ArticleScientific reports2019
Hierarchical Reconstruction of High-Resolution 3D Models of Large Chromosomes.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
- A new efficient immunoprotocol to detect chromosomal/nuclear proteins along with repetitive DNA in squash preparations of formalin-fixed, long-stored root tips.Plant methods · 2025Article
- Tensor-FLAMINGO unravels the complexity of single-cell spatial architectures of genomes at high-resolution.Nature communications · 2025Article
- Chronic lymphocytic leukemia (CLL) screening and abnormality detection based on multi-layer fluorescence imaging signal enhancement and compensation.Journal of cancer research and clinical oncology · 2025Article
- geomeTriD: a Bioconductor package for interactive and integrative visualization of 3D structural model with multi-omics data.Bioinformatics advances · 2025Article
- Advancements and future directions in single-cell Hi-C based 3D chromatin modeling.Computational and structural biotechnology journal · 2024Review
- Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics.Nucleic acids research · 2024Article
- Techniques for and challenges in reconstructing 3D genome structures from 2D chromosome conformation capture data.Current opinion in cell biology · 2023Review
- HiC-GNN: A generalizable model for 3D chromosome reconstruction using graph convolutional neural networks.Computational and structural biotechnology journal · 2023Article
- Complementing Hi-C information for 3D chromatin reconstruction by ChromStruct.Frontiers in bioinformatics · 2023Article
- Reconstruct high-resolution 3D genome structures for diverse cell-types using FLAMINGO.Nature communications · 2022Article
- Principal curve approaches for inferring 3D chromatin architecture.Biostatistics (Oxford, England) · 2022Article
- Minimalistic 3D chromatin models: Sparse interactions in single cells drive the chromatin fold and form many-body units.Current opinion in structural biology · 2021Review
- Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data.PLoS computational biology · 2021Article
- Understanding 3D genome organization by multidisciplinary methods.Nature reviews. Molecular cell biology · 2021Review
- Article
- Application of Hi-C and other omics data analysis in human cancer and cell differentiation research.Computational and structural biotechnology journal · 2021Review
- Evidence of constraint in the 3D genome for trans-splicing in human cells.Science China. Life sciences · 2020Article
- An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data.Biological procedures online · 2019Review
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3 authors.
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Abstract
Eukaryotic chromosomes are often composed of components organized into multiple scales, such as nucleosomes, chromatin fibers, topologically associated domains (TAD), chromosome compartments, and chromosome territories. Therefore, reconstructing detailed 3D models of chromosomes in high resolution is useful for advancing genome research. However, the task of constructing quality high-resolution 3D models is still challenging with existing methods. Hence, we designed a hierarchical algorithm, called Hierarchical3DGenome, to reconstruct 3D chromosome models at high resolution (<=5 Kilobase (KB)). The algorithm first reconstructs high-resolution 3D models at TAD level. The TAD models are then assembled to form complete high-resolution chromosomal models. The assembly of TAD models is guided by a complete low-resolution chromosome model. The algorithm is successfully used to reconstruct 3D chromosome models at 5 KB resolution for the human B-cell (GM12878). These high-resolution models satisfy Hi-C chromosomal contacts well and are consistent with models built at lower (i.e. 1 MB) resolution, and with the data of fluorescent in situ hybridization experiments. The Java source code of Hierarchical3DGenome and its user manual are available here https://github.com/BDM-Lab/Hierarchical3DGenome .
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