Bourgeois, Y., Ruggiero R.P., Manthey J.D., Boissinot S. Recent Secondary Contacts, Linked Selection, and Variable Recombination Rates Shape Genomic Diversity in the Model Species Anolis carolinensis. 2020. Genome biology and evolution 11 (7), 2009-2022
Boissinot, S., Bourgeois Y., Manthey J.D., Ruggiero, R.P. The Mobilome of Reptiles: Evolution, Structure, Function. 2019. Cytogenetics and Genome Research 157 (1-2)
Pasquesi, G.I.M, Adams R.H., Card D.C., Schield D.C., Perry B.W., Corbin A.B, Reyez-Velasco J., Ruggiero R.P., Vandewege M.W., Castoe T.A. Squamate reptiles challenge paradigms of genomic repeat evolution set by birds and mammals. 2018. Nature Communications
Bourgeois, S., Ruggiero R.P., Manthey J., Boissinot S. Recent secondary contacts, background selection and variable recombination rates shape genomic diversity in the model species Anolis carolinensis. 2018. bioRxiv
Xue, T.A., Ruggiero R.P., Hickerson M.J., Boissinot S. Differential Effect of Selection against LINE Retrotransposons Among Vertebrates Inferred From Whole-Genome Data and Demographic Modeling. 2018. Genome Biology and Evolution
Ruggiero, R.P., Bourgeois Y., and S. Boissinot. Population genomics of LINEs in Anolis carolinensis inferred from whole genome re-sequencing data. 2017. Frontiers in Genetics 8: 44.
Andrew, A.L., Perry B.W., Card D.C., Scheild D.R., Ruggiero R.P., McGaugh S.E., Choudhary A., Secor S.M., and Castoe T.A. Growth and stress response mechanisms underlying post-feeding regenerative organ growth in the Burmese python. 2017. BMC Genomics 18 (1), 338
Andrew, A.L., Card D.C., Ruggiero R.P., Schield D.R., Adams R.H., Pollock D.D., Secor S.M., and T.A. Castoe. Rapid changes in gene expression direct rapid shifts in intestinal form and function in the Burmese python after feeding. 2015. Physiological Genomics, (5):147-57
Shaney, K.J., D.R. Schield, D.C. Card, R.P. Ruggiero, D.D. Pollock. S.P. Mackessy, T.A. Castoe. Squamate reptile genomics and evolution. 2014. In: Handbook of Toxinology: Venom Genomics and Proteomics, P. Gopalakrishnakone (Ed.), Springer Reference Press, New York, NY.
Wacholder A.C., Cox C., Meyer T.J., Ruggiero R.P., Vemulapalli V., Damert A., Carbone L., and D.D. Pollock. Inference of transposable element ancestry. 2014. PLoS Genetics 8:e1004482
Card, D.C., Schield D.R., Reyes-Velasco J., Andrew A.L., Ruggiero R.P., Pollock D.D., Tomback D.F., Oyler-McCance S.J., Fujita M.K., and T.A. Castoe. Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies. 2014. PLoSOne 9: e106649.
Baker N.E., Li K., Quiquand M., Ruggiero R., and L.H. Wang. Eye Development. 2014. Methods. 15;68(1):252-9
Castoe. T.A., de Koning A.P.J., Hall K.T., Card D.C., Schield D.R., Fujita M.K., Ruggiero R.P., Degner J.F., Daza J.M., Gu W., Reyes-Velasco J., Shaney K.J., Castoe J.M., Fox S.E., Poole A.W., Polanco D., Dobry J., Vandewege M.W., Li Q., Schott R., Kapusta A., Minx P., Feschotte C., Uetz P., Ray D.A., Hoffmann F.G., Bogden R., Smith E.N., Chang B.S.W., Vonk F., Casewell N.R., Henkel C.V., Richardson M.K., Mackessy S.P., Bronikowski A.M., Yandell M., Warren W.C., Secor S.M., and D.D. Pollock. The Burmese Python genome reveals the molecular basis for extreme adaptation in snakes. 2013. Proceedings of the National Academy of Sciences, USA 110:20645-20650. -Cover Article –
Ruggiero R., Kale A., Thomas B., and N.E. Baker. Mitosis in neurons: Roughex and APC/C maintain cell cycle exit to prevent cytokinetic and axonal defects in Drosophila photoreceptor neurons. 2012. PLoS Genetics 11:e1003049.