The DOI matches its Crossref record; 36 of the 36 references it cites were found in a registry or an index.
MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments
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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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“Chromatin loops were identified between active promoters and distal regulatory regions in microglia, neurons and oligodendrocytes (26).”
From Brain cell type–specific enhancer–promoter interactome maps and disease - risk association (2019) · cites this paper as [26]
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Model-based Analysis of ChIP-Seq (MACS)
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Self-citationA 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.021 · Cited by 9,212
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898
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Capturing Chromosome Conformation
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Formation of chromosomal domains by loop extrusion
Fudenberg, G., Imakaev, M., Lu, C., Goloborodko, A., Abdennur, N., & Mirny, L. A. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.04.085 · Cited by 2,003
Mediator and cohesin connect gene expression and chromatin architecture
Kagey, M. H., Newman, J. J., Bilodeau, S., Zhan, Y., Orlando, D. A., van Berkum, N. L., Ebmeier, C. C., Goossens, J., Rahl, P. B., Levine, S. S., et al. (2010) · Nature · doi:10.1038/nature09380 · Cited by 1,939
Formation of Chromosomal Domains by Loop Extrusion
Fudenberg, G., Imakaev, M., Lu, C. W., Goloborodko, A., Abdennur, N. A., & Mirny, L. (2015) · bioRxiv · doi:10.1101/024620 · Cited by 1,858
Sanborn, A. L., Rao, S. S. P., Huang, S.-C., Durand, N. C., Huntley, M. H., Jewett, A. I., Bochkov, I. D., Chinnappan, D., Cutkosky, A., Li, J., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1518552112 · Cited by 1,730
The long-range interaction landscape of gene promoters
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Research works printed but not linked: 1
- CE Grant, 2011, FIMO: scanning for occurrences of a given motif, Bioinformatics (Oxford, England), 27, 1017, 10.1093/bioinformatics/btr064 · DOI · Paper page
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Ding, W.-Y., Zhou, Y., Liu, Q., Guo, Y.-Y., Zhang, C., & Jin, S. (2026) · Briefings Bioinform. · doi:10.1093/bib/bbag292
“…calling without significance testing [ 12]; MAPS (Model-based Analysis of PLAC-seq and HiChIP) employs zero-inflated models on contact matrices [ 13]; FitHiChIP adjusts for genomic distance and local coverage [ 14]; HiC-DC + incorporates Hi-C normalization strategies to stabilize interaction…”
Tan, J., Wu, Y., Head, R., & Sun, Y. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.30.715320
“For MAPS [7] , which models background interactions in fixed-size genomic bins, the pipeline first quantified average mappability at RE fragment ends.”
InfluentialPickering, S. H., Galigniana, N., Abdelhalim, M., Sørensen, A., Zucknick, M., Collas, P., & Briand, N. (2025) · bioRxiv · doi:10.1101/2025.03.28.645896
“0 (Juric et al. 2019) as implemented within the Arima Genomics pipeline (https://github.com/HuMingLab/MAPS/tree/master/Arima_Genomics).”
E-box independent chromatin recruitment turns MYOD into a transcriptional repressorPreprint
Nicoletti, C., Massenet, J., Pintado-Urbanc, A. P., Connor, L. J., Nicolau, M., Sundar, S., Xu, M., Schmitt, A. D., Zhang, W., Fang, Z., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.05.627024 · Cited by 3
THUNDER: A reference-free deconvolution method to infer cell type proportions from bulk Hi-C data
Rowland, B. T., Huh, R., Hou, Z., Hu, M., Shen, Y., & Li, Y. (2020) · bioRxiv · doi:10.1101/2020.11.12.379941
Self-citationWei, X., Xiang, Y., Abnousi, A., Sun, T., Lin, X., Li, W., Hu, M., & Diao, Y.-R. (2020) · bioRxiv · doi:10.1101/2020.11.02.366062
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Metadata
- Authors
- Juric, I., Yu, M., Abnousi, A., Raviram, R., Fang, R., Zhao, Y., Zhang, Y., Qiu, Y., Yang, Y., Li, Y., Ren, B., & Hu, M.
- Affiliations
- Ludwig Cancer Research (US)
- Cleveland Clinic (US)
- University of California San Diego (US)
- University of North Carolina at Chapel Hill (US)
- Corresponding author
- Ren, Bing
- Hu, Ming
- ORCID
- Venue
- PLOS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2019-04-15
- Volume
- 15
- Issue
- 4
- Pages
- e1006982
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- PMC
- PMC6483256
- OpenAlex
- W2951448241
- Cited by
- 121
- References
- 35
- Citations by year
- 2026: 11 · 2025: 10 · 2024: 22 · 2023: 12 · 2022: 23 · 2021: 22 · 2020: 10 · 2019: 10
- FWCI
- 5.62
- Type
- journal article
- Language
- en
- Update notices
- new_version (2019-04-25)
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Computational Biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Carolina Digital Repository (University of North Carolina at Chapel Hill) (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- UNC Libraries
- Funders
- Foundation for the National Institutes of Health (U54DK107977, R01HL129132)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- long-range chromatin interactions, HiChIP, Hi-C, transcription factor binding sites, histone modifications, model-based analysis, maps
- MeSH terms
- Chromatin, Chromosome Mapping, Computer Simulation, Humans, Software, Genome, Sequence Analysis, DNA, Computational Biology, Genomics, Chromatin Assembly and Disassembly, Histone Code, Chromatin Immunoprecipitation, High-Throughput Nucleotide Sequencing
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