TY - JOUR AU - Koning, A. P. J. AU - Gu, W. AU - Castoe, T. A. AU - Batzer, M. A. AU - Pollock, D. D. PY - 2011 DA - 2011// TI - Repetitive elements may comprise over two-thirds of the human genome JO - PLoS Genet VL - 7 UR - https://doi.org/10.1371/journal.pgen.1002384 DO - 10.1371/journal.pgen.1002384 ID - Koning2011 ER - TY - JOUR AU - Lander PY - 2001 DA - 2001// TI - Initial sequencing and analysis of the human genome JO - Nature VL - 409 UR - https://doi.org/10.1038/35057062 DO - 10.1038/35057062 ID - Lander2001 ER - TY - JOUR AU - Ray, D. A. AU - Pagan, H. J. T. AU - Thompson, M. L. AU - Stevens, R. D. PY - 2007 DA - 2007// TI - Bats with hATs: Evidence for recent DNA transposon activity in genus Myotis JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msl192 DO - 10.1093/molbev/msl192 ID - Ray2007 ER - TY - JOUR AU - Pritham, E. J. AU - Feschotte, C. PY - 2007 DA - 2007// TI - Massive amplification of rolling-circle transposons in the lineage of the bat Myotis lucifugus JO - Proc Natl Acad Sci VL - 104 UR - https://doi.org/10.1073/pnas.0609601104 DO - 10.1073/pnas.0609601104 ID - Pritham2007 ER - TY - JOUR AU - Thomas, J. AU - Phillips, C. D. AU - Baker, R. J. AU - Pritham, E. J. PY - 2014 DA - 2014// TI - Rolling-circle transposons catalyze genomic innovation in a mammalian lineage JO - Genome Biol Evol VL - 6 UR - https://doi.org/10.1093/gbe/evu204 DO - 10.1093/gbe/evu204 ID - Thomas2014 ER - TY - JOUR AU - Ray, D. A. AU - Feschotte, C. AU - Pagan, H. J. T. AU - Smith, J. D. AU - Pritham, E. J. AU - Arensburger, P. PY - 2008 DA - 2008// TI - Multiple waves of recent DNA transposon activity in the bat, Myotis lucifugus JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.071886.107 DO - 10.1101/gr.071886.107 ID - Ray2008 ER - TY - JOUR AU - Platt, R. N. AU - Vandewege, M. W. AU - Kern, C. AU - Schmidt, C. J. AU - Hoffmann, F. G. AU - Ray, D. A. PY - 2014 DA - 2014// TI - Large numbers of novel miRNAs originate from DNA transposons and are coincident with a large species radiation in bats JO - Mol Biol Evol VL - 31 UR - https://doi.org/10.1093/molbev/msu112 DO - 10.1093/molbev/msu112 ID - Platt2014 ER - TY - JOUR AU - Thomas, J. AU - Sorourian, M. AU - Ray, D. AU - Baker, R. J. AU - Pritham, E. J. PY - 2011 DA - 2011// TI - The limited distribution of Helitrons to vesper bats supports horizontal transfer JO - Gene VL - 474 UR - https://doi.org/10.1016/j.gene.2010.12.007 DO - 10.1016/j.gene.2010.12.007 ID - Thomas2011 ER - TY - JOUR AU - Miller-Butterworth, C. M. AU - Murphy, W. J. AU - O'Brien, S. J. AU - Jacobs, D. S. AU - Springer, M. S. AU - Teeling, E. C. PY - 2007 DA - 2007// TI - A family matter: Conclusive resolution of the taxonomic position of the long-fingered bats, Miniopterus JO - Mol Biol Evol VL - 24 UR - https://doi.org/10.1093/molbev/msm076 DO - 10.1093/molbev/msm076 ID - Miller-Butterworth2007 ER - TY - STD TI - Eckalbar WL, Schlebusch SA, Mason MK, Gill Z, Parker AV, Booker BM et al. Transcriptomic and epigenomic characterization of the developing bat wing. Nat Genet. 2016;advance online publication. doi:10.1038/ng.3537. ID - ref10 ER - TY - JOUR AU - Platt, R. N. AU - Blanco-Berdugo, L. AU - Ray, D. A. PY - 2016 DA - 2016// TI - Accurate transposable element annotation is vital when analyzing new genome assemblies JO - Genome Biol Evol VL - 8 UR - https://doi.org/10.1093/gbe/evw009 DO - 10.1093/gbe/evw009 ID - Platt2016 ER - TY - STD TI - Smit A, Hubley R. RepeatModeler Open-1.0. 2008-2015. ID - ref12 ER - TY - STD TI - Smit A, Hubley R, P G. RepeatMasker Open-4.0. 2013-2015. ID - ref13 ER - TY - JOUR AU - Altschul, S. F. AU - Madden, T. L. AU - Schäffer, A. A. AU - Zhang, J. AU - Zhang, Z. AU - Miller, W. PY - 1997 DA - 1997// TI - Gapped BLAST and PSI-BLAST: a new generation of protein database search programs JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.17.3389 DO - 10.1093/nar/25.17.3389 ID - Altschul1997 ER - TY - JOUR AU - Edgar, R. C. PY - 2004 DA - 2004// TI - MUSCLE: multiple sequence alignment with high accuracy and high throughput JO - Nucleic Acids Res VL - 32 UR - https://doi.org/10.1093/nar/gkh340 DO - 10.1093/nar/gkh340 ID - Edgar2004 ER - TY - STD TI - Hall T. BioEdit version 7.0.0. 2004. ID - ref16 ER - TY - JOUR AU - Xiong, W. AU - He, L. AU - Lai, J. AU - Dooner, H. K. AU - Du, C. PY - 2014 DA - 2014// TI - HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes JO - Proc Natl Acad Sci VL - 111 UR - https://doi.org/10.1073/pnas.1410068111 DO - 10.1073/pnas.1410068111 ID - Xiong2014 ER - TY - JOUR AU - Rice, P. AU - Longden, I. AU - Bleasby, A. PY - 2000 DA - 2000// TI - EMBOSS: The European Molecular Biology Open Software Suite JO - Trends Genet VL - 16 UR - https://doi.org/10.1016/S0168-9525(00)02024-2 DO - 10.1016/S0168-9525(00)02024-2 ID - Rice2000 ER - TY - STD TI - Kent WJ. BLAT--the BLAST-like alignment tool. Genome research. 2002;12(4):656-64. doi:10.1101/gr.229202. article published online before march 2002. ID - ref19 ER - TY - JOUR AU - Bao, W. AU - Kojima, K. K. AU - Kohany, O. PY - 2015 DA - 2015// TI - Repbase Update, a database of repetitive elements in eukaryotic genomes JO - Mob DNA VL - 6 UR - https://doi.org/10.1186/s13100-015-0041-9 DO - 10.1186/s13100-015-0041-9 ID - Bao2015 ER - TY - JOUR AU - Wheeler, D. L. AU - Barrett, T. AU - Benson, D. A. AU - Bryant, S. H. AU - Canese, K. AU - Chetvernin, V. PY - 2007 DA - 2007// TI - Database resources of the National Center for Biotechnology Information JO - Nucleic Acids Res VL - 35 UR - https://doi.org/10.1093/nar/gkl1031 DO - 10.1093/nar/gkl1031 ID - Wheeler2007 ER - TY - JOUR AU - Wicker, T. AU - Sabot, F. AU - Hua-Van, A. AU - Bennetzen, J. L. AU - Capy, P. AU - Chalhoub, B. PY - 2007 DA - 2007// TI - A unified classification system for eukaryotic transposable elements JO - Nat Rev Genet VL - 8 UR - https://doi.org/10.1038/nrg2165 DO - 10.1038/nrg2165 ID - Wicker2007 ER - TY - STD TI - Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol.16(2):111-20. doi:10.1007/bf01731581. ID - ref23 ER - TY - JOUR AU - Xing, J. AU - Hedges, D. J. AU - Han, K. AU - Wang, H. AU - Cordaux, R. AU - Batzer, M. A. PY - 2004 DA - 2004// TI - Alu Element Mutation Spectra: Molecular Clocks and the Effect of DNA Methylation JO - J Mol Biol VL - 344 UR - https://doi.org/10.1016/j.jmb.2004.09.058 DO - 10.1016/j.jmb.2004.09.058 ID - Xing2004 ER - TY - JOUR AU - Eick, G. N. AU - Jacobs, D. S. AU - Matthee, C. A. PY - 2005 DA - 2005// TI - A nuclear DNA phylogenetic perspective on the evolution of echolocation and historical biogeography of extant bats (Chiroptera) JO - Mol Biol Evol VL - 22 UR - https://doi.org/10.1093/molbev/msi180 DO - 10.1093/molbev/msi180 ID - Eick2005 ER - TY - JOUR AU - Ray, D. A. AU - Pagan, H. J. AU - Platt, R. N. AU - Kroll, A. R. AU - Schaack, S. AU - Stevens, R. D. PY - 2015 DA - 2015// TI - Differential SINE evolution in vesper and non-vesper bats JO - Mob DNA VL - 6 UR - https://doi.org/10.1186/s13100-015-0038-4 DO - 10.1186/s13100-015-0038-4 ID - Ray2015 ER - TY - JOUR AU - Platt, R. N. AU - Zhang, Y. AU - Witherspoon, D. J. AU - Xing, J. AU - Suh, A. AU - Keith, M. S. PY - 2015 DA - 2015// TI - Targeted capture of phylogenetically informative Ves SINE Insertions in genus Myotis JO - Genome Biol Evol VL - 7 UR - https://doi.org/10.1093/gbe/evv099 DO - 10.1093/gbe/evv099 ID - Platt2015 ER - TY - STD TI - Thomas J, Pritham EJ. Helitrons, the eukaryotic rolling-circle transposable elements. Microbiol Spectr. 2015;3(4). doi:10.1128/microbiolspec.MDNA3-0049-2014. ID - ref28 ER - TY - JOUR AU - Smit, A. F. AU - Riggs, A. D. PY - 1996 DA - 1996// TI - Tiggers and DNA transposon fossils in the human genome JO - Proc Natl Acad Sci U S A VL - 93 UR - https://doi.org/10.1073/pnas.93.4.1443 DO - 10.1073/pnas.93.4.1443 ID - Smit1996 ER - TY - JOUR AU - Schaack, S. AU - Gilbert, C. AU - Feschotte, C. PY - 2010 DA - 2010// TI - Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution JO - Trends Ecol Evol VL - 25 UR - https://doi.org/10.1016/j.tree.2010.06.001 DO - 10.1016/j.tree.2010.06.001 ID - Schaack2010 ER - TY - JOUR AU - Lack, J. B. AU - Roehrs, Z. P. AU - Stanley, C. E. AU - Ruedi, M. AU - Bussche, R. A. PY - 2010 DA - 2010// TI - Molecular phylogenetics of Myotis indicate familial-level divergence for the genus Cistugo (Chiroptera) JO - J Mammal VL - 91 UR - https://doi.org/10.1644/09-MAMM-A-192.1 DO - 10.1644/09-MAMM-A-192.1 ID - Lack2010 ER - TY - JOUR AU - Pagan, H. J. T. AU - Smith, J. D. AU - Hubley, R. M. AU - Ray, D. A. PY - 2010 DA - 2010// TI - PiggyBac-ing on a Primate genome: Novel elements, recent activity and horizontal transfer JO - Genome Biol Evol VL - 2 UR - https://doi.org/10.1093/gbe/evq021 DO - 10.1093/gbe/evq021 ID - Pagan2010 ER - TY - JOUR AU - Roehrs, Z. P. AU - Lack, J. B. AU - Bussche, R. A. PY - 2010 DA - 2010// TI - Tribal phylogenetic relationships within Vespertilioninae (Chiroptera: Vespertilionidae) based on mitochondrial and nuclear sequence data JO - J Mammal VL - 91 UR - https://doi.org/10.1644/09-MAMM-A-325.1 DO - 10.1644/09-MAMM-A-325.1 ID - Roehrs2010 ER - TY - JOUR AU - Pace, J. K. AU - Feschotte, C. PY - 2007 DA - 2007// TI - The evolutionary history of human DNA transposons: Evidence for intense activity in the primate lineage JO - Genome Res VL - 17 UR - https://doi.org/10.1101/gr.5826307 DO - 10.1101/gr.5826307 ID - Pace2007 ER - TY - JOUR AU - Vandewege, M. W. AU - Platt, R. N. AU - Ray, D. A. AU - Hoffmann, F. G. PY - 2016 DA - 2016// TI - Transposable element targeting by piRNAs in Laurasiatherians with distinct transposable element histories JO - Genome Biol Evol ID - Vandewege2016 ER - TY - STD TI - Gilbert C, Chateigner A, Ernenwein L, Barbe V, Bézier A, Herniou EA et al. Population genomics supports baculoviruses as vectors of horizontal transfer of insect transposons. Nat Commun. 2014;5. doi:10.1038/ncomms4348. ID - ref36 ER - TY - JOUR AU - Feschotte, C. AU - Pritham, E. J. PY - 2007 DA - 2007// TI - DNA Transposons and the Evolution of Eukaryotic Genomes JO - Annu Rev Genet VL - 41 UR - https://doi.org/10.1146/annurev.genet.40.110405.090448 DO - 10.1146/annurev.genet.40.110405.090448 ID - Feschotte2007 ER - TY - JOUR AU - Oliver, K. R. AU - Greene, W. K. PY - 2011 DA - 2011// TI - Mobile DNA and the TE-Thrust hypothesis: supporting evidence from the primates JO - Mob DNA VL - 2 UR - https://doi.org/10.1186/1759-8753-2-8 DO - 10.1186/1759-8753-2-8 ID - Oliver2011 ER - TY - JOUR AU - Hedges, S. B. AU - Marin, J. AU - Suleski, M. AU - Paymer, M. AU - Kumar, S. PY - 2015 DA - 2015// TI - Tree of Life Reveals Clock-Like Speciation and Diversification JO - Mol Biol Evol VL - 32 UR - https://doi.org/10.1093/molbev/msv037 DO - 10.1093/molbev/msv037 ID - Hedges2015 ER - TY - JOUR AU - Stadelmann, B. AU - Lin, L. K. AU - Kunz, T. H. AU - Ruedi, M. PY - 2007 DA - 2007// TI - Molecular phylogeny of New World Myotis (Chiroptera, Vespertilionidae) inferred from mitochondrial and nuclear DNA genes JO - Mol Phylogenet Evol VL - 43 UR - https://doi.org/10.1016/j.ympev.2006.06.019 DO - 10.1016/j.ympev.2006.06.019 ID - Stadelmann2007 ER -