Profile
Zhana Duren
Genetics and Biochemistry
Adjunct Asst Professor
864-656-6878
Self Regional Hall (Greenwood Genetic Center) 153 [Office]
Research Interests
A person’s genome typically contains millions of variants which represent the differences between this personal genome and the reference human genome. It is challenging to understand the mechanism of how these genetic variants contribute to disease because over 90% of trait-associated genetic variants are located in non-coding regions which don’t encode any protein-coding genes but may have regulatory functions. My research goal is to answer the key scientific question” How non-coding genetic variant act through cellular context specific gene regulatory network to influence phenotype”. To do this, we develop novel statistical machine learning methods and bioinformatics tools. Specific directions include 1) inference method of gene regulatory network by integrating different types of genomics data, 2) single-cell genomics data analysis, and 3) identification of causal variants for complex diseases by using cellular context specific gene regulatory networks.
Selected Publications
Qiuyue Yuan and Zhana Duren. Integration of single-cell multi-omics data by regression analysis on unpaired observations. Genome Biology (2022).
Zhana Duren*, Fengge Chang*, Fnu Naqing, Jingxue Xin, Qiao Liu, and Wing Hung Wong. Regulatory analysis of single cell multiome gene expression and chromatin accessibility data with scREG. Genome Biology (2022). (* Co-first)
Zhana Duren*, Wenhui Sophia Lu*, Joseph G Arthur, Preyas Shah, Jingxue Xin, Francesca Meschi, Miranda Lin Li, Corey M Nemec, Yifeng Yin, and Wing Hung Wong. Sc-compReg enables the comparison of gene regulatory networks between conditions using single-cell data. Nature Communications (2021). (* Co-first)
David G. Gennert, Rachel C. Lynn, Jeffrey M. Granja, Evan W. Weber, Maxwell R. Mumbach, Yang Zhao, Zhana Duren, Elena Sotillo, William J. Greenleaf, Wing H. Wong, Ansuman T. Satpathy, Crystal L. Mackall, and Howard Y. Chang. Dynamic chromatin regulatory landscape of human CAR T cell exhaustion. Proceedings of the National Academy of Sciences 118, no. 30 (2021): e2104758118.
Xiang Zhu, Zhana Duren, and Wing Hung Wong. Modeling regulatory network topology improves genome-wide analyses of complex human traits. Nature Communications (2021).
Jingxue Xin*, Hui Zhang*, Yaoxi He*, Zhana Duren*, Chaoying Cui*, Lang Chen, Xin Luo, Dong-Sheng Yan, Chaoyu Zhang, Xiang Zhu, Qiuyue Yuan, Xuebing Qi, Ouzhuluobu, Wing Hung Wong, Yong Wang, and Bing Su. Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation. Nature Communications (2020). (* Co-first)
Wenran Li*, Zhana Duren*, Rui Jiang, and Wing Hung Wong. A method for scoring the cell-type specific impacts of non-coding variants in personal genomics. Proceedings of the National Academy of Sciences (2020). (*Co-first)
Zhana Duren, Xi Chen, Jingxue Xin, Yong Wang and Wing Hung Wong. Time course regulatory analysis based on paired expression and chromatin accessibility data. Genome Research (2020): gr-257063.
Xianglong Zhang, David Hong, Shining Ma, Thomas Ward, Marcus Ho, Reenal Pattni, Zhana Duren, Atanas Stankov, Sharon Bade Shrestha, Joachim Hallmayer, Wing Hung Wong, Allan L. Reiss, and Alexander E. Urban. Integrated functional genomic analyses of Klinefelter and Turner syndromes reveal global network effects of altered X chromosome dosage. Proceedings of the National Academy of Sciences 117, no. 9 (2020): 4864-4873.
Xiang Zhu, Zhana Duren, Wing Hung Wong. Modeling regulatory network topology improves genome-wide analyses of complex human traits. BioRxiv (2020).
Wanwen Zeng*, Xi Chen*, Zhana Duren*, Yong Wang, Rui Jiang, and Wing Hung Wong. DC3 is a method for deconvolution and coupled clustering from bulk and single-cell genomics data. Nature Communications, 10.1 (2019): 1-11. (* Co-first)
Lingjie Li, Yong Wang, Jessica L.Torkelson, Gautam Shankar, Jillian M.Pattison, Hanson H.Zhen, Fengqin Fang, Zhana Duren, JingxueXin, Sadhana Gaddam, Sandra P.Melo, Samantha N.Piekos, Jiang Li, Eric J.Liaw, Lang Chen, Rui Li, Marius Wernig, Wing H. Wong, Howard Y. Chang, Anthony E. Oro. TFAP2C-and p63-Dependent Networks Sequentially Rearrange Chromatin Landscapes to Drive Human Epidermal Lineage Commitment. Cell stem cell 24.2 (2019): 271-284.
Zhana Duren, Xi Chen, Mahdi Zamanighomi, Wanwen Zeng, Ansuman T. Satpathy, Howard Y. Chang, Yong Wang, and Wing Hung Wong. Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations. Proceedings of the National Academy of Sciences 115.30 (2018): 7723-7728.
Mahdi Zamanighomi, Zhixiang Lin, Timothy Daley, Xi Chen, Zhana Duren, Alicia Schep, William J. Greenleaf, Wing Hung Wong. Unsupervised clustering and epigenetic classification of single cells. Nature Communications, 9.1 (2018): 2410.
Zhana Duren, Xi Chen, Rui Jiang, Yong Wang, and Wing Hung Wong. Modeling gene regulation from paired expression and chromatin accessibility data. Proceedings of the National Academy of Sciences (2017): 201704553.
