ArticleNature communications2025
A high-resolution, nanopore-based artificial intelligence assay for DNA replication stress in human cancer cells.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
21 citing papers in PubMed.
- S-phase targeted treatment triggers caspase-dependent lytic immunogenic cell death with pyroptotic features in cancers.Cell death and differentiation · 2026Article
- RepliSage: a stochastic graph-based framework for 3D chromatin modeling across the cell cycle.Nucleic acids research · 2026Article
- Replication origin firing capacity indicates ATR inhibitor sensitivity.Nature communications · 2026Article
- Spatial organization and dynamics of genome replication: from forks to foci.Nucleic acids research · 2026Review
- Decision tree with randomized grid search-based hyperparameter tuning and optimal feature scaling for diabetes diagnosis.BMC bioinformatics · 2026Article
- Adaptive Replication Fork Acceleration by CDK1-Cyclin B1 Sustains Genome Duplication despite Impaired Origin Firing.bioRxiv : the preprint server for biology · 2026Article
- Dynamic regulation of origin firing factors links CDK activity to dormant origin activation.Nature communications · 2026Article
- Nanopore-based sequencing of active DNA replication reveals key principles of metazoan replication dynamics.Science advances · 2026Article
- DNAi: an open-source AI tool for unbiased DNA fiber analysis.Nucleic acids research · 2026Article
- Therapy as a State-Generator: Dynamic Phenotypic Landscapes and Adaptive Stress Circuits in Chemotherapy Resistance of Breast Cancer.Antioxidants (Basel, Switzerland) · 2026Review
- Multiplexed TrAEL-seq captures DNA replication dynamics in mammalian cells.Nucleic acids research · 2026Article
- Automated mapping of DNA replication fork progression in human cells with ForkML.Nature communications · 2026Article
- Article
- Nanopore-based sequencing of active DNA replication reveals key principles of metazoan replication fork progression, origin and termination sites.bioRxiv : the preprint server for biology · 2025Article
- ecDNA replication is disorganized and vulnerable to replication stress.Nucleic acids research · 2025Article
- Most human DNA replication initiation is dispersed throughout the genome with only a minority within previously identified initiation zones.Genome biology · 2025Article
- The double life of mammalian DNA replication origins.Genes & development · 2025Review
- DNA replication dynamics are associated with genome composition in Plasmodium species.Nucleic acids research · 2025Article
- Roles for the 3D genome in the cell cycle, DNA replication, and double strand break repair.Frontiers in cell and developmental biology · 2025Review
- Quantifying DNA replication speeds in single cells by scEdU-seq.Nature methods · 2024Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
DNA replication stress is a hallmark of cancer that is exploited by chemotherapies. Current assays for replication stress have low throughput and poor resolution whilst being unable to map the movement of replication forks genome-wide. We present a new method that uses nanopore sequencing and artificial intelligence to map forks and measure their rates of movement and stalling in melanoma and colon cancer cells treated with chemotherapies. Our method can differentiate between fork slowing and fork stalling in cells treated with hydroxyurea, as well as inhibitors of ATR, WEE1, and PARP1. These different therapies yield different characteristic signatures of replication stress. We assess the role of the intra-S-phase checkpoint on fork slowing and stalling and show that replication stress dynamically changes over S-phase. Finally, we demonstrate that this method is applicable and consistent across two different flow cell chemistries (R9.4.1 and R10.4.1) from Oxford Nanopore Technologies. This method requires sequencing on only one nanopore flow cell per sample, and the cost-effectiveness enables functional screens to determine how human cancers respond to replication-targeted therapies.
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Registered trials
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