Nakombo-Gbassault P., Arenas S., Affortit P., Faye A., Flis P., Sine B., Moukouanga D., Gantet P., Komba E. K., Kane N., Bennett M., Wells D., Cubry P., Bailey E., Grondin A., Vigouroux Y., Laplaze L.. 2025. Genetic control of the leaf ionome in pearl millet and correlation with root and agromorphological traits. PLOS ONE. 20(5). e0319140.

Vi T., Le T. N., Cubry P., Phan V. H., Dinh T. T. O., Tran T. B. N., Nguyen V. T., Millet C. P., Kambale J.-L., Gba Kossia Manzan K., Musoli P., Sumirat U., Mahinga J. C., Stoffelen P., Zhang D., Marraccini P., Vigouroux Y., Khong G. N., Poncet V.. 2025. Out of Africa: The genomic footprints of Vietnamese Robusta coffee. PLOS ONE. 20(5). e0324988.

Kaczmarek T., Cubry P., Champion L., Causse S., Couderc M., Orjuela J., Uyoh E. A., Oselebe H. O., Dachi S. N., Adje C. O. A., Sekloka E., Achigan-Dako E. G., Ibrahim Bio Yerima A. R., Idi Saidou S., Bakasso Y., Diop B. M., Gueye M. C., Agyare R. Y., Adjebeng-Danquah J., Gueye M., Wieringa J. J., Vigouroux Y., Billot C., Barnaud A., Lecler C.. 2025. Independent domestication and cultivation histories of two West African indigenous fonio millet crops. Nature Communications. 16. 4067.

Aqbouch L., Abou-Saaid O., Sarah G., Zunino L., Segura V., Mournet P., Bonal F., Zaher H., El Bakkali A., Cubry P., Costes E., Khadari B.. 2025. Genome-wide association analysis of flowering date in a collection of cultivated olive tree. Horticulture Research. 12(1). uhae265.

Arenas S., Djabali Y., Rincent R., Cubry P., Martin M. L., Blein-Nicolas M., Laplaze L., Schneider H., Grondin A.. 2025. Modeling plant phenotypic plasticity and its underlying genetic architecture: a comparative study. Journal of Experimental Botany. 76:8. 2239–2251.

Zunino L., Cubry P., Sarah G., Mournet P., El Bakkali A., Aqbouch L., Sidibe-Bocs S., Costes E., Khadari B.. 2024. Genomic evidence of genuine wild versus admixed olive populations evolving in the same natural environments in western Mediterranean Basin. PLOS ONE. 19(1). e0295043.

Belton S., Cubry P., Roche J. R., Kelleher C. T.. 2024. Molecular characterisation of Pinus sylvestris (L.) in Ireland at the western limit of the species distribution. BMC Ecology and Evolution. 24. 12.

Ntakirutimana F., Tranchant-Dubreuil C., Cubry P., Chougule K., Zhang J., Wing RA., Adam H., Lorieux M., Jouannic S.. 2023. Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud. G3: Genes| Genomes| Genetics. 13(10). jkad174.

Sedah P., Djedatin L. G., Loko L. Y. E., Ewedje Eebk, Orobiyi A., Gbemavo C. D. S. J., Toffa J., Tchakpa C., Cubry P., Sabot F.. 2023. Impact of seed origin and genetic drift of improved rice variety IR841 in Benin. Rice. 16. 48.

Scotti I., Lalague H., Oddou-Muratorio S., Ruiz Daniels R., Grivet D., Lefevre F., Cubry P., Fady B., Gonzalez-Martinez S. C., Roig A., Lesur Kupin I., Bagnoli F., Guerin V., Plomion C., Rozneberg P., Vendramin G.. 2023. Common microgeographical selection patterns revealed in four European conifers. Molecular Ecology. 32(2). 393-411.

Robson J. K., Ferguson J. N., Mcausland L., Atkinson J. A., Tranchant-Dubreuil C., Cubry P., Sabot F., Wells D. M., Price A. H., Wilson Z. A., Murchie E. H.. 2023. Chlorophyll fluorescence-based high-throughput phenotyping facilitates the genetic dissection of photosynthetic heat tolerance in African (Oryza glaberrima) and Asian (Oryza sativa) rice. Journal of Experimental Botany. 74(17). 5181-5197.

Gain C., Rhoné B., Cubry P., Salazar I., Forbes F., Vigouroux Y., Jay F., François O.. 2023. A Quantitative Theory for Genomic Offset Statistics. Molecular Biology and Evolution. 40(6). msad140.

Vi T., Vigouroux Y., Cubry P., Marraccini P., Phan H.V., Khong G. N., Poncet V.. 2023. Genome-wide admixture mapping identifies wild ancestry-of-origin segments in cultivated Robusta coffee. Genome Biology and Evolution (GBE). 15(5). evad065.

Faye A., Barnaud A., Kane N. A., Cubry P., Mariac C., Burgarella C., Rhoné B., Faye A., Olodo K. F., Cissé A., Couderc M., Dequincey A., Zekraoui L., Moussa D., Tidjani M., Vigouroux Y., Berthouly-Salazar C.. 2022. Genomic footprints of selection in early-and late-flowering pearl millet landraces. Frontiers in Plant Science. 13. 880631.

Cubry P., Oddou-Muratorio S., Scotti I., Lefèvre F.. 2022. Interactions between microenvironment, selection and genetic architecture drive multiscale adaptation in a simulation experiment. Journal of Evolutionary Biology. 35(3). 451-466.

De Aquino Oliveira S., Kiwuka C., Tournebize R., Gain C., Marraccini P., Mariac C., Bethune K., Couderc M., Cubry P., Andrade A., Lepelley M., Darracq O., Crouzillat D., Anten N., Musoli P., Vigouroux Y., De Kochko A., Manel S., François O., Poncet V.. 2022. Adaptive potential of Coffea canephora from Uganda in response to climate change. Molecular Ecology. 31(6). 1800-1819.

De la Fuente Canto C., Diouf M. N., Ndour P. M. S., Debieu M., Grondin A., Passot S., Champion A., Barrachina C., Pratlong M., Gantet P., Assigbetse K., Kane N. A., Cubry P., Diedhiou A., Heulin T., Achouak W., Vigouroux Y., Cournac L., Laplaze L.. 2022. Genetic control of rhizosheath formation in pearl millet. Scientific Reports. 12. 9205.

Affortit P., Effa-Effa B., Ndoye M. S., Moukouanga D., Luchaire N., Cabrera-Bosquet L., Peralvarez M., Pilloni R., Welcker C., Champion A., Gantet P., Diedhiou A. G., Manneh B., Aroca R., Vadez V., Laplaze L., Cubry P., Grondin A.. 2022. Physiological and genetic control of transpiration efficiency in African rice, Oryza glaberrima Steud. Journal of Experimental Botany. 73(15). 5279-5293.

Barro M., Konate K.A., Wonni I., Kassankogno A.I., Sabot F., Albar L., Somda I., Bena G., Ghesquière A., Kam H., Sie M., Cubry P., Tollenaere C.. 2021. Assessment of genetic diversity of rice in registered cultivars and farmers' fields in Burkina Faso. Crops. 1(3). 129-141.

Varshney R., Roorkiwal M., Sun S., Bajaj P., Chitikineni A., Thudi M., Singh N., Du X., Upadhyaya H., Khan A., Wang Y., Garg V., Fan G., Cowling W., Crossa J., Gentzbittel L., Voss-Fels K. P., Valluri V. K., Sinha P., Singh V., Ben C., Rathore A., Punna R., Singh M., Taran B., Bharadwaj C., Yasin M., Pithia M., Singh S., Soren K. R., Kudapa H., Jarquin D., Cubry P., Hickey L., Dixit G. P., Thuillet A.-C., Hamwieh A., Kumar S., Deokar A., Chaturvedi S., Francis A., Howard R., Chattopadhyay D., Edwards D., Lyons E., Vigouroux Y., Hayes B., Von Wettberg E., Datta S., Yang H., Nguyen H., Wang J., Siddique K., Mohapatra T., Bennetzen J., Xu X., Liu X.. 2021. A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature. 599. 622-627.

Peros J., Cousins P., Launay A., Cubry P., Walker A., Prado E., Peressotti E., Wiedemann-Merdinoglu S., Laucou V., Merdinoglu D., This P., Boursiquot J., Doligez A.. 2021. Genetic diversity and population structure in Vitis species illustrate phylogeographic patterns in eastern North America. Molecular Ecology. 30(10). 2333-2348.

Belton S., Cubry P., Fox E., Kelleher C. T.. 2021. Novel post-glacial haplotype evolution in birch: a case for conserving local adaptation. Forests. 12(9). 1246.

Cubry P., Pidon H., Ta KN., Tranchant-Dubreuil C., Thuillet A-C., Holzinger M., Adam H., Kam H., Chrestin H., Ghesquière A., François O., Sabot F., Vigouroux Y., Albar L., Jouannic S.. 2020. Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima. Rice. 13. 66.

Rhoné B., Defrance D., Berthouly-Salazar C., Mariac C., Cubry P., Couderc M., Dequincey A., Assoumanne A., Kane N. A., Sultan B., Barnaud A., Vigouroux Y.. 2020. Pearl millet genomic vulnerability to climate change in West Africa highlights the need for regional collaboration. Nature Communications. 11. 5274.

Labouisse J.-P., Cubry P., Austerlitz F., Rivallan R., Nguyen H. A.. 2020. New insights on spatial genetic structure and diversity of Coffea canephora (Rubiaceae) in Upper Guinea based on old herbaria. Plant Ecology and Evolution. 153(1). 82-100.

Abrouk M., Ahmed H. I., Cubry P., Imonikova D., Cauet S., Pailles Y., Bettgenhaeuser J., Gapa L., Scarcelli N., Couderc M., Zekraoui L., Kathiresan N., Čižkova J., Hřibova E., Doležel J., Arribat S., Berges H., Wieringa J., Gueye M., Kane N., Leclerc C., Causse S., Vancoppenolle S., Billot C., Wicker T., Vigouroux Y., Barnaud A., Krattinger S.. 2020. Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate. Nature Communications. 11. 4488.

Varshney R. K., Thudi M., Roorkiwal M., He W., Upadhyaya H. D., Yang W., Bajaj P., Cubry P., Rathore A., Jian J., Doddamani D., Khan A., Garg V., Chitikineni A., Xu D., Gaur P. M., Singh N. P., Chaturvedi S. K., Nadigatla G., Krishnamurthy L., Dixit G. P., Fikre A., Kimurto P., Sreeman S. M., Bharadwaj C., Tripathi S., Wang J., Lee S.-H., Edwards D., Polavarapu K. K. B., Penmetsa R. V., Crossa J., Nguyen H. T., Siddique K. H. M., Colmer T. D., Sutton T., Von Wettberg E., Vigouroux Y., Xu X., Liu X.. 2019. Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits. Nature Genetics. 51. 857-864.

Scarcelli N., Cubry P., Akakpo R., Thuillet A.-C., Obidiegwu J., Baco M. N., Otoo E., Sonké B., Dansi A., Djedatin G., Mariac C., Couderc M., Causse S., Alix K., Chair H., François O., Vigouroux Y.. 2019. Yam genomics supports West Africa as a major cradle of crop domestication. Science Advances. 5(5). aaw1947.