Epigenome overlap measure (EPOM) for comparing tissue/cell types based on chromatin states. - Wei Vivian Li; Zahra S. Razaee; Jingyi Jessica Li (BMC Genom., 2016)

Modeling and analysis of RNA-seq data: a review from a statistical perspective. - Wei Vivian Li; Jingyi Jessica Li (Quant. Biol., 2018)

A statistical simulator scDesign for rational scRNA-seq experimental design. - Wei Vivian Li; Jingyi Jessica Li (Bioinform., 2019)

Bridging Cost-sensitive and Neyman-Pearson Paradigms for Asymmetric Binary Classification. - Wei Vivian Li; Xin Tong; Jingyi Jessica Li (CoRR, 2020)

Selecting gene features for unsupervised analysis of single-cell gene expression data. - Jie Sheng; Wei Vivian Li (Briefings Bioinform., 2021)

scLink: Inferring Sparse Gene Co-expression Networks from Single-cell Expression Data. - Wei Vivian Li; Yanzeng Li (Genom. Proteom. Bioinform., 2021)

A Novel Matrix Factorization Model for Interpreting Single-Cell Gene Expression from Biologically Heterogeneous Data. - Kun Qian; Shiwei Fu; Hongwei Li 003; Wei Vivian Li (RECOMB, 2022)

Phitest for analyzing the homogeneity of single-cell populations. - Wei Vivian Li (Bioinform., 2022)

The scINSIGHT Package for Integrating Single-Cell RNA-Seq Data from Different Biological Conditions. - Kun Qian; Shiwei Fu; Hongwei Li 003; Wei Vivian Li (J. Comput. Biol., 2022)

Simulating Single-Cell Gene Expression Count Data with Preserved Gene Correlations by scDesign2. - Tianyi Sun; Dongyuan Song; Wei Vivian Li; Jingyi Jessica Li (J. Comput. Biol., 2022)

Benchmarking cell-type clustering methods for spatially resolved transcriptomics data. - Andrew Cheng; Guanyu Hu; Wei Vivian Li (Briefings Bioinform., 2023)

Differential variability analysis of single-cell gene expression data. - Jiayi Liu; Anat Kreimer; Wei Vivian Li (Briefings Bioinform., 2023)

scAce: an adaptive embedding and clustering method for single-cell gene expression data. - Xinwei He; Kun Qian; Ziqian Wang; Shirou Zeng; Hongwei Li 003; Wei Vivian Li (Bioinform., 2023)

Predicting and comparing transcription start sites in single cell populations. - Shiwei Fu; Wei Vivian Li (PLoS Comput. Biol., 2025)

Generalized probabilistic canonical correlation analysis for multi-modal data integration with full or partial observations. - Tianjian Yang; Wei Vivian Li (CoRR, 2025)