ArticleResearch (Washington, D.C.)2022
Accurate Identification of DNA Replication Origin by Fusing Epigenomics and Chromatin Interaction Information.
Article in Research (Washington, D.C.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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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
17 citing papers in PubMed, 38 citations in OpenAlex.
- Interpretable prediction of DNA replication origins in S. cerevisiae using DNABERT and DNABERT-2.BMC bioinformatics · 2026Article
- Computational prediction of replication origins: a comparative review of methods, benchmarks, and trends from heuristics to deep learning.Briefings in bioinformatics · 2026Review
- Multidimensional cfRNA response modeling identifies a 5-gene pair signature for high-robust pulmonary tuberculosis diagnosis.iScience · 2026Article
- ResNet-Powered Multi-Class Identification of Sequence Patterns for Genome Replication Timing Analysis.Interdisciplinary sciences, computational life sciences · 2025Article
- Hypertension Increases Susceptibility to Lead-Induced Microglial Polarization via ANT1-Mediated Mitochondrial DNA/cGAS/STING Signaling.Research (Washington, D.C.) · 2025Article
- Human essential gene identification based on feature fusion and feature screening.IET systems biology · 2024Article
- Exploration of Alkyne-Based Multilayered 3D Polymers and Oligomers: Subtle Aggregation-Induced Emission, Chromium(VI) Ion Detection, and Chiral Properties Characterization.Molecules (Basel, Switzerland) · 2024Article
- Development of pharmacological immunoregulatory anti-cancer therapeutics: current mechanistic studies and clinical opportunities.Signal transduction and targeted therapy · 2024Review
- Prediction of blood-brain barrier penetrating peptides based on data augmentation with Augur.BMC biology · 2024Article
- IGCNSDA: unraveling disease-associated snoRNAs with an interpretable graph convolutional network.Briefings in bioinformatics · 2024Article
- Article
- Progesterone Enhances Niraparib Efficacy in Ovarian Cancer by Promoting Palmitoleic-Acid-Mediated Ferroptosis.Research (Washington, D.C.) · 2024Article
- Unveiling human origins of replication using deep learning: accurate prediction and comprehensive analysis.Briefings in bioinformatics · 2023Article
- ORI-Explorer: a unified cell-specific tool for origin of replication sites prediction by feature fusion.Bioinformatics (Oxford, England) · 2023Article
- Prediction of CTCF loop anchor based on machine learning.Frontiers in genetics · 2023Article
- Prediction of apoptosis protein subcellular location based on amphiphilic pseudo amino acid composition.Frontiers in genetics · 2023Article
- Recognition of outer membrane proteins using multiple feature fusion.Frontiers in genetics · 2023Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA replication initiation is a complex process involving various genetic and epigenomic signatures. The correct identification of replication origins (ORIs) could provide important clues for the study of a variety of diseases caused by replication. Here, we design a computational approach named iORI-Epi to recognize ORIs by incorporating epigenome-based features, sequence-based features, and 3D genome-based features. The iORI-Epi displays excellent robustness and generalization ability on both training datasets and independent datasets of K562 cell line. Further experiments confirm that iORI-Epi is highly scalable in other cell lines (MCF7 and HCT116). We also analyze and clarify the regulatory role of epigenomic marks, DNA motifs, and chromatin interaction in DNA replication initiation of eukaryotic genomes. Finally, we discuss gene enrichment pathways from the perspective of ORIs in different replication timing states and heuristically dissect the effect of promoters on replication initiation. Our computational methodology is worth extending to ORI identification in other eukaryotic species.
Identifiers
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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 OpenQuestion graph.