Yong Chen, Ph.D.

Yong Chen, Ph.D.

Yong Chen, Ph.D.
Assistant Professor

Yong Chen, Ph.D.

Contact Info
856-256-4500 ext. 53589
Science Hall 256E

Biography

 
Education:
BS (Mathematics), Shandong University
Joint PhD (Bioinformatics and Mathematics), University of Georgia and Shandong University
Postdoctoral (Bioinformatics and computational system biology), Tsinghua University
Postdoctoral (Cancer Epigenetics), University of Texas at Dallas
Lecturer (Mathematics), University of Texas at Dallas
 
Research Expertise: 
Bioinformatics | Cancer Epigenetics | Chromatin Interaction
 
My research has focused on omics studies, bioinformatics and mathematical modeling to study cancer for the purpose of understanding cancer biology as well as to discover clinical biomarkers. We are especially interested in designing novel experimental and computational methods to dissect 3-D chromatin interactions and how the disordered interactions (and epigenetic modifications) are associated with cancer/disease development. We have designed several methods/pipelines/database for omics data integration, deciphering cancer driver genes and pathways, and analysis of chromatin interaction data. We have also designed several mathematical models/methods to not only analyze next-generation sequencing data (bulk and single cell data), but also to understand biological mechanisms by using Bayesian statistics, differential equation system, network optimization and machine learning.
 
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)
 
Selected Publications:

(more here)

Xin Liu*, Yuanyu Zhang*,Yong Chen*, Mushan Li*, Feng Zhou*, Kailong Li, Hui Cao, Min Ni, Yuxuan Liu, Zhimin Gu, Kathryn E. Dickerson, Shiqi Xie, Gary C. Hon, Zhenyu Xuan, Michael Q. Zhang, Zhen Shao, Jian Xu. In Situ Capture of Chromatin Interactions by Biotinylated dCas9. Cell (170), 1-16. 2017 Aug; (*Co-first Author)

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

Haitao Li*, Congmin Wang*, Yong Chen*, Shaoqiang Zhang, Rongya Yang, Integrated transcriptomic analysis of Trichosporon Asahii uncovers the core genes and pathways of fluconazole resistance. Scientific Reports, 2017 19;7(1):17847. doi: 10.1038/s41598-017-18072-9. (*Co-first Author)

Yong Chen, Yunfei Wang, Zhenyu Xuan, Min Chen, Michael Q. Zhang. De novo deciphering three-dimensional chromatin interaction and topological domains by wavelet transformation of epigenetic profiles. Nucleic Acids Research. 2016 April; 44(11) 10.1093/nar/gkw225.

Yong Chen, Dandan Geng, Kristina Ehrhardt and Shaoqiang Zhang. Investigating Evolutionary Dynamics of RHA1 Operons. Evolutionary Bioinformatics. 2016:12 157-163.

Shaoqiang Zhang, Yong Chen*. CLIMP: Clustering Motifs via Maximal Cliques with Parallel Computing Design. PLOS ONE 2016, 11(8): E0160435. (*corresponding author)

Yong Chen, YunFeng Ding, Li Yang, Jinhai Yu, et al. Integrated omics studies delineates the dynamics of lipid droplets in Rhodococcus opacus PD630. Nucleic Acids Research. 2014 Jan; 42(2):1052-64.

Yong Chen, Thibault Jacquemin, Shuyan Zhang, Rui Jiang. Prioritizing protein complexes implicated in human diseases by network optimization. BMC System Biology 2014, 8:S2.

Yang Zhang*, Chen Yong*, Yu Jinhai, Liu Guiming, Huang Zhigang. Integrated transcriptome analysis reveals miRNA-mRNA crosstalk in laryngeal squamous cell carcinoma. Genomics, 2014 Jun 28, S0888-7543(14)00097-4. (*Co-first Author).

Yong Chen, Jingjing Hao, Wei Jiang, Xuegong Zhang, Tao Jiang, Rui Jiang. Identifying potential cancer driver genes by genomic data integration, Scientific Reports, 2013, doi:10.1038/srep03528.

11. Yong Chen, Xuebing Wu, Rui Jiang. Integrating human omics data to prioritize candidate genes. BMC Medical Genomics, 2013 6:57.

Yong Chen, Li Yang, Yunfeng Ding, Shuyan Zhang, Huina Zhang, Tong He, Fenglou Mao, Congyan Zhang, Chaoxing Huo, Pingsheng Liu, Tracing evolutionary footprints to identify novel gene functional linkages, PLOS ONE 2013, 8(6):e66817.

Huimin Na, Peng Zhang, Yong Chen, Xiaotong Zhu, Li Yang, Shimeng Xu, Fuquan Yang, Pingsheng Liu. Identification of Lipid Droplet Structure-like/ Resident Proteins in Caenorhabditis elegans. Biochim Biophys Acta. 2015 May 27. Pii: S0167-4889(15)00174-3.

Su Wen, Wang Y, Jia X, Wu W, Li L, Tian X, Li S, Wang C, Xu H, Cao J, Han Q, Xu S, Chen Yong, Zhong Y, Zhang X, Liu P, Gustafsson JA, Guan Y. Comparative proteomic study reveals 17β-HSD13 as a pathogenic protein innonalcoholic fatty liver disease. Proc Natl Acad Sci USA, 2014 Aug 5;111(31):111437-42.

Zhang P, Na H, Liu Z, Zhang S, Xue P, Yong Chen, Pu J, Peng G, Huang X, Yang F, Xie Z, Xu T, Xu P, Ou G, Zhang SO, Liu P. Proteomic study and marker protein identification of Caenorhabditis elegans lipid droplets. Mol Cell Proteomics. 2012 Apr 9.

Ding Y, Zhang S, Yang L, Na H, Zhang P, Zhang H, Wang Y, Yong Chen, Yu J, Huo C, Xu S, Martina Garaiova, Cong Y, Liu P. Isolating lipid droplets from multiple species. Nature Protocols. 8, 43-51 Dec 6. 2012.