ArticleBriefings in bioinformatics2025
SMAC: identifying DNA N6-methyladenine (6mA) at the single-molecule level using SMRT CCS data.
Article in Briefings in bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
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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.
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Who cites it
6 citing papers in PubMed.
- A distinct subclade of AlkB family demethylases in ciliates safeguards the positional fidelity of eukaryotic NProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Distribution patterns of N6-methyladenine in the rye genome.Scientific reports · 2025Article
- Revealing long-range heterogeneous organization of nucleoproteins with 6mA footprinting by ipdTrimming.Genome biology · 2025Article
- Identification and characterization of the de novo methyltransferases for eukaryoticScience advances · 2025Article
- Methyl-dependent auto-regulation of the DNA N6-adenine methyltransferase AMT1 in the unicellular eukaryote Tetrahymena thermophila.Nucleic acids research · 2025Article
- FSFT6mA: a feature-synthesis fine-tuning framework for DNA 6mA site prediction.Frontiers in genetics · 2025Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
DNA modifications, such as N6-methyladenine (6mA), play important roles in various processes in eukaryotes. Single-molecule, real-time (SMRT) sequencing enables the direct detection of DNA modifications without requiring special sample preparation. However, most SMRT-based studies of 6mA rely on ensemble-level consensus by combining multiple reads covering the same genomic position, which misses the single-molecule heterogeneity. While recent methods have aimed at single-molecule level detection of 6mA, limitations in sequencing platforms, resolution, accuracy, and usability restrict their application in comprehensive epigenetic studies. Here, we present SMAC (single-molecule 6mA analysis of CCS reads), a novel framework for accurately detecting 6mA at the single-molecule level using SMRT circular consensus sequencing (CCS) data from the Sequel II system. It is an automated method that streamlines the entire workflow by packaging both existing softwares and built-in scripts, with user-defined parameters to allow easy adaptation for various studies. By utilizing the statistical distribution characteristics of enzyme kinetic indicators on single DNA molecules rather than a fixed cutoff, SMAC significantly improves 6mA detection accuracy at the single-nucleotide and single-molecule levels. It simplifies analysis by providing comprehensive information, including quality control, statistical analysis, and site visualization, directly from raw sequencing data. SMAC is a powerful new tool that enables de novo detection of 6mA and empowers investigation of its functions in modulating physiological processes.
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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.