856-256-4500 ext. 53589

Science Hall 256B

Digital Works: https://works.bepress.com/yong-chen/

 

Research Expertise: 
Quantum Computing | Artificial Intelligence (AI) | Deep Learning | Single-Cell Omics | Computational Systems Biology | Cancer Epigenetics | Computational Neuroscience

 

My research integrates artificial intelligence (AI), quantum computing, and systems biology to develop next-generation computational frameworks for analyzing complex biological systems. Building on extensive experience in bioinformatics and computational biology, I design deep-learning, statistical and mathematical models for single-cell and spatial omics data, with applications spanning gene regulatory network inference, chromatin architecture analysis, cancer biology and neuroscience. In cancer research, I develop computational approaches to dissect genome regulation and 3D chromatin organization in tumor contexts and to support mechanistic discovery from large-scale omics datasets. In neuroscience, I apply single-cell and multi-omics methods to study brain function and disease, with a particular focus on memory formation, neuronal plasticity and epilepsy-related molecular mechanisms. A central direction of my work is establishing Quantum Systems Biology, where hybrid quantum-classical algorithms are developed to address computationally hard problems in omics data analysis and biological network optimization. Supported by multiple NSF and NIH grants, I have led projects that combine graph learning, generative AI and quantum algorithms to improve scalability and biological interpretability. My long-term vision is to create open, community-driven platforms that integrate AI, quantum computing and mechanistic modeling to advance systems-level understanding of health and disease and enable transformative biomedical discovery.

 

Member of:
International Society for Computational Biology (ISCB) (https://www.iscb.org/)

the Society of Biological Engineering (SBE) (https://www.aiche.org/sbe)

American Mathematical Society (AMS) (https://www.ams.org/home/page)

IEEE (https://www.ieee.org/)

 

Selected Publications: (IF: Impact Factor; *Co-corresponding Author, ^#Co-first Author)

 

Shuqin Wang, Yuxin Wang, He Zhang, Shiyan Li, Alicia Petrany, Yong Chen*. Attention-guided Dynamic Re-parameterization for Enhancing Multi-Scale Feature Fusion in Convolutional Neural Networks, IEEE Access, vol. 13, pp. 185384-185399, 2025, doi: 10.1109/ACCESS.2025.3626650. (IF 3.6)

 

Madison Dautle, Yong Chen*. Single-Cell Hi-C Technologies and Computational Data Analysis. Adv Sci (Weinh). 2025 Mar;12(9):e2412232. doi: 10.1002/advs.202412232. Epub 2025 Jan 30. PMID: 39887949; PMCID: PMC11884588. (IF 15.10)

 

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. Brief Bioinform. 2025;26(2):bbaf089. doi:10.1093/bib/bbaf089 (IF 5.9)

 

Ruoying Gao, Thomas Ferraro, Liang Chen, Shaoqiang Zhang, Yong Chen*. Enhancing Single-Cell and Bulk Hi-C Data Using a Generative Transformer Model. Biology (Basel). 2025;14(3):288. Published 2025 Mar 12. doi:10.3390/biology14030288. (IF 3.9)

 

Petrany A, Ruoyu Chen, Zhang Shaoqiang Zhang, Yong Chen*. Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data. Genome Res. 2024 Oct 29;34(10):1636-1650. doi: 10.1101/gr.278843.123. PMID: 39406498. (IF 6.2).

 

Lu Qin, Guangya Zhang, Shaoqiang Zhang, Yong Chen*. Deep Batch Integration and Denoise of Single-Cell RNA-Seq Data. Adv Sci (Weinh). 2024 Aug;11(29):e2308934. doi: 10.1002/advs.202308934. Epub 2024 May 22. PMID: 38778573. (IF 15.10).

Xiguo Zhou, Jingyi Pan, Liang Chen, Shaoqiang Zhang, Yong Chen*. DeepIMAGER: Deeply Analyzing Gene Regulatory Networks from scRNA-seq Data. Biomolecules. 2024 Jun 27;14(7):766. doi: 10.3390/biom14070766. PMID: 39062480 (IF 6.06).

Tianyuan Lei, Ruoyu Chen, Shaoqiang Zhang, Yong Chen*. Self-supervised deep clustering of single-cell RNA-seq data to hierarchically detect rare cell populations. Brief Bioinform. 2023 Sep 22;24(6):bbad335. doi: 10.1093/bib/bbad335. PMID: 37769630 (IF 11.62)

Madison Dautle, Shaoqiang Zhang, and 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. https://doi.org/10.3390/ijms241713339. PMID: 37686146. (IF 6.2)

Atlas M Sardoo, Shaoqiang Zhang, Thomas N Ferraro, Thomas M Keck, Yong Chen*. Decoding brain memory formation by single-cell RNA sequencing. Brief in Bioinformatics. 2022 Sep 24:bbac412. doi: 10.1093/bib/bbac412. PMID: 36156112. (IF 11.62)

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 Aug 17;12(8):1130. doi: 10.3390/biom12081130. PMID: 36009024. (IF 4.57)

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. Brief Bioinform. 2021 Nov 5;22(6):bbab236. doi: 10.1093/bib/bbab236. PMID: 34160582. (IF 11.62)

Haipeng Xing, Yingru Wu, Michael Q Zhang, Yong Chen*. Deciphering hierarchical organization of topologically associated domains through change-point testing. BMC Bioinformatics. 2021 Apr 10;22(1):183. doi: 10.1186/s12859-021-04113-8. PMID: 33838653. (IF 3.17)

Haitao Li, Meihong Guo, Congmin Wang, Yibo Li, Anne Marie Fernandez, Thomas N Ferraro, Rongya Yang, Yong Chen*. Epidemiological study ofTrichosporon asahii infections over the past 23 years. Epidemiol Infect. 2020 Jul 24;148:e169. doi: 10.1017/S0950268820001624. PMID: 32703332. (IF 4.43)

Susmita G. Ramanand^#, Yong Chen^#, Jiapei Yuan^#, Kelly Daescu, Maryou Bk Lambros, Kathleen E Houlahan, Suzanne Carreira, Wei Yuan, GuemHee Baek, Adam Sharp, Alec Paschalis, Mohammed Kanchwala, Yunpeng Gao, Adam Aslam, Nida Safdar, Ganesh V Raj, Chao Xing, Paul C Boutros, Johann de Bono, Michael Q Zhang, Ram S Mani. The landscape of RNA polymerase II-associated chromatin interactions in prostate cancer. J Clin Invest. 2020 Aug 3;130(8):3987-4005. doi: 10.1172/JCI134260. PMID: 32343676. (IF 11.84)

Xin Liu^#, Yong Chen^#, Yuannyu Zhang, Yuxuan Liu, Giovanni A Botten, Hui Cao, Nan Liu, Stuart H. Orkin, Michael Q. Zhang, Jian Xu. Multiplexed Capture of Spatial Configuration and Temporal Dynamics of Locus-Specific 3D Chromatin Structure by Biotinylated dCas9, Genome Biology. 21, 59 March 2020. PMID: 32138752. (IF 13.21)

Shaoqiang Zhang, Ying Liang, Xiangyun Wang, Zhengchang Su, and Yong Chen*. FisherMP: Fully parallel algorithm for detecting combinatorial motifs from large ChIP-seq datasets. DNA Research, 10.1093/dnares/dsz004 2019 (IF 5.4).