{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,26]],"date-time":"2026-05-26T11:04:31Z","timestamp":1779793471015,"version":"3.53.1"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2026,5,11]],"date-time":"2026-05-11T00:00:00Z","timestamp":1778457600000},"content-version":"vor","delay-in-days":10,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["1830904"],"award-info":[{"award-number":["1830904"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2124558"],"award-info":[{"award-number":["2124558"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,5,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Advances in high-throughput chromatin conformation capture have provided insight into the three-dimensional structure and organization of chromatin. While bulk Hi-C experiments capture spatio-temporally averaged chromatin interactions across millions of cells, single-cell Hi-C experiments report on the chromatin interactions of individual cells. Supervised and unsupervised algorithms have been developed to embed single-cell Hi-C maps and identify different cell types. However, single-cell Hi-C maps are often difficult to cluster due to their high sparsity, with state-of-the-art algorithms achieving a maximum Adjusted Rand Index (ARI) of only \u22720.4 on several datasets.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We introduce a novel unsupervised algorithm, Single-cell Clustering Using Diagonal Diffusion Operators (SCUDDO), to embed and cluster single-cell Hi-C maps. We evaluate SCUDDO on four previously difficult-to-cluster single-cell Hi-C datasets, and show that it can outperform other current algorithms in ARI by \u22730.2. Further, SCUDDO outperforms all other tested algorithms even when we restrict the number of intrachromosomal maps for each cell type and when we use only a small fraction of contacts in each Hi-C map. Thus, SCUDDO can capture the underlying latent features of single-cell Hi-C maps and provide accurate labelling of cell types even when cell types are not known a priori.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>SCUDDO is freely available at https:\/\/www.github.com\/lmaisuradze\/scuddo as well as https:\/\/doi.org\/10.6084\/m9.figshare.31759915. The tested datasets are publicly available and can be downloaded from the Gene Expression Omnibus.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag284","type":"journal-article","created":{"date-parts":[[2026,5,5]],"date-time":"2026-05-05T11:29:12Z","timestamp":1777980552000},"source":"Crossref","is-referenced-by-count":0,"title":["SCUDDO: an unsupervised clustering algorithm for single-cell Hi-C maps using diagonal diffusion operators"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-1578-5361","authenticated-orcid":false,"given":"Luka","family":"Maisuradze","sequence":"first","affiliation":[{"name":"Yale University Department of Molecular Biophysics and Biochemistry, , New Haven, CT 06520,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark D","family":"Shattuck","sequence":"additional","affiliation":[{"name":"The City College of New York Benjamin Levich Institute and Physics 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