ArticleNucleic acids research2013
The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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32 citing papers in PubMed.
- The challenge of chromatin model comparison and validation: A project from the first international 4D Nucleome Hackathon.PLoS computational biology · 2025Article
- geomeTriD: a Bioconductor package for interactive and integrative visualization of 3D structural model with multi-omics data.Bioinformatics advances · 2025Article
- ParticleChromo3D+: A Web Server for ParticleChromo3D Algorithm for 3D Chromosome Structure Reconstruction.Current issues in molecular biology · 2023Article
- ParticleChromo3D: a Particle Swarm Optimization algorithm for chromosome 3D structure prediction from Hi-C data.BioData mining · 2022Article
- Reconstruct high-resolution 3D genome structures for diverse cell-types using FLAMINGO.Nature communications · 2022Article
- Inferring Single-Cell 3D Chromosomal Structures Based on the Lennard-Jones Potential.International journal of molecular sciences · 2021Article
- A model of active transcription hubs that unifies the roles of active promoters and enhancers.Nucleic acids research · 2021Article
- Application of Hi-C and other omics data analysis in human cancer and cell differentiation research.Computational and structural biotechnology journal · 2021Review
- Revisiting the organization of Polycomb-repressed domains: 3D chromatin models from Hi-C compared with super-resolution imaging.Nucleic acids research · 2020Article
- Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data.Methods (San Diego, Calif.) · 2020Review
- Network-based method for regions with statistically frequent interchromosomal interactions at single-cell resolution.BMC bioinformatics · 2020Article
- Computational methods for predicting 3D genomic organization from high-resolution chromosome conformation capture data.Briefings in functional genomics · 2020Article
- Chromatin 3D structure reconstruction with consideration of adjacency relationship among genomic loci.BMC bioinformatics · 2020Article
- The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance.Genome biology · 2019Article
- Heterogeneous Loop Model to Infer 3D Chromosome Structures from Hi-C.Biophysical journal · 2019Article
- Models of polymer physics for the architecture of the cell nucleus.Wiley interdisciplinary reviews. Systems biology and medicine · 2019Review
- An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data.Biological procedures online · 2019Review
- Producing genome structure populations with the dynamic and automated PGS software.Nature protocols · 2018Article
- Dissecting super-enhancer hierarchy based on chromatin interactions.Nature communications · 2018Article
- Developmentally regulated higher-order chromatin interactions orchestrate B cell fate commitment.Nucleic acids research · 2017Article
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7 authors.
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Abstract
The 3D chromatin structure modeling by chromatin interactions derived from Hi-C experiments is significantly challenged by the intrinsic sequencing biases in these experiments. Conventional modeling methods only focus on the bias among different chromatin regions within the same experiment but neglect the bias arising from different experimental sequencing depth. We now show that the regional interaction bias is tightly coupled with the sequencing depth, and we further identify a chromatin structure parameter as the inherent characteristics of Hi-C derived data for chromatin regions. Then we present an approach for chromatin structure prediction capable of relaxing both kinds of sequencing biases by using this identified parameter. This method is validated by intra and inter cell-line comparisons among various chromatin regions for four human cell-lines (K562, GM12878, IMR90 and H1hESC), which shows that the openness of chromatin region is well correlated with chromatin function. This method has been executed by an automatic pipeline (AutoChrom3D) and thus can be conveniently used.
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