GECO Evolutionary and Computational Genomics

Bioinformatics, Phylogeny and Evolutionary Genomics Group

Flandrois Jean-Pierre

Professeur d'université émérite

UCBL

Address: 43 Bd du 11 novembre 1918
69622 VILLEURBANNE

Tel: 04 72 44 85 60

Email

Linkedin

My Research

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 137 in total

BIBI a bioinformatics bacterial identification tool

G. Devulder, G. Perrière, F. Baty, Jean-Pierre Flandrois

Journal of Clinical Microbiology . 41 : 1785-1787

Journal article

see the publication

A method to study the microscale 3-D spatial distribution of Bacteria in soil.

A. Dechesne, C. Pallud, D. Debouzie, Jean-Pierre Flandrois, J.P. Gaudet, G.L. Grundmann

Mycological Research . 107 : 1221-1230

Journal article

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A novel method for characterizing the microscale 3D spatial distribution of bacteria in soil

A. Dechesne, C. Pallud, D. Debouzie, J. P. Flandrois, T. M. Vogel, J. P. Gaudet...

Soil Biology and Biochemistry . 35 ( 12 ) : 1537-1546

DOI: 10.1016/S0038-0717(03)00243-8

Journal article

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Modelling the competitive growth of Listeria monocytogenes and Listeria innocua in enrichment broths

Marie Cornu, Martin Kalmokoff, Jean-Pierre Flandrois

International Journal of Food Microbiology . 73 ( 2-3 ) : 261-274

DOI: 10.1016/S0168-1605(01)00658-4

Journal article

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What is the relevance of obtaining multiple blood samples for culture? A comprehensive model to optimize the strategy for diagnosing bacteremia

B. Lamy, Pascal Roy, G. Carret, Jean-Pierre Flandrois, Marie Laure Delignette-Muller

Clinical Infectious Diseases . 35 ( 7 ) : 842-850

DOI: 10.1086/342383

Journal article

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Modeling the Lag Time of Listeria monocytogenes from Viable Count Enumeration and Optical Density Data

F. Baty, Jean-Pierre Flandrois, Marie Laure Delignette-Muller

Applied and Environmental Microbiology . 68 : 5816-5825

Journal article

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Spatial Modeling of Nitrifier Microhabitats in Soil

G. Grundmann, A. Dechesne, F. Bartoli, Jean-Pierre Flandrois, J. Chassé, R. Kizungu

Soil Science Society of America Journal . 65 ( 6 ) : 1709

DOI: 10.2136/sssaj2001.1709

Journal article

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A mathematical model describing the thermal virus inactivation

C. Noel, Sandrine Charles, A. Francon, Jean-Pierre Flandrois

Vaccine . 19 : 3575-3582

Journal article

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Fitness and competitive growth advantage of new gentamicin-susceptible MRSA clones spreading in French hospitals

Jean-Pierre Flandrois, F. Laurent

Journal of Antimicrobial Chemotherapy . 47 ( 3 ) : 277-283

DOI: 10.1093/jac/47.3.277

Journal article

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A model describing the relationship between regrowth lag time and mild temperature increase for Listeria monocytogenes

S. Breand, G. Fardel, Jean-Pierre Flandrois, L. Rosso, R. Tomassone

International Journal of Food Microbiology . 46 : 251-261

Journal article

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Characterization of Unexpected Growth of Escherichia coli O157:H7 by Modeling

M. Cornu, Marie Laure Delignette-Muller, Jean-Pierre Flandrois

Applied and Environmental Microbiology . 65 : 5322-5327

Journal article

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Saccharomyces boulardii Fungemia in a Patient Receiving Ultra‐levure Therapy

Jean-Pierre Flandrois, I. Fredenucci, M. Chomarat, C. Boucaud

Clinical Infectious Diseases . 27 ( 1 ) : 222-223

DOI: 10.1086/517685

Journal article

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Model of the influence of time and mild temperature on Listeria monocytogenes nonlinear survival curves

S. Breand, G. Fardel, Jean-Pierre Flandrois, L. Rosso, R. Tomassone

International Journal of Food Microbiology . 40 : 185-195

Journal article

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NEURAL NETWORKS AS AN ALTERNATIVE METHOD FOR PREDICTING BACTERIAL GROWTH RATE FROM THE BEGINNING OF A GROWTH CURVE

M. Delignette-Muller, Jean-Pierre Flandrois

Industrial Applications of Neural Networks . : 451-457

DOI: 10.1142/9789812816955_0053

Book chapter

see the publication

Influence of atmospheric conditions during incubation on the susceptibilities of Streptococcus pneumoniae isolates to five beta- lactam antibiotics

M. Chomarat, L. Chollet, M. Peyret, Jean-Pierre Flandrois

Journal of Antimicrobial Chemotherapy . 40 ( 4 ) : 599-601

DOI: 10.1093/jac/40.4.599

Journal article

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Simple relationship between acid dissociation constant and minimal pH for microbial growth in laboratory medium

Jean-Pierre Flandrois, L. Rosso, E. Zuber, C. Pichat

International Journal of Food Microbiology . 35 ( 1 ) : 75-81

DOI: 10.1016/S0168-1605(96)01231-7

Journal article

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A model describing the relationship between lag time and mild temperature increase duration

S. Breand, G. Fardel, Jean-Pierre Flandrois, L. Rosso, R. Tomassone

International Journal of Food Microbiology . 38 : 157-167

Journal article

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Reappraisal of the effect of temperature on the growth kinetics of Aeromonas salmonicida

V. Guérin-Faublée, Sandrine Charles, M. Chomarat, Jean-Pierre Flandrois

Letters in Applied Microbiology . 25 : 363-366

Journal article

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Homogeneous Two-Site Immunometric Assay Kinetics as a Theoretical Tool for Data Analysis

Emmanuel Zuber, Gérard Mathis, Jean-Pierre Flandrois

Analytical Biochemistry . 251 ( 1 ) : 79-88

DOI: 10.1006/abio.1997.2243

Journal article

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A Descriptive Model for the Kinetics of a Homogeneous Fluorometric Immunoassay

Emmanuel Zuber, Laurent Rosso, Bruno Darbouret, Françoise Socquet, Gérard Mathis, Jean-Pierre Flandrois

Journal of Immunoassay and Immunochemistry . 18 ( 1 ) : 21-47

DOI: 10.1080/01971529708005803

Journal article

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The particular behaviour of Listeria monocytogenes under sub-optimal conditions

S. Bajard, L. Rosso, G. Fardel, J.P. Flandrois

International Journal of Food Microbiology . 29 ( 2-3 ) : 201-211

DOI: 10.1016/0168-1605(95)00031-3

Journal article

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The particular behaviour of Listeria monocytogenes under sub-optimal conditions

S. Bajard, L. Rosso, G. Fardel, Jean-Pierre Flandrois

International Journal of Food Microbiology . 29 : 201-211

Journal article

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Use of mathematics and statistics in nutrition modelling

G Ciuperca, R Tomassone, Jp Flandrois

Annales de zootechnie . 45 ( Suppl1 ) : 143-152

Journal article

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Application of a modified disc diffusion technique to antimicrobial susceptibility testing of Vibrio anguillarum and Aeromonas salmonicida clinical isolates

V. Guerin-Faublée, Marie Laure Delignette-Muller, M. Vigneulle, Jean-Pierre Flandrois

Veterinary Microbiology . 51 : 137-149

Journal article

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Differential growth of Listeria monocytogenes at 4 and 8°C: Consequences for the Shelf Life of Chilled Products

L. Rosso, S. Bajard, Jean-Pierre Flandrois, C. Lahellec, J. Fournaud, P. Veit

Journal of Food Protection . 59 ( 9 ) : 944-949

DOI: 10.4315/0362-028X-59.9.944

Journal article

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Evaluation of an expert system linked to a rapid antibiotic susceptibility testing system for the detection of β-lactam resistance phenotypes

Jean-Pierre Flandrois, G. Vedel, M. Peyret, J.P. Gayral, Patrick Millot

Research in Microbiology . 147 ( 4 ) : 297-309

DOI: 10.1016/0923-2508(96)81390-8

Journal article

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An economic approach to the MIC.

M. Delignette-Muller, Jean-Pierre Flandrois, Catherine Chapuis

Zentralblatt fur Bakteriologie : international journal of medical microbiology . 284 ( 1 ) : 67-74

Journal article

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Olecranon bursitis due toPrototheca wickerhamii, an algal opportunistic pathogen

M. Montclos, G. Chatte, M. Perrin-Fayolle, Jean-Pierre Flandrois

European Journal of Clinical Microbiology and Infectious Diseases . 14 ( 6 ) : 561-562

DOI: 10.1007/bf02113444

Journal article

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The effect of incubation temperature and sodium chloride concentration on the growth kinetics of Vibrio anguillarum and Vibrio anguillarum -related organisms

Véronique Guérin-Faublée, L. Rosso, Martine Vigneulle, J.-P. Flandrois

The Journal of applied bacteriology . 78 ( 6 ) : 621-629

DOI: 10.1111/j.1365-2672.1995.tb03108.x

Journal article

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