James J. Cai - RankMe

17 papers Journal 15Unranked 2

Year	Rank	Type	Title / 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

Kai Greshake, Sahar Abdelnabi, Shailesh Mishra, Christoph Endres, Thorsten Holz, Mario Fritz