ReviewFEBS letters2015
Modeling chromosomes: Beyond pretty pictures.
Review in FEBS letters, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 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
54 citing papers in PubMed.
- RepliSage: a stochastic graph-based framework for 3D chromatin modeling across the cell cycle.Nucleic acids research · 2026Article
- Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks.Bioinformatics (Oxford, England) · 2026Article
- Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation.Nature cell biology · 2026Article
- Design Space and Declarative Grammar for 3D Genomic Data Visualization.IEEE transactions on visualization and computer graphics · 2026Article
- Uchimata: a toolkit for visualization of 3D genome structures on the web and in computational notebooks.ArXiv · 2025Article
- The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon.PLoS computational biology · 2025Article
- Article
- Recipes and ingredients for deep learning models of 3D genome folding.Current opinion in genetics & development · 2025Review
- The Role of Lamins in Genome Organisation: A Modelling Perspective.Sub-cellular biochemistry · 2025Review
- Integrative Modeling of 3D Genome Organization by Bayesian Molecular Dynamics Simulations with Hi-C Metainference.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Advancements and future directions in single-cell Hi-C based 3D chromatin modeling.Computational and structural biotechnology journal · 2024Review
- Multiscale Bayesian simulations reveal functional chromatin condensation of gene loci.PNAS nexus · 2024Article
- Differential roles of positive and negative supercoiling in organizing the E. coli genome.Nucleic acids research · 2024Article
- Interplay between epigenome and 3D chromatin structure.BMB reports · 2023Review
- DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling.Frontiers in microbiology · 2023Review
- Article
- Mapping nucleosome and chromatin architectures: A survey of computational methods.Computational and structural biotechnology journal · 2022Review
- Chromosome Folding Promotes Intrachromosomal Aberrations under Radiation- and Nuclease-Induced DNA Breakage.International journal of molecular sciences · 2021Article
- Single-cell Hi-C data analysis: safety in numbers.Briefings in bioinformatics · 2021Article
- Learning the distribution of single-cell chromosome conformations in bacteria reveals emergent order across genomic scales.Nature communications · 2021Article
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.
Funding
Abstract
Recently, Chromosome Conformation Capture (3C) based experiments have highlighted the importance of computational models for the study of chromosome organization. In this review, we propose 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 two classes of de novo models: structural ensembles and mechanistic ensembles. Finally, we highlight specific questions mechanistic ensembles can address.
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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.