ArticleNature methods2012
Iterative correction of Hi-C data reveals hallmarks of chromosome organization.
Article in Nature methods, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 877 papers, 1 of them a synthesis that pooled it.
What it found
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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.
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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.
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Who cites it
877 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Cross-platform Hi-C meta-analysis identifies functional insulators that actively block enhancer-promoter interactions.Nature communications · 2026Pooled it
- Identification of Genome-Wide Chromatin Structural Aberration in Cancer by Hi-C Analysis.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Controlling for DNA dosage with whole-genome sequencing improves ATAC-seq peak calling.NAR genomics and bioinformatics · 2026Article
- Euchromatin forms condensed domains with short active regions on the surface.Nature genetics · 2026Article
- Nested TAD hierarchy defines cohesion zones on replicated chromosomes.The EMBO journal · 2026Article
- 4D nucleome landscape reveals dissolution of bipartite active X chromosome in liver cancer development.Nature cell biology · 2026Article
- Matrix Rigidity Mechanoprimes Microglia for Inflammation Through Cytoskeletal-to-Nuclear Signaling and 3D Spatio-Epigenomic Remodeling.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Functional Annotation of Alzheimer's Disease-Associated SNPs Based on Three-Dimensional Chromatin Structure.International journal of molecular sciences · 2026Article
- A scaffolding element rewires local 3D chromatin architecture during differentiation.Nature communications · 2026Article
- Overcoming Artificial Structures in Resolution-Enhanced Hi-C Data by Signal Decomposition and Multi-Scale Attention.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Cohesin promotes genomic stability by suppressing unequal sister chromatid exchange.bioRxiv : the preprint server for biology · 2026Article
- De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes.Genome research · 2026Article
- HiCPotts: an R/bioconductor package to identify significant interactions in chromosome conformation capture data and model sources of bias.Bioinformatics (Oxford, England) · 2026Article
- TAL1 is indispensable in ETV2-primed human endothelial cell fate determination.Science advances · 2026Article
- 3D genome organization in tissue regeneration involves long-range chromatin loops.Science advances · 2026Article
- map3C: a computational tool for processing multiomic single-cell Hi-C data.Bioinformatics (Oxford, England) · 2026Article
- Integrating epigenomic features reveals principles of chromatin-state organization.bioRxiv : the preprint server for biology · 2026Article
- Hierarchical Gene Cluster Regulation Across Vertebrate Skins: Developmental Control of Keratin Gene Expression.bioRxiv : the preprint server for biology · 2026Article
- Mapping 3D genome organization at nucleosome-scale with Micro-C and Region Capture Micro-C (RCMC).Nature protocols · 2026Review
- CAD-C: An engineered nuclease enables repair-freebioRxiv : the preprint server for biology · 2026Article
817 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Extracting biologically meaningful information from chromosomal interactions obtained with genome-wide chromosome conformation capture (3C) analyses requires the elimination of systematic biases. We present a computational pipeline that integrates a strategy to map sequencing reads with a data-driven method for iterative correction of biases, yielding genome-wide maps of relative contact probabilities. We validate this ICE (iterative correction and eigenvector decomposition) technique on published data obtained by the high-throughput 3C method Hi-C, and we demonstrate that eigenvector decomposition of the obtained maps provides insights into local chromatin states, global patterns of chromosomal interactions, and the conserved organization of human and mouse chromosomes.
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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.