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)

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)

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)

Moutinho, A. F.; Trancoso, F. F.; Dutheil, J. Y.: The impact of protein architecture on adaptive evolution. Molecular Biology and Evolution 36 (9), pp. 2013 - 2028 (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)

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

Stukenbrock, E. H.; Dutheil, J. Y.: Fine-scale recombination maps of fungal plant pathogens reveal dynamic recombination landscapes and intragenic hotspots. Genetics 208 (3), pp. 1209 - 1229 (2018)

Barroso, G. V.; Puzovic, N.; Dutheil, J. Y.: The evolution of gene-specific transcriptional noise is driven by selection at the pathway level. Genetics 208 (1), pp. 173 - 189 (2018)

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)

Dutheil, J. Y.; Mannhaupt, G.; Schweizer, G.; Sieber, C. M.; Münsterkötter, M.; Güldener, U.; Schirawski, J.; Kahmann, R.: A tale of genome compartmentalization: the evolution of virulence clusters in smut fungi. Genome biology and evolution 8 (3), pp. 681 - 704 (2016)

Nam, K.; Munch, K.; Hobolth, A.; Dutheil, J. Y.; Veeramah, K. R.; Woerner, A. E.; Hammer, M. F.; Great Ape Genome Diversity Project; Mailund, T.; Schierup, M. H.: Extreme selective sweeps independently targeted the X chromosomes of the great apes. Proceedings of the National Academy of Sciences of the United States of America 112 (20), pp. 6413 - 6418 (2015)

Dutheil, J. Y.; Figuet, E.: Optimization of sequence alignments according to the number of sequences vs. number of sites trade-off. BMC Bioinformatics 16, 190 (2015)

Dutheil, J. Y.; Munch, K.; Nam, K.; Mailund, T.; Schierup, M. H.: Strong selective sweeps on the X chromosome in the human-chimpanzee ancestor explain its low divergence. PLoS Genetics 11 (8), e1005451 (2015)

Dutheil, J. Y.: Statistical population genomics. Springer, US (2020), XX, 335 pp.