scCODE: an R package for data-specific differentially expressed gene detection on single-cell RNA-sequencing data. - Jiawei Zou; Fulan Deng; Miaochen Wang; Zhen Zhang; Zheqi Liu; Xiaobin Zhang; Rong Hua; Ke Chen; Xin Zou; Jie Hao (Briefings Bioinform., 2022)

Themis: advancing precision oncology through comprehensive molecular subtyping and optimization. - Yue Xi; Kun Zheng; Fulan Deng; Yujun Liu; Hourong Sun; Yingxia Zheng; Henry H. Y. Tong; Yuan Ji; Yingchun Zhang; Wantao Chen; Yiming Zhang; Xin Zou; et al. (Briefings Bioinform., 2024)

DECEPTICON: a correlation-based strategy for RNA-seq deconvolution inspired by a variation of the Anna Karenina principle. - Fulan Deng; Jiawei Zou; Miaochen Wang; Yida Gu; Jiale Wu; Lianchong Gao; Yuan Ji; Henry H. Y. Tong; Jie Chen; Wantao Chen; Lianjiang Tan; Yaoqing Chu; et al. (Briefings Bioinform., 2025)

Deep scSTAR: leveraging deep learning for the extraction and enhancement of phenotype-associated features from single-cell RNA sequencing and spatial transcriptomics data. - Lianchong Gao; Yujun Liu; Jiawei Zou; Fulan Deng; Zheqi Liu; Zhen Zhang; Xinran Zhao; Lei Chen; Henry H. Y. Tong; Yuan Ji; Huangying Le; Xin Zou; et al. (Briefings Bioinform., 2025)