Names of students and past students are underlined.

2023

[64] Cambon, M.C., Trillat, M., Lesur-Kupin, I., Burlett, R., Chancerel, E., Guichoux, E., Piouceau, L., Castagneyrol, B., Le Provost, G., Robin, S., Ritter, Y., Van Halder, I., Delzon, S., Bohan, D.A., Vacher, C. Microbial biomarkers of tree water status for next-generation biomonitoring of forest ecosystems. Molecular Ecology, accepted

[63] Barroso-Bergadà, D., Tamaddoni-Nezhad, A., Varghese, D., Vacher, C., Galic, N., Laval, V., Suffert, F. and Bohan, D.A. 2023. Unravelling the web of dark interactions: explainable inference of the diversity of microbial interactions, Advances in Ecological Research, accepted

[62] Fournier, P. (*), Jaswa, A. (*), Pellan, L., Vallance, J., Chancerel, E., Bonnard, O., Masneuf-Pomarède, I., Martins, G., Raynal, M., Debord, C., Labarthe, S., Delière, L., Delmotte, F., This, P., Vacher, C. 2023. Towards microbiota-based disease management: analysis of grapevine microbiota in plots with constrasted levels of downy mildew infection. Proceedings of the 22nd GiESCO International Meeting, accepted. (*) co-first authors

[61] Schimann, H., Vacher, C., Coste, S., Louisanna, E., Fort, T., Zinger, L. 2023. Determinants of the vertical distribution of the phyllosphere differ between microbial groups and the epi- and endosphere. Phytobiomes Journal, online (doi: 10.1094/PBIOMES-02-23-0013-R)

[60] Fort, T., Pauvert, C., Chancerel, E., Burlett, R., Wingate, L., Vacher, C. 2023. Leaf microbiome data for European beech (Fagus sylvatica) at the leaf and canopy scales collected in a gallery forest in South-West France. Annals of Forest Science, 80:14 (doi:10.1186/s13595-023-01181-z) [Data and scripts available from Harvard Dataverse (doi: 10.7910/DVN/FFHAQU)]

[59] Barroso-Bergadà, D., Delmotte, F., Faivre d’Arcier, J., Massot, M., Chancerel, E., Demeaux, I., Guimier, S., Guichoux, E., Bohan, D.A., Vacher, C. 2023. Leaf microbiome data for European cultivated grapevine (Vitis vinifera L.) during downy mildew (Plasmopara viticola) epidemics in three wine-producing regions in France. PhytoFrontiers, online (doi: 10.1094/PHYTOFR-11-22-0138-A) [Data and scripts available from Recherche Data Gouv (doi: 10.15454/2YDSBL)]

2022

[58] Fournier P. (*), Pellan L. (*), Barroso-Bergadà D., Bohan D. A., Candresse T., Delmotte F., Dufour M.-C., Lauvergeat V., Le Marrec C., Marais A., Martins G., Masneuf-Pomarède I., Rey P., Sherman D., This P., Frioux C., Labarthe S., Vacher C. 2022. The functional microbiome of grapevine throughout plant evolutionary history and lifetime. Advances in Ecological Research, 67: 27-99. (*) co-first authors (doi: 10.1016/bs.aecr.2022.09.001)

[57] Vacher C., Francioni C., Michel M., Faivre d’Arcier J., Fort T., Chancerel E., Delmotte F., Delmas C. L. 2022. Fungal metabarcoding data for two grapevine varieties (Regent and Vitis vinifera L. cv. Cabernet-Sauvignon) inoculated with powdery mildew (Erysiphe necator) under drought conditions. Phytobiomes Journal, 6:358-367 (doi: 10.1094/PBIOMES-06-22-0037-A) [Data and scripts available from Recherche Data Gouv; doi: 10.15454/KMAU1G and doi:10.15454/PL3HWQ)]

[56] Cambon M. C. (*), Cartry D. (*), Chancerel E., Ziegler C., Levionnois S., Coste S., Stahl C., Delzon S., Buée M., Burban B., Cazal J., Fort T., Goret J-Y., Heuret P., Léger P., Louisanna E., Ritter Y., Bonal D., Roy M., Schimann H. ($), Vacher C ($). 2022. Drought tolerance traits in Neotropical trees correlate with the composition of phyllosphere fungal communities. Phytobiomes Journal, online. (*) co-first authors and ($) co-last authors (doi: 10.1094/PBIOMES-04-22-0023-R) [Data and scripts available from GitLab (project ID: 20709680)]

[55] Barroso-Bergadà, D., Massot, M., Vignolles, N., Faivre d’Arcier, J., Chancerel, E., Guichoux, E., Walker, A-S., Vacher, C., Bohan, D.A., Laval, V., Suffert, F. 2022. Metagenomic next⁃generation sequencing (mNGS) data reveals the phyllosphere microbiome of wheat plants infected by the fungal pathogen Zymoseptoria tritici. Phytobiomes Journal, online (doi: 10.1094/PBIOMES-02-22-0008-FI) [Data and scripts available from Recherche Data Gouv (doi:10.15454/QTXFP9)]

[54] Barroso-Bergadà, D., Tamaddoni-Nezhad A., Muggleton S.H., Vacher C., Galic N., Bohan D.A. 2022. Machine learning of microbial interactions using Abductive ILP and Hypothesis Frequency/Compression Estimation. In: Katzouris N., Artikis A. (eds) Inductive Logic Programming. Lecture Notes in Computer Science, vol 13191. Springer, Cham. (doi: 10.1007/978-3-030-97454-1_3)

[53] Barret M, Buée M, Mougel C, Vacher C. 2020. Plant microbiota : diversity, transmission et function. In Fauvergue X, Malausa T, Rusch A, Jacquin-Joly E, Barret M, Bardin M, Lannou C. (eds). 2020. Extended Biocontrol. Quae editions, collection : Savoir-Faire, Versailles, France (doi: 10.1007/978-94-024-2150-7_9)

2021

[52] Dubart M., Alonso P., Barroso-Bergadà D., Becker N., Bethune K., Bohan D.A., Boury C., Cambon M., Canard E., Chancerel E., Chiquet J., David P., de Manincor N., Donnet S., Duputié A., Facon B., Guichoux E., Le Minh T., Ortiz-Martínez S., Piouceau L., Sacco-Martret de Préville A., Plantegenest M., Poux C., Ravigné V., Robin S., Marine Trillat, Vacher C., Vernière C., Massol F. Coupling ecological network analysis with high-throughput sequencing-based surveys: Lessons from the next-generation biomonitoring project. Advances in Ecological Research, 65: 367-430 (doi: 10.1016/bs.aecr.2021.10.007)

[51] Faticov, M., Abdelfattah, A., Roslin, T., Vacher, C., Hambäck, P., Blanchet, G., Lindahl, B., Tack, A. Climate warming dominates over plant genotype in shaping the seasonal trajectory of foliar fungal communities on oak. New Phytologist, 231: 1770-1783 (doi: 10.1111/nph.17434) [Data available from Dryad (doi:10.5061/dryad.2jm63xsp9)]

[50] Ma Y., Fort T., Marais A., Lefebvre M., Theil S., Vacher C., Candresse T. 2021. Leaf-associated fungal and viral communities of wild plant populations differ between cultivated and natural ecosystems. Plant-Environment Interactions, 2: 87-99 (doi: 10.1002/pei3.10043) [Data and scripts available from Recherche Data Gouv (doi: 10.15454/X23KJF and doi:10.15454/JQPBOW)]

[49] Vacher C., Castagneyrol B., Jousselin E., Schimann H. 2021. Trees and insects have microbiomes: consequences on forest health and management. Current Forestry Reports, 7: 81–96 (doi: 10.1007/s40725-021-00136-9)

[48] Fort T., Pauvert C., Zanne A. E., Ovaskainen O., Caignard T., Barret M., Compant S., Hampe A., Delzon S., Vacher C.  2021. Maternal effects shape the seed mycobiome in Quercus petraea. New Phytologist, 230: 1594–1608 (doi: 10.1111/nph.17153) [Data and scripts available from Recherche Data Gouv (doi:10.15454/0CNFWS)]

[47] Barroso-Bergadà D., Pauvert C., Vallance J., Delière L., Bohan D.A., Buée M., Vacher C. 2021. Microbial networks inferred from environmental DNA data for biomonitoring ecosystem change: strengths and pitfalls. Molecular Ecology Resources, 21: 762–780 (doi: 10.1111/1755-0998.13302) [Raw data, filtered data and scripts available from Recherche Data Gouv (doi: 10.15454/3DPFNJ, doi:10.15454/WOICSE and doi:10.15454/ZWDFJK)]

[46] Compant S., Cambon M., Vacher C., Mitter B., Samad A., Sessitch A. 2021. The plant endosphere world – bacterial life within plants.  Environmental Microbiology, 23(4): 1812–1829 (doi: 10.1111/1462-2920.15240)

2020

[45] Makiola A, Compson ZG, Baird DJ, Barnes MA, Boerlijst SP, Bouchez A, Brennan G, Bush A, Canard E, Cordier T, Creer S, Curry RA, David P, Dumbrell AJ, Gravel D, Hajibabaei M, Hayden B, Hoorn B, Jarne P, Jones JI, Karimi B, Keck F, Kelly M, Knot IE, Krol L, Massol F, Monk WA, Murphy JF, Pawlowski J, Poisot T, Porter TM, Randall KC, Ransome E, Ravigné V, Raybould A, Robin S, Schrama M, Schatz B, Tamaddoni-Nezhad A, Trimbos KB, Vacher C, Vasselon V, Wood S, Woodward G, Bohan DA. 2020. Key questions for next-generation of biomonitoring. Frontiers in environmental science, 7: 197 (doi: 10.3389/fenvs.2019.00197)

[44] Bohan DA, Gravel D, Tamaddoni-Nehzad A, Vacher C, Robin S. 2020. A next-generation of biomonitoring to detect global ecosystem change. E-Book. Frontiers in Ecology and Evolution & Frontiers in Environmental Science (doi: 10.3389/978-2-88966-027-8)

[43] Arnaud-Haond S, Vacher C. 2020. Marine holobiont in the high throughput sequencing era. Recommendation for PCI Ecology (doi : 10.24072/pci.ecology.100045)

[42] Barret M, Buée M, Mougel C, Vacher C. 2020. Le microbiote des plantes : diversité, transmission et fonction. In Fauvergue X, Malausa T, Rusch A, Jacquin-Joly E, Barret M, Bardin M, Lannou C. (eds). 2020. Biocontrôle : Éléments pour une protection agroécologique des cultures. Quae editions, collection : Savoir-Faire, Versailles, France

[41] Pauvert C., Fort T., Calonnec A., Faivre d’Arcier J., Chancerel E., Massot M., Chiquet J., Robin S., Bohan D.A., Vallance J., Vacher C. 2020. Microbial association networks give relevant insights into plant pathobiomes. BioRxiv preprint (doi: 10.1101/2020.02.21.958033)

2019

[40] Pauvert C., Buée M., Laval V., Edel-Hermann V., Fauchery L., Gautier A., Lesur I., Vallance J., Vacher C. 2019. Bioinformatics matters: the accuracy of plant and soil fungal community data is highly dependant on the metabarcoding pipeline. Fungal Ecology, 41: 23-33 (doi: 10.1016/j.funeco.2019.03.005) [Data and scripts available from Recherche Data Gouv (doi:10.15454/8CVWRR and doi:10.15454/VKTWKR)]

[39] Legeay J., Husson C., Cordier T., Vacher C., Marcais B., Buée M. 2019. Comparison and validation of Oomycetes metabarcoding primers for Phytophthora high-throughput sequencing. Journal of Plant Pathology, 101(3), 743-748 (doi: 10.1007/s42161-019-00276-9)

[38] Compant, C., Vacher, C. Sources, niches and routes of colonization by beneficial bacterial endophytes. 2019. In: Endophyte biotechnology: promise for agriculture and pharmacology (Ed. A Schouten), CABI Biotechnology Series (doi: 10.1079/9781786399427.0032)

2018

[37] Derocles, S.A.P., Bohan, D.A., Dumbrell, A.J., Kitson, J.J.N, Massol, F., Pauvert, C., Plantegenest, M., Vacher, C., Evans, D.M. 2018. Biomonitoring for the 21st Century: Integrating Next-Generation Sequencing Into Ecological Network Analysis. Advances in Ecological Research, 58: 1-62 (doi: 10.1016/bs.aecr.2017.12.001)

2017

[36] Bohan, D. A., Vacher, C., Tamaddoni-Nezhad, A., Dumbrell, A.J., Woodward, G. 2017. Next-generation Biomonitoring: large-scale, automatic reconstruction of ecological networks. Trends in Ecology and Evolution, 32(7): 477-487 (doi: 10.1016/j.tree.2017.03.001)

[35] Lemanceau, P., Barret, M., Mazurier, S., Mondy, S., Pivato, B., Fort, T., Vacher C. 2017. Plant communication with associated microbiota in the spermosphere, rhizosphere and phyllosphere. Advances in Botanical Research, 82: 101-133 (doi: 10.1016/bs.abr.2016.10.007)

2016

[34] REX Consortium. 2016. Combining selective pressures to enhance the durability of disease resistance genes. Frontiers in Plant Science 7:1916 (doi: 10.3389/fpls.2016.01916)

[33] Fort, T., Robin, C., Capdevielle, X., Delière, L., Vacher C. 2016. Foliar fungal communities strongly differ between habitat patches in a landcape mosaic. PeerJ, 4:e2656 (doi: 10.7717/peerj.2656)

[32] Jakuschkin, B., Fievet, V., Schwaller, L., Fort, T., Robin, C., Vacher, C. 2016. Deciphering the pathobiome: intra- and inter-kingdom interactions involving the pathogen Erysiphe alphitoides. Microbial Ecology, 72(4):870-880 (doi: 10.1007/s00248-016-0777-x)

[31] Vacher, C., Hampe, A., Porté, A.J., Sauer, U., Compant, S., Morris, C.E. 2016. The phyllosphere: microbial jungle at the plant-climate interface. Annual Review of Ecology, Evolution, and Systematics, vol. 47, 1-24 (doi: 10.1146/annurev-ecolsys-121415-032238)

[30] Vacher, C., Cordier, T., Vallance, J. 2016. Phyllosphere fungal communities differentiate more thoroughly than bacterial communities along an elevation gradient. Microbial Ecology, 72(1):1-3 (doi: 10.1007/s00248-016-0742-8)

[29] QUINTESSENCE Consortium. 2016. Networking our way to better Ecosystem Service provison. Trends in Ecology and Evolution, 31(2):105-115 (doi: 10.1016/j.tree.2015.12.003)

[28] Vacher, C., Tamaddoni-Nezhad A., Kamenova, S., Peyrard, N., Moalic, Y., Sabbadin, R., Schwaller, L., Chiquet, J., Smith, M. A., Vallance, J., Fievet, V., Jakuschkin, B., Bohan, D.A. 2016. Learning Ecological Networks from Next-Generation Sequencing Data. Advances in Ecological Research, 54, 1-39 (doi: 10.1016/bs.aecr.2015.10.004)

[27] Plomion, C., Bastien, C., Bogeat-Triboulot, M.-B., Bouffier, L., Déjardin, A., Duplessis, S., Fady, B., Heuertz, M., Le Gac, A.-L., Le Provost, G., Legué, V., Lelu-Walter, M.-A., Leplé, J.-C., Maury, S., Morel, A., Oddou-Muratorio, S., Pilate, G., Sanchez, L., Scotti, I., Scotti-Saintagne, C., Segura, V., Trontin, J.-F., Vacher, C.. 2016. Forest tree genomics: 10 achievements from the past 10 years and future prospects. Annals of Forest Science, 73:77 (doi: 10.1007/s13595-015-0488-3)

[26] Desprez-Loustau, M-L., Agayo, J. Dutech, C., Hayden, K.J., Husson, C., Jakuschkin, B., Marçais, B., Piou, D., Robin, C.,  Vacher, C. 2016. An evolutionary ecology perspective to address forest pathology challenges of today and tomorrow. Annals of Forest Science, 73:45 (doi: 10.1007/s13595-015-0487-4)

2015

[25] Mulder, C., Bennett, E.M., Bohan, D.A., Bonkowski, M., Carpenter, S.R., Chalmers, R., Cramer, W., Durance, I., Eisenhauer, N., Fontaine, C., Haughton, A.J., Hettelingh, J-P., Hines, J., Ibanez, S., Jeppesen, E., Krumins, J.A., Ma, A., Mancinelli, G., Massol, F., McLaughlin, O., Naeem, S., Pascual, U., Peñuelas, J., Pettorelli, N., Pocock, M.J.O., Raffaelli, D., Rasmussen, J.J., Rusch, G.M., Scherber, C., Setälä, H., Sutherland, W.J., Vacher, C., Voigt, W., Vonk, J.A., Wood, S.A., Woodward, G. 2015. 10 Years Later: Revisiting Priorities for Science and Society a Decade after the Millennium Assessment. Advances in Ecological Research, 53, 1-53 (doi: 10.1016/bs.aecr.2015.10.005)

[24] Leger, J-B., Daudin, J-J., Vacher, C. 2015. Clustering methods differ in their ability to detect patterns in ecological networks. Methods in Ecology and Evolution 6(4): 474-481 (doi: 10.1111/2041-210X.12334)

2014

[23] Coince, A., Cordier, T., Lengellé, J., Defossez, E., Vacher, C., Robin, C., Buée, M., Marçais, C. 2014.  Leaf and root-associated fungal assemblages do not follow similar elevational diversity patterns. PLOS ONE 9(6): e100668 (doi: 10.1371/journal.pone.0100668)

[22] Leger, J-B., Vacher C, Daudin, J-J. 2014. Detection of structurally homogeneous subsets in graphs. Statistics & Computing 24: 675-692 (doi: 10.1007/s11222-013-9395-3)

[21] Castagneyrol, B., Jactel, H., Vacher, C., Koricheva, J., Brockerhoff, E. 2014. Effects of plant phylogenetic diversity on herbivory depend on herbivore specialization. Journal of Applied Ecology 54: 675-692 (doi: 10.1111/1365-2664.12175)

2013

[20] Lagache, L., Leger, J-B., Daudin, J-J., Petit, R., Vacher C. 2013. Putting the biological species concept to the test: using mating networks to delimit species. PLOS ONE, 8(6): e68267 (doi: 10.1371/journal.pone.0068267)

[19] REX Consortium. 2013. Heterogeneity of selection pressures and the evolution of resistance. Trends in Ecology and Evolution 28(2):110-118 (doi: 10.1016/j.tree.2012.09.001)

[18] REX Consortium. 2013. Gestion des résistances: l’importance des modalités de déploiement des substances. Phytoma 669: 10-14

2012

[17] Cordier, T., Robin, C., Capdevielle, X., Fabreguettes, O., Desprez-Loustau, M-L., Vacher C. 2012. The composition of phyllosphere fungal assemblages of European beech (Fagus sylvatica L.) varies significantly along an elevation gradient. New Phytologist 196: 510-519 (doi: 10.1111/j.1469-8137.2012.04284.x)

[16] Cordier, T., Robin, C., Capdevielle, X., Desprez-Loustau, M-L., Vacher C. 2012. Spatial variability of phyllosphere fungal assemblages: genetic distance predominates over geographic distance in a European beech stand (Fagus sylvatica). Fungal Ecology 5: 509-520 (doi: 10.1016/j.funeco.2011.12.004)

2011

[15] Vacher, C., Kossler, T. M., Hochberg, M., Weis, A.E. 2011. Impact of interspecific hybridization between crops and weedy relatives on the evolution of flowering time in weedy phenotypes. PLOS ONE 6(2): e14649 (doi: 10.1371/journal.pone.0014649)

[14] Philibert, A., Desprez-Loustau, M-L., Fabre, B., Frey, P., Halkett, F., Husson, C., Lung-Escarmant, B., Marçais, B. Robin, C., Vacher, C., Makowski, D. 2011. Predicting invasion success of forest pathogenic fungi from species traits. Journal of Applied Ecology 48(6): 1381-1390 (doi: 10.1111/j.1365-2664.2011.02039.x)

2010

[13] REX Consortium. 2010. The skill and style to model the evolution of resistance to pesticide and drugs. Evolutionary Applications 3(4): 375-390 (doi: 10.1111/j.1752-4571.2010.00124.x)

[12] Mariadassou, M., Robin, S., Vacher, C. 2010. Uncovering latent structure in valued graphs: a variational approach. Annals of Applied Statistics 4(2):715-742 (doi : 10.1214/10-AOAS361)

[11] Vacher, C., Daudin, J-J., Piou, D., Desprez-Loustau, M-L. 2010. Ecological integration of alien species into a tree-parasitic fungus network. Biological Invasions 12:3249-3259 (doi: 10.1007/s10530-010-9719-6)

[10] Daudin, J-J., Pierre, L., Vacher, C. 2010. Model for heterogeneous random networks using continuous variables and an application to a tree-fungus network. Biometrics 66:1043-1051 (doi: 10.1111/j.1541-0420.2009.01378.x)

2008

[9] Vacher, C., Piou, D., Desprez-Loustau, M-L. 2008. Architecture of an antagonistic tree/fungus network: the asymmetric influence of past evolutionary history. PLOS ONE 3(3):e1740 (doi: 10.1371/journal.pone.0001740)

[8] Vacher, C., Vile, D., Helion, M. Piou, D., Desprez-Loustau, M-L. 2008. Distribution of parasitic fungal species richness: influence of climate versus host species diversity. Diversity and Distributions 14(5):786-798 (doi: 10.1111/j.1472-4642.2008.00479.x)

2007

[7] REX Consortium. 2007. Structure of the scientific community modelling the evolution of resistance. PloS ONE 2(12):e1275 (doi: 10.1371/journal.pone.0001275)

2006 and before

[6] Vacher, C., Bourguet, D., Desquilbet, M., Lemarié, M., Ambec, S. and M.E. Hochberg. 2006. Fees or refuges: which is better for the sustainable management of insect resistance to transgenic Bt corn? Biology Letters 2: 198-202 (doi: 10.1098/rsbl.2005.0418)

[5] Vacher, C., Brown, S. and M.E. Hochberg. 2005.  Avoid, attack or do both? Behavioral and physiological adaptations in natural enemies faced with novel hosts. BMC Evolutionary Biology 5: 60 (doi: 10.1186/1471-2148-5-60)

[4] Weis, A.E., Winterer, J. A., Vacher, C., Freshwater, M., Kossler, T.M., Young, C.A. and G. LeBuhn. 2005. Phenological assortative mating in flowering plants: the nature and consequences of its frequency-dependance. Evolutionary Ecology Research 7: 161-181

[3] Vacher, C., Weis, A.E., Hermann, D., Kossler, T.M., Young, C. and M.E. Hochberg. 2004. Impact of ecological factors on the initial invasion of Bt transgenes into wild populations. Theoretical and Applied Genetics 109: 806-814 (doi: 10.1007/s00122-004-1696-7)

[2] Vacher, C., Bourguet, D., Rousset, F., Chevillon, C. and M.E. Hochberg. 2004. High dose refuge strategies and genetically modified crops – Reply to Tabashnik et al. Journal of Evolutionary Biology 17: 913-918 (doi: 10.1111/j.1420-9101.2004.00730.x)

[1] Vacher, C., Bourguet, D., Rousset, F., Chevillon, C. and M.E. Hochberg. 2003. Modelling the spatial configuration of refuges for a sustainable control of pests: a case study of Bt cotton. Journal of Evolutionary Biology 16: 378-387 (doi: 10.1046/j.1420-9101.2003.00553.x)