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Orthoptera-TElib: a library of Orthoptera transposable elements for TE annotation
Transposable elements (TEs) are a major component of eukaryotic genomes and are present in almost all eukaryotic organisms. TEs are highly dynamic...
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Teaching transposon classification as a means to crowd source the curation of repeat annotation – a tardigrade perspective
BackgroundThe advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented...
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TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation
Transposable elements (TEs) play powerful and varied evolutionary and functional roles, and are widespread in most eukaryotic genomes. Research into...
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CRISPR-TE: a web-based tool to generate single guide RNAs targeting transposable elements
BackgroundThe CRISPR/Cas systems have emerged as powerful tools in genome engineering. Recent studies highlighting the crucial role of transposable...
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TE Density: a tool to investigate the biology of transposable elements
BackgroundTransposable elements (TEs) are powerful creators of genotypic and phenotypic diversity due to their inherent mutagenic capabilities and in...
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CAULIFINDER: a pipeline for the automated detection and annotation of caulimovirid endogenous viral elements in plant genomes
Plant, animal and protist genomes often contain endogenous viral elements (EVEs), which correspond to partial and sometimes entire viral genomes that...
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Transposable element subfamily annotation has a reproducibility problem
BackgroundTransposable element (TE) sequences are classified into families based on the reconstructed history of replication, and into subfamilies...
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A pangenome-guided manually curated library of transposable elements for Zymoseptoria tritici
ObjectivesHigh-quality species-specific transposable element (TE) libraries are required for studies to elucidate the evolutionary dynamics of TEs...
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Migrators within migrators: exploring transposable element dynamics in the monarch butterfly, Danaus plexippus
BackgroundLepidoptera (butterflies and moths) are an important model system in ecology and evolution. A high-quality chromosomal genome assembly is...
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Software evaluation for de novo detection of transposons
Transposable elements (TEs) are major genomic components in most eukaryotic genomes and play an important role in genome evolution. However, despite...
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Temporo-basal sulcal connections: a manual annotation protocol and an investigation of sexual dimorphism and heritability
The temporo-basal region of the human brain is composed of the collateral, the occipito-temporal, and the rhinal sulci. We manually rated (using a...
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Characterization of transposable elements within the Bemisia tabaci species complex
BackgroundWhiteflies are agricultural pests that cause negative impacts globally to crop yields resulting at times in severe economic losses and food...
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A systematic screen for co-option of transposable elements across the fungal kingdom
How novel protein functions are acquired is a central question in molecular biology. Key paths to novelty include gene duplications, recombination or...
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Teleost genomic repeat landscapes in light of diversification rates and ecology
Repetitive DNA make up a considerable fraction of most eukaryotic genomes. In fish, transposable element (TE) activity has coincided with rapid...
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Spatial transcriptome analysis of long non-coding RNAs reveals tissue specificity and functional roles in cancer
Long non-coding RNAs (lncRNAs) play a significant role in maintaining tissue morphology and functions, and their precise regulatory effectiveness is...
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Identification of transposable element families from pangenome polymorphisms
BackgroundTransposable Elements (TEs) are segments of DNA, typically a few hundred base pairs up to several tens of thousands bases long, that have...
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Expression of down-regulated ERV LTR elements associates with immune activation in human small-cell lung cancers
Small-cell lung cancer (SCLC) is an aggressive cancer characterized by immunosuppressive features leading to poor responses to current...
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Pan-cancer analysis identifies tumor-specific antigens derived from transposable elements
Cryptic promoters within transposable elements (TEs) can be transcriptionally reactivated in tumors to create new TE-chimeric transcripts, which can...
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T3E: a tool for characterising the epigenetic profile of transposable elements using ChIP-seq data
BackgroundDespite the advent of Chromatin Immunoprecipitation Sequencing (ChIP-seq) having revolutionised our understanding of the mammalian genome’s...
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Comprehensive analysis of both long and short read transcriptomes of a clonal and a seed-propagated model species reveal the prerequisites for transcriptional activation of autonomous and non-autonomous transposons in plants
BackgroundTransposable element (TE) transcription is a precursor to its mobilisation in host genomes. However, the characteristics of expressed TE...
