James J. Cai

According to our database, James J. Cai authored at least 16 papers between 2005 and 2026.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2026

QuantumXCT: Learning Interaction-Induced State Transformation in Cell-Cell Communication via Quantum Entanglement and Generative Modeling.

Selim Romero, Shreyan Gupta, Robert S. Chapkin, James J. Cai

CoRR, April, 2026

2025

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

Quantum Mach. Intell., December, 2025

A Quantum Generative Framework for Modeling Single-Cell Transcriptomes with Gene-Gene and Cell-Cell Interactions.

Selim Romero, Vignesh Kumar, Robert S. Chapkin, James J. Cai

CoRR, October, 2025

scPOEM: robust co-embedding of peaks and genes revealing peak-gene regulation.

Yan Zhong, Yuntong Hou, Yongjian Yang, Xinyue Zheng, James J. Cai

Bioinform., 2025

2024

Controlled noise: evidence of epigenetic regulation of single-cell expression variability.

Yan Zhong, Siwei Cui, Yongjian Yang, James J. Cai

Bioinform., 2024

2023

Interpretable modeling of time-resolved single-cell gene-protein expression with CrossmodalNet.

Yongjian Yang, Yu-Te Lin, Guanxun Li, Yan Zhong, Qian Xu, James J. Cai

Briefings Bioinform., September, 2023

2022

scTenifoldKnk: An efficient virtual knockout tool for gene function predictions via single-cell gene regulatory network perturbation.

Daniel Osório, Yan Zhong, Guanxun Li, Qian Xu, Yongjian Yang, Yanan Tian, Robert S. Chapkin, Jianhua Z. Huang, James J. Cai

Patterns, 2022

Quantum gene regulatory networks.

Cristhian Roman-Vicharra, James J. Cai

CoRR, 2022

rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database.

Daniel Osório, Marieke L. Kuijjer, James J. Cai

Bioinform., 2022

2021

Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control.

Daniel Osório, James J. Cai

Bioinform., 2021

2020

scTenifoldNet: A Machine Learning Workflow for Constructing and Comparing Transcriptome-wide Gene Regulatory Networks from Single-Cell Data.

Daniel Osório, Yan Zhong, Guanxun Li, Jianhua Z. Huang, James J. Cai

Patterns, 2020

scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis.

James J. Cai

Bioinform., 2020

Single-Cell Gene Regulatory Network Analysis Reveals Potential Mechanisms of Action of Antimalarials Against SARS-CoV-2.

James J. Cai, Daniel Osório

Proceedings of the Computational Advances in Bio and Medical Sciences, 2020

2018

AEGS: identifying aberrantly expressed gene sets for differential variability analysis.

Jinting Guan, Moliang Chen, Congting Ye, James J. Cai, Guoli Ji

Bioinform., 2018

2017

Simulating Variance Heterogeneity in Quantitative Genome Wide Association Studies.

Ahmad Al Kawam, Mustafa Alshawaqfeh, James J. Cai, Erchin Serpedin, Aniruddha Datta

Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

2005

MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution.

James J. Cai, David K. Smith, Xuhua Xia, Kwok-Yung Yuen

BMC Bioinform., 2005