{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,17]],"date-time":"2026-06-17T06:39:53Z","timestamp":1781678393362,"version":"3.54.5"},"reference-count":33,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,12,11]],"date-time":"2023-12-11T00:00:00Z","timestamp":1702252800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Bioinform."],"abstract":"<jats:p>Detailed understanding of the 3D structure of chromatin is a key ingredient to investigate a variety of processes inside the cell. Since direct methods to experimentally ascertain these structures lack the desired spatial fidelity, computational inference methods based on single cell Hi-C data have gained significant interest. Here, we develop a progressive simulation protocol to iteratively improve the resolution of predicted interphase structures by maximum-likelihood association of ambiguous Hi-C contacts using lower-resolution predictions. Compared to state-of-the-art methods, our procedure is not limited to haploid cell data and allows us to reach a resolution of up to 5,000 base pairs per bead. High resolution chromatin models grant access to a multitude of structural phenomena. Exemplarily, we verify the formation of chromosome territories and holes near aggregated chromocenters as well as the inversion of the CpG content for rod photoreceptor cells.<\/jats:p>","DOI":"10.3389\/fbinf.2023.1284484","type":"journal-article","created":{"date-parts":[[2023,12,11]],"date-time":"2023-12-11T10:07:53Z","timestamp":1702289273000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":3,"title":["Reconstructing diploid 3D chromatin structures from single cell Hi-C data with a polymer-based approach"],"prefix":"10.3389","volume":"3","author":[{"given":"Jan","family":"Roth\u00f6rl","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maarten A.","family":"Brems","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tim J.","family":"Stevens","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Virnau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,12,11]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"5342","DOI":"10.1016\/j.jcp.2008.01.047","article-title":"General purpose molecular dynamics simulations fully implemented on graphics processing units","volume":"227","author":"Anderson","year":"2008","journal-title":"J. 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