ArticleGenome biology2020
DeepMILO: a deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 61 citations in OpenAlex.
- Telomere-driven replicative crisis is driven by large-scale changes in genomic architecture.Genome research · 2026Article
- Cross-cell-line conservation-resolved interactions reveal conservation-dependent relationships among CTCF loops.BMC genomics · 2026Article
- GraphChIAr: genome-wide super-resolution reconstruction of protein-mediated remote chromatin interactions by augmenting hi-C interaction maps with multiple ChIP-seq profiles.Briefings in bioinformatics · 2026Article
- TF-loop: deciphering the transcription factor regulatory language for CTCF-mediated chromatin loop based on BERT.Briefings in bioinformatics · 2026Article
- The emerging sequence grammar of 3D genome organisation.Human genetics · 2025Review
- Polymer-derived distance penalties improve chromatin interaction predictions from single-cell data across crop genomes.bioRxiv : the preprint server for biology · 2025Article
- Chrombus-XMBD: a graph convolution model predicting 3D-genome from chromatin features.Briefings in bioinformatics · 2025Article
- Review
- Machine and Deep Learning Methods for Predicting 3D Genome Organization.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Integrative identification of non-coding regulatory regions driving metastatic prostate cancer.Cell reports · 2024Article
- GenomicLinks: deep learning predictions of 3D chromatin interactions in the maize genome.NAR genomics and bioinformatics · 2024Article
- Article
- CD-Loop: a chromatin loop detection method based on the diffusion model.Frontiers in genetics · 2024Article
- DeepCBS: shedding light on the impact of mutations occurring at CTCF binding sites.Frontiers in genetics · 2024Article
- Multimodal learning of noncoding variant effects using genome sequence and chromatin structure.Bioinformatics (Oxford, England) · 2023Article
- Techniques for and challenges in reconstructing 3D genome structures from 2D chromosome conformation capture data.Current opinion in cell biology · 2023Review
- DeepSATA: A Deep Learning-Based Sequence Analyzer Incorporating the Transcription Factor Binding Affinity to Dissect the Effects of Non-Coding Genetic Variants.International journal of molecular sciences · 2023Article
- Analysis of super-enhancer using machine learning and its application to medical biology.Briefings in bioinformatics · 2023Review
- DeepPHiC: predicting promoter-centered chromatin interactions using a novel deep learning approach.Bioinformatics (Oxford, England) · 2023Article
- layerUMAP: A tool for visualizing and understanding deep learning models in biological sequence classification using UMAP.iScience · 2022Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Non-coding variants have been shown to be related to disease by alteration of 3D genome structures. We propose a deep learning method, DeepMILO, to predict the effects of variants on CTCF/cohesin-mediated insulator loops. Application of DeepMILO on variants from whole-genome sequences of 1834 patients of twelve cancer types revealed 672 insulator loops disrupted in at least 10% of patients. Our results show mutations at loop anchors are associated with upregulation of the cancer driver genes BCL2 and MYC in malignant lymphoma thus pointing to a possible new mechanism for their dysregulation via alteration of insulator loops.
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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.