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.
A population biology study of Listeria ushers in a new era in listeriosis surveillance
Seminar “The Evolution of Bacteria Genes and Genomes”
Howard OCHMAN Department of Integrative Biology – University of Texas, Austin, USA Séminaire organisé par le Département GENOMES & GENETIQUE What have we learned from the sequencing of tens of thousands of bacterial genomes? […]
Inception – Institut Convergence for the study of Emergence of Pathology Through Individuals and Populations
Inception 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 […]
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 bacteriaEvolution 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 diversification […]
The imprint of growth
Replication-associated gene dosage effectsMaximal 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 decreases […]
DNA repeats and genome dynamics
The evolutionary roles of repeatsStress 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 facilitated […]
Horizontal gene transfer
Inter-species horizontal transferTuberculosis 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 species. […]
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 genes […]
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 […]
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, […]
2015-… – Associate director for research of the C3BI (Pasteur Institute).
2013-… – Head of the unit Microbial Evolutionary Genomics at Pasteur Institute.
2012-…– President of the CID51 of the National Research Committee (CoNRS).
2010-2015 – Associate director of the GdR BIM.
2009- … – Senior researcher (DR2 then DR1) at the UMR3525 CNRS in Pasteur Institute.
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).
2016Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes, Nat Microbiol 2016 Oct;2:16185.
2016Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis, Sci Rep 2016;6:30379.
2016Regulation of genetic flux between bacteria by restriction-modification systems., Proc Natl Acad Sci U S A. 2016 May 17;113(20):5658-63. doi: 10.1073/pnas.1603257113. .
2016Identification and analysis of integrons and cassette arrays in bacterial genomes., Nucleic Acids Res. 2016 Apr 29. pii: gkw319..
2016Genetic and life-history traits associated with the distribution of prophages in bacteria., ISME J. 2016 Mar 25. doi: 10.1038/ismej.2016.47. .
2016Using Sex to Cure the Genome, PLoS Biol 14(3): e1002417. doi:10.1371/ journal.pbio.1002417.
2016Identification of protein secretion systems in bacterial genomes, Scientific Reports 6, 23080 (2016).
2016The impact of selection, gene conversion, and biased sampling on the assessment of microbial demography, Mol Biol Evol (2016) doi: 10.1093/molbev/msw048 .
2016Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity, Nat. Genet. 2016 Mar;48(3):308-13.
2016Coevolution of the Organization and Structure of Prokaryotic Genomes., Cold Spring Harb Perspect Biol. 2016 Jan 4;8(1).
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