ArticleNature protocols2020
Full-length sequencing of circular DNA viruses and extrachromosomal circular DNA using CIDER-Seq.
Article in Nature protocols, 2020. 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 47 papers, 1 of them a synthesis that pooled it.
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
47 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
- Article
- Novel insights into tomato leaf curl New Delhi virus introduction and evolution in Southeastern France using an advanced long-read sequencing workflow.PLoS pathogens · 2026Article
- Beyond chromosomes: exploring the diverse functions of extrachromosomal circular DNA.Journal of advanced research · 2026Review
- Extrachromosomal circular DNA are functional, heritable units that expand genomic plasticity and confer resilience.Frontiers in plant science · 2026Review
- Antibody-mediated control of anellovirus infection: evidence from people who inject drugs.Journal of virology · 2025Article
- eccDNABase: A Comprehensive and High-Quality Database for Extrachromosomal Circular DNA.Molecular biology and evolution · 2025Article
- Circulating Cell-free DNA Fragmentomics Detection and Beyond.Aging and disease · 2025Review
- 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
- A method for in-depth analysis of circular DNA virus populations by unambiguously profiling the low abundant virus variants and partial genomic components.Nucleic acids research · 2025Article
- Full-Length Sequencing of Circular DNA Viruses Using CIDER-Seq.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Unveiling the mysteries of extrachromosomal circular DNA: from generation to clinical relevance in human cancers and health.Molecular cancer · 2024Review
- Review
- Review
- Beyond the Chromosome: Recent Developments in Decoding the Significance of Extrachromosomal Circular DNA (eccDNA) in Human Malignancies.Life (Basel, Switzerland) · 2024Review
- TA-Cloning for Diabetes Treatment: Expressing Corynebacterium Malic Enzyme Gene in E. coli.Current microbiology · 2024Article
- Long-Read Nanopore-Based Sequencing of Anelloviruses.Viruses · 2024Article
- Categorizing Extrachromosomal Circular DNA as Biomarkers in Serum of Cancer.Biomolecules · 2024Review
- Toward Transgene-Free Transposon-Mediated Biological Mutagenesis for Plant Breeding.International journal of molecular sciences · 2023Review
Corrections and comments
- Erratum issued
Authors and funding
5 authors.
Funding
Abstract
Circular DNA is ubiquitous in nature in the form of plasmids, circular DNA viruses, and extrachromosomal circular DNA (eccDNA) in eukaryotes. Sequencing of such molecules is essential to profiling virus distributions, discovering new viruses and understanding the roles of eccDNAs in eukaryotic cells. Circular DNA enrichment sequencing (CIDER-Seq) is a technique to enrich and accurately sequence circular DNA without the need for polymerase chain reaction amplification, cloning, and computational sequence assembly. The approach is based on randomly primed circular DNA amplification, which is followed by several enzymatic DNA repair steps and then by long-read sequencing. CIDER-Seq includes a custom data analysis package (CIDER-Seq Data Analysis Software 2) that implements the DeConcat algorithm to deconcatenate the long sequencing products of random circular DNA amplification into the intact sequences of the input circular DNA. The CIDER-Seq data analysis package can generate full-length annotated virus genomes, as well as circular DNA sequences of novel viruses. Applications of CIDER-Seq also include profiling of eccDNA molecules such as transposable elements (TEs) from biological samples. The method takes ~2 weeks to complete, depending on the computational resources available. Owing to the present constraints of long-read single-molecule sequencing, the accuracy of circular virus and eccDNA sequences generated by the CIDER-Seq method scales with sequence length, and the greatest accuracy is obtained for molecules <10 kb long.
Indexed as
Identifiers
32246135What OpenQuestion 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 OpenQuestion graph.