ReviewCurrent opinion in structural biology2023
Genome modeling: From chromatin fibers to genes.
Review in Current opinion in structural biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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
29 citing papers in PubMed, 40 citations in OpenAlex.
- Euchromatin forms condensed domains with short active regions on the surface.Nature genetics · 2026Article
- Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie.Genome research · 2026Article
- Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- Linker histones consolidate heterogenous nucleosome fiber contacts by linking together multiple nucleosomes.Nature communications · 2026Article
- Contributions of Local Structural and Energetic Features of DNA to Large-scale Genomic Organization.Journal of molecular biology · 2026Review
- Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks.Bioinformatics (Oxford, England) · 2026Article
- Multiscale chromatin modeling of chromosome X structural changes upon inactivation highlights the differential regulatory mechanism ofbioRxiv : the preprint server for biology · 2026Article
- Physical models reveal indirect reader protein interactions that facilitate epigenetic crosstalk.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Gene-scale in vitro reconstitution reveals histone acetylation directly controls chromatin architecture.Science advances · 2025Article
- Nucleosome Linker Length and Distribution as Major Players in Epigenetic Regulation: Insights from Cryo-Electron Microscopy and Modeling of Retina Cell Maturation.DNA and cell biology · 2025Review
- Deciphering the molecular mechanisms of BPTF interactions with nucleosomes via molecular simulations.Biophysical journal · 2025Article
- Loop Catalog: a comprehensive HiChIP database of human and mouse samples.Genome biology · 2025Article
- Deciphering the Molecular Mechanisms of BPTF Interactions with Nucleosomes via Molecular Simulations.bioRxiv : the preprint server for biology · 2025Article
- Toward decoding the mechanisms that shape sub-megabase-scale genome organization.Current opinion in structural biology · 2025Review
- 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
- Polymer model integrates imaging and sequencing to reveal how nanoscale heterochromatin domains influence gene expression.Nature communications · 2025Article
- Incorporating multiscale methylation effects into nucleosome-resolution chromatin models for simulating mesoscale fibers.The Journal of chemical physics · 2025Article
- Multifunctional histone variants in genome function.Nature reviews. Genetics · 2025Review
- Phase Space Invaders' podcast episode with Tamar Schlick: a trajectory from mathematics to biology.Biophysical reviews · 2025Article
- Integrative Modeling of 3D Genome Organization by Bayesian Molecular Dynamics Simulations with Hi-C Metainference.Methods in molecular biology (Clifton, N.J.) · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
The intricacies of the 3D hierarchical organization of the genome have been approached by many creative modeling studies. The specific model/simulation technique combination defines and restricts the system and phenomena that can be investigated. We present the latest modeling developments and studies of the genome, involving models ranging from nucleosome systems and small polynucleosome arrays to chromatin fibers in the kb-range, chromosomes, and whole genomes, while emphasizing gene folding from first principles. Clever combinations allow the exploration of many interesting phenomena involved in gene regulation, such as nucleosome structure and dynamics, nucleosome-nucleosome stacking, polynucleosome array folding, protein regulation of chromatin architecture, mechanisms of gene folding, loop formation, compartmentalization, and structural transitions at the chromosome and genome levels. Gene-level modeling with full details on nucleosome positions, epigenetic factors, and protein binding, in particular, can in principle be scaled up to model chromosomes and cells to study fundamental biological regulation.
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.