Selected Publications（in the past 5 years）

(1) Yanan Chen; Ruoyu Chen; Shaoqiang Zhang*; Yong Chen*: Navigating cell maps by deep learning integration of single-cell and spatially resolved transcriptomics, Briefings in Bioinformatics, 2026, 27(4):bbag404

(2) Nishi Gupta; Madison Dautle; Shaoqiang Zhang*; Yong Chen*: A Robust Deep Temporal Causal Discovery Platform for Single‐Cell Gene Regulatory Network Reconstruction, Advanced Intelligent Discovery, 2026:e202500247

(3) Liang Chen; Madison Dautle; Ruoying Gao; Shaoqiang Zhang*; Yong Chen*: Inferring Gene Regulatory Networks from Time-Series scRNA-seq Data via Granger Causal Recurrent Autoencoders, Briefings in Bioinformatics, 2025, 26(2):bbaf089

(4) Ruoying Gao; Thomas N. Ferraro; Liang Chen; Shaoqiang Zhang*; Yong Chen*: Enhancing Single-Cell and Bulk Hi-C Data Using a Generative Transformer Model, Biology, 2025, 14(3):288

(5) Lu Qin; Guangya Zhang; Shaoqiang Zhang*; Yong Chen*; Deep Batch Integration and Denoise of Single‐Cell RNA‐Seq Data, Advanced Science, 2024, 11(29): 2308934

(6) Alicia Petrany; Ruoyu Chen; Shaoqiang Zhang*; Yong Chen*, Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data, Genome Research, 2024,34(10):1636-1650

(7) Xiguo Zhou, Jingyi Pan, Liang Chen, Shaoqiang Zhang*, and Yong Chen*. DeepIMAGER: Deeply Analyzing Gene Regulatory Networks from scRNA-seq Data, Biomolecules, 2024, 14(7): 766.

(8) Tianyuan Lei; Ruoyu Chen; Shaoqiang Zhang*; Yong Chen*; Self-supervised deep clustering of single-cell RNA-seq data to hierarchically detect rare cell populations, Briefings in Bioinformatics, 2023, 24(6): bbad335

(9) Madison Dautle; Shaoqiang Zhang*; Yong Chen*; scTIGER: A Deep-Learning Method for Inferring Gene Regulatory Networks from Case versus Control scRNA-seq Datasets, International Journal of Molecular Sciences, 2023, 24(17): 13339

(10) Shaoqiang Zhang*; Linjuan Xie; Yaxuan Cui; Benjamin R. Carone; Yong Chen* ; Detecting Fear-Memory-Related Genes from Neuronal scRNA-seq Data by Diverse Distributions and Bhattacharyya Distance, Biomolecules, 2022, 12(8): 1130

(11) Atlas M Sardoo, Shaoqiang Zhang, Thomas N Ferraro, Thomas M Keck, Yong Chen*, Decoding brain memory formation by single-cell RNA sequencing, Briefings in Bioinformatics, 2022, 23(6): bbac412

(12) Yaxuan Cui; Shaoqiang Zhang*; Ying Liang; Xiangyun Wang; Thomas N Ferraro; Yong Chen* ; Consensus clustering of single-cell RNA-seq data by enhancing network affinity, Briefings in Bioinformatics, 2021, 22(6): bbab236