ArticleBMC bioinformatics2017
Repliscan: a tool for classifying replication timing regions.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Replication timing uncovers a two-compartment nuclear architecture of interphase euchromatin.The Plant cell · 2026Article
- OCT4 enhances the firing efficiency of late DNA replication origins in mouse embryonic stem cells.Nature communications · 2026Article
- Comparison of transcriptional activity profiling by metabolic labeling or nuclear RNA sequencing.The Plant journal : for cell and molecular biology · 2025Article
- A comparison of genomic methods to assess DNA replication timing.Scientific reports · 2025Article
- Replication timing alterations are associated with mutation acquisition during breast and lung cancer evolution.Nature communications · 2024Article
- Coinhibition of topoisomerase 1 and BRD4-mediated pause release selectively kills pancreatic cancer via readthrough transcription.Science advances · 2023Article
- NEDDylated Cullin 3 mediates the adaptive response to topoisomerase 1 inhibitors.Science advances · 2022Article
- From the archives: Polar auxin transport in nodule development, DNA replication timing, and developmentally light-regulated genes.The Plant cell · 2022Article
- LSD1 is required for euchromatic origin firing and replication timing.Signal transduction and targeted therapy · 2022Article
- Globally altered epigenetic landscape and delayed osteogenic differentiation in H3.3-G34W-mutant giant cell tumor of bone.Nature communications · 2020Article
- Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots.PLoS genetics · 2020Article
- Sequence analysis of integrated hepatitis B virus DNA during HBeAg-seroconversion.Emerging microbes & infections · 2018Article
- Genome-Wide Analysis of the Arabidopsis Replication Timing Program.Plant physiology · 2018Article
- Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (The Plant cell · 2017Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundReplication timing experiments that use label incorporation and high throughput sequencing produce peaked data similar to ChIP-Seq experiments. However, the differences in experimental design, coverage density, and possible results make traditional ChIP-Seq analysis methods inappropriate for use with replication timing.
resultsTo accurately detect and classify regions of replication across the genome, we present Repliscan. Repliscan robustly normalizes, automatically removes outlying and uninformative data points, and classifies Repli-seq signals into discrete combinations of replication signatures. The quality control steps and self-fitting methods make Repliscan generally applicable and more robust than previous methods that classify regions based on thresholds.
conclusionsRepliscan is simple and effective to use on organisms with different genome sizes. Even with analysis window sizes as small as 1 kilobase, reliable profiles can be generated with as little as 2.4x coverage.
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