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M. Lyra, S. Kirchhof, S. Goutte, A. Kassie and S. Boissinot (2023). Crossing the Rift Valley: using complete mitogenomes to infer the diversification and biogeographic history of Ethiopian highlands Ptychadena (Anura: Ptychadenidae). Frontiers in Genetics 14: 1215715.

A. Kassie, A. Bekele, B. Afework, S. Goutte and S. Boissinot (2023). Diversity, distribution and habitat association of anuran species from Keffa, southwest Ethiopia. Diversity 15: 300.

S. Goutte, J. Reyes-Velasco, A. Kassie and S. Boissinot (2022). Genetic and morphometric analysis of historical type specimens clarify the taxonomy of Ethiopian Leptopelis (Anura: Arthroleptidae). Zookeys 1128: 63-97.

S. Goutte, I. Hariyani, K.D. Utzinger, Y. Bourgeois, and S. Boissinot (2022). Genomic analysis reveals association of ASIP with a recurrently evolving color pattern in frogs. Molecular Biology and Evolution 39(11): msac235.

J.J.S. Wilcox, B. Arco-Ruibal, J. Samour, V. Mateuta, Y. Idaghdour and S. Boissinot (2022). Linked-reads on eight Falcons reveal a unique genomic architecture in flux. Genome Biology and Evolution 14(6): evac090.

S. Boissinot (2022). On the base composition of transposable elements. International Journal of Molecular Sciences 23(9): 4755.

J.D. Manthey, Y. Bourgeois, M. Yonas and S. Boissinot (2022). Varied diversification patterns and distinct demographic trajectories in Ethiopian montane forest bird (Aves: Passeriformes) populations separated by the Great Rift Valley. Molecular Ecology 31: 2664-2678.

T. Busschau and S. Boissinot (2022). Habitat determines convergent evolution of cephalic horns in vipers. Biological Journal of the Linnean Society 135(4): 652-664.

J. Reyes-Velasco, S. Goutte, X. Freilich and S. Boissinot (2021). Mitogenomics of historical type specimens clarifies the taxonomy of Ethiopian Ptychadena Boulenger 1917 (Anura, Ptychadenidae). Zookeys 1070: 135.

D. Almojil, Y. Bourgeois, M. Falis, I. Hariyani, J. Wilcox and S. Boissinot (2021). The structural, functional and evolutionary impact of transposable elements in eukaryotes. Genes 12(6): 918.

S. Kirchhof, M.L. Lyra, A. Rodriguez, I. Ineich, J. Muller, M.-O. Roedel, J.-F. Trape, M. Vences and S. Boissinot (2021) Mitogenome analyses elucidate the evolutionary relationships of a probable Eocene tropical savanna relic in the arid lizard genus Acanthodactylus. Scientific Reports 11: 4858.

S. Goutte, J Reyes-Velasco, X. Freilich, A. Kassie and S. Boissinot (2021) Taxonomic revision of the grass frogs (Ptychadenidae, Ptychadena) endemic to the Ethiopian highlands. Zookeys 1016: 77-141.

Y. Bourgeois, R.P. Ruggiero, I. Hariyani, and S. Boissinot (2020). Disentangling the determinants of transposable elements dynamics in vertebrate genomes using empirical evidence and simulation. PLoS Genetics 16(10): e1009082.

R.P. Ruggiero and S. Boissinot (2020). Variation in base composition underlies functional and evolutionary divergence in non-LTR retrotransposons. Mobile DNA 11: 14.

J. Reyes-Velasco, R.H. Adams, S. Boissinot, C.L. Parkinson, J.A. Campbell, T.A. Castoe and E.N. Smith (2020). Genome-wide SNPs clarify lineage diversity confused by coloration in coralsnakes of the Micrurus diastema species complex (Serpentes: Elapidae). Molecular Phylogenetics and Evolution 147: 106770.

Y. Bourgeois and S. Boissinot (2019) Selection at behavioural, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer. Molecular Ecology. DOI: 10.1111/mec.15162.

J. J. S. Wilcox, S. Boissinot, Y. Idaghdour (2019) Falcon genomics in the context of conservation, speciation, and human culture. Ecology and Evolution. DOI: 10.1002/ece3.5864.

D. Ray, N. Paulat, W. An, S. Boissinot, R. Cordeaux, T. Kaul, B. Freeman and V. Belancio (2019). The Mobile DNA conference: 25 years of discussion and research. FASEB J 33(11): 11625-11628.

Y. Bourgeois and S. Boissinot (2019). On the population dynamics of junk: a review on the population dynamics of transposable elements. Genes 10(6): 419.

S. Goutte, J. Reyes-Velasco, S. Boissinot (2019) A new species of puddle frog from an unexplored mountain in southwestern Ethiopia (Anura, Phrynobatrachidae, Phrynobatrachus). ZooKeys 824: 53–70.

A. Sookdeo, M. Ruiz-Garcia, H. Schneider and S. Boissinot (2018). Contrasting rates of LINE-1 amplification among New World primates of the Atelidae family. Cytogenetics and Genome Research 154 (4): 217-228.

A. Sookdeo, C.M. Hepp, and S. Boissinot (2018). Contrasted patterns of evolution of the LINE-1 retrotransposon in perissodactyls: the history of a LINE-1 extinction. Mobile DNA 9(1): 12. 

A.T. Xue, R.P. Ruggiero, M. Hickerson, and S. Boissinot (2018). Differential effect of selection againt LINE retrotransposons among vertebrates inferred from whole genome data and demographic modeling. Genome Biology and Evolution 10(5): 1265-1281. 

J.D. Manthey, S. Boissinot and R. Moyle (2019). Biodiversity genomics of North American Dryobates woodpeckers reveals little gene flow across the D. nuttalli x D. scalaris contact zone. The Auk 136(2): ukz015.

Y. Bourgeois, Ruggiero, R., Manthey, J., & Boissinot, S. (2019). Recent secondary contacts, background selection and variable recombination rates shape genomic diversity in the model species Anolis carolinensis. bioRxiv, 352922.

J.D. Manthey, Moyle, R. G., & Boissinot, S. (2018). Multiple and independent phases of transposable element amplification in the genomes of Piciformes (woodpeckers and allies). Genome biology and evolution, 10(6), 1445-1456.

I. Roman, I., Y. Bourgeois, J. Reyes-Velasco, O. P. Jensen, J. Waldman & S. Boissinot. (2018). Contrasted patterns of divergence and gene flow among five fish species in a Mongolian rift lake following glaciation. Biological Journal of the Linnean Society. XX, 1 - 11.

J. Reyes‐Velasco, Manthey, J. D., Freilich, X., & Boissinot, S. (2018). Diversification of African tree frogs (genus Leptopelis) in the highlands of Ethiopia. Molecular ecology, 27(9), 2256-2270. pdf

C. Grünwald, , J. Reyes-Velasco, H. Franz-Chávez, K. I. Morales-Flores, I. T. Ahumada-Carrillo, J. M. Jones, and S. Boissinot (2018). Six new species of Eleutherodactylus (Anura: Eleutherodactylidae: subgenus Syrrhophus) from Mexico, with a discussion of their systematic relationships and the validity of related species. Mesoamerican Herpetology. 5(1): 7-81.

J. Reyes-Velasco, Manthey, J. D., Bourgeois, Y., Freilich, X., & Boissinot, S. (2018). Revisiting the phylogeography, demography and taxonomy of the frog genus Ptychadena in the Ethiopian highlands with the use of genome-wide SNP data. PloS one, 13(2), e0190440.

J. Liang, Y. Shaulov, C. Savage-Dunn, S. Boissinot and T. Hoque (2017). Chloride intracellular channel proteins respond to heat stress in Caenorhabditis elegans. PLoS One 12 (9): e0184308. [A, W]

J.D. Manthey, Reyes-Velasco, J., Freilich, X., & Boissinot, S. (2017). Diversification in a biodiversity hotspot: genomic variation in the river frog Amietia nutti across the Ethiopian Highlands. Biological Journal of the Linnean Society, 122(4), 801-813.

R. Ruggiero, Y. Bourgeois and S. Boissinot (2017). LINE insertion polymorphisms are abundant but at low frequencies across populations of Anolis carolinensis. Frontiers in Genetics 4: 44.

S. Boissinot and A. Sookdeo (2016). The evolution of LINE-1 in vertebrates.  Genome Biology and Evolution 8(12): 3485-3507.

J.D. Manthey, M. Tollis, A.R. Lemmon, E. Moriarty Lemmon and S. Boissinot (2016). Diversification in wild populations of the model organism Anolis carolinensis: a genome-wide phylogeographic investigation. Ecology and Evolution 6(22): 8115-8125.

X. Freilich, J.D. Anadon, J. Bukala, O. Calderon, R. Chakraborty, Evolutionary Genetics – Class of 2013 and S. Boissinot (2016). Comparative phylogeography of Ethiopian anurans: impact of the Great Rift Valley and Pelistocene climate change. BMC Evolutionary Biology 16(1): 206.

I. Fish and S. Boissinot (2016). Functional evolution of the OAS1 viral sensor: insights from Old World primates. Infection, Genetics and Evolution 44: 341-350.

I. Fish and S. Boissinot (2015). Contrasted patterns of variation and evolutionary convergence at the antiviral OAS1 gene in Old World primates. Immunogenetics 67(9): 487-499.

S. Boissinot, L. Alvarez, J. Giraldo-Ramirez and M. Tollis (2014). Neutral nuclear variation in baboons (genus Papio) provides insights into their evolutionary and demographic histories. Am. J. of Physical Anthropology 155: 621-634.

X. Freilich, M. Tollis and S. Boissinot (2014). Hiding in the highlands: evolution of a frog species complex of the genus Ptychadena in the Ethiopian highlands. Molecular Phylogenetics and Evolution 71: 157-169. pdf

M. Tollis and S. Boissinot (2014). Genetic variation in the green anole lizard (Anolis carolinensis) reveals island refugia and a fragmented Florida during the quaternary. Genetica 142: 59-72.

M. Tollis and S. Boissinot (2013). Lizards and LINEs: selection and demography affect the fate of L1 retrotransposons in the genome of the green anole (Anolis carolinensis). Genome Biology and Evolution 5(9): 1754-1768. pdf

A. Sookdeo, C. Hepp, M. McClure and S. Boissinot (2013). Revisiting the evolution of mouse LINE-1 in the genomic era. Mobile DNA 4(1): 3. pdf

E. Blass, M. Bell and S. Boissinot (2012). Accumulation and rapid decay of non-LTR retrotransposons in the genome of the three-spine stickleback. Genome Biology and Evolution 4: 687-702. pdf

M. Tollis and S. Boissinot (2012). The Evolutionary Dynamics of Transposable Elements in Eukaryote Genomes. Genome Dynamics Vol.7: Repetitive DNA: 68-91.  

M. Tollis, G. Ausubel, D. Ghmire and S. Boissinot (2012). Multi-locus Phylogeographic and Population Genetic Analysis of Anolis carolinensis: Historical Demography of a Genomic Model Species. PLoS ONE 7: e38474. pdf

W. Ferguson, S. Dvora, R. Fikes, A.C. Stone, and S. Boissinot (2012). Long-term balancing selection at the anti-viral gene OAS1 maintains functionally different alleles in chimpanzees. Molecular Biology and Evolution. 29(4): 1093-1103.

K. Kusumi, R.J. Kulathinal, A. Abzhanov, S. Boissinot, N.G. Crawford, B.C. Faircloth, T.C. Glenn, J.B. Losos, D.B. Menke, T.J. Sanger, C. Schneider, J. Wade, J. Wilson-Rawls (2011). Developing a community-based genetic nomenclature and comparative analysis of the anole lizard. BMC Genomics 12: 554.  

M. Tollis and S. Boissinot (2011). The transposable element profile of the Anolis genome: how a lizard can provide insights into the evolution of vertebrate genome size and structure. Mobile Genetics Elements 1: 107-111.

J. Alfoldi, F. Di Palma, M. Grabherr,..S. Boissinot,..P. Novick… et al. [47 authors] (2011). The genome of Anolis carolinensis, the green anole lizard, and a comparative analysis with birds and mammals. Nature 477: 587-591.

P. Novick, J. Smith, M. Floumanhaft, D. Ray and S. Boissinot (2011). The evolution and diversity of DNA transposons in the genome of the lizard Anolis carolinensis. Genome Biology and Evolution 3: 1-14. pdf

M. Song, R.M. Haralick, and S. Boissinot (2010). Efficient and exact maximum likelihood quantization of genomic features using dynamic programming. Int. J. Data mining and Bioinformatics 4(2): 123-141. 

P. Novick, J. Smith, D. Ray and S. Boissinot (2010). Independent and parallel lateral transfer of DNA transposons in tetrapod genomes. Gene 449: 85-94. pdf

P. Novick, H. Basta, M. Floumanhaft, M. McClure, and S. Boissinot (2009). The evolutionary dynamics of non-LTR retrotransposons in the lizard Anolis carolinensis shows more similarity to fish than mammals. Mol. Biol. Evol. 26: 1811-1822. pdf

A.V. Furano and S. Boissinot (2008). Long Interspersed Nuclear Elements (LINEs): Evolution (version 2.0). In: Encyclopedia of Life Sciences (ELS). John Wiley & Sons, Ltd: Chichester.

W. Ferguson, S. Dvora, J. Gallo, A. Orth and S. Boissinot (2008). Long term balancing selection at the West Nile virus resistance gene, Oas1b, maintains trans-specific polymorphism in the house mouse. Mol. Biol. Evol. 25(8): 1609-1618.

M. Song and S. Boissinot (2007). Selection against LINE-1 retrotransposons results principally from their ability to mediate ectopic recombination. Gene 390 (1-2): 206-213. 

D.J. Witherspoon, E.E. Marchani, W.S. Watkins, C.T. Ostler, S.P. Wooding, B.A. Anders, J.D. Fowlkes, S. Boissinot, A.V. Furano, A.R. Rogers, M.A. Batzer and L.B. Jorde (2006). Analysis of human population genetic structure and diversity comparing polymorphic L1 (LINE-1) and Alu insertions. Human heredity 62 (1): 30-46.  

S. Boissinot, J. Davis, A. Entezam, D. Petrov and A.V. Furano (2006). Fitness cost of LINE-1 (L1) activity in humans. Proc. Natl. Acad. Sci. USA 103 (25): 9590-9594. pdf

T. Graham and S. Boissinot (2006). The genomic distribution of L1 elements: the role of insertion bias and natural selection. Journal of Biomedicine and Biotechnology 2006: 1-5.  

H. Khan, A. Smit and S. Boissinot (2006). The evolution of human LINE-1 retrotransposons since the origin of primates. Genome Research 16(1): 78-87. pdf

S. Boissinot and A.V. Furano (2005). The recent evolution of human L1 retrotransposons. Cytogenetics and Genome Research 110(1-4): 402-406.

S.L. Martin, W-LP Li, AV Furano and S. Boissinot (2005). The structure of mouse and human L1 elements reflect their insertion mechanism. Cytogenetics and Genome Research 110(1-4): 223-228.

S. Boissinot, Entezam A, Young L, Munson P, and Furano AV (2004). The insertional history of an active family of LINE-1 retrotransposons in humans. Genome Research 14: 1221-1231.

A.V. Furano, D. Duvernell and S. Boissinot (2004). L1 (LINE-1) retrotransposon diversity differs dramatically between mammals and fish. Trends in Genetics 20(1): 9-14.

S. Boissinot, C. Roos and A.V. Furano (2004). Different rates of LINE-1 retrotransposons amplification and evolution in New World monkeys. J. Mol. Evol. 58: 122-130.

M. Song, S. Boissinot, R.M. Haralick, I.T. Phillips (2003). Estimating recombination rate distribution by optimal quantization. Proceedings of IEEE Computational Systems Bioinformatics Conference 2003: 403-406.

A.V. Furano and S. Boissinot (2002). Long Interspersed Nuclear Elements (LINEs): Evolution in the "Nature Encyclopedia of the human Genome", McMillan Publisher, Pp 746-752.

S. Boissinot and A.V. Furano (2001). Adaptive evolution in LINE-1 retrotransposons. Mol. Biol. Evol. 18(12): 2186-2194.

S. Boissinot, A. Entezam and A.V. Furano (2001). Selection against deleterious LINE-1-containing loci in the human lineage. Mol. Biol. Evol. 18: 926-935.

S. Boissinot, P. Chevret and A.V. Furano (2000). L1 (LINE-1) retrotransposon evolution and amplification in recent human history. Mol. Biol. Evol. 17(6): 915-928.  

W.-H. Li, S. Boissinot, Y. Tan,  S.-K. Shyue and D. Hewett-Emmett (2000). Evolutionary genetics of primate color vision: recent progress and potential limits to knowledge. Evol. Biol. 32: 151-178.

W.-H. Li, Y. Tan, S. Boissinot, S.-K. Shyue and D. Hewett-Emmett (2000). Genetic diversity of color vision in primates in "The Biology of Biodiversity" (ed. M. Kato), Springer Verlag, Tokyo, Pp. 259-274.

S. Boissinot, Y. Tan, S.-K. Shyue, H. Schneider, I. Sampaio, K. Neiswanger, D. Hewett-Emmett and W.-H. Li (1998). Origins and antiquity of X-linked triallelic color vision systems in New World monkeys. Proc. Natl. Acad. Sci. USA 95: 13749-13754.

S.-K. Shyue, S. Boissinot, H. Schneider, I. Sampaio, M.P. Schneider, C.R. Abee, L. Williams, D. Hewett-Emmett, H.G. Sperling, J.A. Cowing, K.S. Dulai, D.M. Hunt and W.-H. Li (1998). Molecular genetics of spectral tuning in New World monkey color vision. J. Mol. Evol. 46: 697-702.  

D. Casane, S. Boissinot, B.H.-J. Chang, L. Shimmin and W.-H. Li (1997). Mutation pattern variation among regions of the primate genome. J. Mol. Evol. 45: 216-226.

S. Boissinot and P. Boursot (1997). Discordant phylogeographic patterns between the Y chromosome and mitochondrial DNA in the house mouse: selection on the Y chromosome?. Genetics 46: 1019-1034.

S. Boissinot, I. Ineich, L. Thaler and C.-P. Guillaume (1997). Hybrid origin and clonal diversity in the parthenogenetic gecko, Lepidodactylus lugubris (Reptilia: Lacertilia) in French Polynesia. J. of Herpetology, 31 (2): 295-298.

S. Boissinot, Y.-H. Zhou, D. Hunt, D. Hewett-Emmett and W.-H. Li (1997). Origin and molecular evolution of the X-linked duplicate color vision genes in howler monkeys. Zool. studies 36: 360-369.

A. Orth, E. Lyapunova, A. Kandaurov, S. Boissinot, P. Boursot, N. Vorontsov and F. Bonhomme (1996). The polytypic species Mus musculus in Transcaucasia. C. R. Acad. Sci. Paris, Serie III, 319: 435-441.

C.P. Guillaume, I. Ineich and S. Boissinot (1994). Allozyme evidence for specific status of the two French Polynesian skink species in the genus Emoia ( Reptilia : Lacertilia). Copeia, 1994 (4): 548-556.

P. Geniez, M. Geniez, S. Boissinot, P.C. Beaubrun and J. Bons (1991). The Moroccan herpetofauna: new observations, 2 [in french]. Bull. Soc. Herp. Fr., 59 : 19-27.