{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,15]],"date-time":"2025-11-15T14:41:44Z","timestamp":1763217704222,"version":"3.45.0"},"reference-count":75,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2025,11,15]],"date-time":"2025-11-15T00:00:00Z","timestamp":1763164800000},"content-version":"vor","delay-in-days":14,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Basic Science Research Program through the National Research Foundation of Korea","award":["RS-2021-NR060140","RS-2024-00342721","RS-2023-00220207","RS-2024-00440285"],"award-info":[{"award-number":["RS-2021-NR060140","RS-2024-00342721","RS-2023-00220207","RS-2024-00440285"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Tumor tissues are composed of malignant subclones with diverse genetic profiles. Reconstructing the evolutionary trajectory of these subclones is crucial for understanding how tumors acquire malignant traits. However, current approaches to subclonal tree reconstruction are limited either by their reliance on single-cell DNA sequencing (scDNA-seq) that involve a small number of cells and thus yield low-resolution results, or using single-cell RNA sequencing (scRNA-seq) data, which despite including larger cell populations, remain susceptible to bias from high dropout rates and technical noise. Here, we introduce CluVar, an autoencoder-based framework for inferring the phylogeny of cancer subclones from scRNA-seq data using mutation profile analysis. To address the extensive missing variant information inherent in scRNA-seq datasets, CluVar incorporates a customized loss function and multiple hidden layers optimized for clustering. CluVar demonstrated superior performance in reconstructing phylogenetic trees of cancer subclones under a range of erroneous conditions. When applied to cancer scRNA-seq data, the phylogenetic tree predicted using CluVar aligned well with the transcriptomic profiles. These findings highlight its utility for tracing evolutionary trajectories and identifying novel variants associated with cancer progression.<\/jats:p>","DOI":"10.1093\/bib\/bbaf603","type":"journal-article","created":{"date-parts":[[2025,11,15]],"date-time":"2025-11-15T14:37:51Z","timestamp":1763217471000},"source":"Crossref","is-referenced-by-count":0,"title":["CluVar: clustering of variants using autoencoder for inferring cancer subclones from single cell RNA sequencing data"],"prefix":"10.1093","volume":"26","author":[{"given":"Chae Won","family":"Kim","sequence":"first","affiliation":[{"name":"Department of Bioinformatics, Soongsil University , 369 Sangdo-Ro, Dongjak-Gu, Seoul 06978 ,","place":["Republic of Korea"]}]},{"given":"Heewon","family":"Park","sequence":"additional","affiliation":[{"name":"Department of Intelligent Semiconductors, Soongsil University , 369 Sangdo-Ro, Dongjak-Gu, Seoul 06978 ,","place":["Republic of Korea"]}]},{"given":"Dohyeon","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Soongsil University , 369 Sangdo-Ro, Dongjak-Gu, Seoul 06978 ,","place":["Republic of Korea"]},{"name":"Center for Natural Product Systems Biology, Korea Institute of Science and Technology , 679 Saimdang-Ro, Gangneung 25451 ,","place":["Republic of Korea"]}]},{"given":"Yuchang","family":"Seong","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Soongsil University , 369 Sangdo-Ro, Dongjak-Gu, Seoul 06978 ,","place":["Republic of Korea"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8807-3719","authenticated-orcid":false,"given":"Minhae","family":"Kwon","sequence":"additional","affiliation":[{"name":"Department of Intelligent Semiconductors, Soongsil University , 369 Sangdo-Ro, Dongjak-Gu, Seoul 06978 ,","place":["Republic of Korea"]},{"name":"School of Electronic Engineering, Soongsil University , 369 Sangdo-Ro, Dongjak-Gu, Seoul 06978 ,","place":["Republic of Korea"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1202-1808","authenticated-orcid":false,"given":"Junil","family":"Kim","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Soongsil University , 369 Sangdo-Ro, Dongjak-Gu, Seoul 06978 ,","place":["Republic of Korea"]},{"name":"School of Systems Biomedical Science, Soongsil University , 369 Sangdo-Ro, Dongjak-Gu, Seoul 06978 ,","place":["Republic of Korea"]}]}],"member":"286","published-online":{"date-parts":[[2025,11,15]]},"reference":[{"key":"2025111509374611600_ref1","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1126\/science.959840","article-title":"The clonal evolution of tumor cell populations","volume":"194","author":"Nowell","year":"1976","journal-title":"Science"},{"key":"2025111509374611600_ref2","doi-asserted-by":"publisher","first-page":"328","DOI":"10.1038\/nature12624","article-title":"Tumour heterogeneity and cancer cell 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