Langebrake, C.; Manthey, G.; Lugo Ramos, J. S.; Dutheil, J. Y.; Chetverikova, R.; Solov'yov, I.; Mouritsen, H.; Liedvogel, M.: Adaptive evolution and loss of a putative magnetoreceptor in passerines. Proceedings of the Royal Society B: Biological Sciences 291 (2016), 0232308 (2024)

Dutheil, J. Y.; Hamidi, D.; Pajot, B.: The Site/Group Extended Data format and tools. Genome Biology and Evolution 16 (2), evae011 (2024)

Bascón-Cardozo, K.; Bours, A.; Manthey, G.; Pruisscher, P.; Durieux, G.; Dutheil, J. Y.; Odenthal-Hesse, L.; Liedvogel, M.: Fine-scale map reveals highly variable recombination rates associated with genomic features in the European blackcap. Genome Biology and Evolution 16 (1), evad233 (2024)

Rivas-González, I.; Rousselle, M.; Li, F.; Zhou, L.; Dutheil, J. Y.; Munch, K.; Shao, Y.; Wu, D.; Schierup, M. H.; Zhang, G.: Pervasive incomplete lineage sorting illuminates speciation and selection in primates. Science 380, 925 (2023)

Raas, M. W. D.; Dutheil, J. Y.: The rate of adaptive molecular evolution in wild and domesticated Saccharomyces cerevisiae populations. Molecular Ecology 00 (00), pp. 1 - 21 (2023)

Barroso, G.; Dutheil, J. Y.: The landscape of nucleotide diversity in Drosophila melanogaster is shaped by mutation rate variation. Peer Community Journal 3, e40 (2023)

Puzović, N.; Madaan, T.; Dutheil, J. Y.: Being noisy in a crowd: differential selective pressure on gene expression noise in model gene regulatory networks. PLoS Computational Biology 19 (4), e1010982 (2023)

Moutinho, A. F.; Eyre-Walker, A.; Dutheil, J. Y.: Strong evidence for the adaptive walk model of gene evolution in Drosophila and Arabidopsis. PLoS Biology 20 (9), e3001775 (2022)

Chaurasia, S.; Dutheil, J. Y.: The structural determinants of intra-protein compensatory substitutions. Molecular Biology and Evolution 39 (4), msac063 (2022)

Soni, V.; Moutinho, A. F.; Eyre-Walker, A.: Changing population size in McDonald–Kreitman style analyses: artifactual correlations and adaptive evolution between humans and chimpanzees. Genome Biology and Evolution 14 (2), evac022 (2022)

Meteyer, C. U.; Dutheil, J. Y.; Keel, M. K.; Boyles, J. G.; Stukenbrock, E. H.: Plant pathogens provide clues to the potential origin of bat white-nose syndromePseudogymnoascus destructans. Virulence 13 (1), pp. 1020 - 1031 (2022)

Schweizer, G.; Haider, M. B.; Barroso, G. V.; Rossel, N.; Munch, K.; Kahmann, R.; Dutheil, J. Y.: Population genomics of the maize pathogen Ustilago maydis: demographic history and role of virulence clusters in adaptation. Genome Biology and Evolution 13 (5), evab073 (2021)

Dutheil, J. Y.; Münch, K.; Schotanus, K.; Stukenbrock, E. H.; Kahmann, R.: The insertion of a mitochondrial selfish element into the nuclear genome and its consequences. Ecology and Evolution 10 (20), pp. 11117 - 11132 (2020)

Moutinho, A. F.; Bataillon, T.; Dutheil, J. Y.: Variation of the adaptive substitution rate between species and within genomes. Evolutionary Ecology 34 (3), pp. 315 - 338 (2020)

Moutinho, A. F.; Serén, N.; Paupério, J.; Silva, T. L.; Martínez-Freiría, F.; Sotelo, G.; Faria, R.; Mappes, T.; Alves, P. C.; Brito, J. C. et al.; Boratyński, Z.: Evolutionary history of two cryptic species of northern African jerboas. BMC Evolutionary Biology 20, 26 (2020)

Potgieter, L.; Feurtey, A.; Dutheil, J. Y.; Stukenbrock, E. H.: On variant discovery in genomes of fungal plant pathogens. Frontiers in Microbiology 11, 626 (2020)

Barroso, G.; Puzović, N.; Dutheil, J. Y.: Inference of recombination maps from a single pair of genomes and its application to ancient samples. PLoS Genetics 15 (11), e1008449 (2019)

Grandaubert, J.; Dutheil, J. Y.; Stukenbrock, E. H.: The genomic determinants of adaptive evolution in a fungal pathogen. Evolution Letters 3 (3), pp. 299 - 312 (2019)

Schweizer, G.; Münch, K.; Mannhaupt, G.; Schirawski, J.; Kahmann, R.; Dutheil, J. Y.: Positively selected effector genes and their contribution to virulence in the smut fungus Sporisorium reilianum. Genome Biology and Evolution 10 (2), pp. 629 - 645 (2018)

Odenthal-Hesse, L.; Dutheil, J. Y.; Klötzl, F.; Haubold, B.: hotspot: software to support sperm-typing for investigating recombination hotspots. Bioinformatics 32 (16), pp. 2554 - 2555 (2016)