ArticleGenome biology2018
Predicting double-strand DNA breaks using epigenome marks or DNA at kilobase resolution.
Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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
29 citing papers in PubMed, 46 citations in OpenAlex.
- Using the DNA language model, GROVER, to parse effects of sequence, chromatin and regulatory features on genome stability.Bioinformatics (Oxford, England) · 2026Article
- AI-based methods for the assessment of DNA damage and repair mechanisms.Frontiers in systems biology · 2026Review
- The interplay of DNA damage, epigenetics and tumour heterogeneity in driving cancer cell fitness.Nature communications · 2025Review
- Article
- ChromInSight: Revealing DNA Double-Strand Breaks Through Chromatin Structural Insights With an Interpretable Graph Neural Network Framework.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Coordinated regulation by lncRNAs results in tight lncRNA-target couplings.Cell genomics · 2025Article
- Enhancing R-loop prediction with high-throughput sequencing data.NAR genomics and bioinformatics · 2025Article
- Deep learning reveals determinants of transcriptional infidelity at nucleotide resolution in the allopolyploid line by goldfish and common carp hybrids.Briefings in bioinformatics · 2025Article
- Towards the genomic sequence code of DNA fragility for machine learning.Nucleic acids research · 2024Article
- Pervasive structural heterogeneity rewires glioblastoma chromosomes to sustain patient-specific transcriptional programs.Nature communications · 2024Article
- SSBlazer: a genome-wide nucleotide-resolution model for predicting single-strand break sites.Genome biology · 2024Article
- DSB profiles in human spermatozoa highlight the role of TMEJ in the male germline.Frontiers in genetics · 2024Article
- A graph neural network-based interpretable framework reveals a novel DNA fragility-associated chromatin structural unit.Genome biology · 2023Article
- Breaking the paradigm: early insights from mammalian DNA breakomes.The FEBS journal · 2022Review
- Epigenomic signatures associated with spontaneous and replication stress-induced DNA double strand breaks.Frontiers in genetics · 2022Article
- Review
- Medium levels of transcription and replication related chromosomal instability are associated with poor clinical outcome.Scientific reports · 2021Article
- Article
- Predicted Cellular Interactors of the Endogenous Retrovirus-K Integrase Enzyme.Microorganisms · 2021Article
- Epigenetic Marks and Variation of Sequence-Based Information Along Genomic Regions Are Predictive of Recombination Hot/Cold Spots inFrontiers in genetics · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Double-strand breaks (DSBs) result from the attack of both DNA strands by multiple sources, including radiation and chemicals. DSBs can cause the abnormal chromosomal rearrangements associated with cancer. Recent techniques allow the genome-wide mapping of DSBs at high resolution, enabling the comprehensive study of their origins. However, these techniques are costly and challenging. Hence, we devise a computational approach to predict DSBs using the epigenomic and chromatin context, for which public data are readily available from the ENCODE project. We achieve excellent prediction accuracy at high resolution. We identify chromatin accessibility, activity, and long-range contacts as the best predictors.
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What Socratic holds
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.