ArticleNAR genomics and bioinformatics2020
PHi-C: deciphering Hi-C data into polymer dynamics.
Article in NAR genomics and bioinformatics, 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.
- Integrative modeling of the genome structure and dynamics in fission yeast.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon.PLoS computational biology · 2025Article
- Integrative Modeling of 3D Genome Organization by Bayesian Molecular Dynamics Simulations with Hi-C Metainference.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Transcription-coupled changes in genomic region proximities during transcriptional bursting.Science advances · 2024Article
- 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
- Hi-C-guided many-polymer model to decipher 3D genome organization.Biophysical journal · 2024Article
- Multiscale Bayesian simulations reveal functional chromatin condensation of gene loci.PNAS nexus · 2024Article
- Large-scale data-driven and physics-based models offer insights into the relationships among the structures, dynamics, and functions of chromosomes.Journal of molecular cell biology · 2023Review
- Quantifying the large-scale chromosome structural dynamics during the mitosis-to-G1 phase transition of cell cycle.Open biology · 2023Article
- Competition between transcription and loop extrusion modulates promoter and enhancer dynamics.Research square · 2023Article
- Strong interactions between highly dynamic lamina-associated domains and the nuclear envelope stabilize the 3D architecture of Drosophila interphase chromatin.Epigenetics & chromatin · 2023Article
- Competition between transcription and loop extrusion modulates promoter and enhancer dynamics.bioRxiv : the preprint server for biology · 2023Article
- A maximum-entropy model to predict 3D structural ensembles of chromatin from pairwise distances with applications to interphase chromosomes and structural variants.Nature communications · 2023Article
- Multidimensional scaling methods can reconstruct genomic DNA loops using Hi-C data properties.PloS one · 2023Article
- Insights into the cell fate decision-making processes from chromosome structural reorganizations.Biophysics reviews · 2022Article
- PHi-C2: interpreting Hi-C data as the dynamic 3D genome state.Bioinformatics (Oxford, England) · 2022Article
- Dissecting the cosegregation probability from genome architecture mapping.Biophysical journal · 2022Article
- Heterogeneous interactions and polymer entropy decide organization and dynamics of chromatin domains.Biophysical journal · 2022Article
- Single-nucleosome imaging reveals steady-state motion of interphase chromatin in living human cells.Science advances · 2022Article
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genomes are spatiotemporally organized within the cell nucleus. Genome-wide chromosome conformation capture (Hi-C) technologies have uncovered the 3D genome organization. Furthermore, live-cell imaging experiments have revealed that genomes are functional in 4D. Although computational modeling methods can convert 2D Hi-C data into population-averaged static 3D genome models, exploring 4D genome nature based on 2D Hi-C data remains lacking. Here, we describe a 4D simulation method, PHi-C (polymer dynamics deciphered from Hi-C data), that depicts 4D genome features from 2D Hi-C data by polymer modeling. PHi-C allows users to interpret 2D Hi-C data as physical interaction parameters within single chromosomes. The physical interaction parameters can then be used in the simulations and analyses to demonstrate dynamic characteristics of genomic loci and chromosomes as observed in live-cell imaging experiments. PHi-C is available at https://github.com/soyashinkai/PHi-C.
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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.