ArticleNucleic acids research2021
A benchmark and an algorithm for detecting germline transposon insertions and measuring de novo transposon insertion frequencies.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed, 56 citations in OpenAlex.
- Ancient Transposable Elements Sustain Global Ecological Adaptation Despite Chronically Low Nucleotide Diversity.Molecular ecology · 2026Article
- Somatic mobility of transposons is explosive and shaped by distinct integration biases in Arabidopsis thaliana.Genome biology · 2026Article
- Leveraging long-read assemblies and machine learning to enhance short-read transposable element detection and genotyping.Genetics · 2026Article
- Meiotic double-strand DNA breaks and spontaneous mutation in Drosophila melanogaster.G3 (Bethesda, Md.) · 2026Article
- Transgenerational effects of heat shock on gene regulation and fitness-related traits in natural Drosophila populations.Molecular biology and evolution · 2026Article
- Chromosome-scale Genome Assembly of the Most Abundant Ectomycorrhizal Fungus Cenococcum Geophilum Reveals Massive TE Expansion and RIP Defense Mechanism.Genome biology and evolution · 2026Article
- Jumping in the human brain: A review on somatic transposition.Fundamental research · 2026Review
- Historic transposon mobilisation waves create distinct pools of adaptive variants in a major crop pathogen.Nature communications · 2025Article
- The contribution of transposable element insertions to genetic diversity inbioRxiv : the preprint server for biology · 2025Article
- Translesion DNA polymerases Rev1 and PolH promote LTR-retrotransposon transcription by safeguarding Pol II occupancy in both germline and somatic tissues of Drosophila.Nucleic acids research · 2025Article
- The Roles of tRNA-Derived Fragments in Cancer: Updates and Perspectives.International journal of molecular sciences · 2025Review
- Article
- A mechanistic basis for genetic assimilation in natural fly populations.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Exploring unsolved cases of lissencephaly spectrum: integrating exome and genome sequencing for higher diagnostic yield.Journal of human genetics · 2024Article
- A unified framework to analyze transposable element insertion polymorphisms using graph genomes.Nature communications · 2024Article
- Article
- Mobile element insertions in rare diseases: a comparative benchmark and reanalysis of 60,000 exome samples.European journal of human genetics : EJHG · 2024Article
- The Structural Abnormalities Are Deeply Involved in the Cause ofInternational journal of molecular sciences · 2023Article
- Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast.Mobile DNA · 2023Article
- Epigenetic and chromosomal features drive transposon insertion in Drosophila melanogaster.Nucleic acids research · 2023Article
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
Transposons are genomic parasites, and their new insertions can cause instability and spur the evolution of their host genomes. Rapid accumulation of short-read whole-genome sequencing data provides a great opportunity for studying new transposon insertions and their impacts on the host genome. Although many algorithms are available for detecting transposon insertions, the task remains challenging and existing tools are not designed for identifying de novo insertions. Here, we present a new benchmark fly dataset based on PacBio long-read sequencing and a new method TEMP2 for detecting germline insertions and measuring de novo 'singleton' insertion frequencies in eukaryotic genomes. TEMP2 achieves high sensitivity and precision for detecting germline insertions when compared with existing tools using both simulated data in fly and experimental data in fly and human. Furthermore, TEMP2 can accurately assess the frequencies of de novo transposon insertions even with high levels of chimeric reads in simulated datasets; such chimeric reads often occur during the construction of short-read sequencing libraries. By applying TEMP2 to published data on hybrid dysgenic flies inflicted by de-repressed P-elements, we confirmed the continuous new insertions of P-elements in dysgenic offspring before they regain piRNAs for P-element repression. TEMP2 is freely available at Github: https://github.com/weng-lab/TEMP2.
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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.