Single-cell and spatial detection of senescent cells using DeepScence.
Publication
, Journal Article
Qu, Y; Ji, B; Dong, R; Gu, L; Chan, C; Xie, J; Glass, C; Wang, X-F; Nixon, AB; Ji, Z
Published in: Cell Genom
December 10, 2025
Accurately identifying senescent cells is essential for studying their spatial and molecular features. We developed DeepScence, a method based on deep neural networks, to identify senescent cells in single-cell and spatial transcriptomics data. DeepScence is based on CoreScence, a senescence-associated gene set we curated that incorporates information from multiple published gene sets. We demonstrate that DeepScence can accurately identify senescent cells in single-cell gene expression data collected both in vitro and in vivo, as well as in spatial transcriptomics data generated by different platforms, substantially outperforming existing methods.
Duke Scholars
Published In
Cell Genom
DOI
EISSN
2666-979X
Publication Date
December 10, 2025
Volume
5
Issue
12
Start / End Page
101035
Location
United States
Related Subject Headings
- Transcriptome
- Single-Cell Analysis
- Neural Networks, Computer
- Mice
- Humans
- Gene Expression Profiling
- Cellular Senescence
- Animals
Citation
APA
Chicago
ICMJE
MLA
NLM
Qu, Y., Ji, B., Dong, R., Gu, L., Chan, C., Xie, J., … Ji, Z. (2025). Single-cell and spatial detection of senescent cells using DeepScence. Cell Genom, 5(12), 101035. https://doi.org/10.1016/j.xgen.2025.101035
Qu, Yilong, Beijie Ji, Runze Dong, Liangcai Gu, Cliburn Chan, Jichun Xie, Carolyn Glass, Xiao-Fan Wang, Andrew B. Nixon, and Zhicheng Ji. “Single-cell and spatial detection of senescent cells using DeepScence.” Cell Genom 5, no. 12 (December 10, 2025): 101035. https://doi.org/10.1016/j.xgen.2025.101035.
Qu Y, Ji B, Dong R, Gu L, Chan C, Xie J, et al. Single-cell and spatial detection of senescent cells using DeepScence. Cell Genom. 2025 Dec 10;5(12):101035.
Qu, Yilong, et al. “Single-cell and spatial detection of senescent cells using DeepScence.” Cell Genom, vol. 5, no. 12, Dec. 2025, p. 101035. Pubmed, doi:10.1016/j.xgen.2025.101035.
Qu Y, Ji B, Dong R, Gu L, Chan C, Xie J, Glass C, Wang X-F, Nixon AB, Ji Z. Single-cell and spatial detection of senescent cells using DeepScence. Cell Genom. 2025 Dec 10;5(12):101035.
Published In
Cell Genom
DOI
EISSN
2666-979X
Publication Date
December 10, 2025
Volume
5
Issue
12
Start / End Page
101035
Location
United States
Related Subject Headings
- Transcriptome
- Single-Cell Analysis
- Neural Networks, Computer
- Mice
- Humans
- Gene Expression Profiling
- Cellular Senescence
- Animals