ArticleMobile DNA2015
A call for benchmarking transposable element annotation methods.
Article in Mobile DNA, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
55 citing papers in PubMed, 98 citations in OpenAlex.
- Diversity and genome engineering applications of R2 non-LTR retrotransposons.RNA (New York, N.Y.) · 2026Review
- Transposable elements in the era of data science EMBO course: a call for open, accessible, and collaborative TE resources.Mobile DNA · 2026Article
- TE_Bench: a foundational benchmarking workflow for transposable element annotation pipelines.Mobile DNA · 2026Article
- Genomic resources for two apex avian predators from Saudi Arabia: Falco biarmicus and Falco peregrinus.G3 (Bethesda, Md.) · 2026Article
- The dynamics of transposable element content in the genome of the human pathogen Histoplasma.Fungal genetics and biology : FG & B · 2026Article
- TEPEAK: A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations.PLoS computational biology · 2026Article
- Differences in GenBank and RefSeq annotations may affect genomics data interpretation formSphere · 2025Article
- TEtrimmer: a tool to automate the manual curation of transposable elements.Nature communications · 2025Article
- A phylogenetic approach uncovers cryptic endogenous retrovirus subfamilies in the primate lineage.Science advances · 2025Article
- GenomeDelta: detecting recent transposable element invasions without repeat library.Genome biology · 2024Article
- Discovery of numerous novel Helitron-like elements in eukaryote genomes using HELIANO.Nucleic acids research · 2024Article
- Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges.Genome research · 2023Article
- Young SINEs in pig genomes impact gene regulation, genetic diversity, and complex traits.Communications biology · 2023Article
- Genome ARTIST_v2-An Autonomous Bioinformatics Tool for Annotation of Natural Transposons in Sequenced Genomes.International journal of molecular sciences · 2022Article
- Software evaluation for de novo detection of transposons.Mobile DNA · 2022Article
- Methodologies for theGenes · 2022Review
- Finding and Characterizing Repeats in Plant Genomes.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Genome-wide characterization of Mariner-like transposons and their derived MITEs in the Whitefly Bemisia tabaci (Hemiptera: Aleyrodidae).G3 (Bethesda, Md.) · 2021Article
- Engines of change: Transposable element mutation rates are high and variable within Daphnia magna.PLoS genetics · 2021Article
- TE Hub: A community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotation.Mobile DNA · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
18 authors at 9 institutions in 4 countries.
Funding
Abstract
DNA derived from transposable elements (TEs) constitutes large parts of the genomes of complex eukaryotes, with major impacts not only on genomic research but also on how organisms evolve and function. Although a variety of methods and tools have been developed to detect and annotate TEs, there are as yet no standard benchmarks-that is, no standard way to measure or compare their accuracy. This lack of accuracy assessment calls into question conclusions from a wide range of research that depends explicitly or implicitly on TE annotation. In the absence of standard benchmarks, toolmakers are impeded in improving their tools, annotators cannot properly assess which tools might best suit their needs, and downstream researchers cannot judge how accuracy limitations might impact their studies. We therefore propose that the TE research community create and adopt standard TE annotation benchmarks, and we call for other researchers to join the authors in making this long-overdue effort a success.
Identifiers
What OpenQuestion holds
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.