ArticleMethods in molecular biology (Clifton, N.J.)2023
An Overview of Best Practices for Transposable Element Identification, Classification, and Annotation in Eukaryotic Genomes.
Article in Methods in molecular biology (Clifton, N.J.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
10 citing papers in PubMed, 18 citations in OpenAlex.
- Transposable elements as evolutionary catalysts of ant macrodiversity.Science advances · 2026Article
- SwarmGenomics: A Unified Pipeline for Individual-Based Whole-Genome Analyses.Molecular ecology resources · 2026Article
- panHiTE: A comprehensive and accurate pipeline for TE detection in large-scale population genomes.Plant communications · 2026Article
- Transposable elements as drivers of genome evolution in Drosophila virilis.Nucleic acids research · 2026Article
- Characterization of the transposable element landscape shaping the Ectocarpus genome.Genome biology · 2025Article
- Chromosome-level assembly of the 400-year-old Goethe's Palm (Chamaerops humilis L.).Scientific data · 2025Article
- Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide.Frontiers in zoology · 2025Review
- GenomeDelta: detecting recent transposable element invasions without repeat library.Genome biology · 2024Article
- De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms - a brief guide.Frontiers in zoology · 2024Review
- Genome-Wide Tool for Sensitive de novo Identification and Visualisation of Interspersed and Tandem Repeats.Bioinformatics and biology insights · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Transposable elements (TEs) exert an increasingly diverse spectrum of influences on eukaryotic genome structure, function, and evolution. A deluge of genomic, transcriptomic, and proteomic data provides the foundation for turning essentially any non-model eukaryotic species into an emerging model to study any and all aspects of organismal biology, ultimately shaping future directions for biomedical, environmental, and biodiversity research. However, identification and annotation of the mobile genome component still lags behind the standards accepted for host gene annotation. To achieve the objective of providing every genome project with a comprehensive description of its mobilome component in addition to the standard genic and transcriptomic datasets, each step of TE identification, classification, and annotation should be focused on improving TE boundary designation, reducing identification error rates, and providing accurate information on the type and integrity of TE insertions. Here, we offer practical advice for generating TE models in de novo assemblies for non-model organisms, provide step-by-step instructions to guide inexperienced TE annotators through some of the commonly utilized TE analysis pipelines, and entertain suggestions for tool improvement which could be implemented by interested developers.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.