Harrison College of Pharmacy

Faculty and Staff Directory

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Bio

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Research Interests

Dr. Zongliang Yue is an assistant research professor at Auburn University. His past research has focused on utilizing biological data mining, systems biology, network biology, machine learning, visual analytics, and translational informatics to improve human health. He has also constructed several web servers and applications for functional genomics analysis and drug repositioning. Working at Harrison College of Pharmacy allows me to engage in interdisciplinary projects focused on developing machine learning models that enable tailored interventions in prescription and treatment to enhance patient outcomes.

Dr. Yue's research involves characterizing driving genes and underlying molecular mechanisms using multi-omics and single-cell data. He expanded his research to focus on cohort discovery and risk stratification for precision medicine, leveraging advanced AI methodologies. Additionally, he is a session chair of the Midsouth Computational Biology and Bioinformatics Society and serves on the editorial boards of JMIR Bioinformatics and Biotechnology, and DNA and Cell Biology Reports. He is also a topic editor in Frontiers in Artificial Intelligence and special guest editor of Biology (MDPI).

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Funded Research

University of Alabama-Birmingham
6/1/2025-6/1/2026
Development of PAGER 3.0 in Advancing Functional Genomics Analysis
Role: Principle Investigator
Total project funding awarded: $30,000

NASEM Early Career Fellow
9/1/2025-8/31/2027
Research Fellowship Human Health and Community Resilience Track
Role: Principle Investigator
Total project funding awarded: $76,000

Department of Energy (DOE) Joint Genome Institute (JGI)
5/1/2025-4/30/2027
Unraveling the Crosstalk in Poplar's Transcriptional Regulatory Network for Drought Tolerance and Wood Formation using DAP-seq Technology
Role: Co-Principle Investigator

Department of Energy (DOE) Joint Genome Institute (JGI)
11/1/2025-10/31/2027
Linking Lignin Engineering to drought Stress Resilience: RNA-Seq and Metabolomic Insights in Lignin Biosynthetic Pathway Edited Populus
Role: Co-Principle Investigator

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Selected Publications

Full Publication Listing

1. Fengyuan Huang, Robert S. Welner, Jake Y. Chen*, Zongliang Yue*, (2024) PAGER-scFGA: Unveiling Cell Functions and Molecular Mechanisms in Cell Trajectories through Single-Cell Functional Genomics Analysis, Front. in Bioinformatics. https://doi.org/10.3389/fbinf.2024.1336135.
2. Zongliang Yue, Nicholas P. McCormick, Oluchukwu M. Ezeala, Spencer H. Durham, Salisa C. Westrick. (2024) EMSIG: Uncovering Factors Influencing COVID-19 Vaccination Across Different Subgroups Charactered by Embedding-based Spatial Information Gain Vaccines. Vaccines. https://doi.org/10.3390/vaccines12111253.
3. Zongliang Yue, Sara Jaradat, Jingjing Qian. (2024) Prediction of cognitive impairment among Medicare beneficiaries using a machine learning approach. Archives of Gerontology and Geriatrics. https://doi.org/10.1016/j.archger.2024.105623.
4. Zongliang Yue, Xiangzhong Xue, Jingjing Qian. (2024) The association between polypharmacy and health-related quality of life among older adults with prostate cancer, Journal of Geriatric Oncology. https://doi.org/10.1016/j.jgo.2024.101772.
5. Zongliang Yue, Radomir Slominski, Samuel Bharti and Jake Y. Chen*, (2022) PAGER Web APP: An interactive, online gene set and network interpretation tool for functional genomics, Front. in Genetics. https://doi.org/10.3389/fgene.2022.820361.
6. Zongliang Yue#, Eric Zhang#, Clark Xu, Sunny Khurana, Nishant Batra, Son Dang, and Jake Y. Chen* (2021) PAGER-CoV: A Pathway, Annotated-list and Gene-signature Electronic Repository for Coronavirus Diseases Studies. Nucleic Acids Research. https://doi.org/10.1093/nar/gkaa1094.
7. Zongliang Yue, Qi Zheng, Michael T. Neylon, Minjae Yoo, Jimin Shin, Zhiying Zhao, Aik Choon Tan, and Jake Y. Chen§ (2017) PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology. Nucleic Acids Research. https://doi.org/10.1093/nar/gkx1040.

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Teaching

AU Engineering College Capstone Project COMP-7980
AU Honor College HONOR-3987

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Graduate Students Advised

Santoshi Borra, M.S. Program, Luddy School of Informatics, Indiana University Computing, and Engineering, IU (advisor)
Quang-Huy Nguyen, Ph.D. Program, Computer Science Department, Samuel Ginn College of Engineering (co-chair)
Sabina Tiwari, Ph.D. Program, College of Forestry, Wildlife and Environment (co-chair)
Liangliang Xu, Ph.D. Program, Computer Science Department, Samuel Ginn College of Engineering (co-chair)

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