ArticleAdvanced science (Weinheim, Baden-Wurttemberg, Germany)2019
Circular Trajectory Reconstruction Uncovers Cell-Cycle Progression and Regulatory Dynamics from Single-Cell Hi-C Maps.
Article in Advanced science (Weinheim, Baden-Wurttemberg, Germany), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 27 citations in OpenAlex.
- Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie.Genome research · 2026Article
- CellLoop: Identifying single-cell 3D genome chromatin loops.Nature communications · 2026Article
- Recent advances in single-cell bioinformatics for inferring higher-order chromatin contact maps.BMB reports · 2025Review
- Dynamic modelling of cell cycle arrest through integrated single-cell and mathematical modelling approaches.PLoS computational biology · 2025Article
- HiC4D-SPOT: a spatiotemporal outlier detection tool for Hi-C data.Briefings in bioinformatics · 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
- Advancements and future directions in single-cell Hi-C based 3D chromatin modeling.Computational and structural biotechnology journal · 2024Review
- ImputeHiFI: An Imputation Method for Multiplexed DNA FISH Data by Utilizing Single-Cell Hi-C and RNA FISH Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- scHiCyclePred: a deep learning framework for predicting cell cycle phases from single-cell Hi-C data using multi-scale interaction information.Communications biology · 2024Article
- [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
- scHi-CSim: a flexible simulator that generates high-fidelity single-cell Hi-C data for benchmarking.Journal of molecular cell biology · 2023Article
- Deciphering Hierarchical Chromatin Domains and Preference of Genomic Position Forming Boundaries in Single Mouse Embryonic Stem Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- Integrated investigation of DNA methylation, gene expression and immune cell population revealed immune cell infiltration associated with atherosclerotic plaque formation.BMC medical genomics · 2022Article
- Integrative approaches in genome structure analysis.Structure (London, England : 1993) · 2022Review
- TinGa: fast and flexible trajectory inference with Growing Neural Gas.Bioinformatics (Oxford, England) · 2020Article
- Circular Trajectory Reconstruction Uncovers Cell-Cycle Progression and Regulatory Dynamics from Single-Cell Hi-C Maps.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2019Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-cell Hi-C technology is emerging and will provide unprecedented opportunities to elucidate chromosomal dynamics with high resolution. How to characterize pseudo time-series of single cells using single-cell Hi-C maps is an essential and challenging topic. To this end, a powerful circular trajectory reconstruction tool CIRCLET is developed to resolve cell cycle phases of single cells by considering multiscale features of chromosomal architectures without specifying a starting cell. CIRCLET reveals its best superiority based on the combination of one feature set about global information and another two feature sets about local interactional information in terms of designed evaluation indexes and verification strategies from a collection of cell-cycle Hi-C maps of 1171 single cells. Further division of the reconstructed trajectory into 12 stages helps to accurately characterize the dynamics of chromosomal structures and explain the special regulatory events along cell-cycle progression. Last but not the least, the reconstructed trajectory helps to uncover important regulatory genes related with dynamic substructures, providing a novel framework for discovering regulatory regions even cancer markers at single-cell resolution.
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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.