ArticleFrontiers in plant science2021
ecc_finder: A Robust and Accurate Tool for Detecting Extrachromosomal Circular DNA From Sequencing Data.
Article in Frontiers in plant science, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers, 1 of them a synthesis that pooled it.
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Who cites it
38 citing papers in PubMed, 1 synthesis or guideline pooled it, 69 citations in OpenAlex.
- Characterization, biogenesis model, and current bioinformatics of human extrachromosomal circular DNA.Frontiers in genetics · 2024Pooled it
- An active Helitron transposon family in wheat.Nature plants · 2026Article
- Fast and accurate resolution of ecDNA sequence using Cycle-Extractor.bioRxiv : the preprint server for biology · 2026Article
- DeepECC: a deep learning framework for genome-wide identification and analysis of human cancer eccDNAs.Nucleic acids research · 2026Article
- Comparative analysis of eccDNA and circRNA tools shows increased accuracy of tool combination.GigaScience · 2026Article
- CircleBase V2: an eccDNA annotation platform across cancers and species.Nucleic acids research · 2026Article
- Research Advances of Extrachromosomal Circular DNA in Breast Cancer.Cancer medicine · 2025Review
- PAFAH1B3 Exists in Linear Chromosomal and Extrachromosomal Circular DNA and Promotes HCC Progression via EMT.International journal of molecular sciences · 2025Article
- A comprehensive atlas of full-length Arabidopsis eccDNA populations identifies their genomic origins and epigenetic regulation.PLoS biology · 2025Article
- Adaptive dynamics of extrachromosomal circular DNA in rice under nutrient stress.Nature communications · 2025Article
- Identification of eccDNA in Extracellular Vesicles Derived from Human Dermal Fibroblasts Through Nanopore Sequencing.International journal of molecular sciences · 2025Article
- Exploring the potential of extrachromosomal DNA as a novel oncogenic driver.Science China. Life sciences · 2025Review
- Unveiling the mysteries of extrachromosomal circular DNA: from generation to clinical relevance in human cancers and health.Molecular cancer · 2024Review
- Comparative Analysis of Active LTR Retrotransposons in Sunflower (International journal of molecular sciences · 2024Article
- Comparative analysis of methodologies for detecting extrachromosomal circular DNA.Nature communications · 2024Article
- Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil.Genome research · 2024Article
- Review
- Review
- Categorizing Extrachromosomal Circular DNA as Biomarkers in Serum of Cancer.Biomolecules · 2024Review
- Dynamics of extrachromosomal circular DNA in rice.Nature communications · 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 at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Extrachromosomal circular DNA (eccDNA) has been observed in different species for decades, and more and more evidence shows that this specific type of DNA molecules may play an important role in rapid adaptation. Therefore, characterizing the full landscape of eccDNA has become critical, and there are several protocols for enriching eccDNAs and performing short-read or long-read sequencing. However, there is currently no available bioinformatic tool to identify eccDNAs from Nanopore reads. More importantly, the current tools based on Illumina short reads lack an efficient standardized pipeline notably to identify eccDNA originating from repeated loci and cannot be applied to very large genomes. Here, we introduce a comprehensive tool to solve both of these two issues. Applying ecc_finder to eccDNA-seq data (either mobilome-seq, Circle-Seq and CIDER-seq) from
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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.