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Xue, Alexander T., Robert P. Ruggiero, Michael J. Hickerson, and Stéphane Boissinot. "Differential Effect of Selection against LINE Retrotransposons among Vertebrates Inferred from Whole-Genome Data and Demographic Modeling." Genome biology and evolution 10, no. 5 (2018): 1265-1281.
Manthey, Joseph D., Robert G. Moyle, and Stéphane Boissinot. "Multiple and independent phases of transposable element amplification in the genomes of Piciformes (woodpeckers and allies)." Genome biology and evolution 10, no. 6 (2018): 1445-1456.
Roman, Ivana, Yann Bourgeois, Jacobo Reyes-Velasco, Olaf P. Jensen, John Waldman, and Stephane Boissinot. "Contrasted patterns of divergence and gene flow among five fish species in a Mongolian rift lake following glaciation." Biological Journal of the Linnean Society 125, no. 1 (2018): 115-125.
Reyes‐Velasco, Jacobo, Joseph D. Manthey, Xenia Freilich, and Stéphane Boissinot. "Diversification of African tree frogs (genus Leptopelis) in the highlands of Ethiopia." Molecular ecology 27, no. 9 (2018): 2256-2270.
Ruggiero, Robert P., Yann Bourgeois, and Stéphane Boissinot. "LINE insertion polymorphisms are abundant but at low frequencies across populations of Anolis carolinensis." Frontiers in genetics 8 (2017).
Boissinot, Stéphane, and Akash Sookdeo. "The evolution of Line-1 in vertebrates." Genome biology and evolution 8, no. 12 (2016): 3485-3507.
Manthey, Joseph D., Marc Tollis, Alan R. Lemmon, Emily Moriarty Lemmon, and Stéphane Boissinot. "Diversification in wild populations of the model organism Anolis carolinensis: A genome‐wide phylogeographic investigation." Ecology and evolution 6, no. 22 (2016): 8115-8125.
Freilich, Xenia, José D. Anadón, Jolanta Bukala, Ordaliza Calderon, Ronveer Chakraborty, and Stéphane Boissinot. "Comparative Phylogeography of Ethiopian anurans: impact of the Great Rift Valley and Pleistocene climate change." BMC evolutionary biology 16, no. 1 (2016): 206.
Fish, Ian, and Stéphane Boissinot. "Functional evolution of the OAS1 viral sensor: Insights from old world primates." Infection, Genetics and Evolution 44 (2016): 341-350.
Fish, Ian, and Stéphane Boissinot. "Contrasted patterns of variation and evolutionary convergence at the antiviral OAS1 gene in old world primates." Immunogenetics 67, no. 9 (2015): 487-499.
Freilich, Xenia, Marc Tollis, and Stéphane Boissinot. "Hiding in the highlands: Evolution of a frog species complex of the genus Ptychadena in the Ethiopian highlands." Molecular phylogenetics and evolution 71 (2014): 157-169.
Sookdeo, Akash, Crystal M. Hepp, Marcella A. McClure, and Stéphane Boissinot. "Revisiting the evolution of mouse LINE-1 in the genomic era." Mobile DNA 4, no. 1 (2013): 3.
Blass, Eryn, Michael Bell, and Stéphane Boissinot. "Accumulation and rapid decay of non-LTR retrotransposons in the genome of the three-spine stickleback." Genome biology and evolution 4, no. 5 (2012): 687-702.
Ferguson, William, Shira Dvora, Ronald W. Fikes, Anne C. Stone, and Stéphane Boissinot. "Long-term balancing selection at the antiviral gene OAS1 in Central African chimpanzees." Molecular biology and evolution 29, no. 4 (2011): 1093-1103.