DeepCI: a deep learning based clustering method for single cell RNA-seq data. - Zhenlan Liang; Ruiqing Zheng; Siqi Chen; Xuhua Yan; Min Li 007 (BIBM, 2021)

MKG: a mutual information based method to infer single cell gene regulatory network. - Yanping Zeng; Xuhua Yan; Zhenlan Liang; Ruiqing Zheng; Min Li 007 (BIBM, 2021)

SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement. - Zhenlan Liang; Min Li 007; Ruiqing Zheng; Yu Tian; Xuhua Yan; Jin Chen 004; Fang-Xiang Wu; Jianxin Wang 001 (Genom. Proteom. Bioinform., 2021)

GLOBE: a contrastive learning-based framework for integrating single-cell transcriptome datasets. - Xuhua Yan; Ruiqing Zheng; Min Li 007 (Briefings Bioinform., 2022)

Bubble: a fast single-cell RNA-seq imputation using an autoencoder constrained by bulk RNA-seq data. - Siqi Chen; Xuhua Yan; Ruiqing Zheng; Min Li 007 (Briefings Bioinform., 2023)

CLAIRE: contrastive learning-based batch correction framework for better balance between batch mixing and preservation of cellular heterogeneity. - Xuhua Yan; Ruiqing Zheng; Fang-Xiang Wu; Min Li 007 (Bioinform., 2023)

scNCL: transferring labels from scRNA-seq to scATAC-seq data with neighborhood contrastive regularization. - Xuhua Yan; Ruiqing Zheng; Jinmiao Chen; Min Li 007 (Bioinform., 2023)