ArticleNucleic acids research2010
Mathematical modelling of whole chromosome replication.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
- RepliSage: a stochastic graph-based framework for 3D chromatin modeling across the cell cycle.Nucleic acids research · 2026Article
- Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes.Genome biology · 2025Article
- Regulation of replication timing in Saccharomyces cerevisiae.PLoS computational biology · 2025Article
- DNA replication timing reveals genome-wide features of transcription and fragility.Nature communications · 2025Article
- Rif1 restrains the rate of replication origin firing in Xenopus laevis.Communications biology · 2023Article
- Neural network and kinetic modelling of human genome replication reveal replication origin locations and strengths.PLoS computational biology · 2023Article
- DNA replication timing: Biochemical mechanisms and biological significance.BioEssays : news and reviews in molecular, cellular and developmental biology · 2022Article
- Genome-wide mapping of individual replication fork velocities using nanopore sequencing.Nature communications · 2022Article
- Review
- Chromosomal Mcm2-7 distribution and the genome replication program in species from yeast to humans.PLoS genetics · 2021Article
- Genome-wide mapping of human DNA replication by optical replication mapping supports a stochastic model of eukaryotic replication.Molecular cell · 2021Article
- Article
- The capacity of origins to load MCM establishes replication timing patterns.PLoS genetics · 2021Article
- Article
- FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing.Genome biology · 2020Article
- DNA copy-number measurement of genome replication dynamics by high-throughput sequencing: the sort-seq, sync-seq and MFA-seq family.Nature protocols · 2020Article
- Genomic methods for measuring DNA replication dynamics.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2020Review
- The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems.PLoS computational biology · 2020Article
- Stochasticity of replication forks' speeds plays a key role in the dynamics of DNA replication.PLoS computational biology · 2019Article
- Replication dynamics of individual loci in single living cells reveal changes in the degree of replication stochasticity through S phase.Nucleic acids research · 2019Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
All chromosomes must be completely replicated prior to cell division, a requirement that demands the activation of a sufficient number of appropriately distributed DNA replication origins. Here we investigate how the activity of multiple origins on each chromosome is coordinated to ensure successful replication. We present a stochastic model for whole chromosome replication where the dynamics are based upon the parameters of individual origins. Using this model we demonstrate that mean replication time at any given chromosome position is determined collectively by the parameters of all origins. Combining parameter estimation with extensive simulations we show that there is a range of model parameters consistent with mean replication data, emphasising the need for caution in interpreting such data. In contrast, the replicated-fraction at time points through S phase contains more information than mean replication time data and allowed us to use our model to uniquely estimate many origin parameters. These estimated parameters enable us to make a number of predictions that showed agreement with independent experimental data, confirming that our model has predictive power. In summary, we demonstrate that a stochastic model can recapitulate experimental observations, including those that might be interpreted as deterministic such as ordered origin activation times.
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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.