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.

Grégoire L., Kholova J., Srivastava R., Hash C. T., Vigouroux Y., Vadez V. 2024. Transpiration efficiency variations in the pearl millet reference collection PMiGAP. PLOS ONE. 19(7). e0299686.

De la Fuente C., Grondin A., Sine B., Debieu M., Belin C., Hajjarpoor A., Atkinson J., Passot S., Salson M., Orjuela J., Tranchant-Dubreuil C., Brossier J.-R., Steffen M., Morgado C., Dinh H. N., Pandey B., Darmau J., Champion A., Petitot A.-S., Barrachina C., Pratlong M., Mounier T., Gantet P., Gangashetty P., Guedon Y., Vadez V., Reichheld J.-P., Bennett M., Kane N., Guyomarc'h S., Wells D., Vigouroux Y., Laplaze L. 2024. Glutaredoxin regulation of primary root growth confers early drought stress tolerance in pearl millet. eLife. 12.

Salson M., Orjuela J., Mariac C., Zekraoui L., Couderc M., Arribat S., Rodde N., Faye A., Kane N., Vigouroux Y., Tranchant-Dubreuil C., Berthouly-Salazar C. 2023. An improved assembly of the pearl millet reference genome using Oxford Nanopore long reads and optical mapping. G3: Genes| Genomes| Genetics. 13(5). 1-7.

Tranchant-Dubreuil C., Chenal C., Blaison M., Albar L., Klein V., Mariac C., Wing R. A., Vigouroux Y., Sabot F. 2023. FrangiPANe, a tool for creating a panreference using left behind reads. NAR Genomics and Bioinformatics. 5(1). lqad013.

Tenaillon M. I., Burban E., Huynh S., Wojcik A., Thuillet A.-C., Manicacci D., Gerard P. R., Alix K., Belcram H., Cornille A., Brault M., Stevens R., Lagnel J., Dogimont C., Vigouroux Y., Glemin S. 2023. Crop domestication as a step toward reproductive isolation. American Journal of Botany. 110(7). e16173.

Kaczmarek T., Causse S., Abdul S. D., Abraham S., Achigan‐dako E. G., Adje C., Adjebeng-Danquah J., Agyare R. Y., Akanvou L., Bakasso Y., Barry M. B., Bonsy S. K., Calatayyd C., Conde S., Couderc M., Dachi S. N., Diallo T., Diop B. M., Deu M., Gueye M. C., Ibrahim Bio Yerima A. R., Issah A. R., Kane N. A., Keita Y., James K., Ngom A., Noyer J.-L., Olodo K., Oselebe H. O., Pham J.-L., Piquet M., Puozaa D. K., Rivallan R., Saidou S., Sekloka E., Tengey T. K., Uyoh E. A., Vancoppenolle S., Vigouroux Y., Zekraoui L., Leclerc C., Barnaud A., Billot C. 2023. Towards conservation and sustainable use of an indigenous crop: A large partnership network enabled the genetic diversity assessment of 1539 fonio (Digitaria exilis) accessions. Plants, People, Planet. 7(3). 621-630.

Escobar S., Vigouroux Y., Karubian J., Zekraoui L., Balslev H., Montufar R. 2023. Limited seed dispersal shapes fine‐scale spatial genetic structure in a Neotropical dioecious large‐seeded palm. Biotropica. 55(1). 160-172.

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.

Diop B., Guèye M., Leclerc C., Deu M., Zekraoui L., Calatayud C., Rivallan R., Kaly J., Cisse M., Piquet M., Diack O., Ngom A., Berger A., Ndoye I., Ndir K., Vigouroux Y., Kane N., Barnaud A., Billot C. 2023. Ethnolinguistic and genetic diversity of fonio (Digitaria exilis) in Senegal. Plants, People, Planet. 7(3). 666-678.

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.

Tournebize R., Borner L., Manel S., Meynard C., Vigouroux Y., Crouzillat D., Fournier C., Kassam M., Descombes P., Tranchant-Dubreuil C., Parrinello H., Kiwuka C., Sumirat U., Legnate H., Kambale J., Sonké B., Mahinga J. C., Musoli P., Janssens S. B., Stoffelen P., De Kochko A., Poncet V. 2022. Ecological and genomic vulnerability to climate change across native populations of Robusta coffee (Coffea canephora). Global Change Biology. 28(13). 4124-4142.

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.

De La Fuente Canto C., Vigouroux Y. 2022. Evaluation of nine statistics to identify QTLs in bulk segregant analysis using next generation sequencing approaches. BMC Genomics. 23(1). 490.

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.

Mofini M.-T., Diedhiou A., Simonin M., Dondjou D. T., Pignoly S., Ndiaye C., Min D., Vigouroux Y., Laplaze L., Kane A. 2022. Cultivated and Wild Pearl Millet Display Contrasting Patterns of Abundance and Co-occurrence in their root mycobiome. Scientific Reports. 12. 207.

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.

Mariac C., Renno J.-F., Garcia-Davila C., Vigouroux Y., Mejia E., Angulo C., Castro Ruiz D., Estivals G., Nolorbe C., Garcia Vasquez A., Nunez J., Cochonneau G., Florez M., Alvarado J., Vertiz J., Chota-Macuyama W., Sanchez H., Miranda G., Duponchelle F. 2021. Species-level ichthyoplankton dynamics for 97 fishes in two major river basins of the Amazon using quantitative metabarcoding. Molecular Ecology. 31(6). 1627-1648.

Rimlinger A., Avana M.-L., Awono A., Chakocha A., Gakwavu A., Lemoine T., Marie L., Mboujda F., Vigouroux Y., Jognson V., Vinceti B., Carriere S., Duminil J. 2021. Trees and their seed networks: The social dynamics of urban fruit trees and implications for genetic diversity. PLOS ONE. 16(3). e0243017.

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.

Olodo K., Barnaud A., Kane N., Mariac C., Faye A., Couderc M., Zekraoui L., Dequincey A., Diouf D., Vigouroux Y., Berthouly-Salazar C. 2020. Abandonment of pearl millet cropping and homogenization of its diversity over a 40 year period in Senegal. PLOS ONE. 15(9). e0239123.

Le Corre V., Siol M., Vigouroux Y., Tenaillon M. I., Délye C. 2020. Adaptive introgression from maize has facilitated the establishment of teosinte as a noxious weed in Europe. Proceedings of the National Academy of Sciences of the United States of America (PNAS). 117(41). 25618-25627.

Diack O., Kanfany G., Gueye M. C., Sy O., Fofana A., Tall H., Serba D., Zekraoui L., Berthouly-Salazar C., Vigouroux Y., Diouf D., Kane N. A. 2020. GWAS unveils features between early- and late-flowering pearl millets. BMC Genomics. 21. 777.

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.

Grondin A., Affortit P., Tranchant-Dubreuil C., De la Fuente-Canto C., Mariac C., Gantet P., Vadez V., Vigouroux Y., Laplaze L. 2020. Aquaporins are main contributors to root hydraulic conductivity in pearl millet [Pennisetum glaucum (L) R. Br.]. PLOS ONE. 15(10). e0233481.

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.

Tournebize R., Poncet V., Jakobsson M., Vigouroux Y., Manel S. 2019. McSwan: A joint site frequency spectrum method to detect and date selective sweeps across multiple population genomes. Molecular Ecology Resources. 19(1). 283-295.

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.

Olodo K. F., Gueye M. C., Calatayud C., Diop B. M., Kane N. A., Ngom A., Ntui V. O., Barreto M.-M., Uyoh E. A., Abraham S., Vigouroux Y., Billot C., Barnaud A. 2019. EST-SSR development for Digitaria exilis and its relatives D. iburua and D. longiflora from transcriptome sequences. Plant Genetic Resources. 17(3). 280-284.

Magwe-Tindo J., Wieringa J. J., Sonké B., Zapfack L., Vigouroux Y., Couvreur T. L. P., Scarcelli N. 2019. Complete plastome sequences of 14 African yam species (Dioscorea spp.). Mitochondrial DNA Part B: Resources. 4(1). 74-76.

Burgarella C., Barnaud A., Kane N. A., Jankowski F., Scarcelli N., Billot C., Vigouroux Y., Berthouly-Salazar C. 2019. Adaptive Introgression: An Untapped Evolutionary Mechanism for Crop Adaptation. Frontiers in Plant Science. 10. 1-17.

Bethune K., Mariac C., Couderc M., Scarcelli N., Santoni S., Ardisson M., Martin J.-F., Montufar R., Klein V., Sabot F., Vigouroux Y., Couvreur T. L. P. 2019. Long-fragment targeted capture for long-read sequencing of plastomes. Applications in Plant Sciences. 7(5). e1243.