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Repository for all published articles on softwares, databases, and methodologies. Submit your updates and new submissions on not yet covered databases and other tools for analyzing and categorizing transposable elements. 

  1. Interspersed repeats occupy a large part of many eukaryotic genomes, and thus their accurate annotation is essential for various genome analyses. Database-free de novo repeat detection approaches are powerful ...

    Authors: Atsushi Takeda, Daisuke Nonaka, Yuta Imazu, Tsukasa Fukunaga and Michiaki Hamada
    Citation: Mobile DNA 2025 16:16
    Content type: Software Published on:

  3. The advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented resources for the study of genome evolution. Within this context, the...

    Authors: Valentina Peona, Jacopo Martelossi, Dareen Almojil, Julia Bocharkina, Ioana Brännström, Max Brown, Alice Cang, Tomàs Carrasco-Valenzuela, Jon DeVries, Meredith Doellman, Daniel Elsner, Pamela Espíndola-Hernández, Guillermo Friis Montoya, Bence Gaspar, Danijela Zagorski, Paweł Hałakuc…
    Citation: Mobile DNA 2024 15:10
    Content type: Research Published on:

  4. Plant genomes include large numbers of transposable elements. One particular type of these elements is flanked by two Long Terminal Repeats (LTRs) and can translocate using RNA. Such elements are known as LTR-...

    Authors: Anthony B. Garza, Emmanuelle Lerat and Hani Z. Girgis
    Citation: Mobile DNA 2024 15:8
    Content type: Software Published on:

  5. Repeat elements (REs) play important roles for cell function in health and disease. However, RE enrichment analysis in short-read high-throughput sequencing (HTS) data, such as ChIP-seq, is a challenging task.

    Authors: Michel Choudalakis, Pavel Bashtrykov and Albert Jeltsch
    Citation: Mobile DNA 2024 15:6
    Content type: Methodology Published on:

  8. Many computational methods have been developed to detect non-reference transposable element (TE) insertions using short-read whole genome sequencing data. The diversity and complexity of such methods often pre...

    Authors: Jingxuan Chen, Preston J. Basting, Shunhua Han, David J. Garfinkel and Casey M. Bergman
    Citation: Mobile DNA 2023 14:8
    Content type: Research Published on:

  9. In the study of transposable elements (TEs), the generation of a high confidence set of consensus sequences that represent the diversity of TEs found in a given genome is a key step in the path to investigate ...

    Authors: Clement Goubert, Rory J. Craig, Agustin F. Bilat, Valentina Peona, Aaron A. Vogan and Anna V. Protasio
    Citation: Mobile DNA 2022 13:7
    Content type: Methodology Published on:

    The Correction to this article has been published in Mobile DNA 2022 13:15

  11. Retroelements (REs) occupy a significant part of all eukaryotic genomes including humans. The majority of retroelements in the human genome are inactive and unable to retrotranspose. Dozens of active copies ar...

    Authors: Alexander Y. Komkov, Shamil Z. Urazbakhtin, Maria V. Saliutina, Ekaterina A. Komech, Yuri A. Shelygin, Gaiaz A. Nugmanov, Vitaliy P. Shubin, Anastasia O. Smirnova, Mikhail Y. Bobrov, Alexey S. Tsukanov, Anastasia V. Snezhkina, Anna V. Kudryavtseva, Yuri B. Lebedev and Ilgar Z. Mamedov
    Citation: Mobile DNA 2020 11:33
    Content type: Methodology Published on:

  12. Nearly half the human genome consists of repeat elements, most of which are retrotransposons, and many of which play important biological roles. However repeat elements pose several unique challenges to curren...

    Authors: Jason D. Fernandes, Armando Zamudio-Hurtado, Hiram Clawson, W. James Kent, David Haussler, Sofie R. Salama and Maximilian Haeussler
    Citation: Mobile DNA 2020 11:13
    Content type: Software Published on:

  13. Mobile elements are ubiquitous components of mammalian genomes and constitute more than half of the human genome. Polymorphic mobile element insertions (pMEIs) are a major source of human genomic variation and...

    Authors: Jui Wan Loh, Hongseok Ha, Timothy Lin, Nawei Sun, Kathleen H. Burns and Jinchuan Xing
    Citation: Mobile DNA 2020 11:12
    Content type: Methodology Published on:

  14. Ligation-mediated PCR protocols have diverse uses including the identification of integration sites of insertional mutagens, integrating vectors and naturally occurring mobile genetic elements. For approaches ...

    Authors: Joanna C. Dawes, Philip Webster, Barbara Iadarola, Claudia Garcia-Diaz, Marian Dore, Bruce J. Bolt, Hamlata Dewchand, Gopuraja Dharmalingam, Alex P. McLatchie, Jakub Kaczor, Juan J. Caceres, Alberto Paccanaro, Laurence Game, Simona Parrinello and Anthony G. Uren
    Citation: Mobile DNA 2020 11:7
    Content type: Methodology Published on:

  15. Retrotransposons are one of the oldest evolutionary forces shaping mammalian genomes, with the ability to mobilize from one genomic location to another. This mobilization is also a significant factor in human ...

    Authors: Tiffany Kaul, Maria E. Morales, Alton O. Sartor, Victoria P. Belancio and Prescott Deininger
    Citation: Mobile DNA 2020 11:2
    Content type: Methodology Published on:

  16. Transposable elements (TEs) are an important source of genomic variability in eukaryotic genomes. Their activity impacts genome architecture and gene expression and can lead to drastic phenotypic changes. Ther...

    Authors: Pol Vendrell-Mir, Fabio Barteri, Miriam Merenciano, Josefa González, Josep M. Casacuberta and Raúl Castanera
    Citation: Mobile DNA 2019 10:53
    Content type: Methodology Published on:

  17. Sequencing technologies give access to a precise picture of the molecular mechanisms acting upon genome regulation. One of the biggest technical challenges with sequencing data is to map millions of reads to a...

    Authors: Aurélie Teissandier, Nicolas Servant, Emmanuel Barillot and Deborah Bourc’his
    Citation: Mobile DNA 2019 10:52
    Content type: Methodology Published on:

  19. Transposable elements make up a significant portion of the human genome. Accurately locating these mobile DNAs is vital to understand their role as a source of structural variation and somatic mutation. To thi...

    Authors: Jared P. Steranka, Zuojian Tang, Mark Grivainis, Cheng Ran Lisa Huang, Lindsay M. Payer, Fernanda O. R. Rego, Thiago Luiz Araujo Miller, Pedro A. F. Galante, Sitharam Ramaswami, Adriana Heguy, David Fenyö, Jef D. Boeke and Kathleen H. Burns
    Citation: Mobile DNA 2019 10:8
    Content type: Methodology Published on:

  20. Thanks to their ability to move around and replicate within genomes, transposable elements (TEs) are perhaps the most important contributors to genome plasticity and evolution. Their detection and annotation a...

    Authors: Joëlle Amselem, Guillaume Cornut, Nathalie Choisne, Michael Alaux, Françoise Alfama-Depauw, Véronique Jamilloux, Florian Maumus, Thomas Letellier, Isabelle Luyten, Cyril Pommier, Anne-Françoise Adam-Blondon and Hadi Quesneville
    Citation: Mobile DNA 2019 10:6
    Content type: Software Published on:

  21. Similar to retro−/lenti- virus system, DNA transposons are useful tools for stable expression of exogenous genes in mammalian cells. Sleeping Beauty (SB) transposon has adopted for integrating genes into host ...

    Authors: Kaishun Hu, Yu Li, Wenjing Wu, Hengxing Chen, Zhen Chen, Yin Zhang, Yabin Guo and Dong Yin
    Citation: Mobile DNA 2018 9:33
    Content type: Research Published on:

    The Correction to this article has been published in Mobile DNA 2019 10:2

  22. There is increasing evidence that the transpositional activity of retroelements (REs) is not limited to germ line cells, but often occurs in tumor and normal somatic cells. Somatic transpositions were found in...

    Authors: Alexander Y. Komkov, Anastasia A. Minervina, Gaiaz A. Nugmanov, Mariia V. Saliutina, Konstantin V. Khodosevich, Yuri B. Lebedev and Ilgar Z. Mamedov
    Citation: Mobile DNA 2018 9:31
    Content type: Methodology Published on:

  28. The National Cancer Institute-60 (NCI-60) cell lines are among the most widely used models of human cancer. They provide a platform to integrate DNA sequence information, epigenetic data, RNA and protein expre...

    Authors: John G. Zampella, Nemanja Rodić, Wan Rou Yang, Cheng Ran Lisa Huang, Jane Welch, Veena P. Gnanakkan, Toby C. Cornish, Jef D. Boeke and Kathleen H. Burns
    Citation: Mobile DNA 2016 7:20
    Content type: Research Published on:

  31. A critical topic of insertional mutagenesis experiments performed on model organisms is mapping the hits of artificial transposons (ATs) at nucleotide level accuracy. Mapping errors may occur when sequencing a...

    Authors: Alexandru Al. Ecovoiu, Iulian Constantin Ghionoiu, Andrei Mihai Ciuca and Attila Cristian Ratiu
    Citation: Mobile DNA 2016 7:3
    Content type: Software Published on:

  32. DNA derived from transposable elements (TEs) constitutes large parts of the genomes of complex eukaryotes, with major impacts not only on genomic research but also on how organisms evolve and function. Althoug...

    Authors: Douglas R. Hoen, Glenn Hickey, Guillaume Bourque, Josep Casacuberta, Richard Cordaux, Cédric Feschotte, Anna-Sophie Fiston-Lavier, Aurélie Hua-Van, Robert Hubley, Aurélie Kapusta, Emmanuelle Lerat, Florian Maumus, David D. Pollock, Hadi Quesneville, Arian Smit, Travis J. Wheeler…
    Citation: Mobile DNA 2015 6:13
    Content type: Commentary Published on:

  34. The active human mobile element, long interspersed element 1 (L1) currently populates human genomes in excess of 500,000 copies per haploid genome. Through its mobility via a process called target primed rever...

    Authors: Travis B White, Adam M McCoy, Vincent A Streva, Joshua Fenrich and Prescott L Deininger
    Citation: Mobile DNA 2014 5:30
    Content type: Research Published on:

  35. LINE-1 (L1) retrotransposons are common occupants of mammalian genomes representing about a fifth of the genetic content. Ongoing L1 retrotransposition in the germ line and somatic tissues has contributed to s...

    Authors: Mark Sokolowski, Cecily B DeFreece, Geraldine Servant, Kristine J Kines, Dawn L deHaro and Victoria P Belancio
    Citation: Mobile DNA 2014 5:29
    Content type: Methodology Published on:

  38. Accurate and complete identification of mobile elements is a challenging task in the current era of sequencing, given their large numbers and frequent truncations. Group II intron retroelements, which consist ...

    Authors: Michael Abebe, Manuel A Candales, Adrian Duong, Keyar S Hood, Tony Li, Ryan A E Neufeld, Abat Shakenov, Runda Sun, Li Wu, Ashley M Jarding, Cameron Semper and Steven Zimmerly
    Citation: Mobile DNA 2013 4:28
    Content type: Software Published on:

  39. High-throughput deep-sequencing technology has generated an unprecedented number of expressed sequence reads that offer the opportunity to get insight into biological systems. Several databases report the sequ...

    Authors: Jeremy Dufourt, Pierre Pouchin, Pierre Peyret, Emilie Brasset and Chantal Vaury
    Citation: Mobile DNA 2013 4:1
    Content type: Software Published on:

  40. Functional regulatory sequences are present in many transposable element (TE) copies, resulting in TEs being frequently exapted by host genes. Today, many examples of TEs impacting host gene expression can be ...

    Authors: Rita Rebollo, Sharareh Farivar and Dixie L Mager
    Citation: Mobile DNA 2012 3:9
    Content type: Short Report Published on:

  41. The transposon-based gene delivery technique is emerging as a method of choice for gene therapy. The Sleeping Beauty (SB) system has become one of the most favored methods, because of its efficiency and its rando...

    Authors: Orsolya Kolacsek, Virág Krízsik, Anita Schamberger, Zsuzsa Erdei, Ágota Apáti, György Várady, Lajos Mátés, Zsuzsanna Izsvák, Zoltán Ivics, Balázs Sarkadi and Tamás I Orbán
    Citation: Mobile DNA 2011 2:5
    Content type: Methodology Published on:

    The Erratum to this article has been published in Mobile DNA 2013 4:11

  42. Completed genome projects have revealed an astonishing diversity of transposable genetic elements, implying the existence of novel element families yet to be discovered from diverse life forms. Concurrently, s...

    Authors: Maria I Pajunen, Tiina S Rasila, Lotta J Happonen, Arja Lamberg, Saija Haapa-Paananen, Saija Kiljunen and Harri Savilahti
    Citation: Mobile DNA 2010 1:24
    Content type: Research Published on:

  43. Retrotransposons are abundant components of plant genomes, and although some plant retrotransposons have been used as insertional mutagens, these mobile genetic elements have not been widely exploited for plan...

    Authors: Yi Hou, Jyothi Rajagopal, Phillip A Irwin and Daniel F Voytas
    Citation: Mobile DNA 2010 1:19
    Content type: Research Published on: