ArticleNAR genomics and bioinformatics2023
3D models of fungal chromosomes to enhance visual integration of omics data.
Article in NAR genomics and bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed, 5 citations in OpenAlex.
- Hybrid CNN and multi-head attention model for analyzing epigenetic mechanisms and gene expression across fungal phylogenetic distances.iScience · 2026Article
- Bacteriophage PAK_P3 genome structuration and dynamics during infection ofScience advances · 2026Article
- A constitutive heterochromatic region shapes genome organization and impacts gene expression in Neurospora crassa.BMC genomics · 2024Article
- A Constitutive Heterochromatic Region Shapes Genome Organization and Impacts Gene Expression inbioRxiv : the preprint server for biology · 2024Article
- Understanding the molecular mechanisms of human diseases: the benefits of fission yeasts.Microbial cell (Graz, Austria) · 2024Article
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The functions of eukaryotic chromosomes and their spatial architecture in the nucleus are reciprocally dependent. Hi-C experiments are routinely used to study chromosome 3D organization by probing chromatin interactions. Standard representation of the data has relied on contact maps that show the frequency of interactions between parts of the genome. In parallel, it has become easier to build 3D models of the entire genome based on the same Hi-C data, and thus benefit from the methodology and visualization tools developed for structural biology. 3D modeling of entire genomes leverages the understanding of their spatial organization. However, this opportunity for original and insightful modeling is underexploited. In this paper, we show how seeing the spatial organization of chromosomes can bring new perspectives to omics data integration. We assembled state-of-the-art tools into a workflow that goes from Hi-C raw data to fully annotated 3D models and we re-analysed public omics datasets available for three fungal species. Besides the well-described properties of the spatial organization of their chromosomes (Rabl conformation, hypercoiling and chromosome territories), our results highlighted (i) in
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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.