(Q38387036)

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A survey of transposable element classification systems--a call for a fundamental update to meet the challenge of their diversity and complexity.

scientific article published on 20 March 2015

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3 March 2020

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Europe PubMed Central

A survey of transposable element classification systems--a call for a fundamental update to meet the challenge of their diversity and complexity (English)

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25797922%20AND%20SRC:MED&resulttype=core&format=json

3 March 2020

1

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3 March 2020

author name string

Solenne Bire

2

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3 March 2020

Peter Arensburger

3

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3 March 2020

Yves Bigot

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3 March 2020

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20 March 2015

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3 March 2020

Molecular Phylogenetics and Evolution

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3 March 2020

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3 March 2020

90-109

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3 March 2020

Recently agreed changes to the International Code of Virus Classification and Nomenclature

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Distribution and phylogeny of Penelope-like elements in eukaryotes

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Origin and evolution of LINE-1 derived "half-L1" retrotransposons (HAL1)

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Ginger DNA transposons in eukaryotes and their evolutionary relationships with long terminal repeat retrotransposons

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Homing endonucleases residing within inteins: evolutionary puzzles awaiting genetic solutions

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Two for the price of one: a bifunctional intron-encoded DNA endonuclease-RNA maturase.

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Genetics: Junk DNA as an evolutionary force

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Characteristics of inteins in invertebrate iridoviruses and factors controlling insertion in their viral hosts.

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Classification and nomenclature of endogenous retroviral sequences (ERVs): problems and recommendations

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Zisupton--a novel superfamily of DNA transposable elements recently active in fish

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

A proposed mechanism for IS607-family serine transposases

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Convergent evolution of similar enzymatic function on different protein folds: the hexokinase, ribokinase, and galactokinase families of sugar kinases

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Identification of non-autonomous non-LTR retrotransposons in the genome of Trypanosoma cruzi

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

The current source of human Alu retroposons is a conserved gene shared with Old World monkey

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Relationships between transposable elements based upon the integrase-transposase domains: is there a common ancestor?

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Procapsid assembly, maturation, nuclear exit: dynamic steps in the production of infectious herpesvirions

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Profile of the mosaic element BTMR1 in the genome of the bumble bee Bombus terrestris (Hymenoptera: Apidae).

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Breaking and joining single-stranded DNA: the HUH endonuclease superfamily

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

The International Nucleotide Sequence Database Collaboration

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

At the origin of spliceosomal introns: Is multiplication of introner-like elements the main mechanism of intron gain in fungi?

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Unity in transposition reactions

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

The outs and ins of transposition: from mu to kangaroo

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

ORF-less and reverse-transcriptase-encoding group II introns in archaebacteria, with a pattern of homing into related group II intron ORFs

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Repetitive elements may comprise over two-thirds of the human genome

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Small mobile sequences in bacteria display diverse structure/function motifs.

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Provirophages and transpovirons as the diverse mobilome of giant viruses

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Learning to live together: mutualism between self-splicing introns and their hosts

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

The diversity of retrotransposons and the properties of their reverse transcriptases

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Unconventional serine proteases: variations on the catalytic Ser/His/Asp triad configuration

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Protein structure based prediction of catalytic residues

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Eukaryotic transposable elements and genome evolution

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Transposable elements

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

A virophage at the origin of large DNA transposons

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Telomere-associated endonuclease-deficient Penelope-like retroelements in diverse eukaryotes

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

A widespread class of reverse transcriptase-related cellular genes

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Cryptons: a group of tyrosine-recombinase-encoding DNA transposons from pathogenic fungi

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

The diversity of prokaryotic DDE transposases of the mutator superfamily, insertion specificity, and association with conjugation machineries

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

SVA retrotransposons: Evolution and genetic instability

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Integrating DNA: transposases and retroviral integrases

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Clostridium difficile IStron CdISt1: discovery of a variant encoding two complete transposase-like proteins

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

The natural history of group I introns

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Methionyl-tRNA synthetase from Caenorhabditis elegans: a specific multidomain organization for convergent functional evolution

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

The Chinese hamster Alu-equivalent sequence: a conserved highly repetitious, interspersed deoxyribonucleic acid sequence in mammals has a structure suggestive of a transposable element.

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Functional characterization of an active Rag-like transposase

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Integrating prokaryotes and eukaryotes: DNA transposases in light of structure.

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Self-splicing of a group I intron reveals partitioning of native and misfolded RNA populations in yeast

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Transparency tools in gene patenting for informing policy and practice

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Visualizing the substrate-, superoxo-, alkylperoxo-, and product-bound states at the nonheme Fe(II) site of homogentisate dioxygenase

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Repbase Update, a database of eukaryotic repetitive elements

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Attachment of HeT-A sequences to chromosomal termini in Drosophila melanogaster may occur by different mechanisms

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Protein splicing converts the yeast TFP1 gene product to the 69-kD subunit of the vacuolar H(+)-adenosine triphosphatase

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Self-synthesizing DNA transposons in eukaryotes

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Helitrons on a roll: eukaryotic rolling-circle transposons

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

A universal classification of eukaryotic transposable elements implemented in Repbase.

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Simple and fast classification of non-LTR retrotransposons based on phylogeny of their RT domain protein sequences

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Perspective: transposable elements, parasitic DNA, and genome evolution

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

An extraordinary retrotransposon family encoding dual endonucleases

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Crypton transposons: identification of new diverse families and ancient domestication events

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

A superfamily of DNA transposons targeting multicopy small RNA genes

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Recent expansion of a new Ingi-related clade of Vingi non-LTR retrotransposons in hedgehogs

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Group II introns: mobile ribozymes that invade DNA.

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Retrons, msDNA, and the bacterial genome

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Is the evolution of transposable elements modular?

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

An empirical test of convergent evolution in rhodopsins

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Twintrons are not unique to the Euglena chloroplast genome: structure and evolution of a plastome cpn60 gene from a cryptomonad

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Classifications and other ordering systems

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Invasion of protein coding genes by green algal ribosomal group I introns.

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Distribution of conventional and nonconventional introns in tubulin (α and β) genes of euglenids.

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

piggyBac can bypass DNA synthesis during cut and paste transposition

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Transpositional recombination: mechanistic insights from studies of mu and other elements

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Endonuclease domain of the Drosophila melanogaster R2 non-LTR retrotransposon and related retroelements: a new model for transposition

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

The origin and evolution of geminivirus-related DNA sequences in Nicotiana.

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Genomic expansion of the Bov-A2 retroposon relating to phylogeny and breed management

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Threonine aldolase and alanine racemase: novel examples of convergent evolution in the superfamily of vitamin B6-dependent enzymes

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes.

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Identification of a virus intein and a possible variation in the protein-splicing reaction

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Intein spread and extinction in evolution

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

DIRS-1 and the other tyrosine recombinase retrotransposons.

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Group I introns and inteins: disparate origins but convergent parasitic strategies

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

TRUC or the need for a new microbial classification

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Revised nomenclature for transposable genetic elements

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Mystery of intron gain: new data and new models

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution.

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

An intronic enhancer regulates splicing of the twintron of Drosophila melanogaster prospero pre-mRNA by two different spliceosomes

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Protein folds and protein folding

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

The Alu Family of Dispersed Repetitive Sequences

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

A unified classification system for eukaryotic transposable elements should reflect their phylogeny

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Exploring bacterial insertion sequences with ISfinder: objectives, uses, and future developments.

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

SINEs and LINEs: Highly repeated short and long interspersed sequences in mammalian genomes

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Unusual reverse transcriptases

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Homing endonuclease structure and function

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Virus-host co-evolution under a modified nuclear genetic code

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Model-based identification of Helitrons results in a new classification of their families in Arabidopsis thaliana

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Single-stranded DNA transposition is coupled to host replication.

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Structuring the bacterial genome: Y1-transposases associated with REP-BIME sequences.

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Playing second fiddle: second-strand processing and liberation of transposable elements from donor DNA.

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Birth of new spliceosomal introns in fungi by multiplication of introner-like elements.

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Virus species polemics: 14 senior virologists oppose a proposed change to the ICTV definition of virus species

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

SINEBase: a database and tool for SINE analysis

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

The complex intron landscape and massive intron invasion in a picoeukaryote provides insights into intron evolution

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Atomic level architecture of group I introns revealed

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing — a review

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

The discovery of endogenous retroviruses

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

The repetitive landscape of the chicken genome

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

A unified classification system for eukaryotic transposable elements

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Informational gene phylogenies do not support a fourth domain of life for nucleocytoplasmic large DNA viruses

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Green Evolution and Dynamic Adaptations Revealed by Genomes of the Marine Picoeukaryotes Micromonas

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Identification of the endonuclease domain encoded by R2 and other site-specific, non-long terminal repeat retrotransposable elements

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Identifying the mechanisms of intron gain: progress and trends

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

Transposition of hAT elements links transposable elements and V(D)J recombination.

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2015.03.009

7 January 2021

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