ArticleNucleic acids research2014
TEMP: a computational method for analyzing transposable element polymorphism in populations.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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Who cites it
92 citing papers in PubMed.
- Long-read sequencing maps transposable element variation and its regulatory and epigenetic effects in the human brain.bioRxiv : the preprint server for biology · 2026Article
- Leveraging long-read assemblies and machine learning to enhance short-read transposable element detection and genotyping.Genetics · 2026Article
- A reference-free pipeline for detecting shared transposable elements from pan-genomes to retrace their dynamics in a species.Genome biology · 2026Article
- 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
- Image-based DNA sequencing encoding for detecting low-mosaicism somatic mobile element insertions.Nature communications · 2025Article
- Epigenetic reprogramming induced by key metabolite depletion is an evolutionarily ancient path to tumorigenesis.Disease models & mechanisms · 2025Article
- Exploring the Relationship of Transposable Elements and Ageing: Causes and Consequences.Genome biology and evolution · 2025Review
- Ultra-sensitive detection of transposon insertions across multiple families by transposable element display sequencing.Genome biology · 2025Article
- Transposable Element (TE) insertion predictions from RNAseq inputs and TE impact on RNA splicing and gene expression in Drosophila brain transcriptomes.Mobile DNA · 2024Article
- Tolerance thresholds underlie responses to DNA damage during germline development.Genes & development · 2024Article
- Contribution ofmedRxiv : the preprint server for health sciences · 2024Article
- Review
- Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast.Mobile DNA · 2023Article
- Reproducible evaluation of transposable element detectors with McClintock 2 guides accurate inference of Ty insertion patterns in yeast.bioRxiv : the preprint server for biology · 2023Article
- Genotyping of Transposable Element Insertions Segregating in Human Populations Using Short-Read Realignments.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Local assembly of long reads enables phylogenomics of transposable elements in a polyploid cell line.Nucleic acids research · 2022Article
- Role of Transposable Elements in Genome Stability: Implications for Health and Disease.International journal of molecular sciences · 2022Review
- Ongoing transposition in cell culture reveals the phylogeny of diverse Drosophila S2 sublines.Genetics · 2022Article
- Exploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice.Plant communications · 2022Article
32 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
Insertions and excisions of transposable elements (TEs) affect both the stability and variability of the genome. Studying the dynamics of transposition at the population level can provide crucial insights into the processes and mechanisms of genome evolution. Pooling genomic materials from multiple individuals followed by high-throughput sequencing is an efficient way of characterizing genomic polymorphisms in a population. Here we describe a novel method named TEMP, specifically designed to detect TE movements present with a wide range of frequencies in a population. By combining the information provided by pair-end reads and split reads, TEMP is able to identify both the presence and absence of TE insertions in genomic DNA sequences derived from heterogeneous samples; accurately estimate the frequencies of transposition events in the population and pinpoint junctions of high frequency transposition events at nucleotide resolution. Simulation data indicate that TEMP outperforms other algorithms such as PoPoolationTE, RetroSeq, VariationHunter and GASVPro. TEMP also performs well on whole-genome human data derived from the 1000 Genomes Project. We applied TEMP to characterize the TE frequencies in a wild Drosophila melanogaster population and study the inheritance patterns of TEs during hybrid dysgenesis. We also identified sequence signatures of TE insertion and possible molecular effects of TE movements, such as altered gene expression and piRNA production. TEMP is freely available at github: https://github.com/JialiUMassWengLab/TEMP.git.
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