ArticleGenome research2013
Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
What it found
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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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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
65 citing papers in PubMed.
- Long-read sequencing technologies and bioinformatics: a new perspective for decoding DNA methylation modifications.Journal of translational medicine · 2026Review
- Replication-coupled hemimethylation inFrontiers in microbiology · 2026Review
- The emerging role of DNA methylation in the pathogenicity of bacterial pathogens.Journal of bacteriology · 2025Review
- Revealing long-range heterogeneous organization of nucleoproteins with 6mA footprinting by ipdTrimming.Genome biology · 2025Article
- SMAC: identifying DNA N6-methyladenine (6mA) at the single-molecule level using SMRT CCS data.Briefings in bioinformatics · 2025Article
- Understanding prokaryotic adaptation through advanced DNA methylation detection techniques.The ISME journal · 2025Review
- Mapping epigenetic modifications by sequencing technologies.Cell death and differentiation · 2025Review
- Methods for Detection and Mapping of Methylated and Hydroxymethylated Cytosine in DNA.Biomolecules · 2024Review
- Sequencing of NMolecular cell · 2024Article
- Long-read sequencing for brain tumors.Frontiers in oncology · 2024Review
- Adenine methylation is very scarce in theeLife · 2023Article
- Comparison ofEpigenomes · 2023Article
- Shaping eukaryotic epigenetic systems by horizontal gene transfer.BioEssays : news and reviews in molecular, cellular and developmental biology · 2023Article
- Navigating the pitfalls of mapping DNA and RNA modifications.Nature reviews. Genetics · 2023Review
- Single-strand mismatch and damage patterns revealed by single-molecule DNA sequencing.bioRxiv : the preprint server for biology · 2023Article
- Omics and Multi-Omics Analysis for the Early Identification and Improved Outcome of Patients with Psoriatic Arthritis.Biomedicines · 2022Review
- Context-dependent DNA polymerization effects can masquerade as DNA modification signals.BMC genomics · 2022Article
- Critical assessment of DNA adenine methylation in eukaryotes using quantitative deconvolution.Science (New York, N.Y.) · 2022Article
- KAS-seq: genome-wide sequencing of single-stranded DNA by NNature protocols · 2022Review
- Comparison of the Oral Microbiota Structure among People from the Same Ethnic Group Living in Different Environments.BioMed research international · 2022Article
5 more citing papers are in PubMed but not listed here.
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Authors and funding
16 authors.
Funding
Abstract
Current generation DNA sequencing instruments are moving closer to seamlessly sequencing genomes of entire populations as a routine part of scientific investigation. However, while significant inroads have been made identifying small nucleotide variation and structural variations in DNA that impact phenotypes of interest, progress has not been as dramatic regarding epigenetic changes and base-level damage to DNA, largely due to technological limitations in assaying all known and unknown types of modifications at genome scale. Recently, single-molecule real time (SMRT) sequencing has been reported to identify kinetic variation (KV) events that have been demonstrated to reflect epigenetic changes of every known type, providing a path forward for detecting base modifications as a routine part of sequencing. However, to date no statistical framework has been proposed to enhance the power to detect these events while also controlling for false-positive events. By modeling enzyme kinetics in the neighborhood of an arbitrary location in a genomic region of interest as a conditional random field, we provide a statistical framework for incorporating kinetic information at a test position of interest as well as at neighboring sites that help enhance the power to detect KV events. The performance of this and related models is explored, with the best-performing model applied to plasmid DNA isolated from Escherichia coli and mitochondrial DNA isolated from human brain tissue. We highlight widespread kinetic variation events, some of which strongly associate with known modification events, while others represent putative chemically modified sites of unknown types.
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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.