GECO Evolutionary and Computational Genomics
Bioinformatics, Phylogeny and Evolutionary Genomics Group
Flandrois Jean-Pierre
Professeur d'université émérite
UCBL
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
Display of 61 to 90 publications on 129 in total
A mathematical model describing the thermal virus inactivation
Vaccine . 19 : 3575-3582
Journal article
see the publicationFitness and competitive growth advantage of new gentamicin-susceptible MRSA clones spreading in French hospitals
Journal of Antimicrobial Chemotherapy . 47 ( 3 ) : 277-283
DOI: 10.1093/jac/47.3.277
Journal article
see the publicationA model describing the relationship between regrowth lag time and mild temperature increase for Listeria monocytogenes
International Journal of Food Microbiology . 46 : 251-261
Journal article
see the publicationCharacterization of Unexpected Growth of Escherichia coli O157:H7 by Modeling
Applied and Environmental Microbiology . 65 : 5322-5327
Journal article
see the publicationSaccharomyces boulardii Fungemia in a Patient Receiving Ultra‐levure Therapy
Clinical Infectious Diseases . 27 ( 1 ) : 222-223
DOI: 10.1086/517685
Journal article
see the publicationModel of the influence of time and mild temperature on Listeria monocytogenes nonlinear survival curves
International Journal of Food Microbiology . 40 : 185-195
Journal article
see the publicationNEURAL NETWORKS AS AN ALTERNATIVE METHOD FOR PREDICTING BACTERIAL GROWTH RATE FROM THE BEGINNING OF A GROWTH CURVE
Industrial Applications of Neural Networks . : 451-457
Book chapter
see the publicationInfluence of atmospheric conditions during incubation on the susceptibilities of Streptococcus pneumoniae isolates to five beta- lactam antibiotics
Journal of Antimicrobial Chemotherapy . 40 ( 4 ) : 599-601
DOI: 10.1093/jac/40.4.599
Journal article
see the publicationSimple relationship between acid dissociation constant and minimal pH for microbial growth in laboratory medium
International Journal of Food Microbiology . 35 ( 1 ) : 75-81
Journal article
see the publicationReappraisal of the effect of temperature on the growth kinetics of Aeromonas salmonicida
Letters in Applied Microbiology . 25 : 363-366
Journal article
see the publicationA model describing the relationship between lag time and mild temperature increase duration
International Journal of Food Microbiology . 38 : 157-167
Journal article
see the publicationHomogeneous Two-Site Immunometric Assay Kinetics as a Theoretical Tool for Data Analysis
Analytical Biochemistry . 251 ( 1 ) : 79-88
Journal article
see the publicationA Descriptive Model for the Kinetics of a Homogeneous Fluorometric Immunoassay
Journal of Immunoassay and Immunochemistry . 18 ( 1 ) : 21-47
Journal article
see the publicationDifferential growth of Listeria monocytogenes at 4 and 8°C: Consequences for the Shelf Life of Chilled Products
Journal of Food Protection . 59 ( 9 ) : 944-949
Journal article
see the publicationEvaluation of an expert system linked to a rapid antibiotic susceptibility testing system for the detection of β-lactam resistance phenotypes
Research in Microbiology . 147 ( 4 ) : 297-309
Journal article
see the publicationThe particular behaviour of Listeria monocytogenes under sub-optimal conditions
International Journal of Food Microbiology . 29 : 201-211
Journal article
see the publicationUse of mathematics and statistics in nutrition modelling
Annales de zootechnie . 45 ( Suppl1 ) : 143-152
Journal article
see the publicationApplication of a modified disc diffusion technique to antimicrobial susceptibility testing of Vibrio anguillarum and Aeromonas salmonicida clinical isolates
Veterinary Microbiology . 51 : 137-149
Journal article
see the publicationAn economic approach to the MIC.
Zentralblatt fur Bakteriologie : international journal of medical microbiology . 284 ( 1 ) : 67-74
Journal article
see the publicationRelationship between colonial surface and density on agar plate
The Journal of applied bacteriology . 79 ( 5 ) : 542-550
Journal article
see the publicationOlecranon bursitis due toPrototheca wickerhamii, an algal opportunistic pathogen
European Journal of Clinical Microbiology and Infectious Diseases . 14 ( 6 ) : 561-562
DOI: 10.1007/bf02113444
Journal article
see the publicationThe effect of incubation temperature and sodium chloride concentration on the growth kinetics of Vibrio anguillarum and Vibrio anguillarum -related organisms
The Journal of applied bacteriology . 78 ( 6 ) : 621-629
Journal article
see the publicationConvenient Model To Describe the Combined Effects of Temperature and pH on Microbial Growth
Applied and Environmental Microbiology . 61 : 610-616
Journal article
see the publicationAccuracy of microbial growth predictions with square root and polynomial models
International Journal of Food Microbiology . 27 ( 2-3 ) : 139-146
Journal article
see the publicationMathematical model of the interactions between Micrococcus spp. and Pseudomonas aeruginosa on agar surface
The Journal of applied bacteriology . 77 ( 6 ) : 727-732
Journal article
see the publication[Post-antibiotic effect of three aminoglycosides against Klebsiella pneumoniae].
Pathologie Biologie . 42 ( 5 ) : 419-24
Journal article
see the publicationAn accurate diffusion method for determining bacterial sensitivity to antibiotics
Journal of Antimicrobial Chemotherapy . 34 ( 1 ) : 73-81
DOI: 10.1093/jac/34.1.73
Journal article
see the publicationAn unexpected correlation between cardinal temperatures of microbial growth highlighted by a new model
Journal of Theoretical Biology . 162 : 447-463
Journal article
see the publicationActinomyces pyogenes: susceptibility of 103 clinical animal isolates to 22 antimicrobial agents
Veterinary Research . 24 ( 3 ) : 251-259
Journal article
see the publicationMathematical model for comparison of time-killing curves.
Antimicrobial Agents and Chemotherapy . 37 ( 8 ) : 1685-1689
Journal article
see the publication