Research Areas: 

1. The genetic and epigenetic mechanisms of human diseases. 

2. Research of disease-related gene functions. 

3. Bioinformatics.  

My lab concentrates on the exploration of the genetic basis of human diseases. Through classic molecular cytogenetic techniques, genomics, epigenetics, bioinformatics, cell biology and model organism, we accomplished various systematic and original works and achieved multiple significant results in the field of disease genes identification and function exploration. Based on the traditional positional candidate cloning strategy, we identified multiple genes associated with human single gene diseases (Nat Genet, 2001; Nat Genet, 2002; Genomics, 2002; Am J Hum Genet, 2010; J Mol Cell Biol, 2014). Relied on dry-wet combination experiments, we set up an effective statistic and analytic method to identify the core functional variants in the genome of complex diseases (PLoS Genet, 2011; PLoS One, 2010). Further, we have found a series of new rules for gene expression regulation (Genome Biol, 2008; Genome Biol, 2009; Genome Biol, 2009; Cell Res, 2010; Mol Biol Evol, 2013; Nucleic Acids Res, 2014). These studies provide a solid foundation for further illumination of diseases related mechanisms and development for therapeutic drugs. Our proceedings also presented new thoughts for the study on related diseases. Our group published more than 120 papers, and at the same time has been awarded four international patent grants and five national patent grants. Our research achievements have been awarded one national and two provincial major prizes including the second prize of National Natural Science Award, top and second prize of Shanghai Natural Science Award. We are now using integrative multi-omics approaches to unravel mechanisms of tumor initiation and progression. By integrative analyses of multi-omics data, we expect to obtain an in-depth understanding of cancer biology, and contribute our effort to precision medicine by finding new avenues to targeted cancer therapies.  

Brief Biography: 

Education   

Aug. 1995 - Oct.1997: Postdoctoral fellowship, Abt Hans Lehrach In Max-Planck, Institute for Moleculare Genetik  

Sept. 1992 - July 1995: Graduate School, Peking Union Medical College  

Aug. 1988 - Aug. 1992: Department of Cell Biology, Institute of Hematology, Chinese Academy of Medical Science 

Sept. 1983 - July 1988: Medical Department, Shandong University School of Medicine, Bachelor Degree of Medicine 

Sept. 1981 - July 1983: BeiZhen Middle School, Shandong 

Work Experience  

2017 - present: Professor, Principal Investigator, Shanghai Institute of Nutrition and Health, CAS 

Apr. 2002 - 2016: Professor, Principal Investigator, Institute of Health Sciences , Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine  

Aug. 2000 - Mar. 2002: Professor, Principal Investigator, Shanghai Research Center of Biotechnology, Chinese Academy of Sciences  

Jan. 1999 - Aug. 2000: Associate Professor, Principal Investigator, Shanghai Research Center of Biotechnology, Chinese Academy of Sciences 

Dec. 1997 - Dec. 1998: Associate Professor, Shanghai Research Center of Biotechnology, Chinese Academy of Sciences 

Selected Publications: (*Corresponding Author)

1. Wang R, Zhang Y, Guo S, Pei S, Guo W, Wu Z, Wang H, Wang M, Li Y, Zhu Y, Meng LH, Lang J, Jin G*, Xiao Y*, Hu L*, Kong X*. Single-cell RNA sequencing reveals the suppressive effect of PPP1R15A inhibitor Sephin1 in antitumor immunity. iScience 2023 Jan 13;26(2):105954
2. Guo W^#, Zhang Y^#, Guo S^#, Mei Z, Liao H, Dong H, Wu K, Ye H, Zhang Y, Zhu Y, Lang J, Hu L*, Jin G*, Kong X*. Tumor microbiome contributes to an aggressive phenotype in the basal-like subtype of pancreatic cancer. Commun Biol 2021 Aug 31;4(1):1019
3. Liao H^#, Zhang Y, Guo W, Wang X, Wang H, Ye H, Wu K, Zhang YH, Guo L, Zhu Y, Guo Y, Hu L*, Liu G*, Kong X*. Characterization of the Blood and Cerebrospinal Fluid Microbiome in Children with Bacterial Meningitis and Its Potential Correlation with Inflammation. mSystems 2021 Jun 29;6(3):e0004921
4. Huang J, Zhang Y, Ma Q, Zhang Y, Wang M, Zhou Y, Xing Z, Jin M, Hu L, Kong X*. Natural Selection on Exonic SNPs Shapes Allelic Expression Imbalance (AEI) Adaptability in Lung Cancer Progression. Front Genet 2020 Jun 24;11:665
5. Ma Q, Wu K, Li H, Li H, Zhu Y, Hu G*, Hu L*, Kong X*. ONECUT2 overexpression promotes RAS-driven lung adenocarcinoma progression. Sci Rep 2019 Dec 27;9(1):20021
6. Zhang YH^#, Huang T^#, Chen L^#, Xu Y, Hu Y, Hu LD*, Cai Y*, Kong X*. Identifying and analyzing different cancer subtypes using RNA-seq data of blood platelets. Oncotarget 2017 Sep 15;8(50):87494-87511
7. Zhang YH, Xing Z, Liu C, Wang S, Huang T, Cai YD, Kong X*. Identification of the core regulators of the HLA I-peptide binding process. Sci Rep 2017 Feb 17;7:42768
8. Wang M, Zhang P, Shu Y, Yuan F, Zhang Y, Zhou Y, Jiang M, Zhu Y, Hu L, Kong X*, Zhang Z*. Alternative splicing at GYNNGY 5' splice sites: more noise, less regulation. Nucleic Acids Res 2014 Dec 16;42(22):13969-13980
9. Xie J, Wu X, Ren H, Wang W, Wang Z, Pan X, Hao X, Tong J, Ma J, Ye Z, Meng G, Zhu Y, Kiryluk K, Kong X, Hu L*, Chen N*. COL4A3 mutations cause focal segmental glomerulosclerosis. J Mol Cell Biol 2014 Dec;6(6):498-505
10. Yin S, Yang J, Lin B, Deng W, Zhang Y, Yi X, Shi Y, Tao Y, Cai J, Wu CI, Zhao G, Hurst LD, Zhang J, Hu L, Kong X*. Exome sequencing identifies frequent mutation of MLL2 in non-small cell lung carcinoma from Chinese patients. Sci Rep 2014 Aug 12;4:6036
11. Zhang Y, Castillo-Morales A, Jiang M, Zhu Y, Hu L, Urrutia AO, Kong X*, Hurst LD*. Genes that escape X-inactivation in humans have high intraspecific variability in expression, are associated with mental impairment but are not slow evolving. Mol Biol Evol 2013 Dec;30(12):2588-2601
12. Liu Y, Zhang L, Xu S, Hu L, Hurst LD, Kong X*. Identification of two maternal transmission ratio distortion loci in pedigrees of the Framingham heart study. Sci Rep 2013;3:2147
13. Liu Y, Xu H, Chen S, Chen X, Zhang Z, Zhu Z, Qin X, Hu L, Zhu J, Zhao G, Kong X*. Genome-Wide Interaction-Based Association Analysis Identified Multiple New Susceptibility Loci for Common diseases. PLoS Genet 2011;7(3):e1001338
14. Zhang Z, Zhou L, Hu L, Zhu Y, Xu H, Liu Y, Chen X, Yi X, Kong X*, Hurst LD*. Nonsense-mediated decay targets have multiple sequence-related features that can inhibit translation. Mol Syst Biol 2010 Dec 14;6:442
15. Chen X, Li X, Wang P, Liu Y, Zhang Z, Zhao G, Xu H, Zhu J, Qin X, Chen S, Hu L, Kong X*. Novel association strategy with copy number variation for identifying new risk Loci of human diseases. PLoS One 2010 Aug 20;5(8):e12185