ArticleNature communications2024
A unified framework to analyze transposable element insertion polymorphisms using graph genomes.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
21 citing papers in PubMed.
- Updated Transposable Element Libraries forbioRxiv : the preprint server for biology · 2026Article
- Active Human Transposable Elements: Long-Read Sequencing Technologies, Computational Analysis, and Implications for Human Disease.Biomolecules · 2026Review
- Transposable Element Activation: A Hallmark of Cancer.Cancer discovery · 2026Review
- Genomic forecasting for climate-resilient fruit trees.The New phytologist · 2026Review
- Long-read sequencing maps transposable element variation and its regulatory and epigenetic effects in the human brain.bioRxiv : the preprint server for biology · 2026Article
- The evolution of structural variation across 500 million years of vertebrate evolution.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
- Review
- A reference-free pipeline for detecting shared transposable elements from pan-genomes to retrace their dynamics in a species.Genome biology · 2026Article
- Role of LINE-1 in the nervous system and neurological disorders.Chinese medical journal · 2026Review
- TEvarSim: A genome simulator for transposable element (TE) variants.PLoS computational biology · 2026Article
- Jumping in the human brain: A review on somatic transposition.Fundamental research · 2026Review
- Alzheimer's disease: genetic background in the era of next-generation sequencing technologies.Brain communications · 2026Review
- A comparison of 27 Arabidopsis thaliana genomes and the path toward an unbiased characterization of genetic polymorphism.Nature genetics · 2025Article
- Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice.Nature communications · 2025Article
- Reference-free identification and pangenome analysis of accessory chromosomes in a major fungal plant pathogen.NAR genomics and bioinformatics · 2025Article
- Exploring the Relationship of Transposable Elements and Ageing: Causes and Consequences.Genome biology and evolution · 2025Review
- Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements.Genome research · 2025Article
- Advanced analysis of retrotransposon variation in the human genome with nanopore sequencing using RetroInspector.Scientific reports · 2025Article
- Controlling and controlled elements: highlights of the year in mobile DNA research.Mobile DNA · 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
5 authors.
Funding
Abstract
Transposable elements are ubiquitous mobile DNA sequences generating insertion polymorphisms, contributing to genomic diversity. We present GraffiTE, a flexible pipeline to analyze polymorphic mobile elements insertions. By integrating state-of-the-art structural variant detection algorithms and graph genomes, GraffiTE identifies polymorphic mobile elements from genomic assemblies or long-read sequencing data, and genotypes these variants using short or long read sets. Benchmarking on simulated and real datasets reports high precision and recall rates. GraffiTE is designed to allow non-expert users to perform comprehensive analyses, including in models with limited transposable element knowledge and is compatible with various sequencing technologies. Here, we demonstrate the versatility of GraffiTE by analyzing human, Drosophila melanogaster, maize, and Cannabis sativa pangenome data. These analyses reveal the landscapes of polymorphic mobile elements and their frequency variations across individuals, strains, and cultivars.
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What Socratic 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 Socratic graph.