ArticleGenome research2017
Model-based analysis of DNA replication profiles: predicting replication fork velocity and initiation rate by profiling free-cycling cells.
Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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Who cites it
13 citing papers in PubMed.
- Model-based inference of cell cycle dynamics captures alterations of the DNA replication programme.PLoS computational biology · 2025Article
- Regulation of replication timing in Saccharomyces cerevisiae.PLoS computational biology · 2025Article
- Dual genetic level modification engineering accelerate genome evolution of Corynebacterium glutamicum.Nucleic acids research · 2024Article
- Genome replication in asynchronously growing microbial populations.PLoS computational biology · 2024Article
- Genome-wide mapping of individual replication fork velocities using nanopore sequencing.Nature communications · 2022Article
- Rtt109 slows replication speed by histone N-terminal acetylation.Genome research · 2021Article
- Article
- Genomic methods for measuring DNA replication dynamics.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2020Review
- Stochasticity of replication forks' speeds plays a key role in the dynamics of DNA replication.PLoS computational biology · 2019Article
- Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations.Advanced theory and simulations · 2019Article
- Budding yeast Rif1 binds to replication origins and protects DNA at blocked replication forks.EMBO reports · 2018Article
- Cell-to-cell variability and robustness in S-phase duration from genome replication kinetics.Nucleic acids research · 2017Article
- Perturbations in the Replication Program Contribute to Genomic Instability in Cancer.International journal of molecular sciences · 2017Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Eukaryotic cells initiate DNA synthesis by sequential firing of hundreds of origins. This ordered replication is described by replication profiles, which measure the DNA content within a cell population. Here, we show that replication dynamics can be deduced from replication profiles of free-cycling cells. While such profiles lack explicit temporal information, they are sensitive to fork velocity and initiation capacity through the passive replication pattern, namely the replication of origins by forks emanating elsewhere. We apply our model-based approach to a compendium of profiles that include most viable budding yeast mutants implicated in replication. Predicted changes in fork velocity or initiation capacity are verified by profiling synchronously replicating cells. Notably, most mutants implicated in late (or early) origin effects are explained by global modulation of fork velocity or initiation capacity. Our approach provides a rigorous framework for analyzing DNA replication profiles of free-cycling cells.
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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 Socratic graph.