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Zhongshan Cheng, PhD

Zhongshan Cheng, PhD

  • Bioinformatics Research Scientist, Genomics


Postdoc Associate - Yale University, CT, US
Postdoc Associate
- Queen's University, Kingston, Canada
, Microbiology - The University of Hong Kong, Hong Kong


Dr. Zhongshan Cheng specializes in human genetics and cancer genomics. He created a bioinformatics pipeline, Post-GWAS Explorer for Functional Indels and SNPs (PExFInS), to integrate genetic variants with expression quantitative trait loci (eQTLs) data and human genome functional annotation data from public databases. He also discovered a novel signal in the gene, RGMA, predisposing European Americans to opioid dependence. This finding has garnered considerable attentions from multiple media, including CNN and YaleNews. In addition, he found a new host gene, MCOLN1, predisposing African American to opioid overdose.

Research Interests

  • Human genetics
  • Cancer genomics

Selected Publications

Cheng ZS, Yang BZ, Zhou H, Nunez Y, Kranzler HR, Gelernter J, 2019, Genome-wide scan identifies opioid overdose risk locus close to MCOLN1. Addiction Biology, 

Cheng ZS, Zhou H, Sherva R, Farrer L, Kranzler HR, Gelernter J, 2018, Genome-wide association study identifies a regulatory variant of RGMA associated with opioid dependence in European Americans. Biological Psychiatry 84:762-770. 

Cheng ZS, Phokaew C, Chou YL, Lai DB, Meyers J, Agrawal A, Kranzler HR, Farrer L, Gelernter J, 2019, A regulatory variant of CHRM3 is associated with cannabis-induced hallucinations in European Americans. Translational Psychiatry 9(1):309.

Zhou H, Cheng ZS, Nicholas B, John HK, Lindsay AF, Kranzler HR, Gelernter J, 2018. Genome-wide association study identifies glutamate ionotropic receptor GRIA4 as a risk gene for comorbid nicotine dependence and major depression. Translational Psychiatry, 84:762-770. 

Levey DF, Polimanti R, Cheng ZS, Zhou H, Nuñez YZ, Jain S, He F, Sun X, Ursano RJ, Kessler RC, Smoller JW, Stein MB, Kranzler HR, Gelernter J, 2019. Genetic associations with suicide attempt severity and genetic overlap with major depression. Translational Psychiatry, 9, 22. 

Cheng ZS, Zhou J, Chu H, Li C, Wong D, Yang D, Song YQ, Zheng BJ, Yuen KY, 2015. PExFInS: Post-GWAS Explorer for Functional Indels and SNPs. Sci Rep, 5:17302 

Cheng ZS*, Zhou J*, To KK, Chu H, Li C, Wong D, Yang D, Zheng SF, Hao K, Bossé Y, et al, 2015. The identification of TMPRSS2 as the susceptible gene for severe illness of 2009 pandemic A(H1N1) influenza and infection of A(H7N9) influenza. J Infect Dis, 212(8):1214-1221

Chen Y*, Zhou J*, Cheng ZS, Yang SG, Chu H, Fan Y, Li C, Wong BHY, Zheng S, Zhu Y, et al, 2015. Functional variants regulating LGALS1 (Galectin 1) expression affect human susceptibility to influenza A(H7N9). Sci Rep, 17(5):8517.

Chu H*, Zhou J*, Wong BHY, Li C, Cheng ZS, Lin X, Kwok-Man Poon V, Sun T, Choi-Yi Lau C, Fuk-Woo Chan J et al. 2014. Productive replication of Middle East respiratory syndrome coronavirus in monocyte-derived dendritic cells modulates innate immune response. Virology, 454-455:197-205. 

Zhou J*, Chu H*, Li C, Wong BH, Cheng ZS, Poon VK, Sun T, Lau CC, Wong KK, Chan JY et al. 2014.  Active replication of Middle East respiratory syndrome coronavirus and aberrant induction of inflammatory cytokines and chemokines in human macrophages: implications for pathogenesis. J Infect Dis, 209(9):1331-1342. 

Sun SF, Fan J, Cheng ZS, Cai Y, Li GH, Pang Y. 2013. The effect of gamma sterilization on the insecticidal toxicity of engineered and conventional bacillus thuringiensis strains. J Econ Entomol, 106(1):36-42.

To KK, Zhou J, Song YQ, Hung IF, Ip WC, Cheng ZS, Chan AS, Kao RY, Wu AK, Chau S et al. 2013.Surfactant protein B gene polymorphism is associated with severe influenza. Chest, 145:1237-1243. 

Sun SF, Cheng ZS, Fan J, Cheng XH, Pang Y. 2012. The utility of camptothecin as a synergist of bacillus huringiensis var. kurstaki and nucleopolyhedroviruses against trichoplusia ni and spodoptera exigua. J Econ Entomol, 105(4):1164-1170. 

Zhou J, To KKW, Dong H, Cheng ZS, Lau CCY, Poon VKM, Fan YH, Song YQ, Tse H, Chan KH et al. 2012. A functional variation in CD55 increases the severity of 2009 pandemic H1N1 influenza A virus infection. J Infect Dis, 206(4):495-503. 

Last update: June 2020