Modeling chromosomes: beyond pretty pictures
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Summary
This review proposes that current computational models can be grouped into roughly four classes, with two classes of data-driven models: consensus structures and data‐driven ensembles, and twoclasses of de novo models: structural ensemble and mechanistic ensemble.
- Type
- review
- Published
- 2015-09-01
- Cited by
- 96
- References
- 70
- Access
- Open access
- OpenAlex
- https://openalex.org/W1701083935
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:44980109
Keywords
Computational biology, Evolutionary biology, Computer science, Genetics, Biology
References
- Combined collapse by bridging and self-adhesion in a prototypical polymer model inspired by the bacterial nucleoid.
- Condensin- and Replication-Mediated Bacterial Chromosome Folding and Origin Condensation Revealed by Hi-C and Super-resolution Imaging.
- Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions
- A high-throughput imaging-based mapping platform for the systematic identification of gene positioning factors
- A CTCF Code for 3D Genome Architecture
- CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function
- How two meters of DNA fit into a cell nucleus: Polymer models with topological constraints and experimental data
- Reproducibility of 3D chromatin configuration reconstructions.
- Single cell Hi-C reveals cell-to-cell variability in chromosome structure
- A three-dimensional map of the human genome at kilobase resolution reveals principles of chromatin looping
- The role of topological constraints in the kinetics of collapse of macromolecules
- Bayesian Inference of Spatial Organizations of Chromosomes
- A versatile genome-scale PCR-based pipeline for high-definition DNA FISH
- On the stability of fractal globules.
- Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C)
- 3D genome reconstruction from chromosomal contacts
- Looping probabilities in model interphase chromosomes.
- The Three-Dimensional Architecture of a Bacterial Genome
- Effects of topological constraints on globular polymers.
- Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements.
Cited by
- High-resolution 3D models of Caulobacter crescentus chromosome reveal genome structural variability and organization
- Predicting the three-dimensional folding of cis-regulatory regions in mammalian genomes using bioinformatic data and polymer models
- Single-Cell and Single-Molecule Analysis of Gene Expression Regulation
- Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes
- CRISPR Double Cutting through the Labyrinthine Architecture of 3D Genomes.
- The folding landscape of the epigenome
- CTCF and Cohesin in Genome Folding and Transcriptional Gene Regulation.
- Large Scale Chromosome Folding Is Stable against Local Changes in Chromatin Structure
- Formation of Chromosomal Domains by Loop Extrusion
- Genome-wide mapping and analysis of chromosome architecture
- Micro-C XL: assaying chromosome conformation at length scales from the nucleosome to the entire genome
- Identifying Nuclear Matrix–attached DNA across the Genome
- 3D chromatin structure estimation through a constraint-enhanced score function
- Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome
- Chromosome interactome inferred from mitosis-G1 transition
- Capturing pairwise and multi-way chromosomal conformations using chromosomal walks
- Targeted degradation of CTCF decouples local insulation of chromosome domains from higher-order genomic compartmentalization
- The 3D genome organization of Drosophila melanogaster through data integration
- IC-Finder: inferring robustly the hierarchical organization of chromatin folding
- Diffusion of DNA-binding species in the nucleus: A transient anomalous subdiffusion model
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