Institute of Pathogen Biology

Jian YANG Ph.D., Professor

Tel: 86-10-67875146/86-10-81219356
Email: yangj@ipbcams.ac.cn, ipb_yangjian@hotmail.com

Research interests:

Comparative genomics and molecular evolution of bacterial pathogens.

Microbial genomic database construction and data mining.

Microbiome analysis and metagenomics based pathogen discovery.

Selected publications:

Wang C, Chen M, Shao Y, Jiang M, Li Q, Chen L, Wu Y, Cen S, Waterfield NR, Yang J, Yang G: Genome wide analysis revealed conserved domains involved in the effector discrimination of bacterial type VI secretion system. Commun Biol 2023, 6(1):1195.
Liu B, Zhao P, Xu P, Han Y, Wang Y, Chen L, Wu Z, Yang J: A comprehensive dataset of animal-associated sarbecoviruses. Sci Data 2023, 10(1):681.
Yan MY, Zheng D, Li SS, Ding XY, Wang CL, Guo XP, Zhan L, Jin Q, Yang J, Sun YC: Application of combined CRISPR screening for genetic and chemical-genetic interaction profiling in Mycobacterium tuberculosis. Sci Adv 2022, 8(47):eadd5907.
Zhou S, Liu B, Han Y, Wang Y, Chen L, Wu Z, Yang J: ZOVER: the database of zoonotic and vector-borne viruses. Nucleic Acids Res 2022, 50(D1):D943-D949.
Liu B, Zheng D, Zhou S, Chen L, Yang J: VFDB 2022: a general classification scheme for bacterial virulence factors. Nucleic Acids Res 2022, 50(D1):D912-D917.
Song N, Chen L, Zhou Z, Ren X, Liu B, Zhou S, Wang C, Wu Y, Waterfield NR, Yang J, Yang G: Genome-wide dissection reveals diverse pathogenic roles of bacterial Tc toxins. PLoS Pathog 2021, 17(2):e1009102.
Zheng D, Pang G, Liu B, Chen L, Yang J: Learning transferable deep convolutional neural networks for the classification of bacterial virulence factors. Bioinformatics 2020, 36(12):3693-3702.
Chen L, Song N, Liu B, Zhang N, Alikhan NF, Zhou Z, Zhou Y, Zhou S, Zheng D, Chen M, Hapeshi A, Healey J, Waterfield NR, Yang J, Yang G: Genome-wide Identification and Characterization of a Superfamily of Bacterial Extracellular Contractile Injection Systems. Cell Rep 2019, 29(2):511-521.e2.
Liu B, Zheng D, Jin Q, Chen L, Yang J: VFDB 2019: a comparative pathogenomic platform with an interactive web interface. Nucleic Acids Res 2019, 47(D1):D687-D692.
Zhou S, Ren X, Yang J, Jin Q: Evaluating the Value of Defensins for Diagnosing Secondary Bacterial Infections in Influenza-Infected Patients. Front Microbiol 2018, 9:2762.
Hicks ND, Yang J, Zhang X, Zhao B, Grad YH, Liu L, Ou X, Chang Z, Xia H, Zhou Y, Wang S, Dong J, Sun L, Zhu Y, Zhao Y, Jin Q, Fortune SM: Clinically prevalent mutations in Mycobacterium tuberculosis alter propionate metabolism and mediate multidrug tolerance. Nat Microbiol 2018, 3(9):1032-1042.

Zheng J, Chen L, Liu L, Li H, Liu B, Zheng D,Liu T, Dong J, Sun L, Zhu Y, Yang J, Zhang X, Jin Q: Proteogenomic Analysis and Discovery of Immune Antigens in Mycobacterium vaccae. Mol Cell Proteomics 2017, 16(9):1578-1590.
Chen L, Liu B, Wu Z, Jin Q, Yang J: DRodVir: A resource for exploring the virome diversity in rodents. J Genet Genomics 2017, 44(5):259-264.
Chen L, Zheng D, Liu B, Yang J, Jin Q: VFDB 2016: hierarchical and refined dataset for big data analysis--10 years on. Nucleic Acids Res 2016, 44(D1):D694-697.
Yang J, Zhang T, Guo L, Hu Y, Li J, Su H, Xiao Y, Ren X, Dong J, Sun L, Li L, Yang F, Wang J, Yuan H, Jin Q: Mutations of Novel Influenza A(H10N8) Virus in Chicken Eggs and MDCK Cells. Emerg Infect Dis 2014, 20(8):1541-1543.
Chen L, Liu B, Yang J, Jin Q: DBatVir: the database of bat-associated viruses. Database (Oxford) 2014, 2014:bau021.
Chang Z, Lu S, Chen L, Jin Q, Yang J: Causative species and serotypes of shigellosis in mainland china: systematic review and meta-analysis. PLoS One 2012, 7(12):e52515.

Chen L, Xiong Z, Sun L, Yang J, Jin Q: VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res 2012, 40(Database issue):D641-645.
Lu S, Zhang X, Zhu Y, Kim KS, Yang J, Jin Q: Complete genome sequence of the neonatal-meningitis-associated Escherichia coli strain CE10. J Bacteriol 2011, 193(24):7005.
Yang J, Yang F, Ren L, Xiong Z, Wu Z, Dong J, Sun L, Zhang T, Hu Y, Du J, Wang J, Jin Q: Unbiased parallel detection of viral pathogens in clinical samples by use of a metagenomic approach. J Clin Microbiol 2011, 49(10):3463-3469.
Yang J, Yang F, Huang F, Wang J, Jin Q: Subclinical infection with the novel Influenza A (H1N1) virus. Clin Infect Dis 2009, 49(10):1622-1623.
Wu Y, Yang J, Yang F, Liu T, Leng W, Chu Y, Jin Q: Recent dermatophyte divergence revealed by comparative and phylogenetic analysis of mitochondrial genomes. BMC Genomics 2009, 10:238.
Yan Y, Yang J, Dou Y, Chen M, Ping S, Peng J, Lu W, Zhang W, Yao Z, Li H, Liu W, He S, Geng L, Zhang X, Yang F, Yu H, Zhan Y, Li D, Lin Z, Wang Y, Elmerich C, Lin M, Jin Q: Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501. Proc Natl Acad Sci U S A 2008, 105(21):7564-7569.
Yang J, Chen L, Sun L, Yu J, Jin Q: VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics. Nucleic Acids Res 2008, 36(Database issue):D539-542.
Yang J, Chen L, Wang L, Zhang W, Liu T, Jin Q: TrED: the Trichophyton rubrum Expression Database. BMC Genomics 2007, 8:250.
Yang J, Nie H, Chen L, Zhang X, Yang F, Xu X, Zhu Y, Yu J, Jin Q: Revisiting the molecular evolutionary history of Shigella spp. J Mol Evol 2007, 64(1):71-79.
Peng J, Zhang X, Yang J, Wang J, Yang E, Bin W, Wei C, Sun M, Jin Q: The use of comparative genomic hybridization to characterize genome dynamics and diversity among the serotypes of Shigella. BMC Genomics 2006, 7:218.
Nie H, Yang F, Zhang X, Yang J, Chen L, Wang J, Xiong Z, Peng J, Sun L, Dong J, Xue Y, Xu X, Chen S, Yao Z, Shen Y, Jin Q: Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a. BMC Genomics 2006, 7:173.
Yang J, Chen L, Yu J, Sun L, Jin Q: ShiBASE: an integrated database for comparative genomics of Shigella. Nucleic Acids Res 2006, 34(Database issue):D398-401.
Yang F, Yang J, Zhang X, Chen L, Jiang Y, Yan Y, Tang X, Wang J, Xiong Z, Dong J, Xue Y, Zhu Y, Xu X, Sun L, Chen S, Nie H, Peng J, Xu J, Wang Y, Yuan Z, Wen Y, Yao Z, Shen Y, Qiang B, Hou Y, Yu J, Jin Q: Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res 2005, 33(19):6445-6458.
Chen L, Yang J, Yu J, Yao Z, Sun L, Shen Y, Jin Q: VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 2005, 33(Database issue):D325-328.
Yang J, Wang J, Chen L, Yu J, Dong J, Yao ZJ, Shen Y, Jin Q, Chen R: Identification and characterization of simple sequence repeats in the genomes of Shigella species. Gene 2003, 322:85-92.
Yang J, Wang J, Yao ZJ, Jin Q, Shen Y, Chen R: GenomeComp: a visualization tool for microbial genome comparison. J Microbiol Methods 2003, 54(3):423-426.