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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

https://doi.org/10.1016/j.ympev.2015.03.009

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Group II twintron: an intron within an intron in a chloroplast cytochrome b‐559 gene.

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Methionyl‐tRNA synthetase from Caenorhabditis elegans: A specific multidomain organization for convergent functional evolution

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

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

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Procapsid Assembly, Maturation, Nuclear Exit: Dynamic Steps in the Production of Infectious Herpesvirions

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Exploring Bacterial Insertion Sequences with ISfinder: Objectives, Uses, and Future Developments

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Is the evolution of transposable elements modular?

inferredcites →https://doi.org/10.1007/bf00290141openalex-snapshot

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

inferredcites →https://doi.org/10.1007/bf02337546openalex-snapshot

Relationships Between Transposable Elements Based Upon the Integrase-Transposase Domains: Is There a Common Ancestor?

inferredcites →https://doi.org/10.1007/s00335-007-9000-1openalex-snapshot

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

inferredcites →https://doi.org/10.1007/s00705-012-1583-5openalex-snapshot

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

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

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

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

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Eukaryotic transposable elements and genome evolution

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

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Single-Stranded DNA Transposition Is Coupled to Host Replication

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Birth of New Spliceosomal Introns in Fungi by Multiplication of Introner-like Elements

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

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

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Classification and nomenclature of endogenous retroviral sequences (ERVs)

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

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

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Revised nomenclature for transposable genetic elements

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SVA retrotransposons: Evolution and genetic instability

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Atomic level architecture of group I introns revealed

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The natural history of group I introns

inferredcites →https://doi.org/10.1016/j.tig.2007.08.004openalex-snapshot

Helitrons on a roll: eukaryotic rolling-circle transposons

inferredcites →https://doi.org/10.1016/j.tig.2008.11.004openalex-snapshot

Mystery of intron gain: new data and new models

inferredcites →https://doi.org/10.1016/j.virusres.2007.12.010openalex-snapshot

The diversity of retrotransposons and the properties of their reverse transcriptases

inferredcites →https://doi.org/10.1016/j.ympev.2011.09.027openalex-snapshot

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

inferredcites →https://doi.org/10.1016/j.ympev.2013.01.017openalex-snapshot

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

inferredcites →https://doi.org/10.1016/s0021-9258(17)43719-7openalex-snapshot

RNA splicing in Neurospora mitochondria. The large rRNA intron contains a noncoded, 5'-terminal guanosine residue.

inferredcites →https://doi.org/10.1016/s0021-9258(19)39210-5openalex-snapshot

Molecular structure of a gene, VMA1, encoding the catalytic subunit of H(+)-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae.

inferredcites →https://doi.org/10.1016/s0092-8674(00)81997-2openalex-snapshot

Human L1 Retrotransposon Encodes a Conserved Endonuclease Required for Retrotransposition

inferredcites →https://doi.org/10.1016/s0166-6851(02)00167-6openalex-snapshot

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

inferredcites →https://doi.org/10.1016/s0168-9525(01)02365-4openalex-snapshot

Intein spread and extinction in evolution

inferredcites →https://doi.org/10.1016/s0959-437x(05)80108-xopenalex-snapshot

Transposable elements

inferredcites →https://doi.org/10.1016/s0960-9822(07)00409-5openalex-snapshot

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

inferredcites →https://doi.org/10.1016/s0966-842x(00)01757-1openalex-snapshot

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

inferredcites →https://doi.org/10.1016/s1570-9639(03)00050-5openalex-snapshot

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

inferredcites →https://doi.org/10.1017/s0033583505004063openalex-snapshot

Homing endonuclease structure and function

inferredcites →https://doi.org/10.1023/a:1004026821539openalex-snapshot

Is the evolution of transposable elements modular?

inferredcites →https://doi.org/10.1023/a:1016027530962openalex-snapshot

Acquisition/Loss of Modules: the Construction Set of Transposable Elements

inferredcites →https://doi.org/10.1038/443521aopenalex-snapshot

Junk DNA as an evolutionary force

inferredcites →https://doi.org/10.1038/emboj.2008.41openalex-snapshot

piggyBac can bypass DNA synthesis during cut and paste transposition

inferredcites →https://doi.org/10.1038/nature03157openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nbt.2755openalex-snapshot

Transparency tools in gene patenting for informing policy and practice

inferredcites →https://doi.org/10.1038/npre.2009.3886.1openalex-snapshot

The Origin and Evolution of Viruses as Molecular Organisms

inferredcites →https://doi.org/10.1038/nrg2165openalex-snapshot

A unified classification system for eukaryotic transposable elements

inferredcites →https://doi.org/10.1038/nrg2165-c1openalex-snapshot

A universal classification of eukaryotic transposable elements implemented in Repbase

inferredcites →https://doi.org/10.1038/nrg2165-c2openalex-snapshot

A universal classification of eukaryotic transposable elements implemented in Repbase

inferredcites →https://doi.org/10.1038/nrg2165-c3openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nrg2165-c4openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nrg2384openalex-snapshot

A sense of identity helps stressed-out plants

inferredcites →https://doi.org/10.1038/nrm1241openalex-snapshot

The outs and ins of transposition: from Mu to Kangaroo

inferredcites →https://doi.org/10.1038/nrmicro3067openalex-snapshot

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

inferredcites →https://doi.org/10.1038/nsmb.2338openalex-snapshot

Functional characterization of an active Rag-like transposase

inferredcites →https://doi.org/10.1038/sj.hdy.6800431openalex-snapshot

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

inferredcites →https://doi.org/10.1042/bst0390169openalex-snapshot

Homing endonucleases residing within inteins: evolutionary puzzles awaiting genetic solutions

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Classifications and other ordering systems

inferredcites →https://doi.org/10.1073/pnas.0600833103openalex-snapshot

Self-synthesizing DNA transposons in eukaryotes

inferredcites →https://doi.org/10.1073/pnas.0702741104openalex-snapshot

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

inferredcites →https://doi.org/10.1073/pnas.1100266108openalex-snapshot

A widespread class of reverse transcriptase-related cellular genes

inferredcites →https://doi.org/10.1073/pnas.1104208108openalex-snapshot

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

inferredcites →https://doi.org/10.1073/pnas.1208835109openalex-snapshot

Provirophages and transpovirons as the diverse mobilome of giant viruses

inferredcites →https://doi.org/10.1073/pnas.1302144110openalex-snapshot

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

inferredcites →https://doi.org/10.1073/pnas.86.10.3718openalex-snapshot

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

inferredcites →https://doi.org/10.1073/pnas.96.14.7847openalex-snapshot

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

inferredcites →https://doi.org/10.1074/jbc.270.42.24623openalex-snapshot

Unusual Reverse Transcriptases

inferredcites →https://doi.org/10.1080/10635150601077683openalex-snapshot

Distribution and Phylogeny of Penelope-Like Elements in Eukaryotes

inferredcites →https://doi.org/10.1093/gbe/evt189openalex-snapshot

The Complex Intron Landscape and Massive Intron Invasion in a Picoeukaryote Provides Insights into Intron Evolution

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The Diversity of Prokaryotic DDE Transposases of the Mutator Superfamily, Insertion Specificity, and Association with Conjugation Machineries

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Recent Expansion of a New Ingi-Related Clade of Vingi non-LTR Retrotransposons in Hedgehogs

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Zisupton--A Novel Superfamily of DNA Transposable Elements Recently Active in Fish

inferredcites →https://doi.org/10.1093/molbev/mst171openalex-snapshot

An Empirical Test of Convergent Evolution in Rhodopsins

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Distribution of Conventional and Nonconventional Introns in Tubulin (α and β) Genes of Euglenids

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

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The International Nucleotide Sequence Database Collaboration

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The International Nucleotide Sequence Database Collaboration

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

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SINEBase: a database and tool for SINE analysis

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Protein folds and protein folding

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Systematics Agenda 2020: The Mission Evolves

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

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Group II Introns: Mobile Ribozymes that Invade DNA

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

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The repetitive landscape of the chicken genome

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The repetitive landscape of the chicken genome

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An extraordinary retrotransposon family encoding dual endonucleases

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

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PERSPECTIVE: TRANSPOSABLE ELEMENTS, PARASITIC DNA, AND GENOME EVOLUTION

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

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Small mobile sequences in bacteria display diverse structure/function motifs

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International Code of Nomenclature of Bacteria Bacteriological Code, 1990 Revision

inferredcites →https://doi.org/10.1126/science.1167222openalex-snapshot

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

inferredcites →https://doi.org/10.1126/science.1199412openalex-snapshot

A Virophage at the Origin of Large DNA Transposons

inferredcites →https://doi.org/10.1126/science.1239181openalex-snapshot

Pandoraviruses: Amoeba Viruses with Genomes Up to 2.5 Mb Reaching That of Parasitic Eukaryotes

inferredcites →https://doi.org/10.1126/science.2146742openalex-snapshot

Protein Splicing Converts the Yeast TFP1 Gene Product to the 69-kdDSubunit of the Vacuolar H + -Adenosine Triphosphatase

inferredcites →https://doi.org/10.1126/science.270.5234.253openalex-snapshot

Unity in Transposition Reactions

inferredcites →https://doi.org/10.1126/science.341.6143.226openalex-snapshot

Ever-Bigger Viruses Shake Tree of Life

inferredcites →https://doi.org/10.1126/science.6281889openalex-snapshot

The Alu Family of Dispersed Repetitive Sequences

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Expression of animal virus genomes

inferredcites →https://doi.org/10.1128/jb.00675-09openalex-snapshot

Group I Introns and Inteins: Disparate Origins but Convergent Parasitic Strategies

inferredcites →https://doi.org/10.1128/jb.186.8.2508-2510.2004openalex-snapshot

Clostridium difficileIStron CdISt1: Discovery of a Variant Encoding Two Complete Transposase-Like Proteins

inferredcites →https://doi.org/10.1128/mcb.1.7.573openalex-snapshot

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

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Attachment of HeT-A Sequences to Chromosomal Termini in Drosophila melanogaster May Occur by Different Mechanisms

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An Intronic Enhancer Regulates Splicing of the Twintron of Drosophila melanogaster prospero Pre-mRNA by Two Different Spliceosomes

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Insertion Sequences

inferredcites →https://doi.org/10.1146/annurev.bi.61.070192.005051openalex-snapshot

TRANSPOSITIONAL RECOMBINATION: Mechanistic Insights from Studies of Mu and Other Elements

inferredcites →https://doi.org/10.1146/annurev.micro.53.1.245openalex-snapshot

Integrating DNA: Transposases and Retroviral Integrases

inferredcites →https://doi.org/10.1159/000084979openalex-snapshot

Repbase Update, a database of eukaryotic repetitive elements

inferredcites →https://doi.org/10.1159/000084982openalex-snapshot

Retrons, msDNA, and the bacterial genome

inferredcites →https://doi.org/10.1159/000084991openalex-snapshot

DIRS-1 and the other tyrosine recombinase retrotransposons

inferredcites →https://doi.org/10.1159/000354269openalex-snapshot

TRUC or the Need for a New Microbial Classification

inferredcites →https://doi.org/10.1186/1471-2105-14-63openalex-snapshot

Protein structure based prediction of catalytic residues

inferredcites →https://doi.org/10.1186/1471-2148-6-94openalex-snapshot

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

inferredcites →https://doi.org/10.1186/1741-7007-9-22openalex-snapshot

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

inferredcites →https://doi.org/10.1186/1742-4690-3-67openalex-snapshot

The discovery of endogenous retroviruses

inferredcites →https://doi.org/10.1186/1743-422x-10-158openalex-snapshot

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

inferredcites →https://doi.org/10.1186/1745-6150-7-29openalex-snapshot

Identifying the mechanisms of intron gain: progress and trends

inferredcites →https://doi.org/10.1186/1759-8753-1-3openalex-snapshot

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

inferredcites →https://doi.org/10.1186/1759-8753-2-12openalex-snapshot

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

inferredcites →https://doi.org/10.1186/1759-8753-4-12openalex-snapshot

Homologues of bacterial TnpB_IS605 are widespread in diverse eukaryotic transposable elements

inferredcites →https://doi.org/10.1186/1759-8753-4-14openalex-snapshot

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

inferredcites →https://doi.org/10.1186/1759-8753-4-24openalex-snapshot

A proposed mechanism for IS607-family serine transposases

inferredcites →https://doi.org/10.1201/9780203833445openalex-snapshot

Molecular Biology of the Cell

inferredcites →https://doi.org/10.1261/rna.184206openalex-snapshot

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

inferredcites →https://doi.org/10.1261/rna.2126203openalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.pbio.0030181openalex-snapshot

RAG1 Core and V(D)J Recombination Signal Sequences Were Derived from Transib Transposons

inferredcites →https://doi.org/10.1371/journal.pgen.1002384openalex-snapshot

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

inferredcites →https://doi.org/10.1371/journal.pone.0021080openalex-snapshot

Informational Gene Phylogenies Do Not Support a Fourth Domain of Life for Nucleocytoplasmic Large DNA Viruses

inferredcites →https://doi.org/10.1371/journal.pone.0068260openalex-snapshot

A Superfamily of DNA Transposons Targeting Multicopy Small RNA Genes

inferredcites →https://doi.org/10.3109/10409230903505596openalex-snapshot

Integrating prokaryotes and eukaryotes: DNA transposases in light of structure

inferredcites →https://doi.org/10.3389/fgene.2013.00063openalex-snapshot

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

inferredcites →https://doi.org/10.4161/cib.23147openalex-snapshot

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

inferredcites →https://doi.org/10.7717/peerj.50openalex-snapshot

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

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Insertion Sequence Driven Evolution of the Microbiota Revealed by a Novel Metagenomics Pipeline

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Genomic and Transcriptomic Perspectives on the Origin, Evolution, and Application of Numts in Orthoptera

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Transposable Elements in Eukaryotes

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A Naturally Active Spy Transposon Discovered from the Insect Genome of Colletes gigas as a Promising Novel Gene Transfer Tool

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Curation Guidelines for de novo Generated Transposable Element Families

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RNA ‐based regulation of transposon expression

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Retrotransposable Elements: DNA Fingerprinting and the Assessment of Genetic Diversity

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New Insights on the Evolution of Genome Content: Population Dynamics of Transposable Elements in Flies and Humans

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DDE Transposon as Public Goods

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The Apple Genome and Epigenome

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Transposable Elements in Pines

inferred← citeshttps://doi.org/10.1007/978-3-319-71740-1_2openalex-snapshot

Fungal Inteins: Distribution, Evolution, and Applications

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Genome-wide analysis of transposable elements in the coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae): description of novel families

inferred← citeshttps://doi.org/10.1007/s10142-023-01206-wopenalex-snapshot

From parasites to partners: exploring the intricacies of host-transposon dynamics and coevolution

inferred← citeshttps://doi.org/10.1007/s10577-019-09609-xopenalex-snapshot

The mobilome of Drosophila incompta, a flower-breeding species: comparison of transposable element landscapes among generalist and specialist flies

inferred← citeshttps://doi.org/10.1007/s10709-017-9964-zopenalex-snapshot

Transposable elements in the Anopheles funestus transcriptome

inferred← citeshttps://doi.org/10.1007/s10709-018-0007-1openalex-snapshot

A Mos1 transposase in vivo assay to screen new HIV-1 integrase inhibitors

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Genome wide annotation and characterization of young, intact long terminal repeat retrotransposons (In-LTR-RTs) of seven legume species

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Investigation of rice (Oryza sativa L.) retrotransposons in different taxa

inferred← citeshttps://doi.org/10.1007/s13353-024-00916-6openalex-snapshot

Polymorphic insertions of DcSto miniature inverted-repeat transposable elements reveal genetic diversity structure within the cultivated carrot

inferred← citeshttps://doi.org/10.1016/b978-0-323-91909-8.00035-9openalex-snapshot

Transposable Elements Shaping the Epigenome

inferred← citeshttps://doi.org/10.1016/bs.abr.2018.09.001openalex-snapshot

Transposable Elements as Tool for Crop Improvement

inferred← citeshttps://doi.org/10.1016/j.arr.2023.101881openalex-snapshot

Transposable elements and their role in aging

inferred← citeshttps://doi.org/10.1016/j.biotechadv.2024.108343openalex-snapshot

Mobile genetic element-based gene editing and genome engineering: Recent advances and applications

inferred← citeshttps://doi.org/10.1016/j.chom.2024.03.005openalex-snapshot

A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota

inferred← citeshttps://doi.org/10.1016/j.ibmb.2015.09.003openalex-snapshot

Transposition burst of mariner-like elements in the sequenced genome of Rhodnius prolixus

inferred← citeshttps://doi.org/10.1016/j.jhazmat.2025.137886openalex-snapshot

Differential size-dependent response patterns and antibiotic resistance development mechanism in anammox consortia

inferred← citeshttps://doi.org/10.1016/j.jmb.2020.166805openalex-snapshot

The C-terminal Domain of piggyBac Transposase Is Not Required for DNA Transposition

inferred← citeshttps://doi.org/10.1016/j.jmb.2021.166839openalex-snapshot

The piggyBac-derived protein 5 (PGBD5) transposes both the closely and the distantly related piggyBac-like elements Tcr-pble and Ifp2

inferred← citeshttps://doi.org/10.1016/j.scienta.2018.03.055openalex-snapshot

Identification of repetitive DNA sequences in the Chrysanthemum boreale genome

inferred← citeshttps://doi.org/10.1016/j.shpsc.2016.02.016openalex-snapshot

Are viruses alive? The replicator paradigm sheds decisive light on an old but misguided question

inferred← citeshttps://doi.org/10.1016/j.tim.2026.03.003openalex-snapshot

From ancient catalytic folds to retrotransposons and retroviruses

inferred← citeshttps://doi.org/10.1016/j.trecan.2018.05.008openalex-snapshot

Deregulation of Retroelements as an Emerging Therapeutic Opportunity in Cancer

inferred← citeshttps://doi.org/10.1016/j.ygeno.2021.03.032openalex-snapshot

Two repeated motifs enriched within some enhancers and origins of replication are bound by SETMAR isoforms in human colon cells

inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107090openalex-snapshot

A genomic survey of Tc1-mariner transposons in nematodes suggests extensive horizontal transposon transfer events

inferred← citeshttps://doi.org/10.1016/j.ympev.2021.107236openalex-snapshot

In and out: Evolution of viral sequences in the mitochondrial genomes of legumes (Fabaceae)

inferred← citeshttps://doi.org/10.1016/j.ympev.2024.108221openalex-snapshot

Genomic and transcriptomic perspectives on the origin and evolution of NUMTs in Orthoptera

inferred← citeshttps://doi.org/10.1017/thg.2023.42openalex-snapshot

Cap Analysis of Gene Expression Clarifies Transcriptomic Divergence Within Monozygotic Twin Pairs

inferred← citeshttps://doi.org/10.1021/acs.chemrev.6b00003openalex-snapshot

DNA Transposition at Work

inferred← citeshttps://doi.org/10.1038/s12276-018-0112-3openalex-snapshot

Patterns and mechanisms of structural variations in human cancer

inferred← citeshttps://doi.org/10.1038/s41467-026-69550-6openalex-snapshot

Arms races between selfish genetic elements and their host defence in termites

inferred← citeshttps://doi.org/10.1038/s41576-018-0050-xopenalex-snapshot

Computational tools to unmask transposable elements

inferred← citeshttps://doi.org/10.1038/s41576-020-0251-yopenalex-snapshot

Measuring and interpreting transposable element expression

inferred← citeshttps://doi.org/10.1038/s41598-017-08194-5openalex-snapshot

Rapid amplification of four retrotransposon families promoted speciation and genome size expansion in the genus Panax

inferred← citeshttps://doi.org/10.1038/s41598-019-56383-1openalex-snapshot

Repetitive DNA landscape in essential A and supernumerary B chromosomes of Festuca pratensis Huds

inferred← citeshttps://doi.org/10.1071/fp18098openalex-snapshot

Use of retrotransposon-derived genetic markers to analyse genomic variability in plants

inferred← citeshttps://doi.org/10.1073/pnas.1921046117openalex-snapshot

RepeatModeler2 for automated genomic discovery of transposable element families

inferred← citeshttps://doi.org/10.1073/pnas.2301424120openalex-snapshot

Replitrons: A major group of eukaryotic transposons encoding HUH endonuclease

inferred← citeshttps://doi.org/10.1080/10985549.2025.2594182openalex-snapshot

Impact of Transposable Elements on DNA Double-Strand Break Repair and Genomic Stability

inferred← citeshttps://doi.org/10.1080/2159256x.2016.1256852openalex-snapshot

The future of transposable element annotation and their classification in the light of functional genomics - what we can learn from the fables of Jean de la Fontaine?

inferred← citeshttps://doi.org/10.1080/2159256x.2017.1314236openalex-snapshot

Somatizing the transposons action

inferred← citeshttps://doi.org/10.1080/2159256x.2017.1393490openalex-snapshot

tRNAs as primers and inhibitors of retrotransposons

inferred← citeshttps://doi.org/10.1093/aob/mcy186openalex-snapshot

Comparative analysis of repetitive sequences among species from the potato and the tomato clades

inferred← citeshttps://doi.org/10.1093/database/baae044openalex-snapshot

FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research

inferred← citeshttps://doi.org/10.1093/ee/nvad105openalex-snapshot

Transposable elements differ between geographic populations of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae)

inferred← citeshttps://doi.org/10.1093/g3journal/jkab287openalex-snapshot

Genome-wide characterization of Mariner-like transposons and their derived MITEs in the Whitefly Bemisia tabaci (Hemiptera: Aleyrodidae)

inferred← citeshttps://doi.org/10.1093/gbe/evab135openalex-snapshot

Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant Pathogen Verticillium dahliae

inferred← citeshttps://doi.org/10.1093/gbe/evag155openalex-snapshot

Ancient Persistence and Newfound Diversity of CR1-Group Retrotransposons Across Vertebrates

inferred← citeshttps://doi.org/10.1093/gbe/evw006openalex-snapshot

Recent Mobility of Casposons, Self-Synthesizing Transposons at the Origin of the CRISPR-Cas Immunity

inferred← citeshttps://doi.org/10.1093/gbe/evw264openalex-snapshot

Evolution and Diversity of Transposable Elements in Vertebrate Genomes

inferred← citeshttps://doi.org/10.1093/jhered/esaa060openalex-snapshot

Opinion: Genetic Conflict With Mobile Elements Drives Eukaryotic Genome Evolution, and Perhaps Also Eukaryogenesis

inferred← citeshttps://doi.org/10.1093/nar/gkae327openalex-snapshot

Systematic identification of cargo-mobilizing genetic elements reveals new dimensions of eukaryotic diversity

inferred← citeshttps://doi.org/10.1093/nar/gkag139openalex-snapshot

Transposable elements as drivers of genome evolution in Drosophila virilis

inferred← citeshttps://doi.org/10.1093/nar/gkw1115openalex-snapshot

Temporal self-regulation of transposition through host-independent transposase rodlet formation

inferred← citeshttps://doi.org/10.1098/rsta.2015.0065openalex-snapshot

The meaning of biological information

inferred← citeshttps://doi.org/10.1101/115030openalex-snapshot

First landscape of binding to chromosomes for a domesticated mariner transposase in the human genome: diversity of genomic targets of SETMAR isoforms in two colorectal cell lines

inferred← citeshttps://doi.org/10.1101/2020.09.21.307181openalex-snapshot

Engines of change: Transposable element mutation rates are high and vary widely among genotypes and populations of Daphnia magna

inferred← citeshttps://doi.org/10.1101/2022.06.02.494618openalex-snapshot

600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges

inferred← citeshttps://doi.org/10.1101/2022.12.15.520654openalex-snapshot

Replitrons: a new group of eukaryotic transposons encoding HUH endonuclease

inferred← citeshttps://doi.org/10.1101/2023.03.21.533716openalex-snapshot

Integrating long-read RNA sequencing improves locus-specific quantification of transposable element expression

inferred← citeshttps://doi.org/10.1101/gr.277387.122openalex-snapshot

Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges

inferred← citeshttps://doi.org/10.1111/1744-7917.70276openalex-snapshot

Coevolutionary interactions between transposable elements and host silencing factors in genome gigantism of Caeliferans (Orthoptera)

inferred← citeshttps://doi.org/10.1111/imb.12220openalex-snapshot

Insect transformation with piggyBac : getting the number of injections just right

inferred← citeshttps://doi.org/10.1111/imb.12577openalex-snapshot

Characterization of Herves ‐like transposable elements ( hAT s) in Drosophila species and their evolutionary scenario

inferred← citeshttps://doi.org/10.1111/jeu.12891openalex-snapshot

Epigenetic influences of mobile genetic elements on ciliate genome architecture and evolution

inferred← citeshttps://doi.org/10.1111/mec.14794openalex-snapshot

The impact of transposable elements in adaptive evolution

inferred← citeshttps://doi.org/10.1111/tpj.16599openalex-snapshot

Repeat turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets

inferred← citeshttps://doi.org/10.1126/science.abk3112openalex-snapshot

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

inferred← citeshttps://doi.org/10.1126/sciimmunol.adf8838openalex-snapshot

Selective control of transposable element expression during T cell exhaustion and anti–PD-1 treatment

inferred← citeshttps://doi.org/10.1134/s1022795419010113openalex-snapshot

Transposable Elements in the Evolution of Gene Regulatory Networks

inferred← citeshttps://doi.org/10.1139/gen-2022-0066openalex-snapshot

Transposable elements in the transcriptome of the velvetbean caterpillar Anticarsia gemmatalis Hübner, 1818 (Lepidoptera: Erebidae)

inferred← citeshttps://doi.org/10.11606/d.41.2022.tde-11112022-151353openalex-snapshot

Evolução genômica dos Medusozoa (Cnidaria), com ênfase em elementos repetitivos nos Scyphozoa

inferred← citeshttps://doi.org/10.1186/s12052-016-0057-8openalex-snapshot

A naturalists guide to mobile genetic elements

inferred← citeshttps://doi.org/10.1186/s12864-016-3015-5openalex-snapshot

Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools

inferred← citeshttps://doi.org/10.1186/s12864-016-3432-5openalex-snapshot

Proteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti

inferred← citeshttps://doi.org/10.1186/s12864-023-09499-8openalex-snapshot

Comparative genomics reveals insights into anuran genome size evolution

inferred← citeshttps://doi.org/10.1186/s13059-025-03522-9openalex-snapshot

LocusMasterTE: integrating long-read RNA sequencing improves locus-specific quantification of transposable element expression

inferred← citeshttps://doi.org/10.1186/s13100-015-0049-1openalex-snapshot

Identification and characterization of a minisatellite contained within a novel miniature inverted-repeat transposable element (MITE) of Porphyromonas gingivalis

inferred← citeshttps://doi.org/10.1186/s13100-017-0103-2openalex-snapshot

Using bioinformatic and phylogenetic approaches to classify transposable elements and understand their complex evolutionary histories

inferred← citeshttps://doi.org/10.1186/s13100-019-0163-6openalex-snapshot

MGERT: a pipeline to retrieve coding sequences of mobile genetic elements from genome assemblies

inferred← citeshttps://doi.org/10.1186/s13100-019-0190-3openalex-snapshot

Stowaway miniature inverted repeat transposable elements are important agents driving recent genomic diversity in wild and cultivated carrot

inferred← citeshttps://doi.org/10.1186/s13100-020-00230-yopenalex-snapshot

The Dfam community resource of transposable element families, sequence models, and genome annotations

inferred← citeshttps://doi.org/10.1186/s13100-021-00244-0openalex-snapshot

TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation

inferred← citeshttps://doi.org/10.1186/s13100-021-00259-7openalex-snapshot

A beginner’s guide to manual curation of transposable elements

inferred← citeshttps://doi.org/10.1186/s13100-022-00270-6openalex-snapshot

Characterization of transposable elements within the Bemisia tabaci species complex

inferred← citeshttps://doi.org/10.1186/s13100-023-00311-8openalex-snapshot

Evolutionary dynamics of the LTR-retrotransposon crapaud in the Podospora anserina species complex and the interaction with repeat-induced point mutations

inferred← citeshttps://doi.org/10.1186/s13100-024-00316-xopenalex-snapshot

Orthoptera-TElib: a library of Orthoptera transposable elements for TE annotation

inferred← citeshttps://doi.org/10.1266/ggs.18-00024openalex-snapshot

Structural and sequence diversity of eukaryotic transposable elements

inferred← citeshttps://doi.org/10.13140/rg.2.2.16651.49446openalex-snapshot

Conceptual and Empirical Investigations of Eukaryotic Transposable Element Evolution

inferred← citeshttps://doi.org/10.1371/journal.pcbi.1006097openalex-snapshot

A machine learning based framework to identify and classify long terminal repeat retrotransposons

inferred← citeshttps://doi.org/10.1371/journal.pgen.1009768openalex-snapshot

The genomic ecosystem of transposable elements in maize

inferred← citeshttps://doi.org/10.1371/journal.pgen.1009827openalex-snapshot

Engines of change: Transposable element mutation rates are high and variable within Daphnia magna

inferred← citeshttps://doi.org/10.1371/journal.pone.0220539openalex-snapshot

Evolutionary history and classification of Micropia retroelements in Drosophilidae species

inferred← citeshttps://doi.org/10.14232/phd.11254openalex-snapshot

An IS element-mediated synthetic biology approach for engineering multi-copy integration of large genetic constructs into bacterial genomes

inferred← citeshttps://doi.org/10.14411/eje.2017.049openalex-snapshot

An overview of irritans-mariner transposons in two Mayetiola species (Diptera: Cecidomyiidae)

inferred← citeshttps://doi.org/10.14411/eje.2018.064openalex-snapshot

The draft genome sequence of the Japanese honey bee, Apis cerana japonica (Hymenoptera: Apidae)

inferred← citeshttps://doi.org/10.15476/elte.2018.205openalex-snapshot

Molecular genetics of spread of Salmonella Genomic Island 1 (SGI1)

inferred← citeshttps://doi.org/10.17660/actahortic.2024.1393.26openalex-snapshot

Assessment of genetic diversity and population structure of carrot accessions with DcSto Intron Length Polymorphism markers

inferred← citeshttps://doi.org/10.18174/458827openalex-snapshot

Exploring the use of wild relatives in potato breeding through integrated cytogenetic and genomic approaches

inferred← citeshttps://doi.org/10.18174/551238openalex-snapshot

A computational study of genomic rearrangements in plants

inferred← citeshttps://doi.org/10.20944/preprints202112.0040.v1openalex-snapshot

The Comparative Analysis of the DNA Repeat Composition among Cannabis Sativa L., Humulus Lupulus L. And Humulus Japonicus Siebold & Zucc. With Heteromorphic Sex Chromosomes

inferred← citeshttps://doi.org/10.21203/rs.3.rs-5428092/v1openalex-snapshot

Machine learning based pan-plant analyses of transposable elements across 352 species illuminates genome evolution

inferred← citeshttps://doi.org/10.24272/j.issn.2095-8137.2021.426openalex-snapshot

Characterization of NDM-5-producing Enterobacteriaceae isolates from retail grass carp (Ctenopharyngodon idella) and evidence of blaNDM-5-bearing IncHI2 plasmid transfer between ducks and fish

inferred← citeshttps://doi.org/10.3233/jbr-211515openalex-snapshot

Genome-wide analysis of long terminal repeat retrotransposons from the cranberry Vaccinium macrocarpon

inferred← citeshttps://doi.org/10.3389/fpls.2016.01448openalex-snapshot

Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response

inferred← citeshttps://doi.org/10.3389/fpls.2022.917310openalex-snapshot

Variation in the Number and Position of rDNA Loci Contributes to the Diversification and Speciation in Nigella (Ranunculaceae)

inferred← citeshttps://doi.org/10.3390/biology15010059openalex-snapshot

Transformer-Based Classification of Transposable Element Consensus Sequences with TEclass2

inferred← citeshttps://doi.org/10.3390/genes13122374openalex-snapshot

Chemotherapy Drugs Act Differently in the Expression and Somatic Mobilization of the mariner Transposable Element in Drosophila simulans

inferred← citeshttps://doi.org/10.3390/ijms19113653openalex-snapshot

Rex Retroelements and Teleost Genomes: An Overview

inferred← citeshttps://doi.org/10.3390/ijms20143597openalex-snapshot

Transposable Elements Adaptive Role in Genome Plasticity, Pathogenicity and Evolution in Fungal Phytopathogens

inferred← citeshttps://doi.org/10.3390/ijms20153837openalex-snapshot

Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning

inferred← citeshttps://doi.org/10.3390/ijms22126319openalex-snapshot

Expression Quantitative Trait Loci (eQTLs) Associated with Retrotransposons Demonstrate their Modulatory Effect on the Transcriptome

inferred← citeshttps://doi.org/10.3390/ijms222111387openalex-snapshot

The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation

inferred← citeshttps://doi.org/10.3390/ijms24032610openalex-snapshot

Transposable Elements Co-Option in Genome Evolution and Gene Regulation

inferred← citeshttps://doi.org/10.3390/insects15120950openalex-snapshot

Transposable Elements Contribute to the Regulation of Long Noncoding RNAs in Drosophila melanogaster

inferred← citeshttps://doi.org/10.3390/jmp6010001openalex-snapshot

The Transcription of Transposable Elements Differentially Regulated by SVAs in the Major Histocompatibility Complex Class I Region of a Parkinson’s Progression Markers Initiative Cohort

inferred← citeshttps://doi.org/10.3390/microorganisms10020236openalex-snapshot

inPOSE: A Flexible Toolbox for Chromosomal Cloning and Amplification of Bacterial Transgenes

inferred← citeshttps://doi.org/10.3390/ph18101573openalex-snapshot

The Other Side of the Same Coin: Beyond the Coding Region in Amyotrophic Lateral Sclerosis

inferred← citeshttps://doi.org/10.36899/japs.2023.5.0697openalex-snapshot

ANALYSES of P-Tst-1, P-Tst-3 and P-Tst-6 RETROTRANSPOSONS IN CONVENTIONALLY AND ORGANICALLY PRODUCED TOMATOES

inferred← citeshttps://doi.org/10.3892/ijo.2021.5285openalex-snapshot

Transposable elements and Piwi‑interacting RNAs in hemato‑oncology with a focus on myelodysplastic syndrome (Review)

inferred← citeshttps://doi.org/10.4000/books.irdeditions.31237openalex-snapshot

Bibliographie

inferred← citeshttps://doi.org/10.5772/62382openalex-snapshot

DNA Elements Tetris: A Strategy for Gene Correction

inferred← citeshttps://doi.org/10.6084/m9.figshare.13565922openalex-snapshot

Additional file 1 of The Dfam community resource of transposable element families, sequence models, and genome annotations

inferred← citeshttps://doi.org/10.6084/m9.figshare.13565925openalex-snapshot

Additional file 2 of The Dfam community resource of transposable element families, sequence models, and genome annotations

inferred← citeshttps://doi.org/10.6084/m9.figshare.13565931openalex-snapshot

Additional file 4 of The Dfam community resource of transposable element families, sequence models, and genome annotations

inferred← citeshttps://doi.org/10.6084/m9.figshare.19470533openalex-snapshot

Additional file 1 of A beginner’s guide to manual curation of transposable elements

inferred← citeshttps://doi.org/10.6084/m9.figshare.24995496openalex-snapshot

Additional file 1 of Evolutionary dynamics of the LTR-retrotransposon crapaud in the Podospora anserina species complex and the interaction with repeat-induced point mutations

inferred← citeshttps://doi.org/10.6084/m9.figshare.24995586openalex-snapshot

Additional file 2 of Evolutionary dynamics of the LTR-retrotransposon crapaud in the Podospora anserina species complex and the interaction with repeat-induced point mutations

inferred← citeshttps://doi.org/10.6084/m9.figshare.25414889openalex-snapshot

Additional file 1 of Orthoptera-TElib: a library of Orthoptera transposable elements for TE annotation

inferred← citeshttps://doi.org/10.6084/m9.figshare.25415047openalex-snapshot

Additional file 2 of Orthoptera-TElib: a library of Orthoptera transposable elements for TE annotation

inferred← citeshttps://doi.org/10.6084/m9.figshare.26602543openalex-snapshot

Additional file 1 of Comparative genomics reveals insights into anuran genome size evolution

inferred← citeshttps://doi.org/10.6084/m9.figshare.26602546openalex-snapshot

Additional file 2 of Comparative genomics reveals insights into anuran genome size evolution

inferred← citeshttps://doi.org/10.64898/2026.01.13.699120openalex-snapshot

Ancient persistence and newfound diversity of CR1-group retrotransposons across chordates

inferred← citeshttps://doi.org/10.64898/2026.06.16.732638openalex-snapshot

Lineage-specific evolution of LTR retrotransposons under natural selection drives genomic divergence in diploid Oryza species

inferred← citeshttps://doi.org/10.70675/2bc6122fzaa39z46c9za74ezd0da59e1f528openalex-snapshot

Définition des cibles chromosomiques de PGBD5 dans les neurones pyramidaux du système nerveux central des vertébrés

inferred← citeshttps://doi.org/10.70675/4193c885z9d9az4014z9a91z7219d45c2ab8openalex-snapshot

Dynamique des éléments transposables et évolution du génome des spartines polyploïdes

inferred← citeshttps://doi.org/10.70675/67774ec7za271z45ebzb84cz0d48d1d2f0efopenalex-snapshot

Caractéristiques génomiques du genre fongique Mucor et évolution adaptative liée à différents modes et conditions de vie au sein du genre

inferred← citeshttps://doi.org/10.70675/6f50b431z92ccz4ccez8b97zed6eccdc71e7openalex-snapshot

Deregulation of genes and transposable elements and hybrid incompatibility among Drosophila mojavensis subspecies and D. arizonae

inferred← citeshttps://doi.org/10.70675/7925c2d0z7ee8z4adazbf69zbc16a3e875a6openalex-snapshot

Le variant d'histone H3.3 dans la spermatogenèse : inactivation des chromosomes sexuels et régulation des piARN

inferred← citeshttps://doi.org/10.70675/89cc8269ze49bz4eabz906dzf93f1457a05aopenalex-snapshot

Les DDEs transposons à l’origine de l’innovation génétique : exemple du transposon RAG

inferred← citeshttps://doi.org/10.70675/921da3d5z46c6z49d0za861z4e751975ac1copenalex-snapshot

Exhaustive Identification of the retroelement Ty1 Integrase partners in yeast Saccharomyces cerevisiae : characterization of the role of Casein kinase II in Ty1 retrotransposition in vivo

inferred← citeshttps://doi.org/10.70675/a4f4a6efz44b4z4777zbcd1z7b96964471e0openalex-snapshot

Contribution des éléments transposables à l’adaptabilité de ravageurs de cultures en absence de reproduction sexuée

inferred← citeshttps://doi.org/10.70675/cef4bacezab19z4a37za5e5z90809f6d6f7eopenalex-snapshot

Annotation des génomes de paramécies

inferred← citeshttps://doi.org/10.70675/d76b18c1zc2c1z4748z9fc2zcc393afc2a86openalex-snapshot

Régulations épigénétiques des éléments transposables au cours de l’ovogenèse de Drosophila melanogaster

inferred← citeshttps://doi.org/10.70675/fcbe20caz6b0fz4133zb162z9197bf1da23fopenalex-snapshot

Comment deux lignées cellulaires stromales mésenchymateuses humaines récapitulent in vitro le microenvironnement hématopoïétique ? : Intérêt en ingénierie

inferred← citeshttps://doi.org/10.7287/peerj.8311v0.1/reviews/1openalex-snapshot

Peer Review #1 of "A systematic review of the application of machine learning in the detection and classification of transposable elements (v0.1)"

inferred← citeshttps://doi.org/10.7287/peerj.8311v0.1/reviews/2openalex-snapshot

Peer Review #2 of "A systematic review of the application of machine learning in the detection and classification of transposable elements (v0.1)"

inferred← citeshttps://doi.org/10.7287/peerj.8311v0.1/reviews/3openalex-snapshot

Peer Review #3 of "A systematic review of the application of machine learning in the detection and classification of transposable elements (v0.1)"

inferred← citeshttps://doi.org/10.7287/peerj.8311v0.2/reviews/1openalex-snapshot

Peer Review #1 of "A systematic review of the application of machine learning in the detection and classification of transposable elements (v0.2)"

inferred← citeshttps://doi.org/10.7287/peerj.8311v0.2/reviews/3openalex-snapshot

Peer Review #3 of "A systematic review of the application of machine learning in the detection and classification of transposable elements (v0.2)"

inferred← citeshttps://doi.org/10.7717/peerj.8311openalex-snapshot

A systematic review of the application of machine learning in the detection and classification of transposable elements

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.