ArticleNature communications2022
Kronos scRT: a uniform framework for single-cell replication timing analysis.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Parallel analysis of replication timing, gene expression, and copy number with PARTAGE.Genome research · 2026Article
- OCT4 enhances the firing efficiency of late DNA replication origins in mouse embryonic stem cells.Nature communications · 2026Article
- The long-standing relationship between replication timing, gene expression, and chromatin accessibility is maintained in early mouse embryogenesis.bioRxiv : the preprint server for biology · 2025Article
- PARTAGE: Parallel analysis of replication timing and gene expression.bioRxiv : the preprint server for biology · 2025Article
- Single cell multiomics approach to analyze replication timing and gene expression in mouse preimplantation embryos.Communications biology · 2025Article
- Mitigating Cell Cycle Effects in Multi-Omics Data: Solutions and Analytical Frameworks.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Replication-dependent histone labeling dissects the physical properties of euchromatin/heterochromatin in living human cells.Science advances · 2025Article
- The double life of mammalian DNA replication origins.Genes & development · 2025Review
- Unravelling single-cell DNA replication timing dynamics using machine learning reveals heterogeneity in cancer progression.Nature communications · 2025Article
- Characterizing the evolutionary dynamics of cancer proliferation in single-cell clones with SPRINTER.Nature genetics · 2025Article
- Single-cell genomics breaks new ground in cell cycle detection.Nature genetics · 2025Article
- Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data.Nature communications · 2024Article
- Quantifying DNA replication speeds in single cells by scEdU-seq.Nature methods · 2024Article
- Cell cycle gene alterations associate with a redistribution of mutation risk across chromosomal domains in human cancers.Nature cancer · 2024Article
- OKseqHMM: a genome-wide replication fork directionality analysis toolkit.Nucleic acids research · 2023Article
- Optimized Repli-seq: improved DNA replication timing analysis by next-generation sequencing.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2022Article
- DNA replication timing: Biochemical mechanisms and biological significance.BioEssays : news and reviews in molecular, cellular and developmental biology · 2022Article
- High-throughput analysis of single human cells reveals the complex nature of DNA replication timing control.Nature communications · 2022Article
- Kronos scRT: a uniform framework for single-cell replication timing analysis.Nature communications · 2022Article
- Review
Corrections and comments
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Authors and funding
11 authors.
Funding
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Abstract
Mammalian genomes are replicated in a cell type-specific order and in coordination with transcription and chromatin organization. Currently, single-cell replication studies require individual processing of sorted cells, yielding a limited number (<100) of cells. Here, we develop Kronos scRT, a software for single-cell Replication Timing (scRT) analysis. Kronos scRT does not require a specific platform or cell sorting, which allows investigating large datasets obtained from asynchronous cells. By applying our tool to published data as well as droplet-based single-cell whole-genome sequencing data generated in this study, we exploit scRT from thousands of cells for different mouse and human cell lines. Our results demonstrate that although genomic regions are frequently replicated around their population average RT, replication can occur stochastically throughout S phase. Altogether, Kronos scRT allows fast and comprehensive investigations of the RT programme at the single-cell resolution for both homogeneous and heterogeneous cell populations.
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