{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,2]],"date-time":"2025-08-02T14:19:22Z","timestamp":1754144362034,"version":"3.41.2"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"Supplement_1","license":[{"start":{"date-parts":[[2025,7,15]],"date-time":"2025-07-15T00:00:00Z","timestamp":1752537600000},"content-version":"vor","delay-in-days":14,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institutes of General Medical Sciences","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R35GM150402"],"award-info":[{"award-number":["R35GM150402"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2153205"],"award-info":[{"award-number":["2153205"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Single-cell Hi-C (scHi-C) data provide critical insights into chromatin interactions at individual cell levels, uncovering unique genomic 3D structures. However, scHi-C datasets are characterized by sparsity and noise, complicating efforts to accurately reconstruct high-resolution chromosomal structures. In this study, we present ScUnicorn, a novel blind super-resolution framework for scHi-C data enhancement. ScUnicorn uses an iterative degradation kernel optimization process, unlike traditional super-resolution approaches, which rely on downsampling, predefined degradation ratios, or constant assumptions about the input data to reconstruct high-resolution interaction matrices. Hence, our approach more reliably preserves critical biological patterns and minimizes noise. Additionally, we propose 3DUnicorn, a maximum likelihood algorithm that leverages the enhanced scHi-C data to infer precise 3D chromosomal structures.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Our evaluation demonstrates that ScUnicorn achieves superior performance over the state-of-the-art methods in terms of Peak Signal-to-Noise Ratio, Structural Similarity Index Measure, and GenomeDisco scores. Moreover, 3DUnicorn\u2019s reconstructed structures align closely with experimental 3D-FISH data, underscoring its biological relevance. Together, ScUnicorn and 3DUnicorn provide a robust framework for advancing genomic research by enhancing scHi-C data fidelity and enabling accurate 3D genome structure reconstruction.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Unicorn implementation is publicly accessible at https:\/\/github.com\/OluwadareLab\/Unicorn.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf177","type":"journal-article","created":{"date-parts":[[2025,7,15]],"date-time":"2025-07-15T13:03:05Z","timestamp":1752584585000},"page":"i475-i483","source":"Crossref","is-referenced-by-count":0,"title":["Unicorn: enhancing single-cell Hi-C data with blind super-resolution for 3D genome structure reconstruction"],"prefix":"10.1093","volume":"41","author":[{"given":"Mohan Kumar B","family":"Chandrashekar","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Colorado, Colorado Springs , 1420 Austin Bluffs Parkway , Colorado Springs, CO, 80918,","place":["United States"]}]},{"given":"Rohit","family":"Menon","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Colorado, Colorado Springs , 1420 Austin Bluffs Parkway , Colorado Springs, CO, 80918,","place":["United States"]}]},{"given":"Samuel","family":"Olowofila","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Colorado, Colorado Springs , 1420 Austin Bluffs Parkway , Colorado Springs, CO, 80918,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5264-2342","authenticated-orcid":false,"given":"Oluwatosin","family":"Oluwadare","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Colorado, Colorado Springs , 1420 Austin Bluffs Parkway , Colorado Springs, CO, 80918,","place":["United States"]},{"name":"Department of Biomedical 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