ArticleMolecular biology and evolution2024
Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline.
Article in Molecular biology and evolution, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 154 papers.
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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
154 citing papers in PubMed, 177 citations in OpenAlex.
- Phenotypic divergence is driven by mobile genetic elements in a heritable insect symbiont.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
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- Genome evolution and long-term demographic history in true crocodiles.G3 (Bethesda, Md.) · 2026Article
- Revisiting the genome assembly of Lupinus species reveals differential diploidization after a shared whole-genome duplication.G3 (Bethesda, Md.) · 2026Article
- Characterization of a draft chromosome-scale genome assembly for the mutton snapper, Lutjanus analis.Genes & genomics · 2026Article
- Accessory regions and horizontal gene transfer shape the evolution of clonal Colletotrichum nymphaeae infecting strawberry.The New phytologist · 2026Article
- A T2T Genome of the Lobed-Lip Iguazu Joana (Crenicichla tuca) Reveals Intrachromosomal Rearrangements and Trans-species Polymorphism in Cichlid Fishes.Genome biology and evolution · 2026Article
- Bacterial DNA invasion triggers transposable element proliferation and genome expansion.bioRxiv : the preprint server for biology · 2026Article
- Transposable element dynamics and regulatory role in sika deer (Cervus nippon) antler development.Mobile DNA · 2026Article
- Programmed DNA elimination was present in the last common ancestor ofbioRxiv : the preprint server for biology · 2026Article
- Chromosome-level genome assembly of the Erythrina gall wasp, Quadrastichus erythrinae (Hymenoptera: Eulophidae).G3 (Bethesda, Md.) · 2026Article
- Chromosomal fusions shaped the genome of the greater hornwrack bryozoan (Flustra foliacea) (Linnaeus, 1758).The Journal of heredity · 2026Article
- Tutorial: annotation of animal genomes.Nature protocols · 2026Review
- Gene body methylation suppresses intragenic transcription and permits epigenetic inheritance in a cnidarian.Nature ecology & evolution · 2026Article
- First genome-wide centromere map of Trypanosoma cruzi suggests linear and 3D compartment boundaries and spatial clustering.BMC genomics · 2026Article
- Hi-C guided genome assembly and karyotype analysis of the Indian population of Maruca vitrata (Lepidoptera: Crambidae) set the stage for structural and functional genomic insights.BMC genomic data · 2026Article
- A chromosome-level genome assembly of the chemosymbiotic species Rugalucina vietnamica (Lucinida: Lucinidae).Scientific data · 2026Article
- An improved Solanum verrucosum genome provides insight into potato centromeres and epigenetic regulation.G3 (Bethesda, Md.) · 2026Article
- Leveraging long-read assemblies and machine learning to enhance short-read transposable element detection and genotyping.Genetics · 2026Article
- Biological Implications of a Detailed Repeat Annotation in Octopus vulgaris.Genome biology and evolution · 2026Article
94 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 2 countries.
Funding
Abstract
Transposable elements (TEs) are major components of eukaryotic genomes and are implicated in a range of evolutionary processes. Yet, TE annotation and characterization remain challenging, particularly for nonspecialists, since existing pipelines are typically complicated to install, run, and extract data from. Current methods of automated TE annotation are also subject to issues that reduce overall quality, particularly (i) fragmented and overlapping TE annotations, leading to erroneous estimates of TE count and coverage, and (ii) repeat models represented by short sections of total TE length, with poor capture of 5' and 3' ends. To address these issues, we present Earl Grey, a fully automated TE annotation pipeline designed for user-friendly curation and annotation of TEs in eukaryotic genome assemblies. Using nine simulated genomes and an annotation of Drosophila melanogaster, we show that Earl Grey outperforms current widely used TE annotation methodologies in ameliorating the issues mentioned above while scoring highly in benchmarking for TE annotation and classification and being robust across genomic contexts. Earl Grey provides a comprehensive and fully automated TE annotation toolkit that provides researchers with paper-ready summary figures and outputs in standard formats compatible with other bioinformatics tools. Earl Grey has a modular format, with great scope for the inclusion of additional modules focused on further quality control and tailored analyses in future releases.
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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.