James J. Cai

17 papers Journal 15Unranked 2
YearRankTypeTitle / Venue / Authors
2025 J jnl
A Quantum Generative Framework for Modeling Single-Cell Transcriptomes with Gene-Gene and Cell-Cell Interactions.
CoRR
Selim Romero, Vignesh Kumar, Robert S. Chapkin, James J. Cai
2025 J jnl
Quantum annealing for enhanced feature selection in single-cell RNA sequencing data analysis.
Quantum Mach. Intell.
Selim Romero, Shreyan Gupta, Victoria Gatlin, Robert S. Chapkin, James J. Cai
2025 J jnl
scPOEM: robust co-embedding of peaks and genes revealing peak-gene regulation.
Bioinform.
Yan Zhong, Yuntong Hou, Yongjian Yang, Xinyue Zheng, James J. Cai
2024 J jnl
Controlled noise: evidence of epigenetic regulation of single-cell expression variability.
Bioinform.
Yan Zhong, Siwei Cui, Yongjian Yang, James J. Cai
2024 J jnl
Quantum Annealing for Enhanced Feature Selection in Single-Cell RNA Sequencing Data Analysis.
CoRR
Selim Romero, Shreyan Gupta, Victoria Gatlin, Robert S. Chapkin, James J. Cai
2023 J jnl
Interpretable modeling of time-resolved single-cell gene-protein expression with CrossmodalNet.
Briefings Bioinform.
Yongjian Yang, Yu-Te Lin, Guanxun Li, Yan Zhong, Qian Xu, James J. Cai
2022 J jnl
Quantum gene regulatory networks.
CoRR
Cristhian Roman-Vicharra, James J. Cai
2022 J jnl
rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database.
Bioinform.
Daniel Osório, Marieke L. Kuijjer, James J. Cai
2022 J jnl
scTenifoldKnk: An efficient virtual knockout tool for gene function predictions via single-cell gene regulatory network perturbation.
Patterns
Daniel Osório, Yan Zhong, Guanxun Li, Qian Xu, Yongjian Yang, Yanan Tian, Robert S. Chapkin, Jianhua Z. Huang, James J. Cai
2021 J jnl
Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control.
Bioinform.
Daniel Osório, James J. Cai
2020 — conf
Single-Cell Gene Regulatory Network Analysis Reveals Potential Mechanisms of Action of Antimalarials Against SARS-CoV-2.
ICCABS
James J. Cai, Daniel Osório
2020 J jnl
scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis.
Bioinform.
James J. Cai
2020 J jnl
scTenifoldNet: A Machine Learning Workflow for Constructing and Comparing Transcriptome-wide Gene Regulatory Networks from Single-Cell Data.
Patterns
Daniel Osório, Yan Zhong, Guanxun Li, Jianhua Z. Huang, James J. Cai
2018 J jnl
AEGS: identifying aberrantly expressed gene sets for differential variability analysis.
Bioinform.
Jinting Guan, Moliang Chen, Congting Ye, James J. Cai, Guoli Ji
2018 J jnl
Simulating variance heterogeneity in quantitative genome wide association studies.
BMC Bioinform.
Ahmad Al Kawam, Mustafa Alshawaqfeh, James J. Cai, Erchin Serpedin, Aniruddha Datta
2017 — conf
Simulating Variance Heterogeneity in Quantitative Genome Wide Association Studies.
BCB
Ahmad Al Kawam, Mustafa Alshawaqfeh, James J. Cai, Erchin Serpedin, Aniruddha Datta
2005 J jnl
MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution.
BMC Bioinform.
James J. Cai, David K. Smith, Xuhua Xia, Kwok-Yung Yuen