@article{zheng2024scnovel,title={scNovel: a scalable deep learning-based network for novel rare cell discovery in single-cell transcriptomics},author={Zheng, Chuanyang and Wang, Yixuan and Cheng, Yuqi and Wang, Xuesong and Wei, Hongxin and King, Irwin and Li, Yu},journal={Briefings in Bioinformatics},volume={25},number={3},pages={bbae112},year={2024},publisher={Oxford University Press},}
2023
scBalance
A scalable sparse neural network framework for rare cell type annotation of single-cell transcriptome data
@article{cheng2023scalable,title={A scalable sparse neural network framework for rare cell type annotation of single-cell transcriptome data},author={Cheng, Yuqi and Fan, Xingyu and Zhang, Jianing and Li, Yu},journal={Communications Biology},volume={6},number={1},pages={545},year={2023},publisher={Nature Publishing Group UK London},}
2022
Deep autoencoder for interpretable tissue-adaptive deconvolution and cell-type-specific gene analysis
Yanshuo Chen, Yixuan Wang, Yuelong Chen, Yuqi Cheng, and 6 more authors
@article{chen2022deep,author={Chen, Yanshuo and Wang, Yixuan and Chen, Yuelong and Cheng, Yuqi and Wei, Yumeng and Li, Yunxiang and Wang, Jiuming and Wei, Yingying and Chan, Ting-Fung and Li, Yu},journal={Nature Communications},volume={13},number={1},pages={6735},year={2022},publisher={Nature Publishing Group UK London},}
CLEAR
Self-supervised contrastive learning for integrative single cell RNA-seq data analysis
Wenkai Han*, Yuqi Cheng*, Jiayang Chen*, Huawen Zhong, and 6 more authors
@article{han2022self,title={Self-supervised contrastive learning for integrative single cell RNA-seq data analysis},author={Han*, Wenkai and Cheng*, Yuqi and Chen*, Jiayang and Zhong, Huawen and Hu, Zhihang and Chen, Siyuan and Zong, Licheng and King, Irwin and Gao, Xin and Li, Yu},journal={Briefings in Bioinformatics},volume={23},number={5},year={2022},}