ArticleGenome biology2022
MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy.Genome research · 2025Article
- The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon.PLoS computational biology · 2025Article
- StripePy: fast and robust characterization of architectural stripes.Bioinformatics (Oxford, England) · 2025Article
- Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes.Communications biology · 2025Article
- Advancements and future directions in single-cell Hi-C based 3D chromatin modeling.Computational and structural biotechnology journal · 2024Review
- Multiscale molecular modeling of chromatin with MultiMM: From nucleosomes to the whole genome.Computational and structural biotechnology journal · 2024Article
- Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy.bioRxiv : the preprint server for biology · 2024Article
- Congenital microcoria deletion in mouse links Sox21 dysregulation to disease and suggests a role for TGFB2 in glaucoma and myopia.American journal of human genetics · 2024Article
- Computational methods for analysing multiscale 3D genome organization.Nature reviews. Genetics · 2024Review
- Gene regulatory network inference in the era of single-cell multi-omics.Nature reviews. Genetics · 2023Review
- MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions.Genome biology · 2022Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, a computational tool for fast, stochastic modeling of molecular contacts from DNA loop extrusion capable of simulating realistic contact patterns genome wide in a few minutes. MoDLE accurately simulates contact maps in concordance with existing molecular dynamics approaches and with Micro-C data and does so orders of magnitude faster than existing approaches. MoDLE runs efficiently on machines ranging from laptops to high performance computing clusters and opens up for exploratory and predictive modeling of 3D genome structure in a wide range of settings.
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Registered trials
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