ArticleNucleic acids research2025
DNAcycP2: improved estimation of intrinsic DNA cyclizability through data augmentation.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- cgNA+min: computation of sequence-dependent dsDNA energy-minimizing minicircles.Nucleic acids research · 2026Article
- Differential nucleosome organization in human interphase and metaphase chromosomes.Molecular systems biology · 2026Article
- Mlh1-Pms1 couples ATP-driven DNA compaction with nick-dependent endonuclease activation.Nucleic acids research · 2025Article
- Differential nucleosome organization in human interphase and metaphase chromosomes.bioRxiv : the preprint server for biology · 2025Article
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Authors and funding
6 authors.
Funding
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Abstract
Loop-seq is a pioneering high-throughput assay that enables the simultaneous quantification of intrinsic cyclizability across a large set of DNA fragments. However, the assay's reliance on biotin-tethered elongated DNA fragments introduces a tethering effect, leading to biased cyclizability measurements. We demonstrate that the current de-biasing technique is inadequate for fully mitigating this bias. To address this, we introduce DNAcycP2, an enhanced software tool that extends the capabilities of our previous platform, DNAcycP. DNAcycP2 incorporates a novel data augmentation approach to more effectively eliminate biotin tether bias, yielding more accurate estimates of intrinsic DNA cyclizability. Additionally, DNAcycP2 offers improved computational efficiency and expands accessibility through a newly developed R package alongside its existing Python package and web server, ensuring broader utility for the research community.
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Registered trials
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