MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution. - James J. Cai; David K. Smith 001; Xuhua Xia; Kwok-Yung Yuen (BMC Bioinform., 2005)

AEGS: identifying aberrantly expressed gene sets for differential variability analysis. - Jinting Guan; Moliang Chen; Congting Ye; James J. Cai; Guoli Ji (Bioinform., 2018)

Simulating variance heterogeneity in quantitative genome wide association studies. - Ahmad Al Kawam; Mustafa Alshawaqfeh 001; James J. Cai; Erchin Serpedin; Aniruddha Datta (BMC Bioinform., 2018)

Single-Cell Gene Regulatory Network Analysis Reveals Potential Mechanisms of Action of Antimalarials Against SARS-CoV-2. - James J. Cai; Daniel Osório 004 (ICCABS, 2020)

scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis. - James J. Cai (Bioinform., 2020)

scTenifoldNet: A Machine Learning Workflow for Constructing and Comparing Transcriptome-wide Gene Regulatory Networks from Single-Cell Data. - Daniel Osório 004; Yan Zhong 003; Guanxun Li; Jianhua Z. Huang; James J. Cai (Patterns, 2020)

Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control. - Daniel Osório 004; James J. Cai (Bioinform., 2021)

rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database. - Daniel Osório 004; Marieke L. Kuijjer; James J. Cai (Bioinform., 2022)

Quantum gene regulatory networks. - Cristhian Roman-Vicharra; James J. Cai (CoRR, 2022)

scTenifoldKnk: An efficient virtual knockout tool for gene function predictions via single-cell gene regulatory network perturbation. - Daniel Osório 004; Yan Zhong 003; Guanxun Li; Qian Xu; Yongjian Yang 003; Yanan Tian; Robert S. Chapkin; Jianhua Z. Huang; James J. Cai (Patterns, 2022)

Interpretable modeling of time-resolved single-cell gene-protein expression with CrossmodalNet. - Yongjian Yang 003; Yu-Te Lin; Guanxun Li; Yan Zhong 003; Qian Xu; James J. Cai (Briefings Bioinform., 2023)

Quantum Annealing for Enhanced Feature Selection in Single-Cell RNA Sequencing Data Analysis. - Selim Romero; Shreyan Gupta; Victoria Gatlin; Robert S. Chapkin; James J. Cai (CoRR, 2024)