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 1 to 30 publications on 137 in total

The Inca child of the Quehuar volcano: Stable isotopes clue to geographic origin and seasonal diet, with putative seaweed consumption

Eve Poulallion, Violeta Galván, Verónica Seldes, María Fernanda Zigarán, Gabriela Recagno Browning, François Fourel...

Journal of Archaeological Science: Reports . 59 : 104784

DOI: 10.1016/j.jasrep.2024.104784

Journal article

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Diversité et diversification des Pectobacteriaceae, une famille de bactéries phytopathogènes d’importance mondiale

Céline Brochier, Nicole Hugouvieux-Cotte-Pattat, Jean-Pierre Flandrois, Sylvie Reverchon, Jérôme Briolay

Cahiers Scientifiques de la Fondation Pierre Vérots . ( 10 ) : 19-29

Journal article

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Description of a new genus of the Pectobacteriaceae family isolated from water in coastal brackish wetlands of the French Camargue region, Prodigiosinella gen. nov., including the new species Prodigiosinella aquatilis sp. nov

Nicole Hugouvieux-Cotte-Pattat, Jean-Pierre Flandrois, Jérôme Briolay, Sylvie Reverchon, Céline Brochier-Armanet

Systematic and Applied Microbiology . 47 ( 2-3 ) : 126497

DOI: 10.1016/j.syapm.2024.126497

Journal article

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Geographic origin and social status of the Gallic warriors from Ribemont‐sur‐Ancre (France) studied through isotope systematics of bone remains

Thibault Clauzel, Pascale Richardin, Jannick Ricard, Gilles Prilaux, Jeremy Martin, Romain Amiot...

International Journal of Osteoarchaeology . 33 ( 1 ) : 39-50

DOI: 10.1002/oa.3172

Journal article

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Mitigation of the diagenesis risk in biological apatite δ18O interpretation

Christophe Lécuyer, Jean-Pierre Flandrois

Palaeogeography, Palaeoclimatology, Palaeoecology . 630 : 111812

DOI: 10.1016/j.palaeo.2023.111812

Journal article

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δ2H and δ18O of river water from a high-altitude humid plain of the southern Alps: Implications for the interpretation of the isotopic compositions of bioapatite from humans living close to mountain areas

Christophe Lécuyer, François Atrops, François Fourel, Thibault Clauzel, Jean-Pierre Flandrois

Journal of Archaeological Science: Reports . 49 : 104020

DOI: 10.1016/j.jasrep.2023.104020

Journal article

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Geographic origin and social status of the Gallic warriors from Ribemont‐sur‐Ancre (France) studied through isotope systematics of bone remains

Thibault Clauzel, Pascale Richardin, Jannick Ricard, Gilles Prilaux, Jeremy Martin, Romain Amiot...

International Journal of Osteoarchaeology .

DOI: 10.1002/oa.3172

Journal article

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Hydrogen isotope measurements of bone and dental tissues from archaeological human and animal samples and their use as climatic and diet proxies

Thibault Clauzel, Pascale Richardin, Jannick Ricard, Yves Le Béchennec, Romain Amiot, François Fourel...

Journal of Archaeological Science . 147 : 105676

DOI: 10.1016/j.jas.2022.105676

Journal article

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Climate conditions and dietary practices during the Second Iron Age studied through the multi-isotope analysis of bones and teeth from individuals of Thézy-Glimont, Picardie, France

Thibault Clauzel, Pascale Richardin, Jannick Ricard, Yves Le Béchennec, Romain Amiot, François Fourel...

Archaeological and Anthropological Sciences . 14 ( 4 ) : 61

DOI: 10.1007/s12520-022-01534-1

Journal article

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A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea

Monique Aouad, Jean-Pierre Flandrois, Frédéric Jauffrit, Manolo Gouy, Simonetta Gribaldo, Celine Brochier-Armanet

BMC Ecology and Evolution . 22 ( 1 ) : 1-12

DOI: 10.1186/s12862-021-01952-0

Journal article

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Les isotopes de l'hydrogène contenus dans les tissus osseux et dentaires de populations archéologiques et leurs usages comme proxys paléoclimatiques et paléoalimentaires

Thibault Clauzel, Pascale Richardin, Jannick Ricard, Yves Le Béchennec, Romain Amiot, Fourel François...

27e édition de la Réunion des Sciences de la Terre .

Conference paper

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A Comprehensive Evolutionary Scenario of Cell Division and Associated Processes in the Firmicutes

Pierre Garcia, Wandrille Duchemin, Jean-Pierre Flandrois, Simonetta Gribaldo, Christophe Grangeasse, Céline Brochier-Armanet

Molecular Biology and Evolution . 38 ( 6 ) : 2396-2412

DOI: 10.1093/molbev/msab034

Journal article

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Climatic change and diet of the pre-Hispanic population of Gran Canaria (Canary Archipelago, Spain) during the Medieval Warm Period and Little Ice Age

Christophe Lécuyer, Jean Goedert, Johanne Klee, Thibault Clauzel, Pascale Richardin, François Fourel...

Journal of Archaeological Science . 128 : 105336

DOI: 10.1016/j.jas.2021.105336

Journal article

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A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing

Stefan Moritz Neuenschwander, Miguel Angel Terrazos Miani, Heiko Amlang, Carmen Perroulaz, Pascal Bittel, Carlo Casanova...

Journal of Clinical Microbiology . 58 ( 6 ) : 1128

DOI: 10.1128/JCM.00060-20

Journal article

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The Gauls experienced the Roman Warm Period: Oxygen isotope study of the Gallic site of Thézy-Glimont, Picardie, France

Thibault Clauzel, Pascale Richardin, Jannick Ricard, Yves Le Béchennec, Romain Amiot, François Fourel...

Journal of Archaeological Science: Reports . 34 : 102595

DOI: 10.1016/j.jasrep.2020.102595

Journal article

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Metapopulation ecology links antibiotic resistance, consumption, and patient transfers in a network of hospital wards

Julie Teresa Shapiro, Gilles Leboucher, Anne-Florence Myard-Dury, Pascale Girardo, Anatole Luzzati, Mélissa Mary...

eLife . 9

DOI: 10.7554/eLife.54795

Journal article

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Dickeya poaceiphila sp. nov., a plant-pathogenic bacterium isolated from sugar cane (Saccharum officinarum)

Nicole Hugouvieux-Cotte-Pattat, Celine Brochier-Armanet, Jean-Pierre Flandrois, Sylvie Reverchon

International Journal of Systematic and Evolutionary Microbiology . 70 ( 8 ) : 4508-4514

DOI: 10.1099/ijsem.0.004306

Journal article

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δ18O and δ13C of diagenetic land snail shells from the Pliocene (Zanclean) of Lanzarote, Canary Archipelago: Do they still record some climatic parameters?

Christophe Lécuyer, Antonio Sanchez Marco, Alejandro Lomoschitz, Juan-Francisco Betancort, François Fourel, Romain Amiot...

Journal of African Earth Sciences . 162 : 103702

DOI: 10.1016/j.jafrearsci.2019.103702

Journal article

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Isotopic systematics point to wild origin of mummified birds in Ancient Egypt

Marie Linglin, Romain Amiot, Pascale Richardin, Stéphanie Porcier, Ingrid Antheaume, Didier Berthet...

Scientific Reports . 10 ( 1 )

DOI: 10.1038/s41598-020-72326-7

Journal article

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Taxonomic assignment of uncultured prokaryotes with long range PCR targeting the spectinomycin operon

Jean-Pierre Flandrois, Céline Brochier-Armanet, Jérôme Briolay, Danis Abrouk, Guillaume P Schwob, Philippe Normand...

Research in Microbiology . 170 ( 6-7 ) : 280-287

DOI: 10.1016/j.resmic.2019.06.005

Journal article

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Metapopulation ecology links antibiotic resistance, consumption and patient transfers in a network of hospital wards.

Julie Teresa Shapiro, Gilles Leboucher, Anne-Florence Myard-Dury, Pascale Girardo, Anatole Luzatti, Mélissa Mary...

DOI: 10.1101/771790

Preprint

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P2857 Quantifying drivers of antimicrobial resistance in a large network of hospital wards: a meta-population approach.

Julie Teresa Shapiro, Leboucher Gilles, Anatole Luzzati, Jean Francois Sauzon, Olivier Dauwalder, Pascale Girardo...

29TH ECCMID .

Conference paper

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The phytopathogenic nature of Dickeya aquatica 174/2 and the dynamic early evolution of Dickeya pathogenicity

Alexandre Duprey, Najwa Taïb, Simon Leonard, Tiffany Garin, Jean-Pierre Flandrois, William Nasser...

Environmental Microbiology . 21 ( 8 ) : 2809-2835

DOI: 10.1111/1462-2920.14627

Journal article

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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

Andrej Benjak, Charlotte Avanzi, Yvonne Benito, Franck Breysse, Christophe Chartier, Maria-Laura Boschiroli...

MSphere . 3 ( 5 ) : e00405-18

DOI: 10.1128/mSphere.00405-18

Journal article

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Changing patterns of human migrations shaped the global population structure of Mycobacterium tuberculosis in France

Maxime Barbier, Oana Dumitrescu, Catherine Pichat, Gérard Carret, Anne-Sophie Ronnaux-Baron, Ghislaine Blasquez...

Scientific Reports . 8 ( 1 ) : 5855

DOI: 10.1038/s41598-018-24034-6

Journal article

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Tsunami sedimentary deposits of Crete records climate during the ‘Minoan Warming Period’ (≈3350 yr BP)

Christophe Lécuyer, François Atrops, Romain Amiot, Delphine Angst, Valérie Daux, Jean-Pierre Flandrois...

The Holocene .

DOI: 10.1177/0959683617752840

Journal article

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d18O-Derived incubation temperatures of oviraptorosaur eggs.

Romain Amiot, Xu Wang, Shuo Wang, Christophe Lécuyer, Jean-Michel Mazin, Jinyou Mo...

Palaeontology . : 1-15

DOI: 10.1111/pala.12311

Journal article

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δ 18 O-derived incubation temperatures of oviraptorosaur eggs

Romain Amiot, Xu Wang, Shuo Wang, Christophe Lécuyer, Jean-Michel Mazin, Jinyou Mo...

Palaeontology . 60 ( 5 ) : 633-647

DOI: 10.1111/pala.12311

Journal article

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Record of Nile seasonality in Nubian neonates.

Céline Martin, Bruno Maureille, Romain Amiot, Alexandra Touzeau, Aurélien Royer, François Fourel...

Isotopes in Environmental and Health Studies . 53 ( 3 ) : 223-242

DOI: 10.1080/10256016.2016.1229667

Journal article

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Strain-specific estimation of epidemic success provides insights into the transmission dynamics of tuberculosis

Jean-Philippe Rasigade, Maxime Barbier, Oana Dumitrescu, Catherine Pichat, Gérard Carret, Anne-Sophie Ronnaux-Baron...

Scientific Reports . 7 : 45326

DOI: 10.1038/srep45326

Journal article

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