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Generative Modeling of Multi-mapping Reads with mHi-C Advances Analysis of High Throughput Genome-wide Conformation Capture Studies

https://doi.org/10.1101/301705
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Outgoing claims: the papers this work cites, builds on, or argues with.

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CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription
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Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters
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Multiscale 3D Genome Rewiring during Mouse Neural Development
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Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries
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Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom
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Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
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Polycomb-Dependent H3K27me1 and H3K27me2 Regulate Active Transcription and Enhancer Fidelity
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The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries
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Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation
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Topological domains in mammalian genomes identified by analysis of chromatin interactions
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An integrated encyclopedia of DNA elements in the human genome
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A high-resolution map of the three-dimensional chromatin interactome in human cells
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Topology of mammalian developmental enhancers and their regulatory landscapes
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Chromatin architecture reorganization during stem cell differentiation
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Integrative analysis of 111 reference human epigenomes
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Chromosome conformation elucidates regulatory relationships in developing human brain
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DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape
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Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
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Modeling disease risk through analysis of physical interactions between genetic variants within chromatin regulatory circuitry
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The Human Epigenome Browser at Washington University
inferredcites →https://doi.org/10.1038/nmeth.2148openalex-snapshot
Iterative correction of Hi-C data reveals hallmarks of chromosome organization
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Comparison of computational methods for Hi-C data analysis
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Repetitive DNA and next-generation sequencing: computational challenges and solutions
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CTCF: an architectural protein bridging genome topology and function
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Three-dimensional genome architecture: players and mechanisms
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Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages
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Structural variation in the 3D genome
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Integrative detection and analysis of structural variation in cancer genomes
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Fast and accurate long-read alignment with Burrows–Wheeler transform
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FIMO: scanning for occurrences of a given motif
inferredcites →https://doi.org/10.1093/bioinformatics/btu402openalex-snapshot
CNV-guided multi-read allocation for ChIP-seq
inferredcites →https://doi.org/10.1093/bioinformatics/btu801openalex-snapshot
HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements
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GeneCards Version 3: the human gene integrator
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A fast algorithm for matrix balancing
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Subscriptions
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The 3D folding of metazoan genomes correlates with the association of similar repetitive elements
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The UCSC Genome Browser database: 2018 update
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JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework
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CLIP-seq analysis of multi-mapped reads discovers novel functional RNA regulatory sites in the human transcriptome
inferredcites →https://doi.org/10.1101/121889openalex-snapshot
HiGlass: Web-based Visual Exploration and Analysis of Genome Interaction Maps
inferredcites →https://doi.org/10.1101/188755openalex-snapshot
Measuring the reproducibility and quality of Hi-C data
inferredcites →https://doi.org/10.1101/gr.135350.111openalex-snapshot
GENCODE: The reference human genome annotation for The ENCODE Project
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.169417.113openalex-snapshot
Three-dimensional modeling of theP. falciparumgenome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression
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.1067799openalex-snapshot
Capturing Chromosome Conformation
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/10.1146/annurev-cellbio-100616-060531openalex-snapshot
The Three-Dimensional Organization of Mammalian Genomes
inferredcites →https://doi.org/10.1161/circulationaha.117.029430openalex-snapshot
High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure
inferredcites →https://doi.org/10.1186/1471-2105-12-323openalex-snapshot
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
inferredcites →https://doi.org/10.1186/s12859-015-0683-0openalex-snapshot
diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data
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/s13059-015-0831-xopenalex-snapshot
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
inferredcites →https://doi.org/10.1371/journal.pcbi.1002111openalex-snapshot
Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data
inferredcites →https://doi.org/10.1371/journal.pcbi.1004491openalex-snapshot
Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping
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