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QuASAR: Quality Assessment of Spatial Arrangement Reproducibility in Hi-C Data
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1016/j.cell.2012.01.010openalex-snapshot
Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome
inferredcites →https://doi.org/10.1016/j.cell.2014.11.021openalex-snapshot
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
inferredcites →https://doi.org/10.1016/j.cell.2017.05.004openalex-snapshot
Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization
inferredcites →https://doi.org/10.1016/j.molcel.2012.08.031openalex-snapshot
Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains
inferredcites →https://doi.org/10.1016/j.molcel.2015.02.023openalex-snapshot
Widespread Rearrangement of 3D Chromatin Organization Underlies Polycomb-Mediated Stress-Induced Silencing
inferredcites →https://doi.org/10.1016/j.molcel.2017.08.006openalex-snapshot
Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development
inferredcites →https://doi.org/10.1038/nature11082openalex-snapshot
Topological domains in mammalian genomes identified by analysis of chromatin interactions
inferredcites →https://doi.org/10.1038/nature14450openalex-snapshot
Condensin-driven remodelling of X chromosome topology during dosage compensation
inferredcites →https://doi.org/10.1038/nature21429openalex-snapshot
3D structures of individual mammalian genomes studied by single-cell Hi-C
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btq640openalex-snapshot
The uniqueome: a mappability resource for short-tag sequencing
inferredcites →https://doi.org/10.1093/bioinformatics/btr700openalex-snapshot
htSeqTools: high-throughput sequencing quality control, processing and visualization in R
inferredcites →https://doi.org/10.1093/bioinformatics/btx152openalex-snapshot
HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps
inferredcites →https://doi.org/10.1093/nar/gku178openalex-snapshot
Impact of sequencing depth in ChIP-seq experiments
inferredcites →https://doi.org/10.1101/gad.241422.114openalex-snapshot
Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation
inferredcites →https://doi.org/10.1101/gr.136184.111openalex-snapshot
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
inferredcites →https://doi.org/10.1101/gr.220640.117openalex-snapshot
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient
inferredcites →https://doi.org/10.1109/mcse.2011.37openalex-snapshot
The NumPy Array: A Structure for Efficient Numerical Computation
inferredcites →https://doi.org/10.1126/science.1181369openalex-snapshot
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
inferredcites →https://doi.org/10.1186/gb-2012-13-10-r98openalex-snapshot
CHANCE: comprehensive software for quality control and validation of ChIP-seq data
inferredcites →https://doi.org/10.1186/s12859-016-1274-4openalex-snapshot
ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline
inferredcites →https://doi.org/10.1186/s13059-015-0642-0openalex-snapshot
Comparison of the three-dimensional organization of sperm and fibroblast genomes using the Hi-C approach
inferredcites →https://doi.org/10.1186/s13059-015-0753-7openalex-snapshot
Comparison of Hi-C results using in-solution versus in-nucleus ligation
inferredcites →https://doi.org/10.1186/s13059-015-0806-yopenalex-snapshot
HiFive: a tool suite for easy and efficient HiC and 5C data analysis
inferredcites →https://doi.org/10.1534/g3.113.008680openalex-snapshot
Large-Scale Quality Analysis of Published ChIP-seq Data
inferredcites →https://doi.org/10.18632/oncotarget.14291openalex-snapshot
Heterogeneity in sarcoma cell lines reveals enhanced motility of tetraploid versus diploid cells
inferredcites →https://doi.org/10.21873/anticanres.11572openalex-snapshot
Heterogeneous Cell Types in Single-cell-derived Clones of MCF7 and MDA-MB-231 Cells
inferredcites →https://doi.org/10.3389/fgene.2014.00075openalex-snapshot
Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1007/978-1-0716-1390-0_2openalex-snapshot
Methods to Assess the Reproducibility and Similarity of Hi-C Data
inferred← citeshttps://doi.org/10.1007/s12551-018-0489-1openalex-snapshot
Hi-C analysis: from data generation to integration
inferred← citeshttps://doi.org/10.1016/j.copbio.2018.01.023openalex-snapshot
Computational methods for analyzing genome-wide chromosome conformation capture data
inferred← citeshttps://doi.org/10.1016/j.cub.2025.01.044openalex-snapshot
A common molecular mechanism underlying Cornelia de Lange and CHOPS syndromes
inferred← citeshttps://doi.org/10.1016/j.molcel.2020.03.002openalex-snapshot
Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding
inferred← citeshttps://doi.org/10.1021/acs.jpcb.5c08112openalex-snapshot
Spectral Graph Entropy of Chromatin: A von Neumann Framework for Multiscale Polymer Organization from Hi-C
inferred← citeshttps://doi.org/10.1038/s41467-022-31112-xopenalex-snapshot
The 3D architecture of the pepper genome and its relationship to function and evolution
inferred← citeshttps://doi.org/10.1038/s41467-023-41316-4openalex-snapshot
Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors
inferred← citeshttps://doi.org/10.1038/s41588-020-00712-yopenalex-snapshot
CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction
inferred← citeshttps://doi.org/10.1038/s41594-025-01512-wopenalex-snapshot
Reconstruction of diploid higher-order human 3D genome interactions from noisy Pore-C data using Dip3D
inferred← citeshttps://doi.org/10.1038/s41598-021-88115-9openalex-snapshot
VEHiCLE: a Variationally Encoded Hi-C Loss Enhancement algorithm for improving and generating Hi-C data
inferred← citeshttps://doi.org/10.1038/s41598-025-91355-8openalex-snapshot
Novel AI-powered computational method using tensor decomposition for identification of common optimal bin sizes when integrating multiple Hi-C datasets
inferred← citeshttps://doi.org/10.1038/s44320-024-00038-5openalex-snapshot
A continuum of zinc finger transcription factor retention on native chromatin underlies dynamic genome organization
inferred← citeshttps://doi.org/10.1073/pnas.1901423116openalex-snapshot
Robust single-cell Hi-C clustering by convolution- and random-walk–based imputation
inferred← citeshttps://doi.org/10.1093/bib/bbab396openalex-snapshot
scHiCStackL: a stacking ensemble learning-based method for single-cell Hi-C classification using cell embedding
inferred← citeshttps://doi.org/10.1093/bib/bbac385openalex-snapshot
A review and performance evaluation of clustering frameworks for single-cell Hi-C data
inferred← citeshttps://doi.org/10.1093/bib/bbad044openalex-snapshot
HiConfidence: a novel approach uncovering the biological signal in Hi-C data affected by technical biases
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaa048openalex-snapshot
GiniQC: a measure for quantifying noise in single-cell Hi-C data
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty285openalex-snapshot
Unsupervised embedding of single-cell Hi-C data
inferred← citeshttps://doi.org/10.1093/nar/gkaa106openalex-snapshot
Exonuclease combinations reduce noises in 3D genomics technologies
inferred← citeshttps://doi.org/10.1093/nargab/lqae076openalex-snapshot
ENT3C: an entropy-based similarity measure for Hi-C and micro-C derived contact matrices
inferred← citeshttps://doi.org/10.1101/188755openalex-snapshot
Measuring the reproducibility and quality of Hi-C data
inferred← citeshttps://doi.org/10.1101/2020.02.24.961714openalex-snapshot
HiCSR: a Hi-C super-resolution framework for producing highly realistic contact maps
inferred← citeshttps://doi.org/10.1101/2020.09.22.303438openalex-snapshot
Genes on Different Strands Mark Boundaries Associated with Co-regulation Domains
inferred← citeshttps://doi.org/10.1101/2021.04.30.442215openalex-snapshot
A novel framework for single-cell Hi-C clustering based on graph-convolution-based imputation and two-phase-based feature extraction
inferred← citeshttps://doi.org/10.1101/2021.07.14.452365openalex-snapshot
Enhancer-promoter interactions and transcription are maintained upon acute loss of CTCF, cohesin, WAPL, and YY1
inferred← citeshttps://doi.org/10.1101/2022.05.24.493188openalex-snapshot
Context-dependent 3D genome regulation by cohesin and related factors
inferred← citeshttps://doi.org/10.1101/2023.08.29.555243openalex-snapshot
High-resolution diploid 3D genome reconstruction using Pore-C data
inferred← citeshttps://doi.org/10.1101/2025.09.24.678266openalex-snapshot
VECTOR: A Framework to Identify and Quantify Structural Changes in Chromatin using Hi-C Data
inferred← citeshttps://doi.org/10.1101/2025.10.08.681271openalex-snapshot
STRIDE: A Sequencing Depth-Insensitive Metric for Robust Comparison between Sparse Chromosome Conformation Capture Data
inferred← citeshttps://doi.org/10.1109/bibm55620.2022.9995134openalex-snapshot
scHiCSC: A Novel Single-Cell Hi-C Clustering Framework by Contact-Weight-Based Smoothing and Feature Fusion
inferred← citeshttps://doi.org/10.1109/csci62032.2023.00094openalex-snapshot
Deep Learning on Hi-C Contact Data Predicts Biological Replicates
inferred← citeshttps://doi.org/10.1186/s12864-024-10764-7openalex-snapshot
Deep neural network models for cell type prediction based on single-cell Hi-C data
inferred← citeshttps://doi.org/10.1186/s13059-019-1658-7openalex-snapshot
Measuring the reproducibility and quality of Hi-C data
inferred← citeshttps://doi.org/10.1186/s13072-019-0308-3openalex-snapshot
Joint inference and alignment of genome structures enables characterization of compartment-independent reorganization across cell types
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1008978openalex-snapshot
scHiCTools: A computational toolbox for analyzing single-cell Hi-C data
inferred← citeshttps://doi.org/10.3390/cimb43020082openalex-snapshot
HPRep: Quantifying Reproducibility in HiChIP and PLAC-Seq Datasets
inferred← citeshttps://doi.org/10.52810/tc.2021.100043openalex-snapshot
Application of Data Dimension Reduction Method in High-dimensional Data based on Single-cell 3D Genomic Contact Data
inferred← citeshttps://doi.org/10.62762/tiot.2024.186430openalex-snapshot
Application of Dimension Reduction Methods to High-Dimensional Single-Cell 3D Genomic Contact Data
inferred← citeshttps://doi.org/10.64898/2026.02.01.703086openalex-snapshot
HiChIA-Rep quantifies the similarity between enrichment-based chromatin interactions datasets
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