During my Ph.D. training (2016-2021), I became very interested in cellular reprogramming and have been working on this area through statistical model. Mounting important scientific problems are involved in cellular reprogramming, such as cell differentiation, tumor generation, and disease occurrence. I have completed several works through statistics, optimization, and graphical model methods using multi-omics data such as RNA-seq, ATAC-seq, ChIP-seq, and HiC. I investigated the combination of transcription factors by set cover problem, which identified safeguard TFs systematically. This work tried to throw light on the mechanism of cellular reprogramming from a macro perspective. I also focused on several specific cases. ERG fusion always occurs along with the loss of basal cells and increasing luminal cells. I verified the reprogramming from basal to luminal induced by ERG overexpression. I found ERG represses the basal marker Trp63 by binding the enhancers and then regulates the expression of Trp63 by chromatin interaction of enhancers and the promoter of Trp63. I further constructed the regulatory network in the context of wild type and ERG overexpression, comparing them systematically by identifying the regulatory modules. Other cases are the characteristic subtypes of pancreatic carcinoma and hepatocellular carcinoma, which can be taken as the mutual transformation from one subtype to another. I linked the subtype and drug response by statistics, which would guide clinical treatment.
My research interest is to build optimizational and statistical model for cell reprogramming and cell fate determination by integrating multi-omics data.
Yuan, Qiuyue, and Zhana Duren. “Integration of single-cell multi-omics data by regression analysis on unpaired observations.” Genome Biology 23, no. 1 (2022): 160.
Shi, Xiaohan, Yunguang Li, Qiuyue Yuan, Shijie Tang, Shiwei Guo, Yehan Zhang, Juan He et al. “Integrated profiling of human pancreatic cancer organoids reveals chromatin accessibility features associated with drug sensitivity.” Nature Communications 13, no. 1 (2022): 2169.
Qiuyue Yuan, and Yong Wang. 3Scover: Identifying Safeguard TF from Cell Type-TF Specificity Network by an Extended Minimum Set Cover Model[J]. iScience, 2020, 23(6): 101227.
Fei Li, Qiuyue Yuan (Co-first), Wei Di, Xinyi Xia, Zhuang Liu, Ninghui Mao, Lin Li, Chunfeng Li, Juan He, Yunguang Li, Wangxin Guo, Xiaoyu Zhang, Yiqin Zhu, Rebiguli Aji, Shangqian Wang, Xinyuan Tong, Hongbin Ji, Ping Chi, Brett Carver, Yong Wang, Yu Chen, and Dong Gao. ERG orchestrates chromatin interactions to drive prostate cell fate reprogramming [J]. The Journal of Clinical Investigation, 2020, 130(11): 5924-41.
Jingxue Xin, Hui Zhang, Yaoxi He, Zhana Duren, Caijuan Bai, Lang Chen, Xin Luo, DongSheng Yan, Chaoyu Zhang, Xiang Zhu, Qiuyue Yuan, Zhanying Feng, Chaoyiing Cui, Xuebin Qi, Ouzhuluobu NA, Wing Wong, Yong Wang, and Bing Su. Chromatin accessibility landscape and regulatory network of high-altitude hypoxia adaptation[J]. Nature Communications, 2020, 11(1): 1- 20.
Can Jin, Xin Peng, Qing Liu, Xinhan Ye, Lang Chen, Qiuyue Yuan, Xiang-Sun Zhang, LingYun Wu, Yong Wang. An Optimization Method for Calibrating Wireline Conveyance Tension[C] Complex Systems Design & Management: Proceedings of the 4th International Conference on Complex Systems Design & Management Asia and of the 12th Conference on Complex Systems Design & Management CSD&M 2021. Springer Nature, 159.
Zou, Meng, Zhana Duren, Qiuyue Yuan, Henry Li, Andrew Paul Hutchins, Wing Hung Wong, and Yong Wang. “MIMIC: an optimization method to identify cell type-specific marker panel for cell sorting.” Briefings in Bioinformatics (2021).
Zhou, Guofeng, Shaoyan Sun, Qiuyue Yuan, Run Zhang, Ping Jiang, Guangyu Li, Yong Wang, and Xiao Li. “Multiple-Tissue and Multilevel Analysis on Differentially Expressed Genes and Differentially Correlated Gene Pairs for HFpEF.” Frontiers in Genetics 12 (2021).