ReviewAdvanced science (Weinheim, Baden-Wurttemberg, Germany)2025
Single-Cell Hi-C Technologies and Computational Data Analysis.
Review in Advanced science (Weinheim, Baden-Wurttemberg, Germany), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
11 citing papers in PubMed.
- Nuclear mechanotransduction: tools for mechanical perturbation and chromatin characterization.Nucleus (Austin, Tex.) · 2026Review
- ssJSD: A Fusion of Sparsity and Spatial Information for HiC Single-Cell Clustering.bioRxiv : the preprint server for biology · 2026Article
- Chromosomal instability in cancer: sources, consequences and new therapeutic opportunities.Signal transduction and targeted therapy · 2026Review
- Hi-Cformer enables multiscale chromatin contact map modeling for single-cell Hi-C data analysis.Science advances · 2026Article
- Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie.Genome research · 2026Article
- Predicting enhancer-gene links from single-cell multi-omics data by integrating prior Hi-C information.Nucleic acids research · 2026Article
- A unique malignant cell type per patient tumor encoded in each cancer cell transcriptome.iScience · 2026Article
- PB-DiffHiC: a statistical framework for detecting differential chromatin interactions from high resolution pseudo-bulk Hi-C data.BMC genomics · 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
- Article
- Single-Cell Hi-C Technologies and Computational Data Analysis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Single-cell chromatin conformation capture (scHi-C) techniques have evolved to provide significant insights into the structural organization and regulatory mechanisms in individual cells. Although many scHi-C protocols have been developed, they often involve intricate procedures and the resulting data are sparse, leading to computational challenges for systematic data analysis and limited applicability. This review provides a comprehensive overview, quantitative evaluation of thirteen protocols and practical guidance on computational topics. It is first assessed the efficiency of these protocols based on the total number of contacts recovered per cell and the cis/trans ratio. It is then provided systematic considerations for scHi-C quality control and data imputation. Additionally, the capabilities and implementations of various analysis methods, covering cell clustering, A/B compartment calling, topologically associating domain (TAD) calling, loop calling, 3D reconstruction, scHi-C data simulation and differential interaction analysis is summarized. It is further highlighted key computational challenges associated with the specific complexities of scHi-C data and propose potential solutions.
Indexed as
Identifiers
What OpenQuestion holds
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.