Single-cell transcriptomics reveals that human milk feeding shapes neonatal immune cell interleukin signaling pathways in a nonrandomized clinical trial

Michael L Salinas, Bharath Kumar Mulakala, Laurie A Davidson, James J Cai, Sharon M Donovan, Robert S Chapkin, Laxmi Yeruva

Gene function revealed at the moment of sitochastic gene silencing

Shreyan Gupta, and James J. Cai

Quantum Annealing for Enhanced Feature Selection in Single-Cell RNA Sequencing Data Analysis

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

Controlled Noise: Evidence of epigenetic regulation of Single-Cell expression variability

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

Joint Bayesian estimation of cell dependence and gene associations in spatially resolved transcriptomic data

Arhit Chakrabarti, Yang Ni & Bani K. Mallick

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

Quantum gene regulatory networks

D Cristhian Roman-Vicharra & James J. Cai

Gene knockout inference with variational graph autoencoder learning single-cell gene regulatory networks

Yongjian Yang, Guanxun Li, Yan Zhong, Qian Xu, Bo-Jia Chen, Yu-Te Lin, Robert S Chapkin, James J Cai

scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs

D Cristhian Roman-Vicharra & James J. Cai

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

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

Association of pyroptosis and severeness of COVID-19 as revealed by integrated single-cell transcriptome data analysis.

Qian Xu, Yongjian Yang, Xiuren Zhang, James J Cai

A Unified Bayesian Framework for Bi-overlapping-Clustering Multi-omics Data via Sparse Matrix Factorization

Fangting Zhou, Kejun He, James J. Cai, Laurie A. Davidson, Robert S. Chapkin & Yang Ni

scInTime: A Computational Method Leveraging Single-Cell Trajectory and Gene Regulatory Networks to Identify Master Regulators of Cellular Differentiation.

Qian Xu, Guanxun Li, Daniel Osorio, Yan Zhong, Yongjian Yang, Yu-Te Lin, Xiuren Zhang, James J Cai

Single-cell RNA Sequencing Reveals How the Aryl Hydrocarbon Receptor Shapes Cellular Differentiation Potency in the Mouse Colon.

Yongjian Yang, Daniel Osorio, Laurie A Davidson, Huajun Han, Destiny A Mullens, Arul Jayaraman, Stephen Safe, Ivan Ivanov, James J Cai, Robert S Chapkin