Bibliographic references

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Slimani N, Guilbert E, White JC, Hill MJ, Wood PJ, Boumaïza M, Thioulouse J (2022) Unravelling the environmental correlates influencing the seasonal biodiversity of aquatic Heteropteran assemblages in northern Africa. Limnologica - - -

Thioulouse J, Renaud S, Dufour AB, Dray S (2021) Overcoming the Spurious Groups Problem in Between-Group PCA. Evolutionary Biology, 48(4), 458-471. - - -
Slimani N, Sánchez-Fernández D, Guilbert E, Boumaïza M, Thioulouse J (2021) Water Quality Shapes Freshwater Macroinvertebrate Communities in Northern Tunisia. In: Ksibi M et al. (Eds) Recent Advances in Environmental Science from the Euro-Mediterranean and Surrounding Regions (2nd Edition) 2021. -
Hugoni M, Nunan N, Thioulouse J, Dubost A, Abrouk D, Martins J, Goffner D, Prigent-Combaret C, Grundmann G (2020) Small scale variability in bacterial communities' structure in different soil types. Microbial Ecology, 82, 470-483. -

Chiaruzzi M, Barbry A, Muggeo A, Tristan A, Jacquemond I, Badiou C, Cluzeau L, Patot-Bourdeau S, Durand T, Engelmann A, Bosquet D, Bes M, Prigent-Combaret C, Thioulouse J, Muller D, and Lina G (2020) Vaginal tampon colonization by Staphylococcus aureus in healthy women. Applied and Environmental Microbiology 86:18 e01249-20. -
Slimani N, Jiménez JJ, Guilbert E, Boumaïza M, Thioulouse J (2020) Surface water quality assessment in a semiarid Mediterranean region (Medjerda, Northern Tunisia) using partial triadic analysis Environmental Science and Pollution Research 27, 30190-30198 -

Slimani N, Sánchez-Fernández D, Guilbert E, Boumaïza M, Guareschi S, Thioulouse J (2019) Assessing potential surrogates of macroinvertebrate diversity in North-African Mediterranean aquatic ecosystems Ecological Indicators 101, 324-329. -

Thioulouse J, Dray S, Dufour AB, Siberchicot A, Jombart T, Pavoine S (2018) Multivariate Analysis of Ecological Data with ade4. 330p. Springer Statistics books - Front Matter - ISBN: 978-1-4939-8848-8 - - -
Jacquemond I, Muggeo A, Lamblin G, Tristan A, Gillet Y, Bolze PA, Bes M, Gustave CA, Rasigade JP, Golfier F, Ferry T, Dubost A, Abrouk D, Barreto S, Prigent-Combaret C, Thioulouse J, Lina G, and Muller D (2018) Complex ecological interactions of Staphylococcus aureus in tampons during menstruation. Scientific Reports 8:9942. -
Nonfoux L, Chiaruzzi M, Badiou C, Baude J, Tristan A, Thioulouse J, Muller D, Prigent Combaret C, and Lina G. (2018) Impact of currently marketed tampons and menstrual cups on Staphylococcus aureus growth and TSST-1 production in vitro. Applied and Environmental Microbiology 84:12 -

Siberchicot A, Julien-Laferrière A, Dufour AB, Thioulouse J, Dray S (2017) adegraphics: An S4 Lattice-Based Package for the Representation of Multivariate Data. The R Journal 9, 2, 198-212. - -
Duponnois R, Thioulouse J, Baudoin E, Le Roux C, Galiana A, Prin Y (2017) Raisonner l'utilisation des légumineuses ligneuses pour réhabiliter des sols dégradés en milieu méditerranéen et tropical. Innovations Agronomiques 60, 125-131. -
Slimani N, Guilbert E, El Ayni F, Jrad A, Boumaïza M, Thioulouse J (2017) The use of STATICO and COSTATIS, two exploratory three-ways analysis methods. An application to the ecology of aquatic Heteroptera in the Medjerda watershed (Tunisia). Environmental and Ecological Statistics 24, 269-295. - -
Benkhoua N, Hafidi M, Badri W, Baudoin E, Thioulouse J, Prin Y, Galiana A, Ouahmane L, Ouhammou A, Sanguin H, Duponnois R (2017) Management of the mycorrhizal soil infectivity with Crotalaria ochroleuca, an indigenous wild legume in the tropics: Impacts onmicrobial functional diversity involved in phosphorus mobilizationprocesses in a sahelian soil. Ecological Engineering 72, 717-724. - -

Michelland R, Thioulouse J, Kyselková M, Grundmann G (2016) Bacterial Community Structure at the Microscale in Two Different Soils. Microbial Ecology 72, 717-724.
Wahbi S, Prin Y, Thioulouse J, Sanguin H, Baudoin E, Maghraoui T, Oufdou K, Le Roux C, Galiana A, Hafidi M, Duponnois R (2016) Impact of wheat / faba bean mixed cropping or rotation systems on soil microbial functionalities. Frontiers in Plant Science. 7:1364. - -
Deredjian A, Alliot N, Blanchard L, Brothier E, Amane M, Cambier P, Jolivet C, Khelil M N, Nazaret S, Saby N, Thioulouse J, Favre-Bonté S (2016) Occurrence of Stenotrophomonas maltophilia in agricultural soils and antibiotic resistance properties. Research in Microbiology. 167, 313-324.

Wahbi S, Prin Y, Maghraoui T, Sanguin H, Thioulouse J, Oufdou K, Hafidi M, Duponnois R (2015) Field Application of the Mycorrhizal Fungus Rhizophagus irregularis Increases the Yield of Wheat Crop and Affects Soil Microbial Functionalities. American Journal of Plant Sciences. 6, 3205-3215. doi:10.4236/ajps.2015.619312.
Manaut N, Sanguin H, Ouahmane L, Bressan M, Thioulouse J, Baudoin E, Galiana A, Hafidi M, Prin Y, Duponnois R (2015) Potentialities of ecological engineering strategy based on native arbuscular mycorrhizal community for improving afforestation programs with carob trees in degraded environments. Ecological Engineering. 79, 113-119. doi:10.1016/j.ecoleng.2015.03.007.

Dieng A, Baudoin E, Thioulouse J, Brunet D, Toucet J, Sylla S N, Brauman A (2014). Soil Organic Matter Quality, Structure And Activity Of The Denitrifiers Community As Influenced By Decaying Mulched Crop Residues. Applied Ecology And Environmental Research. 13, 655-675. DOI: 10.15666/aeer/1303_655675.
Chemidlin Prévost-Bouré N, Dequiedt S, Thioulouse J, Lelièvre M, Saby NPA, Jolivet C, Arrouays D, Lemanceau P, Ranjard L (2014). Similar processes but different environmental filters for soil bacterial and fungal community composition turnover on a broad spatial scale. PLoS ONE. 9(11): e111667. doi:10.1371/journal.pone.0111667.
Ramanankierana H, Baohanta R, Randriambanona H, Prin Y, Rakotoarimanga N, Baudoin E, Thioulouse J, Galiana A, Lebrun M, Dreyfus B and Duponnois R (2014). Ectomycorrhizal fungi on the early colonizing shrub Sarcolaena oblongifolia F. facilitate the establishment of an endemic tree Uapaca bojeri L. in Madagascarian highland forests. International Journal of Ecology and Ecosolution. 1, 1-15.

Duponnois R, Baudoin E, Sanguin H, Thioulouse J, Le Roux C, Tournier E, Galiana A, Prin Y, Dreyfus B (2013). L'introduction d'acacias australiens pour réhabiliter des écosystèmes dégradés est-elle dépourvue de risques environnementaux ? Bois Et Forêts Des Tropiques. 318, 59-65.
Thioulouse J, Sanguin H, Prin Y, Duponnois R (2013). Méthodes d'analyse multivariée pour l'étude de l'influence de la mycorhizosphère sur la structure et le fonctionnement des communautés bacteriennes du sol. In Duponnois R, Hafidi M, Ndoye I, Ramanankierana H, Bâ A. (Eds.) Des champignons symbiotiques contre la désertification. Ecosystèmes mediterranéens, tropicaux et insulaires. Marseille: IRD Editions. ISBN : 978-2-7099-1827-5, pp 475-508.
Boudiaf I, Baudoin E, Sanguin H, Beddiar A, Thioulouse J, Galiana A, Prin Y, Le Roux C, Lebrun M and Duponnois R. (2013). The exotic legume tree species, Acacia mearnsii, alters microbial soil functionalities and the early development of a native tree species, Quercus suber, in North Africa. Soil Biology & Biochemistry. 65, 172-179.
Hafidi M, Ouahmane L, Thioulouse J, Sanguin H, Boumezzough A, Prin Y, Baudoin E, Galiana A and Duponnois R. (2013). Managing Mediterranean nurse plants-mediated effects on soil microbial functions to improve rock phosphate solubilization processes and early growth of Cupressus atlantica G. Ecological Engineering. 57, 57-64.
Duponnois R, Ramanankierana H, Hafidi M, Baohanta R, Baudoin E, Thioulouse J, Sanguin H, Ba A, Galiana A, Bally R, Lebrun M, and Prin Y. (2013). Des ressources végétales endémiques pour optimiser durablement les opérations de réhabilitation du couvert forestier en milieu méditerranéen et tropical : Exemple des plantes facilitatrices vectrices de propagation des champignons mycorhiziens. Comptes Rendus Biologies. 336, 265-272.
Ranjard L, Dequiedt S, Chemidlin Prévost-Bouré N, Thioulouse J, Saby N P A, Lelievre M, Maron P A, Morin F E R, Bispo A, Jolivet C, Arrouays D, Lemanceau P. (2013). Turnover of soil bacterial diversity driven by wide-scale environmental heterogeneity. Nature Communications. 4 (1434), 1-10. DOI: 10.1038/ncomms2431.
Ndoye I, Soumaré A, Agbangba E C, Thioulouse J, Galiana A, Prin Y, Duponnois R (2013). A new process to promote the use of controlled mycorrhization practice in forest nurseries. African Journal of Agricultural Research. 8, 308-316.
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 (2013). Ectomycorrhizal diversity enhances growth and nitrogen fixation of Acacia mangium seedlings. Soil Biology & Biochemistry, 57, 468-476.
Ramanankierana H, Baohanta R, Thioulouse J, Prin Y, Randriambanona H, Baudoin E, Rakotoarimanga N, Galiana A, Rajaonarimamy E, Lebrun M and Duponnois R (2013). Early Growth Improvement on Endemic Tree Species by Soil Mycorrhizal Management in Madagascar. in Carlos Alberto Busso (Ed.), From Seed Germination to Young Plants: Ecology, Growth and Environmental Influences , Chapter 15, pp 30. Nova Science Publishers.

Thioulouse J, Prin Y, Duponnois R (2012). Multivariate analyses in soil microbial ecology: a new paradigm. Environmental and Ecological Statistics. 19, 499-520.
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.
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.
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.
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.

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 -
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.
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.
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.
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.
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.

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. <hal-00539265> -
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.
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.

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.
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.
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.
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.
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, 259-278.
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.
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.
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.
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.

Remigi P., Faye A., Kane A., Deruaz M., Thioulouse J., Cissoko M., Prin Y., Galiana A., Dreyfus B., & Duponnois R. (2008). The exotic legume tree species Acacia holosericea alters microbial soil functionalities and the structure of the arbuscular mycorrhizal community. Applied and Environmental Microbiology 74, 5, 1485-1493.
Thioulouse J. (2008). Multivariate Data Analysis in Microbial Ecology - New Skin for the old Ceremony. Invited lecture, useR! 2008 conference. August 12-14, Technische Universität Dortmund, Germany.

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.
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.
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.
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.
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. -
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.
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.

Culhane A.C., & Thioulouse J. (2006). A multivariate approach to integrating datasets using made4 and ade4. R News, 6, 5, 54-58.
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.
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. <hal-00128068>
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.
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.
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.
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.
Sanguin, H., Remenant, B., Dechesne, A., Thioulouse, J., Vogel, T.M., Nesme, X., Moenne-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.
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.
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.
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.

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.
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.
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.
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.
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.
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.

Naizot T., Auda Y., Dervieux A., Thioulouse J. & Bellan M.F. (2004). 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. Int. J. Remote Sensing, 25, 1925-1938.
Thioulouse J., Simier M. & Chessel D. (2004). Simultaneous analysis of a sequence of paired ecological tables. Ecology, 85, 272-283.
Chessel D., Dufour A.B., & Thioulouse J. (2004). The ade4 package - I : One-table methods. R News, 4, 1, 5-10.

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.
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.
Dray S., Chessel D., & Thioulouse J. (2003). Co-inertia analysis and the linking of ecological tables. Ecology, 84, 3078-3089.
Dray S., Chessel D., & Thioulouse J. (2003). Procustean co-inertia analysis for the linking of multivariate datasets. Ecoscience, 10, 110-119.
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.
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.
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.

Perrière G., & Thioulouse J. (2002) Use and misuse of correspondence analysis in codon usage studies. Nucleic Acid Research, 30, 4548-4555.
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.
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
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.

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.
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.
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.

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.
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.
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.
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.
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.
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.
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

Duponnois R., Senghor K., Thioulouse J., Ba A. (1999) Susceptibility of several sahelian Acacia to Meloidogyne javanica (Treub) Chitw. Agroforestry Systems, 46, 123-130

Simier M., Thioulouse J., Olivier J.M. (1998) ADE-4 Software: a tool for multivariate analysis and graphical display. Océanis, vol. 24, n° 4, p. 393-416. Institut océanographique, 2001. <hal-03623926>
Robert V., Awono-Ambene H.P. & Thioulouse J. (1998) Ecology of mosquitoes at larval stage with special reference to Anopheles arabiensis (Diptera: Culcidae) in market-garden wells in the urban area of Dakar, Senegal. Journal of Medical Entomology, 35, 948-955.
Cadet P., & Thioulouse J. (1998) Identification of soil factors that relate to the structure of the plant parasitic nematode community. Applied Soil Ecology, 8, 35-49.

Champely S., Guinand B., Thioulouse J., & Clermidy A. (1997) Functional data analysis of curve asymmetry with application to the color pattern of Hydropsyche contubernalis head capsule. Biometrics, 53, 294-305.
Thioulouse J., Chessel D., Dolédec S., & Olivier J.M. (1997) ADE-4: a multivariate analysis and graphical display software. Statistics and Computing, 7, 1, 75-83


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.
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.
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.

Thioulouse J., Chessel D. & Champely S. (1995) Multivariate analysis of spatial patterns: a unified approach to local and global structures. Environmental and Ecological Statistics,2, 1-14.
Thioulouse J. & Lobry J.R. (1995) Co-inertia analysis of amino-acid physico-chemical properties and protein composition with the ADE package. Computer Applications in the Biosciences., 11, 3, 321-329.
Thioulouse J., Doledec S., Chessel D. & Olivier J.M. (1995) ADE software: multivariate analysis and graphical display of environmental data. In: Guariso G. & Rizzoli A. (Eds) Software per l'ambiente, Patron editore, Bologne, pp. 57-62.

Cadet P., Thioulouse J. & Albrecht A. (1994) Relationships between ferrisol properties and the structure of plant parasitic nematode communities on sugarcane in Martinique (French West Indies). Acta Oecologica, 15, 6, 767-780.

Thioulouse J., Royet J.P., Ploye H. & Houllier F. (1993) Evaluation of the Precision of Systematic Sampling : Nugget Effect and Covariogram Modelling. Journal of Microscopy, 172, 249-256.
Devillers J., Thioulouse J. & Karcher W. (1993) Chemometrical Evaluation of Multispecies- Multichemical Data by Means of Graphical Techniques Combined to Multivariate Analyses. Ecotoxicology and Environmental Safety, 26, 333-345.

Thioulouse J. & Chessel D. (1992) A method for reciprocal scaling of species tolerance and sample diversity. Ecology, 73, 2, 670-680.

Devillers J., Thioulouse J., Domine D., Chastrette M. & Karcher W. (1991) Multivariate Analysis of the Input and Output Data in the Fugacity Model Level I. In: Devillers J. & Karcher W. (Eds) Applied Multivariate Analysis in SAR and Environmental Studies, Kluwer Academic Publishers, p. 281-345.
Thioulouse J., Devillers J., Chessel D. & Auda Y. (1991) Graphical Techniques for Multidimensional Data Analysis. In: Devillers J. & Karcher W. (Eds) Applied Multivariate Analysis in SAR and Environmental Studies, Kluwer Academic Publishers, p. 153-205.

Thioulouse J. (1990) MacMul and GraphMu :two Macintosh programs for the display and analysis of multivariate data. Computers and Geosciences, 16, 8, 1235-1240. <hal-00698262>
Chessel D. & Thioulouse J. (1990) Auto-Modélisation en Analyse des Données. In: Brissaud M., Forse M., & Zighed A. (Eds) Modélisation, confluent des Sciences, Editions du CNRS, p. 71-86. <hal-03593117>

Thioulouse J. (1989) Statistical analysis and graphical display of multivariate data on the Macintosh. Computer Applications in the Biosciences., 5, 4, 287-292. <hal-00698254>
Cadet P. & Thioulouse J. (1989) Traitements nématicides et peuplement de nématodes parasites de la canne à sucre au Burkina Faso. I : Repousses. Revue de Nematologie, 12, 1, 35-44. <hal-03602913>

Thioulouse J. & Chessel D. (1987) Les analyses multitableaux en écologie factorielle. I : de la typologie d'état à la typologie de fonctionnement par l'analyse triadique. Acta Oecologica, Oecologia Generalis, 8, 4, 463-480. <hal-00698250>
Thioulouse J. (1987) Space-Time Structure in a Winter Rape Pest Population, Psylliodes chrysocephala (Col. chrysomelidae): methodological proposals and biological interpretations. Journal of Applied Ecology, 24, 435-450. <hal-00698253>

Debouzie D. & Thioulouse J. (1986) Statistics to find spatial and temporal structures in populations. In: Mangel M. (Ed.), Pest control: operations and system analysis in fruit fly managment, NATO ASI Series, Vol. G11, Springer Verlag, p. 263-282. <hal-03602844>
Debouzie D. & Thioulouse J. (1986) Les populations naturelles d'insectes: existence de structures spatiales et temporelles, leur rôle dans la biologie des populations. Actes du Colloque National CNRS "Biologie des populations", p. 90-97. <hal-03602836>

Thioulouse J., Mathy B. & Ploye H. (1985) Estimation d'un Volume à partir de Coupes Seriées : Sous-Echantillonnage, Covariogramme Transitif et Calcul de Précision. Mikroskopie (Wien), 42, 215-224. <hal-00698258>
Thioulouse J., Houllier F. & Onillon J.C. (1985) Variables régionalisées et dénombrement d'Insectes : cas unidimensionnel. Comptes Rendus de l'Academie des Sciences de Paris, 301, 9, 423-428. <hal-00698256>

Thioulouse J., Debouzie D. & Ballanger Y. (1984) Structures spatiales et temporelles des populations d'un ravageur du Colza (Psylliodes chrysocephala L. (Col., Chrysomelidae)) dans plusieurs parcelles de culture. Acta Oecologica, Oecologia Applicata, 5, 4, 335-353. <hal-00698257>