ArticleNucleic acids research2024
Prediction of DNA i-motifs via machine learning.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- RNA i-motif landscapes in plant kingdom and their potential functional roles.Molecular biology and evolution · 2026Article
- AGAPE (Computational G‑Quadruplex Stabilization Prediction): The First Machine Learning Workflow for G‑Quadruplex Stabilization Prediction.ACS omega · 2026Article
- The cellular landscape of i-motifs: genomic insights, methodological challenges, and the road ahead.Genome biology · 2026Review
- Non-B DNA structures and their contributions to genetic diversity, aging, and disease.Nucleic acids research · 2026Review
- High-throughput measurement and prediction of the i-motif DNA stability landscape.Nucleic acids research · 2026Article
- In silico mapping of non-canonical DNA structures across the human ribosomal DNA locus.G3 (Bethesda, Md.) · 2026Article
- i-Motif, not G-quadruplex, stability regulates insulin expression.Nucleic acids research · 2026Article
- Reversible metamorphosis of hierarchical DNA-inorganic crystals.Nature nanotechnology · 2025Article
- G-quadruplex and i-motif DNA structures form in the promoter of the key innate immune adaptorCell reports. Physical science · 2025Article
- i-Motifs as regulatory switches: Mechanisms and implications for gene expression.Molecular therapy. Nucleic acids · 2025Review
- The iMab antibody selectively binds to intramolecular and intermolecular i-motif structures.Nucleic acids research · 2025Article
- Asymmetric distribution of G-quadruplex forming sequences in genomes of retroviruses.Scientific reports · 2025Article
- DNA sequence analysis landscape: a comprehensive review of DNA sequence analysis task types, databases, datasets, word embedding methods, and language models.Frontiers in medicine · 2025Review
- Profiling of i-motif-binding proteins reveals functional roles of nucleolin in regulation of high-order DNA structures.Nucleic acids research · 2024Article
- iM-Seeker: a webserver for DNA i-motifs prediction and scoring via automated machine learning.Nucleic acids research · 2024Article
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Authors and funding
7 authors.
Funding
Abstract
i-Motifs (iMs), are secondary structures formed in cytosine-rich DNA sequences and are involved in multiple functions in the genome. Although putative iM forming sequences are widely distributed in the human genome, the folding status and strength of putative iMs vary dramatically. Much previous research on iM has focused on assessing the iM folding properties using biophysical experiments. However, there are no dedicated computational tools for predicting the folding status and strength of iM structures. Here, we introduce a machine learning pipeline, iM-Seeker, to predict both folding status and structural stability of DNA iMs. The programme iM-Seeker incorporates a Balanced Random Forest classifier trained on genome-wide iMab antibody-based CUT&Tag sequencing data to predict the folding status and an Extreme Gradient Boosting regressor to estimate the folding strength according to both literature biophysical data and our in-house biophysical experiments. iM-Seeker predicts DNA iM folding status with a classification accuracy of 81% and estimates the folding strength with coefficient of determination (R2) of 0.642 on the test set. Model interpretation confirms that the nucleotide composition of the C-rich sequence significantly affects iM stability, with a positive correlation with sequences containing cytosine and thymine and a negative correlation with guanine and adenine.
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