{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T14:26:31Z","timestamp":1760711191295,"version":"3.41.2"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2023,5,11]],"date-time":"2023-05-11T00:00:00Z","timestamp":1683763200000},"content-version":"vor","delay-in-days":10,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01GM106023","R01GM110151"],"award-info":[{"award-number":["R01GM106023","R01GM110151"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,5,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Computational inference of genome organization based on Hi-C sequencing has greatly aided the understanding of chromatin and nuclear organization in three dimensions (3D). However, existing computational methods fail to address the cell population heterogeneity. Here we describe a probabilistic-modeling-based method called CscoreTool-M that infers multiple 3D genome sub-compartments from Hi-C data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>The compartment scores inferred using CscoreTool-M represents the probability of a genomic region locating in a specific sub-compartment. Compared to published methods, CscoreTool-M is more accurate in inferring sub-compartments corresponding to both active and repressed chromatin. The compartment scores calculated by CscoreTool-M also help to quantify the levels of heterogeneity in sub-compartment localization within cell populations. By comparing proliferating cells and terminally differentiated non-proliferating cells, we show that the proliferating cells have higher genome organization heterogeneity, which is likely caused by cells at different cell-cycle stages. By analyzing 10 sub-compartments, we found a sub-compartment containing chromatin potentially related to the early-G1 chromatin regions proximal to the nuclear lamina in HCT116 cells, suggesting the method can deconvolve cell cycle stage-specific genome organization among asynchronously dividing cells. Finally, we show that CscoreTool-M can identify sub-compartments that contain genes enriched in housekeeping or cell-type-specific functions.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/scoutzxb\/CscoreTool-M.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad314","type":"journal-article","created":{"date-parts":[[2023,5,11]],"date-time":"2023-05-11T14:51:34Z","timestamp":1683816694000},"source":"Crossref","is-referenced-by-count":2,"title":["CscoreTool-M infers 3D sub-compartment probabilities within cell population"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9599-8525","authenticated-orcid":false,"given":"Xiaobin","family":"Zheng","sequence":"first","affiliation":[{"name":"Department of Embryology, Carnegie Institution for Science , Baltimore, MD 21218, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7467-8995","authenticated-orcid":false,"given":"Joseph R","family":"Tran","sequence":"additional","affiliation":[{"name":"Department of Embryology, Carnegie Institution for Science , Baltimore, MD 21218, United States"}]},{"given":"Yixian","family":"Zheng","sequence":"additional","affiliation":[{"name":"Department of Embryology, Carnegie Institution for Science , Baltimore, MD 21218, United States"}]}],"member":"286","published-online":{"date-parts":[[2023,5,11]]},"reference":[{"key":"2023052412381938900_btad314-B1","doi-asserted-by":"crossref","first-page":"9354","DOI":"10.1038\/s41598-019-45839-z","article-title":"The ENCODE blacklist: identification of problematic regions of the genome","volume":"9","author":"Amemiya","year":"2019","journal-title":"Sci Rep"},{"key":"2023052412381938900_btad314-B2","doi-asserted-by":"crossref","first-page":"1173","DOI":"10.1038\/s41467-020-14974-x","article-title":"Graph embedding and unsupervised 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