Evolutionary Ecology

Quantitative and Evolutionary Ecology of Communities Group

Thioulouse Jean

Directeur de recherche

CNRS

Address: 43 bd du 11 novembre 1918
69622 VILLEURBANNE cedex

Tel: 33 04 72 43 27 56

Site internet

Email

Mendel Building, 1st floor. Office 11.048

Bibliography Web page: You can visit my bibliography web page here: https://jthome.thioulouse.fr/ref/

Reproducible research : A series of paper with graphs and computations reproducibility:

https://jthome.thioulouse.fr/Reproducible_Research/

https://pbil.univ-lyon1.fr/members/thioulouse/RRBibJT/

Google Scholar: https://scholar.google.com/citations?hl=fr&user=1sjOJvSAAAAJO

ORCID ID: https://orcid.org/0000-0001-7664-0598

IdHAL: https://cv.archives-ouvertes.fr/jean-thioulouse

ade4 book: Multivariate Analysis of Ecological Data with ade4
https://link.springer.com/book/10.1007/978-1-4939-8850-1

Evol. Biol. 2021 paper reproducibility:

Overcoming the Spurious Groups Problem in Between-Group PCA

Research activity

My research activities are centred  around innovation in the field of statistical methods in Biology. During the last years, I was mainly interested in statistical analysis methods used for studying bacterial diversity. I have also pursued methodological developments in software, leading to the distribution of several packages for R, and in consulting and teaching in several areas.

The ade4 package for R :ade4

The adegraphics package for R :adegraphics

The ade4TkGUI package for R :ade4TkGUI

 

Publications

Display of 91 to 120 publications on 168 in total

Development of cellular immune responses to Plasmodium falciparum blood stage antigens from birth to 36 months of age in Cameroon

J.Y. Le Hesran, N. Fievet, J. Thioulouse, P. Personne, B. Maubert, S. M'Bidias...

Acta Tropica . 98 : 261-269

Journal article

see the publication

Potential of a 16S rRNA-based taxonomic microarray for analyzing the rhizosphere effects of maize on Agrobacterium spp. and bacterial communities

Hervé Sanguin, B. Remenant, Arnaud Dechesne, J. Thioulouse, Timothy M. Vogel, Xavier Nesme...

Applied and Environmental Microbiology . 72 ( 6 ) : 4302-4312

DOI: 10.1128/AEM.02686-05

Journal article

see the publication

Lavandula species as accompanying plants in Cupressus replanting strategies : Effect on plant growth mycorrhizal soil infectivity and soil microbial catabolic diversity

L. Ouahmane, M. Hafidi, C. Plenchette, M. Kisa, A. Boumezzough, J. Thioulouse...

Applied Soil Ecology . -- : 190-199

Journal article

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Identification of Genomic Species in Agrobacterium Biovar 1 by AFLP Genomic Markers

Perrine Portier, Marion Fischer-Le Saux, Christophe Mougel, Catherine Lerondelle, David Chapulliot, Jean Thioulouse...

Applied and Environmental Microbiology . 72 ( 11 ) : 7123-7131

DOI: 10.1128/AEM.00018-06

Journal article

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Fluorescent pseudomonads occuring in Macrotermes subhyalinus mound structures decrease Cd toxicity and improve its accumulation in sorghum plants

R. Duponnois, M. Kisa, K. Assigbetse, Y. Prin, Jean Thioulouse, M. Issartel...

Science of the Total Environment . 370 : 391-400

DOI: 10.1016/j.scitotenv.2006.07.008

Journal article

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Potential of a 16S rRNA-Based Taxonomic Microarray for Analyzing the Rhizosphere Effects of Maize on Agrobacterium spp. and Bacterial Communities

Hervé Sanguin, Benoit Remenant, Arnaud Dechesne, Jean Thioulouse, Timothy M. Vogel, Xavier Nesme...

Applied and Environmental Microbiology . 72 ( 6 ) : 4302-4312

DOI: 10.1128/AEM.02686-05

Journal article

see the publication

Lavendula species as accompanying plants in Cupressus replanting strategies: Effect on plant growth, mycorrhizal soil infectivity and soil microbial catabolic diversity

Lahcen Ouahmane, Mohamed Hadifi, Christian Plenchette, Marija Kisa, Ali Boumezzough, Jean Thioulouse...

Applied Soil Ecology . 34 ( 2-3 ) : 190-199

DOI: 10.1016/j.apsoil.2006.02.002

Journal article

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Soil bacterial diversity responses to root colonization by an ectomycorrhizal fungus are not root-growth dependent

K. Assigbetse, M. Gueye, J. Thioulouse, R. Duponnois

Microbial ecology . 50 : 350-359

Journal article

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Relationships between plant-parasitic nematode community fallow duration and soil factors in the Sudano-Sahelian area of Senegal

P. Cadet, D. Masse, J. Thioulouse

Agriculture, Ecosystems & Environment . 108 : 302-317

Journal article

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The mycorrhizal fungus Glomus intraradices and rock phosphate amendment influence plant growth and microbial activity in the rhizosphere of Acacia holosericea

R. Duponnois, A. Colombet, V. Hien, J. Thioulouse

Soil Biology and Biochemistry . 37 : 1460-1468

Journal article

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Online synonymous codon usage analyses with the ade4 and seqinR packages

D. Charif, J. Thioulouse, J.R. Lobry, G. Perrière

Bioinformatics . 21 : 545-547

Journal article

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Functional diversity of soil microbial community, rock phosphate dissolution and growth of Acacia seyal as influenced by grass-litter and soil-feeding termite nest structure amendments

R. Duponnois, M. Paugy, Jean Thioulouse, D. Masse, Michel Le Page

Geoderma . 124 : 349-361

Journal article

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MADE4: an R package for multivariate analysis of gene expression data

A.C. Culhane, J. Thioulouse, G. Perrière, D.G. Higgins

Bioinformatics . 21 : 2789-2790

Journal article

see the publication

Simultaneous analysis of a sequence of paired ecological tables with the STATICO method

J. Thioulouse, Monique Simier, D. Chessel

Ecology . 85 : 272-283

Journal article

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The ade4 package - I : One-table methods

D. Chessel, Anne-Béatrice Dufour, J. Thioulouse

R News . 4 : 5-10

Journal article

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Une nouvelle analyse multi-temporelle d`images satellitales les residus de l`Analyse en Composantes Principales. Un cas d`etude: une serie d`images Landsat Thematic Mapper de la Camargue France.

T. Naizot, Y. Auda, A. Dervieux, J. Thioulouse, M.F. Bellan

International Journal of Remote Sensing . 25 : 1925-1938

Journal article

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Relationship of nematode communities to human demographics and environment in agricultural fields and fallow lands in Senegal.

P. Cadet, E. Pate, J. Thioulouse

Journal of Tropical Ecology . 19 : 279-290

Journal article

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Procustean co-inertia analysis for the linking of multivariate datasets

S. Dray, D. Chessel, J. Thioulouse

Ecoscience . 10 : 110-119

Journal article

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Co-inertia analysis and the linking of ecological tables

Stéphane Dray, Daniel Chessel, Jean Thioulouse

Ecology . 84 ( 11 ) : 3078-3089

DOI: 10.1890/03-0178

Journal article

see the publication

Comparing and classifying one-dimensional spatial patterns: an application to laser altimeter profiles

S. Ollier, D. Chessel, Pierre Couteron, R. Pelissier, J. Thioulouse

Remote Sensing of Environment . 85 ( 4 ) : 453-462

DOI: 10.1016/S0034-4257(03)00038-5

Journal article

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Integrated databanks access and sequence/structure analysis services at the PBIL.

G. Perriere, C. Combet, Simon Penel, Christophe Blanchet, J. Thioulouse, C. Geourjon...

Nucleic Acids Research . 31 ( 13 ) : 3393-3399

DOI: 10.1093/nar/gkg530

Journal article

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Relationship between spatial and genetic distance in Agrobacterium spp. in 1 cubic centimeter of soil.

J. Vogel, P. Normand, J. Thioulouse, X. Nesme, G. Grundmann

Applied and Environmental Microbiology . 69 : 1482-1487

DOI: 10.1128/AEM.69.3.1482-1487.2003

Journal article

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Use of Correspondence Discriminant Analysis to predict the subcellular location of bacterial proteins

G. Perrière, J. Thioulouse

Computer Methods and Programs in Biomedicine . 70 : 99-105

Journal article

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Comparing and classifying one-dimensional spatial patterns: an application to laser altimeter profiles.

S. Ollier, D. Chessel, P. Couteron, R. Pélissier, J. Thioulouse

Remote Sensing of Environment . 85 : 453-462

Journal article

see the publication

Relationships between Staphylococcus aureus genetic background, virulence factors, agr groups (alleles), and human disease

S. Jarraud, Christophe Mougel, Jean Thioulouse, Gérard Lina, H. Meugnier, F. Forey...

Infection and Immunity . 70 ( 2 ) : 631-641

Journal article

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Relationships between Staphylococcus aureus genetic background virulence factors agr groups (alleles) and human disease.

S. Jarraud, Christophe Mougel, J. Thioulouse, G. Lina, H. Meugnier, F. Forey...

Infection and Immunity . 70 : 631-641

DOI: 10.1128/IAI.70.2.631-641.2002

Journal article

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Interactions between ectomycorrhizal symbiosis and fluorescent pseudomonads on Acacia holosericea: isolation of mycorrhiza helper bacteria (MHB) from a Soudano-Sahelian soil

H. Founoune, R. Duponnois, J.M. Meyer, J. Thioulouse, D. Masse, J.-L. Chotte...

FEMS Microbiology Ecology . 41 : 37-46

Journal article

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Use and misuse of correspondence analysis in codon usage studies

G. Perrière, J. Thioulouse

Nucleic Acids Research . 30 : 4548-4555

Journal article

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A mathematical method for determining genome divergence and species delineation using AFLP

Christophe Mougel, J. Thioulouse, G. Perrière, X. Nesme

International Journal of Systematic and Evolutionary Microbiology . 52 : 573-586

DOI: 10.1099/00207713-52-2-573

Journal article

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A mathematical method for determining genome divergence and species delineation using AFLP

Christophe Mougel, Jean Thioulouse, Guy Perrière, Xavier Nesme

International Journal of Systematic and Evolutionary Microbiology . 52 : 573-586

Journal article

see the publication