TY - JOUR PY - 2001 DA - 2001// TI - From controlling elements to transposons: Barbara McClintock and the Nobel Prize JO - Trends Genet VL - 17 UR - https://doi.org/10.1016/S0168-9525(01)02383-6 DO - 10.1016/S0168-9525(01)02383-6 ID - ref1 ER - TY - JOUR AU - de 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 - de Koning2011 ER - TY - JOUR AU - Slotkin, R. K. AU - Vaughn, M. AU - Borges, F. AU - Tanurdzic, M. AU - Becker, J. D. AU - Feijó, J. A. PY - 2009 DA - 2009// TI - Epigenetic reprogramming and small RNA silencing of transposable elements in pollen JO - Cell VL - 136 UR - https://doi.org/10.1016/j.cell.2008.12.038 DO - 10.1016/j.cell.2008.12.038 ID - Slotkin2009 ER - TY - JOUR AU - Chuong, E. B. AU - Elde, N. C. AU - Feschotte, C. PY - 2017 DA - 2017// TI - Regulatory activities of transposable elements: from conflicts to benefits JO - Nat Rev Genet VL - 18 UR - https://doi.org/10.1038/nrg.2016.139 DO - 10.1038/nrg.2016.139 ID - Chuong2017 ER - TY - JOUR AU - McCue, A. D. AU - Slotkin, R. K. PY - 2012 DA - 2012// TI - Transposable element small RNAs as regulators of gene expression JO - Trends Genet VL - 28 UR - https://doi.org/10.1016/j.tig.2012.09.001 DO - 10.1016/j.tig.2012.09.001 ID - McCue2012 ER - TY - JOUR AU - Sundaram, V. AU - Cheng, Y. AU - Ma, Z. AU - Li, D. AU - Xing, X. AU - Edge, P. PY - 2014 DA - 2014// TI - Widespread contribution of transposable elements to the innovation of gene regulatory networks JO - Genome Res VL - 24 UR - https://doi.org/10.1101/gr.168872.113 DO - 10.1101/gr.168872.113 ID - Sundaram2014 ER - TY - JOUR AU - Chuong, E. B. AU - Elde, N. C. AU - Feschotte, C. PY - 2016 DA - 2016// TI - Regulatory evolution of innate immunity through co-option of endogenous retroviruses JO - Science VL - 351 UR - https://doi.org/10.1126/science.aad5497 DO - 10.1126/science.aad5497 ID - Chuong2016 ER - TY - JOUR AU - Macfarlan, T. S. AU - Gifford, W. D. AU - Driscoll, S. AU - Lettieri, K. AU - Rowe, H. M. AU - Bonanomi, D. PY - 2012 DA - 2012// TI - Embryonic stem cell potency fluctuates with endogenous retrovirus activity JO - Nature VL - 487 UR - https://doi.org/10.1038/nature11244 DO - 10.1038/nature11244 ID - Macfarlan2012 ER - TY - JOUR AU - Gerdes, P. AU - Richardson, S. R. AU - Mager, D. L. AU - Faulkner, G. J. PY - 2016 DA - 2016// TI - Transposable elements in the mammalian embryo: pioneers surviving through stealth and service JO - Genome Biol VL - 17 ID - Gerdes2016 ER - TY - JOUR AU - Kapusta, A. AU - Kronenberg, Z. AU - Lynch, V. J. AU - Zhuo, X. AU - Ramsay, L. AU - Bourque, G. PY - 2013 DA - 2013// TI - Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs JO - PLoS Genet VL - 9 UR - https://doi.org/10.1371/journal.pgen.1003470 DO - 10.1371/journal.pgen.1003470 ID - Kapusta2013 ER - TY - JOUR AU - Horváth, V. AU - Merenciano, M. AU - Gonzalez, J. PY - 2017 DA - 2017// TI - Revisiting the Relationship between Transposable Elements and the Eukaryotic Stress Response JO - Trends Genet VL - 33 UR - https://doi.org/10.1016/j.tig.2017.08.007 DO - 10.1016/j.tig.2017.08.007 ID - Horváth2017 ER - TY - JOUR AU - Klein, S. J. AU - O'Neill, R. J. PY - 2018 DA - 2018// TI - Transposable elements: genome innovation, chromosome diversity, and centromere conflict JO - Chromosom Res VL - 2012 ID - Klein2018 ER - TY - JOUR AU - Mateo, L. AU - Gonzalez, J. PY - 2014 DA - 2014// TI - Pogo-like transposases have been repeatedly domesticated into CENP-B-related proteins JO - Genome Biol Evol VL - 6 UR - https://doi.org/10.1093/gbe/evu153 DO - 10.1093/gbe/evu153 ID - Mateo2014 ER - TY - JOUR AU - George, J. A. AU - DeBaryshe, P. G. AU - Traverse, K. L. AU - Celniker, S. E. AU - Pardue, M. -. L. PY - 2006 DA - 2006// TI - Genomic organization of the Drosophila telomere retrotransposable elements JO - Genome Res VL - 16 UR - https://doi.org/10.1101/gr.5348806 DO - 10.1101/gr.5348806 ID - George2006 ER - TY - JOUR AU - Reilly, M. T. AU - Faulkner, G. J. AU - Dubnau, J. AU - Ponomarev, I. AU - Gage, F. H. PY - 2013 DA - 2013// TI - The role of transposable elements in health and diseases of the central nervous system JO - J Neurosci VL - 33 UR - https://doi.org/10.1523/JNEUROSCI.3369-13.2013 DO - 10.1523/JNEUROSCI.3369-13.2013 ID - Reilly2013 ER - TY - JOUR AU - Wylie, A. AU - Jones, A. E. AU - Abrams, J. M. PY - 2016 DA - 2016// TI - p53 in the game of transposons JO - BioEssays VL - 38 UR - https://doi.org/10.1002/bies.201600115 DO - 10.1002/bies.201600115 ID - Wylie2016 ER - TY - JOUR AU - Burns, K. H. PY - 2017 DA - 2017// TI - Transposable elements in cancer JO - Nat Rev Cancer VL - 17 UR - https://doi.org/10.1038/nrc.2017.35 DO - 10.1038/nrc.2017.35 ID - Burns2017 ER - TY - JOUR AU - Faulkner, G. J. AU - Forrest, A. R. R. AU - Chalk, A. M. AU - Schroder, K. AU - Hayashizaki, Y. AU - Carninci, P. PY - 2008 DA - 2008// TI - A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE JO - Genomics VL - 91 UR - https://doi.org/10.1016/j.ygeno.2007.11.003 DO - 10.1016/j.ygeno.2007.11.003 ID - Faulkner2008 ER - TY - JOUR AU - Gardner, E. J. AU - Lam, V. K. AU - Harris, D. N. AU - Chuang, N. T. AU - Scott, E. C. AU - Pittard, W. S. PY - 2017 DA - 2017// TI - The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology JO - Genome Res VL - 27 UR - https://doi.org/10.1101/gr.218032.116 DO - 10.1101/gr.218032.116 ID - Gardner2017 ER - TY - JOUR AU - Keane, T. M. AU - Wong, K. AU - Adams, D. J. PY - 2013 DA - 2013// TI - RetroSeq: transposable element discovery from next-generation sequencing data JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/bts697 DO - 10.1093/bioinformatics/bts697 ID - Keane2013 ER - TY - JOUR AU - Daron, J. AU - Slotkin, R. K. PY - 2017 DA - 2017// TI - EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels JO - Genome Biol VL - 18 UR - https://doi.org/10.1186/s13059-017-1232-0 DO - 10.1186/s13059-017-1232-0 ID - Daron2017 ER - TY - JOUR AU - Nelson, M. G. AU - Linheiro, R. S. AU - Bergman, C. M. PY - 2017 DA - 2017// TI - McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data JO - G3 VL - 7 UR - https://doi.org/10.1534/g3.117.043893 DO - 10.1534/g3.117.043893 ID - Nelson2017 ER - TY - JOUR AU - Fiston-Lavier, A. -. S. AU - Carrigan, M. AU - Petrov, D. A. AU - Gonzalez, J. PY - 2011 DA - 2011// TI - T-lex: a program for fast and accurate assessment of transposable element presence using next-generation sequencing data JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkq1291 DO - 10.1093/nar/gkq1291 ID - Fiston-Lavier2011 ER - TY - JOUR AU - Daron, J. AU - Glover, N. AU - Pingault, L. AU - Theil, S. AU - Jamilloux, V. AU - Paux, E. PY - 2014 DA - 2014// TI - Organization and evolution of transposable elements along the bread wheat chromosome 3B JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/s13059-014-0546-4 DO - 10.1186/s13059-014-0546-4 ID - Daron2014 ER - TY - JOUR AU - Jin, Y. AU - Tam, O. H. AU - Paniagua, E. AU - Hammell, M. PY - 2015 DA - 2015// TI - TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets JO - Bioinformatics VL - 31 UR - https://doi.org/10.1093/bioinformatics/btv422 DO - 10.1093/bioinformatics/btv422 ID - Jin2015 ER - TY - JOUR AU - Jin, Y. AU - Hammell, M. PY - 2018 DA - 2018// TI - Analysis of RNA-Seq Data Using TEtranscripts JO - Methods Mol Biol VL - 1751 UR - https://doi.org/10.1007/978-1-4939-7710-9_11 DO - 10.1007/978-1-4939-7710-9_11 ID - Jin2018 ER - TY - JOUR AU - Panda, K. AU - Ji, L. AU - Neumann, D. A. AU - Daron, J. AU - Schmitz, R. J. AU - Slotkin, R. K. PY - 2016 DA - 2016// TI - Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation JO - Genome Biol VL - 17 UR - https://doi.org/10.1186/s13059-016-1032-y DO - 10.1186/s13059-016-1032-y ID - Panda2016 ER - TY - JOUR AU - Breese, M. R. AU - Liu, Y. PY - 2013 DA - 2013// TI - NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/bts731 DO - 10.1093/bioinformatics/bts731 ID - Breese2013 ER - TY - JOUR AU - Nuthikattu, S. AU - McCue, A. D. AU - Panda, K. AU - Fultz, D. AU - DeFraia, C. AU - Thomas, E. N. PY - 2013 DA - 2013// TI - The Initiation of Epigenetic Silencing of Active Transposable Elements Is Triggered by RDR6 and 21-22 Nucleotide Small Interfering RNAs JO - Plant Physiol VL - 162 UR - https://doi.org/10.1104/pp.113.216481 DO - 10.1104/pp.113.216481 ID - Nuthikattu2013 ER - TY - JOUR AU - Johnson, N. R. AU - Yeoh, J. M. AU - Coruh, C. AU - Axtell, M. J. PY - 2016 DA - 2016// TI - Improved Placement of Multi-Mapping Small RNAs JO - G3 VL - 6 UR - https://doi.org/10.1534/g3.116.030452 DO - 10.1534/g3.116.030452 ID - Johnson2016 ER - TY - STD TI - Martinez G, Wolff P, Wang Z, Moreno-Romero J, Lez JS–GX, Conze LL. et al, Paternal easiRNAs regulate parental genome dosage in Arabidopsis. Nat Genet. 2018;50:193–98. ID - ref31 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 - McCue, A. D. AU - Panda, K. AU - Nuthikattu, S. AU - Choudury, S. G. AU - Thomas, E. N. AU - Slotkin, R. K. PY - 2015 DA - 2015// TI - ARGONAUTE 6 bridges transposable element mRNA-derived siRNAs to the establishment of DNA methylation JO - EMBO J VL - 34 UR - https://doi.org/10.15252/embj.201489499 DO - 10.15252/embj.201489499 ID - McCue2015 ER - TY - JOUR AU - Ewing, A. D. PY - 2015 DA - 2015// TI - Transposable element detection from whole genome sequence data JO - Mob DNA VL - 6 UR - https://doi.org/10.1186/s13100-015-0055-3 DO - 10.1186/s13100-015-0055-3 ID - Ewing2015 ER - TY - JOUR AU - Ivics, Z. AU - Li, M. A. AU - Mátés, L. AU - Boeke, J. D. AU - Nagy, A. AU - Bradley, A. PY - 2009 DA - 2009// TI - Transposon-mediated genome manipulation in vertebrates JO - Nat Methods VL - 6 UR - https://doi.org/10.1038/nmeth.1332 DO - 10.1038/nmeth.1332 ID - Ivics2009 ER - TY - JOUR AU - Buenrostro, J. D. AU - Wu, B. AU - Chang, H. Y. AU - Greenleaf, W. J. PY - 2015 DA - 2015// TI - ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide JO - Curr Protoc Mol Biol VL - 109 UR - https://doi.org/10.1002/0471142727.mb2129s109 DO - 10.1002/0471142727.mb2129s109 ID - Buenrostro2015 ER - TY - JOUR AU - Picelli, S. AU - Björklund, A. K. AU - Reinius, B. AU - Sagasser, S. AU - Winberg, G. AU - Sandberg, R. PY - 2014 DA - 2014// TI - Tn5 transposase and tagmentation procedures for massively scaled sequencing projects JO - Genome Res VL - 24 UR - https://doi.org/10.1101/gr.177881.114 DO - 10.1101/gr.177881.114 ID - Picelli2014 ER - TY - JOUR AU - Koonin, E. V. AU - Makarova, K. S. PY - 2017 DA - 2017// TI - Mobile Genetic Elements and Evolution of CRISPR-Cas Systems: All the Way There and Back JO - Genome Biol Evol VL - 9 UR - https://doi.org/10.1093/gbe/evx192 DO - 10.1093/gbe/evx192 ID - Koonin2017 ER - TY - JOUR AU - Sudmant, P. H. AU - Rausch, T. AU - Gardner, E. J. AU - Handsaker, R. E. AU - Abyzov, A. AU - Huddleston, J. PY - 2015 DA - 2015// TI - An integrated map of structural variation in 2,504 human genomes JO - Nature VL - 526 UR - https://doi.org/10.1038/nature15394 DO - 10.1038/nature15394 ID - Sudmant2015 ER -