ArticleNucleic acids research2024
BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Integrative Epigenomics: Bioinformatics Strategies for Multi-Omics Data Analysis in Health and Disease.Epigenomes · 2026Review
- map3C: a computational tool for processing multiomic single-cell Hi-C data.Bioinformatics (Oxford, England) · 2026Article
- Cell-to-cell variability and gain of methylation at polycomb CpG islands as a hallmark of aging.Nature communications · 2026Article
- The genetic basis for DNA methylation variation across tissues and development.Nature communications · 2026Article
- Long-read sequencing identifies aberrant fragmentation patterns linked to elevated cell-free DNA levels in cancer.Genome biology · 2026Article
- MidbrainbioRxiv : the preprint server for biology · 2026Article
- M-PACT leverages cell-free DNA methylomes to achieve robust classification of pediatric brain tumors.Nature cancer · 2026Article
- Unnatural Cytosine Analogs Potentiate a Customizable, Enzymatic Method for Integrated Epigenetic and Four-Base Genetic Sequencing.Journal of the American Chemical Society · 2026Article
- Genetics and environment distinctively shape the human immune cell epigenome.Nature genetics · 2026Article
- Dnmt3a2 expression during embryonic development is required for phenotypic stability.Communications biology · 2025Article
- An allele-resolved nanopore-guided tour of the human placental methylome.Nature communications · 2025Article
- map3C: a computational tool for processing multiomic single-cell Hi-C data.bioRxiv : the preprint server for biology · 2025Article
- Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard.Nucleic acids research · 2025Article
- Article
- Scalable screening of ternary-code DNA methylation dynamics associated with human traits.Cell genomics · 2025Article
- High-coverage allele-resolved single-cell DNA methylation profiling reveals cell lineage, X-inactivation state, and replication dynamics.Nature communications · 2025Article
- AutoMethyc: an automated methylation analysis for massively parallel sequencing data.Briefings in bioinformatics · 2025Article
- Genetic/epigenetic DNA markers for linking suspects and tissues in complex crime scenes.Briefings in bioinformatics · 2025Article
- Charting the regulatory landscape of TP53 on transposable elements in cancer.Genome research · 2025Article
- Methyl-Micro-C: simultaneous characterization of chromatin accessibility, interactions, and DNA methylation.NAR genomics and bioinformatics · 2025Article
Corrections and comments
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13 authors.
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Abstract
Data from both bulk and single-cell whole-genome DNA methylation experiments are under-utilized in many ways. This is attributable to inefficient mapping of methylation sequencing reads, routinely discarded genetic information, and neglected read-level epigenetic and genetic linkage information. We introduce the BISulfite-seq Command line User Interface Toolkit (BISCUIT) and its companion R/Bioconductor package, biscuiteer, for simultaneous extraction of genetic and epigenetic information from bulk and single-cell DNA methylation sequencing. BISCUIT's performance, flexibility and standards-compliant output allow large, complex experimental designs to be characterized on clinical timescales. BISCUIT is particularly suited for processing data from single-cell DNA methylation assays, with its excellent scalability, efficiency, and ability to greatly enhance mappability, a key challenge for single-cell studies. We also introduce the epiBED format for single-molecule analysis of coupled epigenetic and genetic information, facilitating the study of cellular and tissue heterogeneity from DNA methylation sequencing.
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Registered trials
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