Volume 4, issue 1, December 2013

28 articles in this issue

A pipeline of programs for collecting and analyzing group II intron retroelement sequences from GenBank

Authors (first, second and last of 12)
- Michael Abebe
- Manuel A Candales
- Steven Zimmerly
- Content type: Software
- Open Access
- Published: 20 December 2013
- Article: 28
Distinctive patterns of epigenetic marks are associated with promoter regions of mouse LINE-1 and LTR retrotransposons

Authors
- Danny Rangasamy
- Content type: Short Report
- Open Access
- Published: 02 December 2013
- Article: 27
Analysis of western lowland gorilla (Gorilla gorilla gorilla) specific Alu repeats

Authors (first, second and last of 8)
- Adam T McLain
- Glenn W Carman
- Mark A Batzer
- Content type: Research
- Open Access
- Published: 22 November 2013
- Article: 26
Identification of three new Alu Yb subfamilies by source tracking of recently integrated Alu Yb elements

Authors
- Musaddeque Ahmed
- Wen Li
- Ping Liang
- Content type: Research
- Open Access
- Published: 12 November 2013
- Article: 25
A proposed mechanism for IS607-family serine transposases

Authors
- Martin R Boocock
- Phoebe A Rice
- Content type: Research
- Open Access
- Published: 06 November 2013
- Article: 24
PGBD5: a neural-specific intron-containing piggyBac transposase domesticated over 500 million years ago and conserved from cephalochordates to humans

Authors (first, second and last of 5)
- Thomas Pavelitz
- Lucas T Gray
- Alan M Weiner
- Content type: Research
- Open Access
- Published: 01 November 2013
- Article: 23
Translocation junctions in TCF3-PBX1 acute lymphoblastic leukemia/lymphoma cluster near transposable elements

Authors (first, second and last of 5)
- Nemanja Rodić
- John G Zampella
- Kathleen H Burns
- Content type: Research
- Open Access
- Published: 17 October 2013
- Article: 22
Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera

Authors (first, second and last of 5)
- Christine A Lavoie
- Roy N Platt II
- David A Ray
- Content type: Research
- Open Access
- Published: 02 October 2013
- Article: 21
In and out of the rRNA genes: characterization of Pokey elements in the sequenced Daphnia genome

Authors (first, second and last of 4)
- Tyler A Elliott
- Deborah E Stage
- Thomas H Eickbush
- Content type: Research
- Open Access
- Published: 23 September 2013
- Article: 20
Endonuclease-containing Penelope retrotransposons in the bdelloid rotifer Adineta vaga exhibit unusual structural features and play a role in expansion of host gene families

Authors
- Irina R Arkhipova
- Irina A Yushenova
- Fernando Rodriguez
- Content type: Research
- Open Access
- Published: 27 August 2013
- Article: 19
The Putzig partners DREF, TRF2 and KEN are involved in the regulation of the Drosophila telomere retrotransposons, HeT-A and TART

Authors
- Rute Silva-Sousa
- Míriam Díaz Varela
- Elena Casacuberta
- Content type: Research
- Open Access
- Published: 03 July 2013
- Article: 18
Nuclear group I introns in self-splicing and beyond

Authors
- Annica Hedberg
- Steinar D Johansen
- Content type: Review
- Open Access
- Published: 05 June 2013
- Article: 17
This is part of 1 collection:
Mobile introns review series
LINE-1 and Alu retrotransposition exhibit clonal variation

Authors
- Vincent A Streva
- Zachary J Faber
- Prescott L Deininger
- Content type: Short Report
- Open Access
- Published: 03 June 2013
- Article: 16
Regulation of DNA transposition by CpG methylation and chromatin structure in human cells

Authors (first, second and last of 4)
- Tobias Jursch
- Csaba Miskey
- Zoltán Ivics
- Content type: Research
- Open Access
- Published: 15 May 2013
- Article: 15
Now on display: a gallery of group II intron structures at different stages of catalysis

Authors
- Marco Marcia
- Srinivas Somarowthu
- Anna Marie Pyle
- Content type: Review
- Open Access
- Published: 01 May 2013
- Article: 14
This is part of 1 collection:
Mobile introns review series
Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina

Authors
- Bárbara Negre
- Pat Simpson
- Content type: Research
- Open Access
- Published: 03 April 2013
- Article: 13
Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements

Authors
- Weidong Bao
- Jerzy Jurka
- Content type: Research
- Open Access
- Published: 01 April 2013
- Article: 12
Erratum to: Reliable transgene-independent method for determining sleeping beauty transposon copy numbers

Authors (first, second and last of 11)
- Orsolya Kolacsek
- Virág Krízsik
- Tamás I Orbán
- Content type: Erratum
- Open Access
- Published: 15 March 2013
- Article: 11
Cell division promotes efficient retrotransposition in a stable L1 reporter cell line

Authors (first, second and last of 6)
- Yi Xie
- Lajos Mates
- Wenfeng An
- Content type: Short Report
- Open Access
- Published: 06 March 2013
- Article: 10
Sirevirus LTR retrotransposons: phylogenetic misconceptions in the plant world

Authors
- Alexandros Bousios
- Nikos Darzentas
- Content type: Commentary
- Open Access
- Published: 04 March 2013
- Article: 9
Highly diverse chromoviruses of Beta vulgaris are classified by chromodomains and chromosomal integration

Authors (first, second and last of 8)
- Beatrice Weber
- Tony Heitkam
- Thomas Schmidt
- Content type: Research
- Open Access
- Published: 01 March 2013
- Article: 8
Evolution of a transposon in Daphnia hybrid genomes

Authors (first, second and last of 5)
- Roland Vergilino
- Tyler A Elliott
- France Dufresne
- Content type: Research
- Open Access
- Published: 06 February 2013
- Article: 7
Striking structural dynamism and nucleotide sequence variation of the transposon Galileo in the genome of Drosophila mojavensis

Authors (first, second and last of 5)
- Mar Marzo
- Xabier Bello
- Alfredo Ruiz
- Content type: Research
- Open Access
- Published: 04 February 2013
- Article: 6
Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)

Authors (first, second and last of 6)
- Farid Benachenhou
- Göran O Sperber
- Jonas Blomberg
- Content type: Research
- Open Access
- Published: 01 February 2013
- Article: 5
Reviewer acknowledgement 2013

Authors
- Nancy L Craig
- Thomas H Eikbush
- Daniel F Voytas
- Content type: Reviewer Acknowledgement
- Open Access
- Published: 25 February 2013
- Article: 4
Revisiting the evolution of mouse LINE-1 in the genomic era

Authors (first, second and last of 4)
- Akash Sookdeo
- Crystal M Hepp
- Stéphane Boissinot
- Content type: Research
- Open Access
- Published: 03 January 2013
- Article: 3
The site-specific integration reaction of Listeria phage A118 integrase, a serine recombinase

Authors (first, second and last of 5)
- Sridhar Mandali
- Gautam Dhar
- Reid C Johnson
- Content type: Research
- Open Access
- Published: 03 January 2013
- Article: 2
NucBase, an easy to use read mapper for small RNAs

Authors (first, second and last of 5)
- Jeremy Dufourt
- Pierre Pouchin
- Chantal Vaury
- Content type: Software
- Open Access
- Published: 01 January 2013
- Article: 1

Volume 4, issue 1, December 2013

A pipeline of programs for collecting and analyzing group II intron retroelement sequences from GenBank

Distinctive patterns of epigenetic marks are associated with promoter regions of mouse LINE-1 and LTR retrotransposons

Analysis of western lowland gorilla (Gorilla gorilla gorilla) specific Alu repeats

Identification of three new Alu Yb subfamilies by source tracking of recently integrated Alu Yb elements

A proposed mechanism for IS607-family serine transposases

PGBD5: a neural-specific intron-containing piggyBac transposase domesticated over 500 million years ago and conserved from cephalochordates to humans

Translocation junctions in TCF3-PBX1 acute lymphoblastic leukemia/lymphoma cluster near transposable elements

Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera

In and out of the rRNA genes: characterization of Pokey elements in the sequenced Daphnia genome

Endonuclease-containing Penelope retrotransposons in the bdelloid rotifer Adineta vaga exhibit unusual structural features and play a role in expansion of host gene families

The Putzig partners DREF, TRF2 and KEN are involved in the regulation of the Drosophila telomere retrotransposons, HeT-A and TART

Nuclear group I introns in self-splicing and beyond

LINE-1 and Alu retrotransposition exhibit clonal variation

Regulation of DNA transposition by CpG methylation and chromatin structure in human cells

Now on display: a gallery of group II intron structures at different stages of catalysis

Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina

Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements

Erratum to: Reliable transgene-independent method for determining sleeping beauty transposon copy numbers

Cell division promotes efficient retrotransposition in a stable L1 reporter cell line

Sirevirus LTR retrotransposons: phylogenetic misconceptions in the plant world

Highly diverse chromoviruses of Beta vulgaris are classified by chromodomains and chromosomal integration

Evolution of a transposon in Daphnia hybrid genomes

Striking structural dynamism and nucleotide sequence variation of the transposon Galileo in the genome of Drosophila mojavensis

Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)

Reviewer acknowledgement 2013

Revisiting the evolution of mouse LINE-1 in the genomic era

The site-specific integration reaction of Listeria phage A118 integrase, a serine recombinase

NucBase, an easy to use read mapper for small RNAs

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