GECO Evolutionary and Computational Genomics
Bioinformatics, Phylogeny and Evolutionary Genomics Group
Professeur d'université émérite
Two flagship projects
BIBI-DB BIBI-DB is a taxonomy-hierarchized set of databases and oriented to facilitate the phylogeny of Archaea and Bacteria. Thanks to a web interface it allows the phylogenetic placement of unknown nucleic acid sequences (this may precede identification). RiboDB is a ribosomal protein database of Bacteria and Archaea freely searchable via the Internet. RiboDB construction process is versatile and can be used to construct proteins databases from freshly assembled and annotated genomes.
leBIBI is a web application used worldwide to identify bacteria in hospital laboratories, industrial, environmental.
The leBIBI and RiboDB databases are useful to classify more rigorously the Bacteria and Archaea and may highlight new pathogen species. Their use helps to explain the evolution of the microbial world. RiboDB will allow to improve the quality of diagnosis of infections.
Ancient Ecosystems and stable isotopes
I am very pleased to cooperate since 2012 in some work Christophe Lecuyer and his team as a physiologist, biologist and physician. This topic is now a real scientific center of interest for me!
The first studies were on ancient climates reconstruction by using the informations recorded in bone and teeth of egyptian mummies but of course we get also informations on human and animal nutrition.
Climate reconstruction may also be done outside egypt with other types of samples.
We were also proud to show that the hatching temperature of Oviraptosaurs were not so different from that of actual birds...
This are works I have initiated or using datas that have been collected during my previous position as Head of the Microbiology Laboratory CH Lyon-Sud 1979-2013.
Display of 1 to 30 publications on 126 in total
A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea
BMC Ecology and Evolution . 22 ( 1 ) : 1-12
A Comprehensive Evolutionary Scenario of Cell Division and Associated Processes in the Firmicutes
Molecular Biology and Evolution . 38 ( 6 ) : 2396-2412
Climatic change and diet of the pre-Hispanic population of Gran Canaria (Canary Archipelago, Spain) during the Medieval Warm Period and Little Ice Age
Journal of Archaeological Science . 128 : 105336
A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing
Journal of Clinical Microbiology . 58 ( 6 )
Isotopic systematics point to wild origin of mummified birds in Ancient Egypt
Scientific Reports . 10 ( 1 )
The Gauls experienced the Roman Warm Period: Oxygen isotope study of the Gallic site of Thézy-Glimont, Picardie, France
Journal of Archaeological Science: Reports . 34 : 102595
Metapopulation ecology links antibiotic resistance, consumption, and patient transfers in a network of hospital wards
eLife . 9
Dickeya poaceiphila sp. nov., a plant-pathogenic bacterium isolated from sugar cane (Saccharum officinarum)
International Journal of Systematic and Evolutionary Microbiology . 70 ( 8 ) : 4508-4514
δ18O and δ13C of diagenetic land snail shells from the Pliocene (Zanclean) of Lanzarote, Canary Archipelago: Do they still record some climatic parameters?
Journal of African Earth Sciences . 162 : 103702
Taxonomic assignment of uncultured prokaryotes with long range PCR targeting the spectinomycin operon
Research in Microbiology . 170 ( 6-7 ) : 280-287
Metapopulation ecology links antibiotic resistance, consumption and patient transfers in a network of hospital wards.
Preprintsee the publication
P2857 Quantifying drivers of antimicrobial resistance in a large network of hospital wards: a meta-population approach.
29TH ECCMID .
Conference papersee the publication
The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity
Environmental Microbiology . 21 ( 8 ) : 2809-2835
Highly Reduced Genome of the New Species Mycobacterium uberis, the Causative Agent of Nodular Thelitis and Tuberculoid Scrotitis in Livestock and a Close Relative of the Leprosy Bacilli
MSphere . 3 ( 5 ) : e00405-18
Changing patterns of human migrations shaped the global population structure of Mycobacterium tuberculosis in France
Scientific Reports . 8 ( 1 ) : 5855
Tsunami sedimentary deposits of Crete records climate during the ‘Minoan Warming Period’ (≈3350 yr BP)
The Holocene .
d18O-Derived incubation temperatures of oviraptorosaur eggs.
Palaeontology . : 1-15
δ 18 O-derived incubation temperatures of oviraptorosaur eggs
Palaeontology . 60 ( 5 ) : 633-647
Record of Nile seasonality in Nubian neonates.
Isotopes in Environmental and Health Studies . 53 ( 3 ) : 223-242
Strain-specific estimation of epidemic success provides insights into the transmission dynamics of tuberculosis
Scientific Reports . 7 : 45326
Oxygen isotope fractionation between bird eggshell calcite and body water: application to fossil eggs from Lanzarote (Canary Islands)
The Science of Nature Naturwissenschaften . 103 ( 9-10 )
RiboDB database: a comprehensive resource for prokaryotic systematics
Molecular Biology and Evolution . 33 ( 8 ) : 2170--2172
Combined Genotypic, Phylogenetic, and Epidemiologic Analyses of Mycobacterium tuberculosis Genetic Diversity in the Rhône Alpes Region, France
PLoS ONE . 11 ( 4 ) : e0153580
Nontuberculous Mycobacteria: An Underestimated Cause of Bioprosthetic Valve Infective Endocarditis
Open Forum Infectious Diseases . 2 ( 2 )
Assessment of polycarbonate filter in a molecular analytical system for the microbiological quality monitoring of recycled waters onboard ISS
Life Sciences in Space Research . 6 : 29-35
A Toolbox for Nonlinear Regression in R: The Package nistools
Journal of Statistical Software . 66 : 1-21
leBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences
BMC Bioinformatics . 16 ( 1 ) : 251
Diet of ancient Egyptians inferred from stable isotope systematics
Journal of Archaeological Science . 46 : 114-124
MUBII-TB-DB: a database of mutations associated with antibiotic resistance in Mycobacterium tuberculosis.
BMC Bioinformatics . 15 ( 1 ) : 107
Mycobacterium Species Related to M. leprae and M. lepromatosis from Cows with Bovine Nodular Thelitis
Emerging Infectious Diseases . 20 : 2111-4