ArticleInternational journal of molecular sciences2021
Inferring Single-Cell 3D Chromosomal Structures Based on the Lennard-Jones Potential.
Article in International journal of molecular sciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie.Genome research · 2026Article
- Navigating the 3D genome at single-cell resolution: techniques, computation, and mechanistic landscapes.Briefings in bioinformatics · 2025Review
- The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon.PLoS computational biology · 2025Article
- Unicorn: enhancing single-cell Hi-C data with blind super-resolution for 3D genome structure reconstruction.Bioinformatics (Oxford, England) · 2025Article
- ChromMovie: A Molecular Dynamics Approach for Simultaneous Modeling of Chromatin Conformation Changes from Multiple Single-Cell Hi-C Maps.bioRxiv : the preprint server for biology · 2025Article
- Reconstructing 3D chromosome structures from single-cell Hi-C data with SO(3)-equivariant graph neural networks.NAR genomics and bioinformatics · 2025Article
- Advancements and future directions in single-cell Hi-C based 3D chromatin modeling.Computational and structural biotechnology journal · 2024Review
- Article
- [Advances in methods and applications of single-cell Hi-C data analysis].Sheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi · 2023Article
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Authors and funding
4 authors.
Funding
Abstract
Reconstructing three-dimensional (3D) chromosomal structures based on single-cell Hi-C data is a challenging scientific problem due to the extreme sparseness of the single-cell Hi-C data. In this research, we used the Lennard-Jones potential to reconstruct both 500 kb and high-resolution 50 kb chromosomal structures based on single-cell Hi-C data. A chromosome was represented by a string of 500 kb or 50 kb DNA beads and put into a 3D cubic lattice for simulations. A 2D Gaussian function was used to impute the sparse single-cell Hi-C contact matrices. We designed a novel loss function based on the Lennard-Jones potential, in which the ε value, i.e., the well depth, was used to indicate how stable the binding of every pair of beads is. For the bead pairs that have single-cell Hi-C contacts and their neighboring bead pairs, the loss function assigns them stronger binding stability. The Metropolis-Hastings algorithm was used to try different locations for the DNA beads, and simulated annealing was used to optimize the loss function. We proved the correctness and validness of the reconstructed 3D structures by evaluating the models according to multiple criteria and comparing the models with 3D-FISH data.
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