ArticlePLoS computational biology2019
MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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Who cites it
87 citing papers in PubMed.
- Article
- LAWS-HiC: A Locally Adaptive Weighting and Screening (LAWS) Approach to Improve Detection of Long-Range Chromatin Interactions from Hi-C Data.Methods and protocols · 2026Article
- dcHiChIP: a comprehensive Nextflow-based pipeline for multiscale analysis of chromatin architecture from HiChIP data.Bioinformatics (Oxford, England) · 2026Article
- Integrative Epigenomics: Bioinformatics Strategies for Multi-Omics Data Analysis in Health and Disease.Epigenomes · 2026Review
- A high-penetrance intergenic variant at 9p21 confers melanoma susceptibility.Research square · 2026Article
- Accurate and efficient HiChIP interaction detection by modeling restriction enzyme cut site density as biological signal.Briefings in bioinformatics · 2026Article
- Trimodal single-cell profiling of transcriptome, epigenome and 3D genome in complex tissues with scHiCAR.Nature biotechnology · 2026Article
- Multimodal epigenetic and enhancer network remodeling shape the transcriptional landscape of human beige adipocytes.Communications biology · 2026Article
- Epigenetic regulation in osteoarthritis: recent updates and emerging mechanisms.Frontiers in genetics · 2026Review
- Article
- Accurate and robust 3D genome feature discovery from multiplexed DNA FISH.bioRxiv : the preprint server for biology · 2025Article
- A subset of transposable elements as mechano-response enhancer elements in controlling human embryonic stem cell fate.Nature cell biology · 2025Article
- Critical roles of IKAROS and HDAC1 in regulation of heterochromatin and tumor suppression in T-cell acute lymphoblastic leukemia.Leukemia · 2025Article
- Genomic convergence in hibernating mammals elucidates the genetics of metabolic regulation in the hypothalamus.Science (New York, N.Y.) · 2025Article
- Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding.Genome research · 2025Article
- Loop Catalog: a comprehensive HiChIP database of human and mouse samples.Genome biology · 2025Article
- Unveiling Multi-Scale Architectural Features in Single-Cell Hi-C Data Using scCAFE.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes.Communications biology · 2025Article
- Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues.Nature structural & molecular biology · 2025Article
- Pioneer factor GATA6 promotes colorectal cancer through 3D genome regulation.Science advances · 2025Article
27 more citing papers are in PubMed but not listed here.
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12 authors.
Funding
Abstract
Hi-C and chromatin immunoprecipitation (ChIP) have been combined to identify long-range chromatin interactions genome-wide at reduced cost and enhanced resolution, but extracting information from the resulting datasets has been challenging. Here we describe a computational method, MAPS, Model-based Analysis of PLAC-seq and HiChIP, to process the data from such experiments and identify long-range chromatin interactions. MAPS adopts a zero-truncated Poisson regression framework to explicitly remove systematic biases in the PLAC-seq and HiChIP datasets, and then uses the normalized chromatin contact frequencies to identify significant chromatin interactions anchored at genomic regions bound by the protein of interest. MAPS shows superior performance over existing software tools in the analysis of chromatin interactions from multiple PLAC-seq and HiChIP datasets centered on different transcriptional factors and histone marks. MAPS is freely available at https://github.com/ijuric/MAPS.
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