ArticleQuantitative plant biology2022
MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant whole-genome bisulfite sequencing data.
Article in Quantitative plant biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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
15 citing papers in PubMed.
- metileneNature communications · 2026Article
- Epigenetic orchestration of sugar signaling in plant development and stress adaptation.Horticulture research · 2026Article
- Methylome differences among barley inbreds and their association with genomic, transcriptomic, and phenotypic variation.Journal of experimental botany · 2026Article
- Major alleles of CDCA7 shape CG methylation in Arabidopsis thaliana.Nature plants · 2025Article
- Computational Workflow for Genome-Wide DNA Methylation Profiling and Differential Methylation Analysis.Bio-protocol · 2025Article
- Heat stress response and transposon control in plant shoot stem cells.Plant physiology · 2025Article
- Subfunctionalization and epigenetic regulation of a biosynthetic gene cluster inProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Population epigenetics: DNA methylation in the plant omics era.Plant physiology · 2024Article
- Exploring Cereal Metagenomics: Unravelling Microbial Communities for Improved Food Security.Microorganisms · 2024Review
- Moving targets: Mechanisms regulating siRNA production and DNA methylation during plant development.Current opinion in plant biology · 2023Review
- Differentially methylated genomic regions of lettuce seeds relate to divergence across morphologically distinct horticultural types.AoB PLANTS · 2023Article
- On the causes of gene-body methylation variation in Arabidopsis thaliana.PLoS genetics · 2023Article
- Canalization of genome-wide transcriptional activity in Arabidopsis thaliana accessions by MET1-dependent CG methylation.Genome biology · 2022Article
- Predictable and stable epimutations induced during clonal plant propagation with embryonic transcription factor.PLoS genetics · 2022Article
- Conditional GWAS of non-CG transposon methylation in Arabidopsis thaliana reveals major polymorphisms in five genes.PLoS genetics · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Whole-genome bisulfite sequencing (WGBS) is the standard method for profiling DNA methylation at single-nucleotide resolution. Different tools have been developed to extract differentially methylated regions (DMRs), often built upon assumptions from mammalian data. Here, we present MethylScore, a pipeline to analyse WGBS data and to account for the substantially more complex and variable nature of plant DNA methylation. MethylScore uses an unsupervised machine learning approach to segment the genome by classification into states of high and low methylation. It processes data from genomic alignments to DMR output and is designed to be usable by novice and expert users alike. We show how MethylScore can identify DMRs from hundreds of samples and how its data-driven approach can stratify associated samples without prior information. We identify DMRs in the
Indexed as
Identifiers
What 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.