
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 […]
Population biology of the bacterial pathogen Klebsiella pneumoniae
Klebsiella pneumoniae is one of the most urgent threats to public health given its increasing resistance to antimicrobial agents including carbapenems, considered as last-resort antibiotics. In this project we aim to understand the ecological, epidemiological and […]
Selection and mutation in bacteria Evolution is an intrinsically stochastic process that involves a time lag between the generation of the polymorphisms and their moderation by selection. During the very initial stages of sequence […]
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 […]
DNA repeats and genome dynamics
The evolutionary roles of repeats Stress is often faced in nature, whether from lack of nutrients, arrival of competitors or predators, or the presence of toxic substances. The survival of stressed organisms can be […]
Horizontal gene transfer
Inter-species horizontal transfer Tuberculosis was initially considered as a clonal population with no known acquisition of genetic material by horizontal genetic transfer, although it carries IS elements with similarity to IS elements from other […]
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). Integrons are major genetic element, notorious for their major […]
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 […]
T3SSscan and FLAGscan use hmm profiles to scan a set of bacterial protein sequences for the presence of key components of: non-flagellar type III secretion systems (“NF-T3SS” database), flagella (“Flagellum”) or both (“NF-T3SS+Flagellum”).Eight proteins […]
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
Non-Flagellar Type III Secretion Systems (NF-T3SS, or injectisomes) are bacterial machineries partially homologous to the bacterial flagellum, which allow direct injection of bacterial effectors from bacterial cytoplasm to eukaryotic cells via a molecular needle […]
ConjDB – a database of conjugative & mobilization systems and T4SS
This website allows to query a dataset of 947 conjugative systems, 646 non-conjugative T4SS and 1,180 mobilization systems retrieved from 2,269 complete genome sequences. These systems were detected with protein profiles of T4SS components, […]
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).
2019Ultrafast search of all deposited bacterial and viral genomic data, Nat. Biotechnol. 2019 Feb;37(2):152-159.
2018Genetic exchanges are more frequent in bacteria encoding capsules, PLoS Genet. 2018 12;14(12):e1007862.
2018HflXr, a homolog of a ribosome-splitting factor, mediates antibiotic resistance, Proc. Natl. Acad. Sci. U.S.A. 2018 12;115(52):13359-13364.
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.
2018Host range and genetic plasticity explain the co-existence of integrative and extrachromosomal mobile genetic elements, Mol. Biol. Evol. 2018 Jun;.
2018Parallels between experimental and natural evolution of legume symbionts, Nat Commun 2018 06;9(1):2264.
2018Neutral Theory, Microbial Practice: Challenges in Bacterial Population Genetics, Mol. Biol. Evol. 2018 Jun;35(6):1338-1347.
2018Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement, Microb Biotechnol 2018 01;11(1):3-17.
2017Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria, Nature Communications 8, 2094..
2017The chromosomal organization of horizontal gene transfer in bacteria, Nat Commun 2017 Oct;8(1):841.
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