ArticleGenome research2024
Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data using Decoil.
Article in Genome research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Micronuclear ecDNA constrains tumor cell fitness and is associated with favorable patient survival.Nature genetics · 2026Article
- Extrachromosomal DNA as a platform for epigenetic reprogramming in cancer.Molecular cancer · 2026Review
- Quantitative and sensitive neuroblastoma minimal residual disease detection using extrachromosomal DNA (ecDNA) breakpoints.bioRxiv : the preprint server for biology · 2026Article
- Extrachromosomal DNA in urothelial carcinoma: mechanisms and clinical applications.Nature reviews. Urology · 2026Review
- A bibliometric analysis of extrachromosomal DNA in cancer over six decades.Discover oncology · 2026Article
- Targeting extrachromosomal DNA in human cancers.Nature reviews. Drug discovery · 2026Review
- Chromosome-arm-specific telomere length governs dual modes of structural genome evolution in IDH-mutant astrocytoma.bioRxiv : the preprint server for biology · 2026Article
- Fast and accurate resolution of ecDNA sequence using Cycle-Extractor.bioRxiv : the preprint server for biology · 2026Article
- Juvenile-Onset Cerebrotendinous Xanthomatosis with Novel Compound Heterozygous CYP27A1 Mutations: Case Series and Literature Review.Cerebellum (London, England) · 2026Review
- Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D.Nature communications · 2025Article
- Extrachromosomal DNA: shaping the evolutionary dynamics of cancer.Trends in cancer · 2025Review
- A Guide to Extrachromosomal DNA: Cancer's Dynamic Circular Genome.Cancer discovery · 2025Review
- Chromothripsis-associated chromosome 21 amplification orchestrates transformation to blast-phase MPN through targetable overexpression of DYRK1A.Nature genetics · 2025Article
- Unraveling the hidden complexity of cancer through long-read sequencing.Genome research · 2025Review
- Chromothripsis in cancer.Nature reviews. Cancer · 2025Review
- Modern biology of extrachromosomal DNA: A decade-long voyage of discovery.Cell research · 2025Review
- CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing.Genome research · 2024Article
- CytoCellDB: a comprehensive resource for exploring extrachromosomal DNA in cancer cell lines.NAR cancer · 2024Article
- CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing.bioRxiv : the preprint server for biology · 2024Article
- eccDNA-pipe: an integrated pipeline for identification, analysis and visualization of extrachromosomal circular DNA from high-throughput sequencing data.Briefings in bioinformatics · 2024Article
Corrections and comments
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Authors and funding
13 authors.
Funding
Abstract
Circular extrachromosomal DNA (ecDNA) is a form of oncogene amplification found across cancer types and associated with poor outcome in patients. ecDNA can be structurally complex and can contain rearranged DNA sequences derived from multiple chromosome locations. As the structure of ecDNA can impact oncogene regulation and may indicate mechanisms of its formation, disentangling it at high resolution from sequencing data is essential. Even though methods have been developed to identify and reconstruct ecDNA in cancer genome sequencing, it remains challenging to resolve complex ecDNA structures, in particular amplicons with shared genomic footprints. We here introduce Decoil, a computational method that combines a breakpoint-graph approach with
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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.