ArticlePLoS genetics2018
Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling.
Article in PLoS genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 160 papers.
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Who cites it
160 citing papers in PubMed, 285 citations in OpenAlex.
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- Physics-Based Modeling of Sparse Single-Cell Hi-C Uncovers Structural and Epigenetic Variability.International journal of molecular sciences · 2026Article
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- Recurrence plot reconstruction reveals chromosomal reorganization before territory formation.NAR genomics and bioinformatics · 2026Article
- The functional organization of chromosome territories in single nuclei during zygotic genome activation.Scientific reports · 2026Article
- Reconstructing the three-dimensional architecture of extrachromosomal DNA with ec3D.Nature communications · 2025Article
- High-throughput single-virion DNA-PAINT reveals structural diversity, cooperativity, and flexibility during selective packaging in influenza.Nucleic acids research · 2025Article
- Differential regulation of mesoscale chromosome conformations in osteoblasts and osteosarcoma.Genome biology · 2025Article
- An electrostatic repulsion model of centromere organisation.bioRxiv : the preprint server for biology · 2025Article
- Timing is everything: transcription bursting in development.Genes & development · 2025Review
- DNA O-MAP uncovers the molecular neighborhoods associated with specific genomic loci.bioRxiv : the preprint server for biology · 2025Article
- Polymer-derived distance penalties improve chromatin interaction predictions from single-cell data across crop genomes.bioRxiv : the preprint server for biology · 2025Article
- FAIR sharing of Chromatin Tracing datasets using the newly developed 4DN FISH Omics Format.ArXiv · 2025Article
- Nanoscale 3D DNA tracing in non-denatured cells resolves the Cohesin-dependent loop architecture of the genome in situ.Nature communications · 2025Article
- Geometric Diagrams of Genomes: constructing a visual grammar for 3D genomics.Genome biology · 2025Article
- Herpes simplex virus type 1 reshapes host chromatin architecture via transcription machinery hijacking.Nature communications · 2025Article
- Causal network inference of cis- and trans-gene regulation of expression quantitative trait loci across human tissues.Genetics · 2025Article
- FISHnet: detecting chromatin domains in single-cell sequential Oligopaints imaging data.Nature methods · 2025Article
- RobusTAD: reference panel based annotation of nested topologically associating domains.Genome biology · 2025Article
- Closing the multichannel gap through computational reconstruction of interaction in super-resolution microscopy.Patterns (New York, N.Y.) · 2025Review
100 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
29 authors at 8 institutions in 2 countries.
Funding
Abstract
Chromosome organization is crucial for genome function. Here, we present a method for visualizing chromosomal DNA at super-resolution and then integrating Hi-C data to produce three-dimensional models of chromosome organization. Using the super-resolution microscopy methods of OligoSTORM and OligoDNA-PAINT, we trace 8 megabases of human chromosome 19, visualizing structures ranging in size from a few kilobases to over a megabase. Focusing on chromosomal regions that contribute to compartments, we discover distinct structures that, in spite of considerable variability, can predict whether such regions correspond to active (A-type) or inactive (B-type) compartments. Imaging through the depths of entire nuclei, we capture pairs of homologous regions in diploid cells, obtaining evidence that maternal and paternal homologous regions can be differentially organized. Finally, using restraint-based modeling to integrate imaging and Hi-C data, we implement a method-integrative modeling of genomic regions (IMGR)-to increase the genomic resolution of our traces to 10 kb.
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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.