Comparison of computational methods for Hi-C data analysis
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Summary
Differences in the performance of methods for chromatin interaction identification are revealed, but more comparable results for TAD detection between algorithms are revealed.
- Type
- article
- Published
- 2017-06-12
- Cited by
- 294
- References
- 43
- Access
- Open access
- OpenAlex
- https://openalex.org/W2625231465
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:3057985
Keywords
Chromatin, Genome, Chromosome conformation capture, Domain (mathematical analysis), Computational biology
References
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- Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
- Modeling chromosomes: beyond pretty pictures
- HiFive: a tool suite for easy and efficient HiC and 5C data analysis
- diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data
- A three-dimensional map of the human genome at kilobase resolution reveals principles of chromatin looping
- Comparative analysis of metazoan chromatin organization
- Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture
- Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
- Functional implications of genome topology
- Three-dimensional folding and functional organization principles of the Drosophila genome.
- Genomics: The ENCODE project
- A high-resolution map of three-dimensional chromatin interactome in human cells
- Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions
- Three-dimensional genome architecture: players and mechanisms
- Capturing Chromosome Conformation
- Integrative analysis of 111 reference human epigenomes
- Chromatin Architecture Reorganization during Stem Cell Differentiation
- Comprehensive mapping of long range interactions reveals folding principles of the human genome
- Iterative Correction of Hi-C Data Reveals Hallmarks of Chromosome Organization
Cited by
- HiPiler: Visual Exploration of Large Genome Interaction Matrices with Interactive Small Multiples
- Between form and function: the complexity of genome folding
- Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution
- SHAMAN: bin-free randomization, normalization and screening of Hi-C matrices
- Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element
- Three-dimensional genome architecture and emerging technologies: looping in disease
- Binless normalization of Hi-C data provides significant interaction and difference detection independently of resolution
- Étude des « Topologically Associated Domains (TADs) » dans les anomalies du développement
- Detecting hierarchical genome folding with network modularity
- Contribution of structural variation to genome structure: TAD fusion discovery and ranking
- 3C and 3C-based techniques: the powerful tools for spatial genome organization deciphering
- FIND: difFerential chromatin INteractions Detection using a spatial Poisson process
- 4D Nucleome of Cancer
- Emerging Evidence of Chromosome Folding by Loop Extrusion
- Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries
- SequencEnG: an Interactive Knowledge Base of Sequencing Techniques
- Topologically Associating Domains in Chromosome Architecture and Gene Regulatory Landscapes during Development, Disease, and Evolution.
- Gene regulation in the 3D genome.
- ChromStruct 4: A Python Code to Estimate the Chromatin Structure from Hi-C Data
- Computational methods for analyzing genome-wide chromosome conformation capture data.
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