GECO Génomique Computationnelle et Evolutive
Equipe Bioinformatique, Phylogénie et Génomique Evolutive
Flandrois Jean-Pierre
Professeur d'université émérite
UCBL
Tél : 04 72 44 85 60
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.
Applications
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...
Medical microbiology
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.
Publications
Affichage des publications 31 à 60 sur 137 au total
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 )
Article dans une revue
voir la publicationRiboDB database: a comprehensive resource for prokaryotic systematics
Molecular Biology and Evolution . 33 ( 8 ) : 2170--2172
Article dans une revue
voir la publicationCombined Genotypic, Phylogenetic, and Epidemiologic Analyses of Mycobacterium tuberculosis Genetic Diversity in the Rhône Alpes Region, France
PLoS ONE . 11 ( 4 ) : e0153580
Article dans une revue
voir la publicationNontuberculous Mycobacteria: An Underestimated Cause of Bioprosthetic Valve Infective Endocarditis
Open Forum Infectious Diseases . 2 ( 2 )
DOI: 10.1093/ofid/ofv047
Article dans une revue
voir la publicationAssessment 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
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voir la publicationA Toolbox for Nonlinear Regression in R: The Package nistools
Journal of Statistical Software . 66 : 1-21
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voir la publicationleBIBIQBPP: a set of databases and a webtool for automatic phylogenetic analysis of prokaryotic sequences
BMC Bioinformatics . 16 ( 1 ) : 251
Article dans une revue
voir la publicationDiet of ancient Egyptians inferred from stable isotope systematics
Journal of Archaeological Science . 46 : 114-124
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voir la publicationMUBII-TB-DB: a database of mutations associated with antibiotic resistance in Mycobacterium tuberculosis.
BMC Bioinformatics . 15 ( 1 ) : 107
Article dans une revue
voir la publicationMycobacterium Species Related to M. leprae and M. lepromatosis from Cows with Bovine Nodular Thelitis
Emerging Infectious Diseases . 20 : 2111-4
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voir la publicationOptimization of the reactional medium and a food impact study for a colorimetric in situ Salmonella spp. detection method
International Journal of Food Microbiology . 181 : 48-52
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voir la publicationEnhanced tetrazolium violet reduction of Salmonella spp. by magnesium addition to the culture media
Food Microbiology . 42 : 132-135
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voir la publicationMycobacterium bourgelatii sp. nov., a rapidly growing, non-chromogenic species isolated from the lymph nodes of cattle.
International Journal of Systematic and Evolutionary Microbiology . 63 ( Pt 12 ) : 4669-74
Article dans une revue
voir la publicationCandida albicans and non- Candida albicans fungemia in an institutional hospital during a decade
Medical Mycology . 51 ( 1 ) : 33-37
Article dans une revue
voir la publicationDiminution of 2,3,5-triphenyltetrazolium chloride toxicity on Listeria monocytogenes growth by iron source addition to the culture medium
Food Microbiology . 38 : 1--5
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voir la publicationEgyptian mummies record increasing aridity in the Nile valley from 5500 to 1500yr before present
Earth and Planetary Science Letters . 375 : 92-100
Article dans une revue
voir la publicationSimplified detection of food-borne pathogens: An in situ high affinity capture and staining concept
Journal of Microbiological Methods . 91 : 501--505
Article dans une revue
voir la publicationSpecies-driven interpretation guidelines in case of a single-sampling strategy for blood culture
European Journal of Clinical Microbiology and Infectious Diseases . 30 : 1537-1541
Article dans une revue
voir la publicationA pharmacologically based multiscale mathematical model of angiogenesis and its use in investigating the efficacy of a new cancer treatment strategy.
Journal of Theoretical Biology . 260 ( 4 ) : 545-62
Article dans une revue
voir la publicationA seven-gene multilocus genus-wide approach to the phylogeny of mycobacteria using supertrees
International Journal of Systematic and Evolutionary Microbiology . 58(part 6) : 1432-1441
Article dans une revue
voir la publicationIdentification of Mycobacterium using the EF-Tu encoding (tuf) gene and the tmRNA encoding (ssrA) gene
Journal of Medical Microbiology . 56 ( 8 ) : 1033-1041
Article dans une revue
voir la publicationMycobacterium bovis Infection
Journal of Medical Microbiology . 56 : 1033-1041
Article dans une revue
voir la publicationUse of PCR-Restriction Enzyme Pattern Analysis and Sequencing Database for hsp65 Gene-Based Identification of Nocardia Species
Journal of Clinical Microbiology . 44 ( 2 ) : 536-546
Article dans une revue
voir la publication16S rRNA sequencing in routine bacterial identification : A 30-month experiment
Journal of Microbiological Methods . 67 : 574-581
Article dans une revue
voir la publicationRapid identification of Enterobacteriaceae by sequencing DNA gyrase subunit B encoding gene
Diagnostic Microbiology and Infectious Disease . 55 : 263-268
Article dans une revue
voir la publication[From prevalence to predictive values: considerations on the antimicrobial susceptibility testing dealing with change of susceptibility rates].
Annales de Biologie Clinique . 63 ( 5 ) : 493-502
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voir la publicationA multigene approach to phylogenetic analysis using the genus Mycobacterium as a model
International Journal of Systematic and Evolutionary Microbiology . 55 : 293-302
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voir la publicationDe la prévalence aux valeurs prédictives: L`antibiogramme face à l`évolution de la résistance aux antibiotiques
Annales de Biologie Clinique . 63 : 493-502
Article dans une revue
voir la publicationHow does susceptibility prevalence impact on the performance of disk diffusion susceptibility testing?
Diagnostic Microbiology and Infectious Disease . 49 : 131-139
Article dans une revue
voir la publicationQuelques problèmes statistiques rencontrés dans l`estimation de la température minimale de croissance de Listeria monocytogenes
Revue de Statistique Appliquée . LI : 59-71
Article dans une revue
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