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2012
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Thioulouse J, Prin Y, Duponnois R
(2012).
Multivariate analyses in soil microbial ecology: a new paradigm.
Environmental and Ecological Statistics.
19, 499-520.
Reproducibility page: 
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Diagne N, Thioulouse J, Prin Y, Krasova-Wade T, Sylla S, Galiana A, Baudoin E, Neyra M, Sanguin H,
Svistoonoff S, Lebrun M and Duponnois R
(2012).
Ectomycorrhizal diversity enhances growth and nitrogen fixation of Acacia mangium seedlings.
Soil Biology & Biochemistry,
57, 468-476
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Dray S, Pélissier R, Couteron P, Fortin MJ, Legendre P, Peres-Neto PR, Bellier E, Bivand R, Blanchet FG, De Cáceres M, Dufour AB, Heegaard E, Jombart T, Munoz F, Oksanen J, Thioulouse J and Wagner HH.
(2012).
Community ecology in the age of multivariate multiscale spatial analysis.
Ecological Monographs, 82, 257-275.
Reproducibility page:
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Baohanta, R, Thioulouse J, Ramanankierana H, Prin Y, Rasolomampianina R, Baudoin E, Rakotoarimanga N, Galiana A, Randriambanona H, Lebrun M & Duponnois R.
(2012).
Restoring native forest ecosystems after exotic tree plantation in Madagascar: combination of the local ectotrophic species Leptolena bojeriana and Uapaca bojeri mitigates the negative influence of the exotic species Eucalyptus camaldulensis and Pinus patula.
Biological Invasions, 14, 2407-2421.
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Bilgo A, Sangare S K, Thioulouse J, Prin Y, Hien V, Cissoko M, Galiana A, Baudoin E, Bâ A M, Hafidi M, Dreyfus B, Duponnois R.
(2012).
Response of native soil microbial functions to the controlled mycorrhization of an exotic tree legume, Acacia holosericea in a Sahelian ecosystem.
Mycorrhiza,
22, 175-187.
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Duponnois R, Baudoin E, Thioulouse J, Galiana A, Lebrun M & Prin Y.
(2012).
The impact of mycorrhizosphere bacterial communities on soil biofunctioning in Tropical and Mediterranean forest ecosystems.
in D. K. Maheshwari (Ed.), Bacteria In Agrobiology: Plant Probiotics, pp 79-95.
Springer-Verlag, Berlin.
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2011
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Thioulouse J
(2011).
Simultaneous analysis of a sequence of paired ecological tables: a comparison of several methods.
Annals of Applied Statistics,
5, 2300-2325.
arXiv link - Reproducibility page:
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Duponnois R, Ouahmane L, Kane A, Thioulouse J, Hafidi M, Boumezzough A, Prin Y,
Baudoin E, Galiana A, Dreyfus B.
(2011).
Nurse shrubs increased the early growth of Cupressus seedlings by enhancing
belowground mutualism and soil microbial activity.
Soil Biology & Biochemistry,
43, 2160-2168.
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Vergnes M, Ginevra C, Kay E, Normand P, Thioulouse J, Jarraud S, Maurin M, Schneider D
(2011).
Insertion Sequences as Highly Resolutive Genomic Markers for Sequence Type 1 Legionella pneumophila Paris.
Journal of Clinical Microbiology,
49, 315-324.
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Arrouays D, Saby NPA, Thioulouse J, Jolivet C, Boulonne L, Ratié C (2011).
Large trends in French topsoil characteristics are revealed by spatially constrained multivariate analysis.
Geoderma,
161, 107-114.
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Dequiedt S, Saby NPA, Lelievre M, Jolivet C, Thioulouse J, Toutain B, Arrouays D, Bispo A, Lemanceau P, Ranjard L
(2011).
Biogeographical Patterns of Soil Molecular Microbial Biomass as Influenced by Soil Characteristics and Management.
Global Ecology and Biogeography,
20, 641-652.
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Valiente-Moro C, Thioulouse J, Chauve C, Zenner L.
(2011).
Diversity, geographic distribution and habitat specific variations of microbiota in natural populations of the chicken mite, Dermanyssus gallinae.
Journal of Medical Entomology,
48, 4, 788-796.
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2010
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Thioulouse J, Valiente-Moro C, Zenner L.
(2010).
Online reproducible research: an application to multivariate analysis of bacterial DNA fingerprint data.
R Journal,
2, 44-52.
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Ranjard L, Dequiedt S, Jolivet C, Saby NPA, Thioulouse J, Harmand J, Loisel P, Rapaport A, Fall S, Simonet P, Joffre R, Chemidlin-Prévost Bouré N, Maron PA, Mougel C, Martin MP, Toutain B, Arrouays D, Lemanceau P.
(2010).
Biogeography of soil microbial communities: a review
and a description of the ongoing french national initiative.
Agronomy for Sustainable Development,
30, 359-365.
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-
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Manaut N, Chaffii K, Ouhammou A, Ouahmane L, Thioulouse J, Hafidi M, Boumezzough A, Prin Y, Galiana A, Baudoin E, Lebrun M & Duponnois R
(2010).
Shrub Plants and Associated Mycorrhizal Fungi Sustainably Improve the Native Tree Establishment in Mediterranean Ecosystems.
in G. S. Williams (Ed.), Mediterranean Ecosystems:
Dynamics, Management and Conservation,
Nova Publishers, New York.
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2009
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Saby NPA, Thioulouse J, Jolivet C, Ratié C., Boulonne L, Bispo A, Arrouays D
(2009).
Multivariate analysis of the spatial patterns of 8 trace elements using the French Soil Monitoring Network data.
Science of the Total Environment,
407, 5644-5652.
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Duponnois R, Hafidi M, Thioulouse J, Galiana A, Ouahmane L, Dreyfus B, & Prin Y
(2009).
Monitoring the Development of Nurse Plant Species to Improve the Performances of Reforestation Programs in Mediterranean Areas.
in M.S. Khan et al. (eds.), Microbial Strategies for Crop Improvement,
Springer-Verlag, Berlin, p. 255-265.
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Dequiedt S, Thioulouse J, Jolivet C, Saby NPA, Lelievre M, Maron PA, Martin MP, Chemidlin Prévost-Bouré N, Toutain B, Arrouays D, Lemanceau P & Ranjard L
(2009).
Biogeographical patterns of soil bacterial communities.
Environmental Microbiology Reports
1, 251-255.
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Dequiedt S, Lelièvre M, Jolivet C, Saby NPA, Martin M, Thioulouse J, Maron PA, Mougel C, Chemidlin Prévost-Bouré N, Arrouays D, Lemanceau P, & Ranjard L.
(2009).
Biogéographie microbienne à l'échelle de la France - Etat d'avancement et premiers résultats.
Etude et Gestion des Sols
16, 219-231.
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Sanon A., Andrianjaka Z., Prin Y., Bally R., Thioulouse J., Comte G., & Duponnois R.
(2009).
Rhizosphere microbiota interfers with plant-plant interactions.
Plant & Soil
321, 259Ð278.
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Faye, A., Krasova-Wade, T., Thiao, M., Thioulouse, J., Neyra, M., Prin, Y., Galiana, A., NDoye, I., Dreyfus, B. and Duponnois, R.
(2009).
Controlled ectomycorrhization of an exotic legume tree species Acacia holosericea affects the structure of root nodule bacteria community and their symbiotic effectiveness on Faidherbia albida, a native sahelian Acacia.
Soil Biology & Biochemistry
41, 1245-1252.
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Ouahmane, L., Revel, J.C., Hafidi, M., Thioulouse, J., Prin, Y., Galiana, A., Dreyfus, B. & Duponnois, R.
(2009).
Responses of Pinus halepensis growth, microbial soil functionalities and phosphate-solubilizing bacteria after rock phosphate amendment and ectomycorrhizal inoculation.
Plant & Soil,
320, 169-179.
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Santos C., Tavares F., Thioulouse J., Normand P.
(2009).
A phylogenomic analysis of bacterial helix-turn-helix transcription factors.
FEMS Microbiology Reviews
33, 411-429.
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Valiente Moro C., Thioulouse J., Chauve C., Normand P., Zenner L.
(2009).
Bacterial taxa associated with the hematophagous mite, Dermanyssus gallinae detected by 16S rDNA PCR amplification and TTGE fingerprint.
Research in Microbiology
160, 63-70.
Reproducibility page:
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2007
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Thioulouse J., & Dray S.
(2007).
Interactive Multivariate Data Analysis in R with the ade4 and ade4TkGUI Packages.
Journal of Statistical Software
22, 5, 1-14.
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Andrianjaka Z., Bally R., Lepage M., Thioulouse J., Comte G., & Duponnois, R.
(2007).
Biological control of Striga hermonthica by Cubitermes termite mound powder amendment in sorghum culture.
Applied Soil Ecology
37, 175-183.
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Kisa M., Sanon A., Thioulouse J., Assigbetse K., Sylla S., Dieng L., Berthelin J., Prin Y., Galiana A., Lepage M. & Duponnois R.
(2007).
Arbuscular mycorrhizal symbiosis can counterbalance the negative influence of the exotic tree species Eucalyptus camaldulensis on the structure and functioning of soil microbial communities in a sahelian soil
FEMS Microbiology Ecology,
62, 32-44.
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Ouahmane L., Hafidi M., Thioulouse J., Ducousso M., Kisa M., Prin Y., Galiana A., Boumezzough A., & Duponnois R.
(2007).
Improvement of Cupressus atlantica Gaussen growth by inoculation with native arbuscular mycorrhizal fungi.
Journal of Applied Microbiology
103, 683-690.
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Lasne F., Thioulouse J., Martin L. & de Ceaurriz J.
(2007).
Detection of recombinant human erythropoietin in urine for doping
analysis: interpretation of isoelectric profiles by discriminant analysis.
Electrophoresis
28, 1875-1881.
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Ouahmane L., Thioulouse J., Hafidi M., Prin Y., Galiana A., Plenchette C., Kisa M., & Duponnois R.
(2007).
Soil functional diversity and P solubilization from rock phosphate after inoculation with native or allochtonous arbuscular mycorrhizal fungi.
Forest Ecology and Management
241, 200-208.
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Ramanankierana N., Ducousso M., Rakotoarimanga N., Prin Y., Thioulouse J., Randrianjohany E., Ramaroson L., Kisa M., Galiana A. & Duponnois, R.
(2007).
Arbuscular mycorrhizas and ectomycorrhizas of Uapaca bojeri L. (Euphorbiaceae): sporophore diversity, patterns of root colonization and effects on seedling growth and soil microbial catabolic diversity.
Mycorrhiza,
17, 3, 195-208.
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2006
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Culhane A.C., & Thioulouse J.
(2006).
A multivariate approach to integrating datasets using made4 and ade4.
R News,
6, 5, 54-58.
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Diallo M.D., Duponnois R., Guisse A., Sall S., Chotte J.-L., Thioulouse J.
(2006).
Biological effects of native and exotic plant residues on plant growth,
microbial biomass and N availability under controlled conditions.
European Journal of Soil Biology,
42, 238-246.
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Portier P., Fischer-Le Saux M., Mougel C., Lerondelle C., Chapulliot D., Thioulouse J., and Nesme X.
(2006).
Identification of genomic species from Agrobacterium biovar 1 by AFLP genomic markers.
Applied and Environmental Microbiology,
72, 7123-7131.
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Duponnois R., Assigbetse K., Ramanankierana H., Kisa M., Thioulouse, J. & Lepage, M.
(2006).
Litter-forager termite mounds enhance the ectomycorrhizal symbiosis between
Acacia holosericea A. Cunn. Ex G. Don and Scleroderma dictyosporum isolates.
FEMS Microbiology Ecology,
56, 292-303.
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Le Hesran J.Y., Fievet N., Thioulouse J., Personne P., Maubert B., M'bidias S., Etye'ale D., Cot M., & Deloron P.
(2006).
Development of cellular immune responses to Plasmodium falciparum blood stage antigens from birth
to 36 months of age in Cameroon.
Acta Tropica,
98, 261-269.
|
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Duponnois R., Kisa M., Assigbetse K., Prin Y., Thioulouse J., Issartel M., Moulin P., & Lepage M.
(2006).
Fluorescent pseudomonads occuring in Macrotermes subhyalinus mound structures decrease Cd toxicity and improve its accumulation in sorghum plants.
Science of the Total Environment,
370, 391-400.
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Ouahmane L., Hafidi M., Plenchette C., Kisa M., Boumezouch A., Thioulouse J. & Duponnois R.
(2006).
Lavandula species as accompanying plants in Cupressus replanting strategies:
effect on plant growth, mycorrhizal soil infectivity and soil microbial catabolic diversity.
Applied Soil Ecology,
34, 190-199.
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Sanguin, H., Remenant, B., Dechesne, A., Thioulouse, J., Vogel, T.M., Nesme, X., Moënne-Loccoz, Y., Grundmann, G.L.
(2006).
Potential of a 16S rRNA-Based Taxonomic Microarray for Analyzing the Rhizosphere Effects of Maize on
Agrobacterium spp. and Bacterial Communities.
Applied and Environmental Microbiology,
72, 4302-4312.
|
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Ouahmane L., Duponnois R., Hafidi M., Kisa M., Boumezouch A., Thioulouse J. & Plenchette C.
(2006).
Some Mediterranean plant species (Lavandula spp. and Thymus satureioides) act
as potential "plant nurses" for the early growth of Cupressus atlantica.
Plant Ecology,
185, 123-134.
|
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Ramanankierana N., Rakotoarimanga N., Thioulouse J., Kisa M., Randrianjohany E., Ramaroson L. & Duponnois R.
(2006).
The ectomycorrhizosphere effect influences functional diversity of soil microflora.
International Journal of Soil Science,
1, 8-19.
|
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Sanon A., Martin P., Thioulouse J., Plenchette C., Spichiger R., Lepage M. & Duponnois R.
(2006).
Displacement of an herbaceous plant species community by mycorrhizal and non mycorrhizal Gmelina arborea, an exotic tree, grown in a microcosm experiment.
Mycorrhiza,
16, 125-132.
|
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2005
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Assigbetse K., Gueye M., Thioulouse, J. & Duponnois R.
(2005).
Soil bacterial diversity responses to root colonization by an ectomycorrhizal fungus
are not root-growth dependent.
Microbial Ecology,
50, 350-359.
|
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Duponnois, R., Colombet, A., Hien, V., & Thioulouse, J.
(2005).
The mycorrhizal fungus Glomus intraradices and rock phosphate amendment influence plant growth
and microbial activity in the rhizosphere of Acacia holosericea.
Soil Biology and Biochemistry,
37,1460-1468.
|
|
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Duponnois, R., Paugy, M., Thioulouse J., Masse, D. & Lepage, M.
(2005).
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.
Geoderma,
124, 349-361.
|
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Cadet P., Masse D. & Thioulouse, J.
(2005).
Relationships between plant-parasitic nematode community, fallow duration and soil factors
in the Sudano-Sahelian area of Senegal.
Agriculture, Ecosystems and Environment,
102, 302-317.
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|
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Culhane A.C., Thioulouse J., Perrière G., & Higgins D.G.
(2005).
MADE4: an R package for multivariate analysis of gene expression data.
Bioinformatics,
21, 2789 - 2790.
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Charif, D., Thioulouse, J., Lobry, J.R., & Perrière, G.
(2005).
Online synonymous codon usage analyses with the ade4 and seqinR packages.
Bioinformatics,
21, 545-547.
Reproducibility page:
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2003
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Vogel J., Normand P., Thioulouse J., Nesme X., & Grundmann G.
(2003).
Relationship between spatial and genetic distance in Agrobacterium spp. in 1 cubic centimeter of soil.
Applied and Environmental Microbiology,
69, 1482-1487.
|
|
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Cadet P., Pate E. & Thioulouse J.
(2003).
Relationship of nematode communities to human demographics and environment in agricultural
fields and fallow lands in Senegal.
Journal of Tropical Ecology,
19, 279-290.
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Dray S., Chessel D., & Thioulouse J.
(2003).
Co-inertia analysis and the linking of ecological tables.
Ecology,
84, 3078-3089.
|
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Dray S., Chessel D., & Thioulouse J.
(2003).
Procustean co-inertia analysis for the linking of multivariate datasets.
Ecoscience,
10, 110-119.
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Ollier S., Chessel D., Couteron P., Pélissier R., & Thioulouse J. (2003).
Comparing and classifying one-dimensional spatial patterns: an application to laser altimeter profiles.
Remote Sensing of Environment,
85, 453-462.
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Perrière G., Combet C., Penel S., Blanchet C.Thioulouse J.,
Geourjon C., Grassot J., Charavay C., Gouy M., Duret L. & Deléage G.
(2003).
Integrated databanks access and sequence/structure analysis services at the PBIL.
Nucleic Acids Research,
31, 3393-3399.
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Perrière G., & Thioulouse J.
(2003).
Use of correspondence discriminant analysis to predict the subcellular location
of bacterial proteins.
Computer Methods and Programs in Biomedicine,
70, 99-105.
|
|
2002
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Perrière G., & Thioulouse J.
(2002)
Use and misuse of correspondence analysis in codon usage studies.
Nucleic Acid Research,
30, 4548-4555.
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Founoune, H., Duponnois, R., Meyer, J.M., Thioulouse, J., Masse, D., Chotte, J.L. & Neyra, M.
(2002)
Interactions between ectomycorrhizal symbiosis and fluorescent Pseudomonads on Acacia holosericea: isolation of Mycorrhiza
Helper Bacteria (MHB) from a soudano-sahelian soil.
FEMS Microbiology Ecology,
41, 37-46.
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Pontier D., Say L., Debias F. Bried J., Thioulouse J., Micol T, & Natoli E.
(2002)
The diet of feral cats (Felis catus L.) at five sites on the Grande Terre, Kerguelen archipelago.
Polar Biology,
25, 833-837
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Mougel C., Thioulouse J., Perrière G. & Nesme X.
(2002)
A mathematical method for determining genome divergence and species delineation using AFLP.
International Journal of Systematic and Evolutionary Microbiology,
52, 573-586
|
|
|
Jarraud S., Mougel C., Thioulouse J., Lina G., Meugnier H.,
Forey F., Nesme X., Etienne J. & Vandenesch F.
(2002)
Relationships between Staphylococcus aureus genetic background,
virulence factors, agr type (alleles) and human disease type.
Infection and Immunity,
70, 631-641.
|
|
2001
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Mougel C., Teyssier S., d'Angelo C., Groud K., Neyra M., Sidi-Boumedine K., Cloeckaert A., Peloille M., Baucheron S., Chaslus-Dancla E., Jarraud S.,
Meugnier H., Forey F, Vandenesch F., Lina G., Etienne J, Thioulouse J.,
Manceau C., Robbe P., Nalin R., Briolay J., Nesme X. (2001)
Experimental and theoretical evaluation of typing methods based upon random
amplification of genomic restriction fragments (AFLP) for bacterial
population genetics.
Genet. Sel. Evol.,
33 (Suppl. 1), S319-S338.
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Ranjard L., Poly F., Lata J.C., Mougel C., Thioulouse J. & Nazaret S.
(2001)
Characterisation of bacterial and fungal soil communities by automated-RISA
(Ribosomal Intergenic Spacer Analysis) fingerprints: biological and methodological
variability.
Applied and Environmental Microbiology,
67,4479-4487.
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Duponnois R., Plenchette, C., Thioulouse J., & Cadet P. (2001)
Mycorrhizal soil infectivity and AM fungal spore communities of different aged fallows in Senegal.
Applied Soil Ecology,
17, 239-251.
|
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2000
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Cadet P., Bois J.-F., Chotte J.-L. , Duponnois R., N'Diaye-Faye ND., Floret Ch., FouldS., Manlay R., Masse D.,
Mateille T., Normand Ph., Pate E., Plenchette Ch., Thioulouse J., Villenave C. & Fardoux J. (2000)
Recherche de méthodes de gestion des peuplements de nématodes phytoparasites par les facteurs du sol en zone soudano-sahélienne au Sénégal.
Etude et Gestion des Sols,
2, 435-442.
|
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Duponnois R., Fargette, M., Fould, S., Thioulouse J., & Davies K.G. (2000)
Diversity of the bacterial hyperparasite Pasteuria penetrans in relation to the control of root-knot nematodes (Meloidogyne spp.) on Acacia holosericea.
Nematology,
2, 435-442.
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Ranjard L., Poly F., Combrisson J., Richaume A., Gourbière F., Thioulouse J. & Nazaret S. (2000)
Heterogeneous Cell Density and Genetic Structure of Bacterial Pools Associated with Various
Soil Microenvironments as Determined by Enumeration and DNA Fingerprinting Approach
(RISA).
Microbial Ecology,
39, 263-272.
|
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|
Reynaud P.A. & Thioulouse J. (2000)
Identification of birds as biological markers along a neotropical urban-rural gradient using co-inertia analysis.
Journal of Environmental Management,
59, 121-140.
|
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|
Manlay R., Cadet P., Thioulouse J. & Chotte J.L. (2000)
Relationships between abiotic and biotic soil properties during fallow periods in the sudanian zone of Senegal.
Applied Soil Ecology,
14, 89-101.
|
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Duponnois R., Founoune, H., Lesueur, D., Thioulouse J., & Neyra M. (2000)
Ectomycorrhization of six Acacia auriculiformis provenances from Australia, Papua New Guinea and Senegal
in glasshouse conditions: effect on the plant growth and on the multiplication of plant parasitic nematodes.
Australian Journal of Experimental Agriculture,
40, 443-450.
|
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Pate E., Ndiaye-Faye N., Thioulouse J., Villenave C., Bongers T., Cadet P. & Debouzie D. (2000)
Successional trend in characteristics of soil nematode communities in cropped and fallow lands in Senegal (Sonkorong).
Applied Soil Ecology,
14, 5-15 |
|
|
Ranjard L., Nazaret S., Gourbière F., Thioulouse J., Linet P. & Richaume A. (2000)
A soil microscale study to reveal the heterogeneity of Hg(II) impact on indigenous bacteria by quantification of adapted phenotypes and analysis of community DNA fingerprints.
FEMS Microbiology Ecology,,
31, 107-115 |
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1996
|
|
Thioulouse J. (1996)
Outils logiciels, méthodes statistiques et implications biologiques : une approche
de la biométrie. Mémoire d'Habilitation à Diriger des Recherches.
Université Lyon 1, 106 p.
|
|
|
Perrière G., Lobry J. & Thioulouse J. (1996)
Correspondence discriminant analysis : a multivariate method for comparing classes of
protein and nucleic acid sequences.
Computer Applications in the Biosciences, 12, 6, 519-524.
Reproducibility page:
|
|
Thioulouse J. (1996)
Towards Better Graphics for Multivariate Analysis: the Interactive Factor Map.
Computational Statistics,
11, 11-21.
|
|
Thioulouse J. & Chevenet F. (1996)
NetMul, a World-Wide Web user interface for multivariate analysis sofware.
Computational Statistics and Data Analysis, 21, 3, 369-372.
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Perriere G. & Thioulouse J. (1996)
On-line tools for sequence retrieval and multivariate statistics in molecular biology.
Computer Applications in the Biosciences., 12, 1, 63-69.
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