{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T18:24:08Z","timestamp":1784399048117,"version":"3.55.0"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2019,3,13]],"date-time":"2019-03-13T00:00:00Z","timestamp":1552435200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institutes of General Medical Sciences","doi-asserted-by":"crossref","award":["R15GM120650"],"award-info":[{"award-number":["R15GM120650"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100006686","name":"University of Miami","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006686","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>In contrast to population-based Hi-C data, single-cell Hi-C data are zero-inflated and do not indicate the frequency of proximate DNA segments. There are a limited number of computational tools that can model the 3D structures of chromosomes based on single-cell Hi-C data.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We developed single-cell lattice (SCL), a computational method to reconstruct 3D structures of chromosomes based on single-cell Hi-C data. We designed a loss function and a 2\u2009D Gaussian function specifically for the characteristics of single-cell Hi-C data. A chromosome is represented as beads-on-a-string and stored in a 3\u2009D cubic lattice. Metropolis\u2013Hastings simulation and simulated annealing are used to simulate the structure and minimize the loss function. We evaluated the SCL-inferred 3\u2009D structures (at both 500 and 50\u2009kb resolutions) using multiple criteria and compared them with the ones generated by another modeling software program. The results indicate that the 3\u2009D structures generated by SCL closely fit single-cell Hi-C data. We also found similar patterns of trans-chromosomal contact beads, Lamin-B1 enriched topologically associating domains (TADs), and H3K4me3 enriched TADs by mapping data from previous studies onto the SCL-inferred 3\u2009D structures.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The C++ source code of SCL is freely available at http:\/\/dna.cs.miami.edu\/SCL\/.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz181","type":"journal-article","created":{"date-parts":[[2019,3,12]],"date-time":"2019-03-12T12:38:55Z","timestamp":1552394335000},"page":"3981-3988","source":"Crossref","is-referenced-by-count":37,"title":["SCL: a lattice-based approach to infer 3D chromosome structures from single-cell Hi-C data"],"prefix":"10.1093","volume":"35","author":[{"given":"Hao","family":"Zhu","sequence":"first","affiliation":[{"name":"School of Computing Sciences and Computer Engineering, University of Southern Mississippi , Hattiesburg, MS, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zheng","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Miami , Coral Gables, FL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,3,13]]},"reference":[{"key":"2023013108275644500_btz181-B1","doi-asserted-by":"crossref","first-page":"886.","DOI":"10.1186\/s12864-016-3210-4","article-title":"Chromosome3D: reconstructing three-dimensional chromosomal structures from Hi-C interaction frequency data using distance geometry simulated annealing","volume":"17","author":"Adhikari","year":"2016","journal-title":"BMC Genomics"},{"key":"2023013108275644500_btz181-B2","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1038\/nsmb.1936","article-title":"The three-dimensional folding of the alpha-globin gene domain reveals formation of chromatin globules","volume":"18","author":"Bau","year":"2011","journal-title":"Nat. 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