ArticleBriefings in bioinformatics2022
CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences.
Article in Briefings in bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 29 papers, 1 of them a synthesis that pooled it.
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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
29 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Characterization, biogenesis model, and current bioinformatics of human extrachromosomal circular DNA.Frontiers in genetics · 2024Pooled it
- AI-driven multi-omics deciphering of extrachromosomal circular DNA rescues hidden targets in colorectal cancer.Cell communication and signaling : CCS · 2026Article
- Article
- The potential clinical implications of extrachromosomal circular DNA as a biomarker.Genes & diseases · 2026Review
- Fast and accurate resolution of ecDNA sequence using Cycle-Extractor.bioRxiv : the preprint server for biology · 2026Article
- An enhancement of extrachromosomal circular DNA enrichment and amplification to address the extremely low overlap between replicates.The Journal of biological chemistry · 2026Article
- A Bioinformatics Workflow to Identify eccDNA Using ECCFP From Long-Read Nanopore Sequencing Data.Bio-protocol · 2026Article
- Cytoplasmic circular dsDNA is a key constituent of stress granules.bioRxiv : the preprint server for biology · 2026Article
- Detection of primary cancer types via fragment size selection in circulating cell-free extrachromosomal circular DNA.Genome medicine · 2026Article
- Satellite DNA fragility accompanies complex genome rearrangements and ecDNA oncogene amplification in canine osteosarcomas.bioRxiv : the preprint server for biology · 2025Article
- Extrachromosomal Circular DNA and Transposable Elements in Type 2 Diabetes.International journal of molecular sciences · 2025Review
- Giant mitogenomes in Rhynchospora are a result of nuclear gene and retrotransposon insertions in intergenic spaces.Annals of botany · 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
- Characterization and identification of extrachromosomal circular DNA in cholangiocarcinoma.PloS one · 2025Article
- Unveiling the mysteries of extrachromosomal circular DNA: from generation to clinical relevance in human cancers and health.Molecular cancer · 2024Review
- scEccDNAdb: an integrated single-cell eccDNA resource for human and mouse.Database : the journal of biological databases and curation · 2024Article
- Circle-seq based method for eccDNA synthesis and its application as a canonical promoter independent vector for robust microRNA overexpression.Computational and structural biotechnology journal · 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
Corrections and comments
- Erratum issued
Authors and funding
9 authors.
Funding
Abstract
Extrachromosomal circular DNA (eccDNA) of chromosomal origin is found in many eukaryotic species and cell types, including cancer, where eccDNAs with oncogenes drive tumorigenesis. Most studies of eccDNA employ short-read sequencing for their identification. However, short-read sequencing cannot resolve the complexity of genomic repeats, which can lead to missing eccDNA products. Long-read sequencing technologies provide an alternative to constructing complete eccDNA maps. We present a software suite, Construction-based Rolling-circle-amplification for eccDNA Sequence Identification and Location (CReSIL), to identify and characterize eccDNA from long-read sequences. CReSIL's performance in identifying eccDNA, with a minimum F1 score of 0.98, is superior to the other bioinformatic tools based on simulated data. CReSIL provides many useful features for genomic annotation, which can be used to infer eccDNA function and Circos visualization for eccDNA architecture investigation. We demonstrated CReSIL's capability in several long-read sequencing datasets, including datasets enriched for eccDNA and whole genome datasets from cells containing large eccDNA products. In conclusion, the CReSIL suite software is a versatile tool for investigating complex and simple eccDNA in eukaryotic cells.
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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.