Benchmarking the performance of Pool-seq SNP callers using simulated and real sequencing data Journal Article Forthcoming
Molecular Ecology Resources, Forthcoming.
Temperature, rainfall and wind variables underlie environmental adaptation in natural populations of Drosophila melanogaster Journal Article
Molecular Ecology, 2021.
Transposable Elements in Anopheles Species: Refining Annotation Strategies Towards Population Genomics Analyses Book Chapter
Population Genomics, Springer International Publishing, 2021.
Impact of transposable elements on the genome of the urban malaria vector Anopheles coluzzii Online
Identifying chromosomal subpopulations based on their recombination histories advances the study of the genetic basis of phenotypic traits Journal Article
Genome Research, 2020.
The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe Online
Polymorphic Inversions Underlie the Shared Genetic Susceptibility of Obesity-Related Diseases Journal Article
The American Journal of Human Genetics, 2020.
Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings Journal Article
Nature Communications, 11 (1), 2020.
Genomic analysis of European Drosophila populations reveals major longitudinal structure, continent-wide selection, and unknown DNA viruses Journal Article
Molecular Biology and Evolution, 37 (9), pp. 2661-2678, 2020.
T-lex3: an accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data Journal Article
Transposable elements contribute to the genomic response to insecticides in Drosophila melanogaster Journal Article
Philosophical Transactions of the Royal Society B: Biological Sciences, 375 (1795), pp. 20190341, 2020.
Distinct genotypes and phenotypes in European and American strains of Drosophila suzukii: implications for biology and management of an invasive organism Journal Article
Journal of Pest Science, 93 (1), pp. 77–89, 2020.
A benchmark of transposon insertion detection tools using real data Journal Article
Mobile DNA, 10 (1), 2019.
A new species in the major malaria vector complex sheds light on reticulated species evolution Journal Article
Scientific Reports, 9 (1), 2019.
Broad geographic sampling reveals predictable and pervasive seasonal adaptation in Drosophila Online
New Insights on the Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans Book Chapter
Methods in Molecular Biology, pp. 505–530, Springer New York, 2019.
Diverse families of transposable elements affect the transcriptional regulation of stress-response genes in Drosophila melanogaster Journal Article
Nucleic Acids Research, 2019.
Natural transposable element insertions drive expression changes in genes underlying Drosophila immune response Online
A unique cluster of roo insertions in the promoter region of a stress response gene in Drosophila melanogaster Journal Article
Mobile DNA, 10 (1), 2019.
Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila. Journal Article
PLoS Genetics, 15 (2), pp. e1007900, 2019.
Evolutionary insights from large scale resequencing datasets in Drosophila melanogaster Journal Article
Current Opinion in Insect Science, 31 , pp. 70-76, 2019.
Population specific dynamics and selection patterns of transposable element insertions in European natural populations Journal Article
Molecular Ecology, 2019.
Genome-wide patterns of local adaptation in Western European Drosophila melanogaster natural populations Journal Article
Scientific Reports, 8 , pp. 16143, 2018.
Stress affects the epigenetic marks added by natural transposable element insertions in Drosophila melanogaster Journal Article
Scientific Reports, 8 , pp. 12197, 2018.
Transposable elements contribute to the adaptation of Arabidopsis thaliana Journal Article
Genome Biology and Evolution, 2018.
Revisiting the Relationship between Transposable Elements and the Eukaryotic Stress Response Journal Article
Trends Genet, 33 (11), pp. 832-841, 2017.
Beyond SNPs: how to detect selection on transposable element insertions Journal Article
Methods in Ecology and Evolution, 8 (6), pp. 728-737, 2017.
Natural and laboratory mutations in kuzbanian are associated with zinc stress phenotypes in Drosophila melanogaster Journal Article
Sci Rep, 7 , pp. 42663, 2017.
Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster Journal Article
Mol Ecol., 25 (5), pp. 34, 2016.
Multiple Independent Retroelement Insertions in the Promoter of a Stress Response Gene Have Variable Molecular and Functional Effects in Drosophila Journal Article
PLoS Genet, 12 (8), pp. e1006249, 2016.
Transposable elements: a toolkit for stress and environmental adaptation in bacteria Book Chapter
de Bruijn, Frans J (Ed.): Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria, Chapter 20.10, JohnWiley & Sons, Inc., First edition, 2016.
Lack of population differentiation patterns of previously identified putatively adaptive transposable element insertions at microgeographic scales Journal Article
Biol Direct, 10 , pp. 50, 2015.
T-lex2: genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data Journal Article
Nucleic Acids Res, 43 (4), pp. e22, 2015.
The dominance effect of the adaptive transposable element insertion Bari-Jheh depends on the genetic background Journal Article
Genome Biol Evol, 7 (5), pp. 1260-6, 2015.
Exploring the phenotypic space and the evolutionary history of a natural mutation in Drosophila melanogaster Journal Article
Molecular Biology and Evolution, 32 (7), 2015.
Adaptation through chromosomal inversions in Anopheles Journal Article
Front Genet, 5 , pp. 129, 2014.
Population genomics of transposable elements in Drosophila Journal Article
Annu Rev Genet, 48 , pp. 561-81, 2014.
The transposable element Bari-Jheh mediates oxidative stress response in Drosophila Journal Article
Mol Ecol, 23 (8), pp. 2020-30, 2014.
Pogo-like transposases have been repeatedly domesticated into CENP-B-related proteins Journal Article
Genome Biol Evol, 6 (8), pp. 2008-16, 2014.
A transposable element insertion confers xenobiotic resistance in Drosophila Journal Article
PLoS Genet, 10 (8), pp. e1004560, 2014.
The impact of transposable elements in environmental adaptation Journal Article
Mol Ecol, 22 (6), pp. 1503-17, 2013.
Segmental duplication, microinversion, and gene loss associated with a complex inversion breakpoint region in Drosophila Journal Article
Mol Biol Evol, 29 (7), pp. 1875-89, 2012.
Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans Book Chapter
Methods in Molecular Biology, 2012.
Empirical validation of pooled whole genome population re-sequencing in Drosophila melanogaster Journal Article
PLoS One, 7 (7), pp. e41901, 2012.
T-lex: a program for fast and accurate assessment of transposable element presence using next-generation sequencing data Journal Article
Nucleic Acids Res, 39 (6), pp. e36, 2011.
Population genomics of transposable elements in Drosophila melanogaster Journal Article
Mol Biol Evol, 28 (5), pp. 1633-44, 2011.
Genome-wide patterns of adaptation to temperate environments associated with transposable elements in Drosophila Journal Article
PLoS Genet, 6 (4), pp. e1000905, 2010.
Inferring the strength of selection in Drosophila under complex demographic models Journal Article
Mol Biol Evol, 26 (3), pp. 513-26, 2009.
A recent adaptive transposable element insertion near highly conserved developmental loci in Drosophila melanogaster Journal Article
Mol Biol Evol, 26 (9), pp. 1949-61, 2009.
Bottlenecks, population differentiation and apparent selection at microsatellite loci in Australian Drosophila buzzatii Journal Article
Heredity, 102 (4), pp. 389-401, 2009.