Xiaoqi Zheng, Ph.D., Professor                    

 Director of Bioinformatics Core,

 The Center for Single-Cell Omics (CSCOmics), School of Public Health,

 Shanghai Jiao Tong University School of Medicine

 Address: 227 South Chongqing Road, Shanghai, China

 Email: xqzheng@shsmu.edu.cn or xqzheng@shnu.edu.cn

 Website: https://xiaoqizheng.github.io/index.html

Dr. Xiaoqi Zheng obtained his Ph.D. of Applied Mathematics from Dalian University of Technology in 2009. He then worked in Department of Mathematics of Shanghai Normal University, and prompted to full professor in 2017. In the end of 2022, he joined in School of Public health, Shanghai Jiao Tong University School of Medicine, and served as Bioinformatics Core Director in Center for Single-Cell Omics. Dr. Zheng’s research interests include developing bioinformatics/statistical methods for high-throughput sequencing data, and bio-medical data analyses using deep learning based Artificial Intelligent methods.

Research interests:

1. Computational tools for single cell RNA sequencing and spatial transcriptomics data;

2. Heterogeneity of tumor revealed by DNA methylation

3. AI models (Statistical learning / Deep learning) in biomedical research

Education Experience:

2006 - 2009, Ph.D., Computational Biology, Dalian University of Technology.

2004 - 2006, M.S., Applied Mathematics, Dalian University of Technology.

2000 - 2004, B.S., Applied Mathematics, Shandong Normal University.

Work Experience:

2022.11 - Present, Professor, School of Public Health, Shanghai Jiao Tong University School of Medicine.

2017.09 - 2022.11, Professor, Department of Mathematics, Shanghai Normal University.

2018.07 - 2018.09, Visiting scientist, Hao Wu lab, Department of Biostatistics and Bioinformatics, Emory University.

2012.09 - 2017.09, Associated professor, Department of Mathematics, Shanghai Normal University.

2012.12 - 2014.02, Visiting scientist, Xiaole Shirley Liu lab, Harvard School of Public Health, Harvard University.

2009.06 - 2012.09, Assistant professor, Department of Mathematics, Shanghai Normal University.

Representative publications (#: cofirst author, *: corresponding author) :

[1] Wei N, Nie Y, Liu L*, Zheng X*, Wu HJ*, Secuer: Ultrafast, scalable and accurate clustering of single-cell RNA-seq data, PLoS Computational Biology 2022, doi.org/10.1371/journal.pcbi.1010753.

[2] Ding Y, Cai K, Liu L, Zhang Z, Zheng X*, Shi J*, mHapTk: a comprehensive toolkit for the analysis of DNA methylation haplotypes, Bioinformatics. 2022, 38(22):5141-5143.

[3] Zhang Z#, Dan Y#, Xu Y, Zhang J, Zheng X*, Shi J*: The DNA methylation haplotype (mHap) format and mHapTools, Bioinformatics 2021, 37 (24):4892-4894.

[4] Zhang W#, Li Z, Wei N, Wu H-J, Zheng X*: Detection of differentially methylated CpG sites between tumor samples with uneven tumor purities. Bioinformatics 2020, 36(7):2017-2024.

[5] Qin Y#, Zhang W#, Sun X, Nan S, Wei N, Wu HJ, Zheng X*: Deconvolution of heterogeneous tumor samples using partial reference signals. PLoS Computational Biology 2020, 16(11): e1008452.

[6] T Xu, X Zheng, B Li, P Jin, Z Qin, H Wu: A comprehensive review of computational prediction of genome-wide features, Briefings in bioinformatics 2020, 21(1), 120-134.

[7] Liu X, Liu T, Shang Y, Dai P, Zhang W, Lee BJ, Huang M, Yang D, Wu Q, Liu LD, Zheng X, Zhou BO, Dong J, Yeap LS, Hu J, Xiao T, Zha S, Casellas R, Liu XS, Meng FL: ERCC6L2 promotes DNA orientation-specific recombination in mammalian cells, Cell research 2020, 30 (9):732-744.

[8] Hu X, Zhang J, Wang J, Fu J, Li T, Zheng X, Wang B, Gu S, Jiang P, Fan J, Carroll, MC, Wucherpfennig K, Hacohen N, Zhang F, Zhang P, Liu JS*, Li B*, Liu XS*: Widespread B cell clonal expansions and related mechanism of immune evasion in human cancers, Nature Genetics 2019, 51(3):560-567.

[9] Fan H#, Lv P#, Huo X, Wu J, Wang Q, Cheng L, Liu Y, Tang Q, Zhang L, Zhang F, Zheng X, Wu H, Wen B*: The nuclear matrix protein HNRNPU maintains 3D genome architecture globally in mouse hepatocytes, Genome Research, 2018, 28:192-202.

[10] Niu B#, Paulson JN, Zheng X, Kolter R*: Simplified and Representative Bacterial Community of Maize Roots. P Natl Acad Sci USA 2017, 114 (12): E2450-E2459.

[11] Zheng X#*, Zhang N#, Wu HJ, Wu H*: Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies. Genome Biology 2017, 18:17.

[12] Zheng X#*, Zhong S: From structure to function, how bioinformatics help to reveal functions of our genomes. Genome Biology 2017, 18:183.

[13] Zhang W#, Feng H#, Wu H*, Zheng X*, Accounting for Tumor purity improves cancer subtype classification from DNA methylation data, Bioinformatics 33(17), 2017, 2651–2657.

[14] Ni T#, Li XY#, Lu N#, An T, Liu ZP, Fu R, Lv WC, Zhang YW, Xu XJ, Grant Rowe R, Lin YS, Scherer A, Feinberg T, Zheng XQ, Chen BA, Liu XS, Guo QL, Wu ZQ*, Weiss SJ*: Snail1-dependent p53 repression regulates expansion and activity of tumour-initiating cells in breast cancer. Nat Cell Biol 2016, 18:1221-1232.

[15] Wang F#, Zhang N, Wang J, Wu H#, Zheng X*: Tumor purity and differential methylation in cancer epigenomics. Briefings in Functional Genomics 2016, 15:408-419.

[16] Zhang N#, Wu HJ#, Zhang W, Wang J, Wu H*, Zheng X*: Predicting tumor purity from methylation microarray data. Bioinformatics 2015, 31:3401-3405.

[17] Zhang N#, Wang H#, Fang Y, Wang J*, Zheng X*, Liu XS*: Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model. PLoS Computational Biology 2015, 11:e1004498.

[18] Dong Z#, Zhang N#, Li C, Wang H, Fang Y, Wang J, Zheng X*: Anticancer drug sensitivity prediction in cell lines from baseline gene expression through recursive feature selection. BMC Cancer 2015, 15:489.

[19] Zheng X#, Zhao Q#, Wu H-J#, Li W, Wang H, Meyer CA, Qin QA, Xu H, Zang C, Jiang P, Li F, Hou Y, He J, Wang J, Wang J, Zhang P*, Zhang Y*, Liu XS*: MethylPurify: tumor purity deconvolution and differential methylation detection from single tumor DNA methylomes. Genome Biology 2014, 15:419.

[20] Li L#, Yu S, Xiao W, Li Y, Huang L, Zheng X*, Zhou S*, Yang H*: Sequence-based identification of recombination spots using pseudo nucleic acid representation and recursive feature extraction by linear kernel SVM. BMC bioinformatics 2014, 15:340.

[21] Zhu J#, Qin Y, Liu T, Wang J, Zheng X*: Prioritization of candidate disease genes by topological similarity between disease and protein diffusion profiles. BMC bioinformatics 2013, 14:S5.

[22] Wang J#, Zheng X*: Comparison of protein secondary structures based on backbone dihedral angles. J Theor Biol 2008, 250:382-387.

Core members:

-Director: Xiaoqi Zheng

-Technician: Wanxing Xu