• Muyle A. 2025. Treasurer’s Report for Financial Year 2024. Mol Biol Evol:msaf328.
• Muyle A. 2025. Adaptation beyond the DNA sequence. Nature Plants News and Views. 11:1987–1988. PubMed PMID: 40940426. pdf
• Prentout D, Muyle A, Zemp N, Filali A el, Boussau B, Touzet P, Widmer A, Käfer J, Marais GAB. 2025. Evolution of sex-biased gene expression during transitions to separate sexes in the Silene genus. Molecular Biology and Evolution. 42:msaf229. PubMed PMID: 40991749. pdf
• Eddy Mendoza-Galindo and Aline Muyle. 2025. The contribution of small RNAs to the evolution of separate sexes and sex chromosomes in the plant Silene latifolia. Journal of Evolutionary Biology. 38:952–967. PubMed PMID: 40319379. pdf
• Moraga, C., Branco, C., Rougemont, Q., Jedlička, P., Mendoza-Galindo, E., Veltsos, P., Hanique, M., Rodrı́guez de la Vega, R.C., Tannier, E., Liu, X., Lemaitre, C., Fields, P.D., Cruaud, C., Labadie, K., Belser, C., Briolay, J., Santoni, S., Cegan, R., Linheiro, R., Adam, G., El Filali, A., Mossion, V., Boualem, A., Tavares, R., Chebbi, A., Cordaux, R., Fruchard, C., Prentout, D., Velt, A., Spataro, B., Delmotte, S., Weingartner, L., Toegelová, H., Tulpová, Z., Cápal, P., Šimková, H., Štorchová, H., Krüger, M., Abeyawardana, O.A.J., Taylor, D.R., Olson, Sloan, D.B., Karrenberg, S., Delph, L.F., Charlesworth, D., Muyle, A., Giraud, T., Bendahmane, A., Di Genova, A., Madoui, M.-A., Hobza, R., Marais, G.A.B., 2025. The Silene latifolia genome and its giant Y chromosome. Science 387, 630–636. PubMed PMID: 39913565. pdf
• Muyle A. 2025. Treasurer’s Report for Financial Year (FY) 2023. Molecular Biology and Evolution. 42:msaf046. PubMed PMID: 40036526. pdf
• Saunders PA, Muyle A. 2024. Sex chromosome evolution: hallmarks and question marks. Molecular Biology and Evolution. PubMed PMID: 39417444. Perspective celebrating the 40th anniversary of MBE. pdf
• Martin GT, Solares E, Guadardo-Mendez J, Muyle A, Bousios A, Gaut BS. 2023. miRNA-like secondary structures in maize (Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression. Genome Research 33:1932–1946. PubMed PMID: 37918960. pdf
• Song Y, Peng Y, Liu L, Li G, Zhao X, Wang X, Cao S, Muyle A, Zhou Y, Zhou H. 2023. Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes. Horticulture Research uhad252. PubMed PMID: 38269295. pdf
• Aline Muyle, Gabriel Marais, Václav Bačovský, Roman Hobza, Thomas Lenormand. 2022. Dosage compensation in plants: theories, controversies, mechanisms and emerging evolutionary patterns. Philosophical Transactions of the Royal Society B. 377, 20210222. PubMed PMID: 35306896. pdf
• Aline Muyle, Danelle Seymour, Yuanda Lv, Bruno Huettel, Brandon Gaut. 2022. Gene-body methylation in plants: mechanisms, functions and important implications for understanding evolutionary processes. Genome Biology and Evolution evac038. PubMed PMID: 35298639. pdf
• Muyle A, Ross-Ibarra J, Seymour DK, Gaut BS. 2021. Gene body methylation is under selection in Arabidopsis thaliana. Genetics 218:iyab061. PubMed PMID: 33871638. Featured in Genetics Highlights. pdf
• Muyle A, Seymour D, Darzentas N, Primetis E, Gaut BS, Bousios A. 2021. Gene capture by transposable elements leads to epigenetic conflict in maize. Molecular Plant 14:237–252. PubMed PMID: 33171302. pdf
• Muyle A, Bachtrog D, Marais GAB, Turner JMA. 2021. Epigenetics drive the evolution of sex chromosomes in animals and plants. Philosophical Transactions of the Royal Society B 376:20200124. PubMed PMID: 33866802. pdf
• Muyle A, Martin H, Zemp N, Mollion M, Gallina S, Tavares R, Silva A, Bataillon T, Widmer A, Glémin S, Touzet P, Marais GA. 2021. Dioecy Is Associated with High Genetic Diversity and Adaptation Rates in the Plant Genus Silene. Molecular Biology and Evolution 38:805–818. PubMed PMID: 32926156. pdf
• Boquete MT, Muyle A, Alonso C. 2021. Plant epigenetics: phenotypic and functional diversity beyond the DNA sequence. American Journal of Botany 108:553–558. PubMed PMID: 33887061. pdf
• He L, Jia K-H, Zhang R-G, Wang Y, Shi T-L, Li Z-C, Zeng S-W, Cai X-J, Wagner ND, Hörandl E, Muyle A, Yang K, Charlesworth D, Mao JF. 2021. Chromosome-scale assembly of the genome of Salix dunnii reveals a male-heterogametic sex determination system on chromosome 7. Molecular Ecology Resources. PubMed PMID: 33609314. pdf
• Fruchard C, Badouin H, Latrasse D, Devani RS, Muyle A, Rhoné B, Renner SS, Banerjee AK, Bendahmane A, Marais GAB. 2020. Evidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System. Genes (Basel) 11. PubMed PMID: 32668777. pdf
• Massonnet M, Cochetel N, Minio A, Vondras AM, Muyle A, Lin J, Garcia JF, Zhou Y, Delledonne M, Riaz S, Figueroa-Balderas R, Gaut BS, Cantu D. 2020. The genetic basis of sex determination in grapevines. Nature Communication. 11, 2902. PubMed PMID: 32518223. pdf
• Roessler K, Muyle A, Diez CM, Gaut GRJ, Bousios A, Stitzer MC, Seymour DK, Doebley JF, Liu Q, Gaut BS. 2019. The genome-wide dynamics of purging during selfing in maize. Nature Plants 5:980–990. PubMed PMID: 31477888. pdf
• Muyle A. 2019. How different is the evolution of sex-biased gene expression between plants and animals? A commentary on: “Sexual dimorphism and rapid turnover in gene expression in pre-reproductive seedlings of a dioecious herb.” Annals of Botany 123:iv–v. PubMed PMID: 31282546. pdf
• Veltsos P, Ridout KE, Toups MA, González-Martı́nez SC, Muyle A, Emery O, Rastas P, Hudzieczek V, Hobza R, Vyskot B, et al. 2019. Early Sex-Chromosome Evolution in the Diploid Dioecious Plant Mercurialis annua. Genetics 212:815–835. PubMed PMID: 31113811. pdf
• Martin H, Carpentier F, Gallina S, Godé C, Schmitt E, Muyle A, Marais GA, Touzet P. 2019. Evolution of young sex chromosomes in two dioecious sister plant species with distinct sex determination systems. Genome Biology and Evolution, doi: 10.1093/gbe/evz001. PubMed PMID: 30649306. pdf
• Aline Muyle and Brandon S. Gaut. 2019. Loss of gene body methylation in Eutrema salsugineum is associated with reduced gene expression. Molecular Biology and Evolution 36:155–158. PubMed PMID: 30398664. pdf
• Muyle, A., Zemp, N., Fruchard, C., Cegan, R., Vrana, J., Deschamps, C., Tavares, R., Picard, F., Hobza, R., Widmer, A., Marais, G. 2018. Genomic imprinting mediates dosage compensation in a young plant XY system. Nature Plants, 4(9):677–680. PubMed PMID: 30104649. Recommended by PCI Evol Biol. Highlighted in Nature Plants News and views: Bergero R. 2018. How to solve the gender expression gap. Nature Plants 4:637–638. pdf
• Aline Muyle, Rylan Shearn, Gabriel Marais. 2017. The evolution of sex chromosomes and dosage compensation in plants (review). Genome Biology and Evolution, 9(3), 627–645. PubMed PMID: 28391324. pdf
• Muyle, A., Käfer, J., Zemp, N., Mousset, S., Picard, F., Marais, G. 2016. SEX-DETector: a probabilistic approach to uncover sex chromosomes in non-model organisms. Genome Biology and Evolution, 29;8(8):2530-43. PubMed PMID: 27492231. pdf
• Zemp, N., Tavares, R., Muyle, A., Charlesworth, D., Marais, G., Widmer, A. 2016. Evolution of sex-biased gene expression in a dioecious plant. Nature Plants, 2(11):16168. PubMed PMID: 27808231. pdf
• Blavet, N., Blavet, H., Muyle, A., Kafer, J., Cegan, R., Deschamps, C., Zemp, N., Mousset, S., Aubourg, S., Bergero, R., Charlesworth, D., Hobza, R., Widmer, A., Marais, G. 2015. Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia. BMC Genomics, 16:546. PubMed PMID: 26223308. pdf
• Sylvain Glémin and Aline Muyle. 2014. Mating systems and selection efficacy: a test using chloroplastic sequence data in Angiosperms. Journal of Evolutionary Biology, 27(7):1386-99. PubMed PMID: 24674012. pdf
• Aline Muyle, Niklaus Zemp, Clothilde Deschamps, Sylvain Mousset, Alex Widmer, and Gabriel A. B. Marais. 2012. Rapid de novo evolution of X chromosome dosage compensation in Silene latifolia, a plant with young sex chromosomes. PLoS Biology, 10(4):e1001308. PubMed PMID: 22529744. pdf
• Aline Muyle, Laurana Serres-Giardi, Adrienne Ressayre, Juan Escobar, and Sylvain Glémin. 2011. GC-biased gene conversion and selection affect GC content in the Oryza genus (rice). Molecular Biology and Evolution, 28(9):2695–2706. PubMed PMID: 21504892. pdf
• Aline Muyle and Gabriel Marais. 2016. Breeding systems and genome evolution in plants. In R. Kliman (head editor), Encyclopedia of Evolutionary Biology, 1st Edition, Elsevier. pdf
• Yongfeng Zhou, Aline Muyle and Brandon Gaut. 2019. Evolutionary Genomics and the Domestication of Grapes. The grape genome, Springer.