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Summary
Dr. Zhenqing Ye earned his BS and MS degrees in Cellular Biology from Lanzhou University, China, and completed his Ph.D. in Bioinformatics at Zhejiang University, China. He pursued postdoctoral training at Ohio State University and UT Health San Antonio. In 2016, Dr. Ye joined the Mayo Clinic as an informatics specialist and epigenomics group leader, a role he held until July 2020. Subsequently, he was appointed Assistant Professor (Research) at the Greehey Children’s Cancer Research Institute (GCCRI) at UT Health San Antonio, where he led the Bioinformatics facility as Manager.
In 2024, Dr. Ye joined the Lillehei Heart Institute in the Department of Cardiology at the University of Minnesota Medical School as an Assistant Professor. He has a strong interest in developing algorithms and software tools for analyzing large-scale biomedical datasets, particularly to uncover the molecular mechanisms hidden within high-dimensional data, including single-cell multi-omics and spatial-omics. He has collaborated extensively with biologists and clinicians, resulting in numerous peer-reviewed publications across fields such as cancer research, aging, immunology, and developmental biology.
Ye Z, Hu S, Yu J. (2008). Adaptive clustering algorithm for community detection in complex networks. Physical review E. 78(4):046115. PMID: 18999501.
Ye Z, Chen Z, Sunkel B, Frietze S, Huang TH, Wang Q, Jin VX. (2016) Genome-wide analysis reveals positional-nuclesome-oriented binding pattern of pioneer factor FOXA1. Nucleic Acids Res., 44(16):7540-54. PMID: 27458208.
Zhang P*, Wang D*, Zhao Y, Ren S, Gao K, Ye Z, Wang S, Pan CW, Zhu Y, Yan Y, Yang Y, Wu D, He Y, Zhang J, Lu D, Liu X, Yu L, Zhao S, Li Y, Lin D, Wang Y, Wang L, Chen Y, Sun Y, Wang C, Huang H. (2017). Intrinsic BET inhibitor resistance in SPOP-mutated prostate cancer is mediated by BET protein stabilization and AKT-mTORC1 activation. Nat Med., 23(9):1055-1062. PMID: 28805822.
Ye Z, Dong H, Li Y, Ma T, Huang H, Leong HS, Eckel-Passow JE, Kocher JP, Liang H, Wang L. (2018). Prevalent homozygous deletions of type I interferon and defensing genes in human cancers associate with immunotherapy resistance. Clin. Cancer Res., Doi: 10.1158/1078-0432.CCR-17-3008. PMID: 29618619.
Dr. Ye’s research primarily focuses on bioinformatics data analysis and algorithm development for genomics and epigenomics studies. With a strong interdisciplinary background in bioinformatics and cellular biology, he possesses expertise in high-dimensional, large-scale biomedical data analysis. This expertise is reflected in the development of several bioinformatics tools, including GESS (for exon skipping detection), ePEST (for ChIP-exo analysis), CircularLogo, and Spatial-Live for single-cell spatial-omics. Dr. Ye is passionate about uncovering the hidden molecular mechanisms behind biomedical big data through data mining and computational strategies. Additionally, he is interested in complex network studies, particularly the community structures within biological networks.