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Measuring the reproducibility and quality of Hi-C data

https://doi.org/10.1101/188755
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/jcb.22116openalex-snapshot
ChIP‐based methods for the identification of long‐range chromatin interactions
inferredcites →https://doi.org/10.1016/j.cell.2007.05.009openalex-snapshot
High-Resolution Profiling of Histone Methylations in the Human Genome
inferredcites →https://doi.org/10.1016/j.cell.2007.12.014openalex-snapshot
High-Resolution Mapping and Characterization of Open Chromatin across the Genome
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.molcel.2015.08.024openalex-snapshot
High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila
inferredcites →https://doi.org/10.1016/j.stem.2014.05.017openalex-snapshot
The 3D Genome in Transcriptional Regulation and Pluripotency
inferredcites →https://doi.org/10.1016/j.stem.2016.01.007openalex-snapshot
Cell-of-Origin-Specific 3D Genome Structure Acquired during Somatic Cell Reprogramming
inferredcites →https://doi.org/10.1016/j.ymeth.2014.10.031openalex-snapshot
The Hitchhiker’s guide to Hi-C analysis: Practical guidelines
inferredcites →https://doi.org/10.1038/nature11049openalex-snapshot
Spatial partitioning of the regulatory landscape of the X-inactivation centre
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/nature12593openalex-snapshot
Single-cell Hi-C reveals cell-to-cell variability in chromosome structure
inferredcites →https://doi.org/10.1038/nature12644openalex-snapshot
A high-resolution map of the three-dimensional chromatin interactome in human cells
inferredcites →https://doi.org/10.1038/nature14222openalex-snapshot
Chromatin architecture reorganization during stem cell differentiation
inferredcites →https://doi.org/10.1038/nature14450openalex-snapshot
Condensin-driven remodelling of X chromosome topology during dosage compensation
inferredcites →https://doi.org/10.1038/nature18589openalex-snapshot
Structural organization of the inactive X chromosome in the mouse
inferredcites →https://doi.org/10.1038/nature23001openalex-snapshot
Cell-cycle dynamics of chromosomal organization at single-cell resolution
inferredcites →https://doi.org/10.1038/nbt.1505openalex-snapshot
An integrated software system for analyzing ChIP-chip and ChIP-seq data
inferredcites →https://doi.org/10.1038/ncomms15454openalex-snapshot
An integrated model for detecting significant chromatin interactions from high-resolution Hi-C data
inferredcites →https://doi.org/10.1038/ng.2871openalex-snapshot
Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment
inferredcites →https://doi.org/10.1038/nmeth.2148openalex-snapshot
Iterative correction of Hi-C data reveals hallmarks of chromosome organization
inferredcites →https://doi.org/10.1038/nmeth.3205openalex-snapshot
Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes
inferredcites →https://doi.org/10.1038/nmeth.4155openalex-snapshot
Massively multiplex single-cell Hi-C
inferredcites →https://doi.org/10.1038/nn.3995openalex-snapshot
Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum
inferredcites →https://doi.org/10.1038/nprot.2011.420openalex-snapshot
A computational pipeline for comparative ChIP-seq analyses
inferredcites →https://doi.org/10.1038/nrm.2016.104openalex-snapshot
Genome-wide mapping and analysis of chromosome architecture
inferredcites →https://doi.org/10.1073/pnas.1518552112openalex-snapshot
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
inferredcites →https://doi.org/10.1073/pnas.1609643113openalex-snapshot
Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture
inferredcites →https://doi.org/10.1093/bioinformatics/bts570openalex-snapshot
HiCNorm: removing biases in Hi-C data via Poisson regression
inferredcites →https://doi.org/10.1093/bioinformatics/btv336openalex-snapshot
Mango: a bias-correcting ChIA-PET analysis pipeline
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/bioinformatics/bty164openalex-snapshot
GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs
inferredcites →https://doi.org/10.1093/imanum/drs019openalex-snapshot
A fast algorithm for matrix balancing
inferredcites →https://doi.org/10.1101/204438openalex-snapshot
QuASAR: Quality Assessment of Spatial Arrangement Reproducibility in Hi-C Data
inferredcites →https://doi.org/10.1101/gr.129437.111openalex-snapshot
Physical tethering and volume exclusion determine higher-order genome organization in budding yeast
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.160374.113openalex-snapshot
Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts
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/10.1126/science.1181369openalex-snapshot
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
inferredcites →https://doi.org/10.1126/science.1236083openalex-snapshot
Organization of the Mitotic Chromosome
inferredcites →https://doi.org/10.1186/1471-2164-12-134openalex-snapshot
ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis
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/s13059-014-0572-2openalex-snapshot
De novo assembly of bacterial transcriptomes from RNA-seq data
inferredcites →https://doi.org/10.1186/s13059-015-0728-8openalex-snapshot
Bipartite structure of the inactive mouse X chromosome
inferredcites →https://doi.org/10.1186/s13059-015-0745-7openalex-snapshot
Analysis methods for studying the 3D architecture of the genome
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/s13059-016-0940-1openalex-snapshot
A benchmark for RNA-seq quantification pipelines
inferredcites →https://doi.org/10.1186/s13059-016-0986-0openalex-snapshot
Erratum to: A benchmark for RNA-seq quantification pipelines
inferredcites →https://doi.org/10.1186/s13059-016-0992-2openalex-snapshot
CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data
inferredcites →https://doi.org/10.1214/11-aoas466openalex-snapshot
Measuring reproducibility of high-throughput experiments
inferredcites →https://doi.org/10.1371/journal.pcbi.1005665openalex-snapshot
Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors
inferredcites →https://doi.org/10.3791/1869openalex-snapshot
Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/s12551-018-0489-1openalex-snapshot
Hi-C analysis: from data generation to integration
inferred← citeshttps://doi.org/10.1038/s41421-022-00416-zopenalex-snapshot
Dynamic 3D genome reorganization during development and metabolic stress of the porcine liver
inferred← citeshttps://doi.org/10.1038/s41467-021-27800-9openalex-snapshot
Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis
inferred← citeshttps://doi.org/10.1038/s41467-024-53758-5openalex-snapshot
Decoding the epigenetics and chromatin loop dynamics of androgen receptor-mediated transcription
inferred← citeshttps://doi.org/10.1038/s41588-019-0538-0openalex-snapshot
Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations
inferred← citeshttps://doi.org/10.1038/s41588-022-01223-8openalex-snapshot
Enhancer–promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1
inferred← citeshttps://doi.org/10.1038/s41588-025-02220-3openalex-snapshot
Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance
inferred← citeshttps://doi.org/10.1038/s41592-025-02630-5openalex-snapshot
Comparing chromatin contact maps at scale: methods and insights
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/10.1093/bioinformatics/bty164openalex-snapshot
GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty285openalex-snapshot
Unsupervised embedding of single-cell Hi-C data
inferred← citeshttps://doi.org/10.1096/fj.202402869ropenalex-snapshot
Uncovering Changes in 3D ‐Chromatin Structure and Dynamic Gene Expression During Spermatogenesis
inferred← citeshttps://doi.org/10.1101/301705openalex-snapshot
Generative Modeling of Multi-mapping Reads with mHi-C Advances Analysis of High Throughput Genome-wide Conformation Capture Studies
inferred← citeshttps://doi.org/10.1101/529990openalex-snapshot
Activity-by-Contact model of enhancer specificity from thousands of CRISPR perturbations
inferred← citeshttps://doi.org/10.1186/s12859-020-03652-wopenalex-snapshot
SpectralTAD: an R package for defining a hierarchy of topologically associated domains using spectral clustering
inferred← citeshttps://doi.org/10.1186/s13059-018-1596-9openalex-snapshot
Comparison of computational methods for the identification of topologically associating domains
inferred← citeshttps://doi.org/10.21769/bioprotoc.4879openalex-snapshot
Identification of Topologically Associating Domains (TADs) and Long-distance Enhancer–gene/gene–gene Interactions with Hi-C and HiChIP
inferred← citeshttps://doi.org/10.3390/cimb43020082openalex-snapshot
HPRep: Quantifying Reproducibility in HiChIP and PLAC-Seq Datasets
inferred← citeshttps://doi.org/10.3390/life12111939openalex-snapshot
From Samples to Germline and Somatic Sequence Variation: A Focus on Next-Generation Sequencing in Melanoma Research
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/10.7554/elife.38070openalex-snapshot
Generative modeling of multi-mapping reads with mHi-C advances analysis of Hi-C studies
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