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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)

Moutinho, A. F.; Bataillon, T.; Dutheil, J. Y.: Variation of the adaptive substitution rate between species and within genomes. Evolutionary Ecology n/a (n/a) (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)

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)

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.; 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.

Barroso, G. V.; Moutinho, A. F.; Dutheil, J. Y.: A population genomics lexicon. In: Statistical Population Genomics (Ed. Dutheil, J. Y.). Springer, US (2020)

Dutheil, J. Y.: Processing and analyzing multiple genomes alignments with MafFilter. In: Statistical population genomics (Ed. Dutheil, J. Y.). Springer, US (2020)

Dutheil, J. Y.; Hobolth, A.: Ancestral population genomics. In: Evolutionary Genomics: Statistical and Computational Methods, Vol. 1910, pp. 555 - 589 (Ed. Anisimova, M.). Springer, New York (2019)

Dutheil, J. Y.: Hidden Markov models in population genomics. In: Hidden Markov Models: Methods and Protocols, pp. 149 - 164 (Eds. Westhead, D. R.; Vijayabaskar, M. S.). Springer Science+Business Media LLC, New York (2017)

Dutheil, J. Y.; Hobolth, A.: Ancestral population genomics. In: Evolutionary Genomics: Statistical and Computational Methods, Volume 2, pp. 293 - 313. Humana Press, Totowa, NJ (2012)

Barroso, G.: Darwin throws dice: modelling stochastic processes of molecular evolution. Dissertation, 156 pp., Christian-Albrechts-Universität zu Kiel, Kiel; Plön (2019)

Puzovic, N.: Effect of gene network topology on the evolution of gene-specific expression noise. Master, 64 pp., Christian-Albrechts-Universität, Kiel (2020)

Dutheil, J. Y.; Münch, K.; Schotanus, K.; Stukenbrock, E. H.; Kahmann, R.: The transfer of a mitochondrial selfish element to the nuclear genome and its consequences. bioRxiv (2019), 33 pp.