{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T16:05:10Z","timestamp":1778601910976,"version":"3.51.4"},"reference-count":59,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,5,3]],"date-time":"2024-05-03T00:00:00Z","timestamp":1714694400000},"content-version":"vor","delay-in-days":37,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Yangtze River Delta Project","award":["2023ZY1068"],"award-info":[{"award-number":["2023ZY1068"]}]},{"name":"\u2018Pioneer\u201d and \u201cLeading Goose\u2019 R&D Program of Zhejiang, China","award":["2022C03043"],"award-info":[{"award-number":["2022C03043"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Trajectory inference is a crucial task in single-cell RNA-sequencing downstream analysis, which can reveal the dynamic processes of biological development, including cell differentiation. Dimensionality reduction is an important step in the trajectory inference process. However, most existing trajectory methods rely on cell features derived from traditional dimensionality reduction methods, such as principal component analysis and uniform manifold approximation and projection. These methods are not specifically designed for trajectory inference and fail to fully leverage prior information from upstream analysis, limiting their performance. Here, we introduce scCRT, a novel dimensionality reduction model for trajectory inference. In order to utilize prior information to learn accurate cells representation, scCRT integrates two feature learning components: a cell-level pairwise module and a cluster-level contrastive module. The cell-level module focuses on learning accurate cell representations in a reduced-dimensionality space while maintaining the cell\u2013cell positional relationships in the original space. The cluster-level contrastive module uses prior cell state information to aggregate similar cells, preventing excessive dispersion in the low-dimensional space. Experimental findings from 54 real and 81 synthetic datasets, totaling 135 datasets, highlighted the superior performance of scCRT compared with commonly used trajectory inference methods. Additionally, an ablation study revealed that both cell-level and cluster-level modules enhance the model\u2019s ability to learn accurate cell features, facilitating cell lineage inference. The source code of scCRT is available at https:\/\/github.com\/yuchen21-web\/scCRT-for-scRNA-seq.<\/jats:p>","DOI":"10.1093\/bib\/bbae204","type":"journal-article","created":{"date-parts":[[2024,5,3]],"date-time":"2024-05-03T10:31:34Z","timestamp":1714732294000},"source":"Crossref","is-referenced-by-count":8,"title":["scCRT: a contrastive-based dimensionality reduction model for scRNA-seq trajectory inference"],"prefix":"10.1093","volume":"25","author":[{"given":"Yuchen","family":"Shi","sequence":"first","affiliation":[{"name":"Hangzhou Dianzi University , Hangzhou City, Zhejiang Province , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jian","family":"Wan","sequence":"additional","affiliation":[{"name":"Hangzhou Dianzi University, the Key Laboratory of Biomedical Intelligent Computing Technology of Zhejiang Province, and Zhejiang University of Science and Technology , Hangzhou City, Zhejiang Province , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xin","family":"Zhang","sequence":"additional","affiliation":[{"name":"Hangzhou Dianzi University , Hangzhou City, Zhejiang Province , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tingting","family":"Liang","sequence":"additional","affiliation":[{"name":"Hangzhou Dianzi University , Hangzhou City, Zhejiang Province , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuyu","family":"Yin","sequence":"additional","affiliation":[{"name":"Hangzhou Dianzi University , Hangzhou City, Zhejiang Province , China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,5,2]]},"reference":[{"issue":"2","key":"2024050310311819800_ref1","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/nbt.3102","article-title":"Computational analysis of cell-to-cell heterogeneity in single-cell rna-sequencing data reveals hidden 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