† co-first author       ✉ corresponding author

Comprehensive infectome analysis reveals diverse infectious agents with zoonotic potential in wildlife.
Hou X†✉, Wang J†, Wang DX†, Chen Y†, Li XX†✉, Wu WC, Le SJ, Mei SQ, Liu HL, Feng Y, Yang LF, Shi PB, Ren ZR, Yang L, He HJ, Song WJ, Chen J, Zhu MM, Jiang ZW, Li XM, Guo D, Holmes EC, Deng ZQ✉, Shi M✉. bioRxiv. 2025. 

Using artificial intelligence to document the hidden RNA virosphere.
Hou X†, He Y†, Fang P, Mei SQ, Xu Z, Wu WC, Tian JH, Zhang S, Zeng ZY, Gou QY, Xin GY, Le SJ, Xia YY, Zhou YL, Hui FM, Pan YF, Eden JS, Yang ZH, Han C, Shu YL, Guo D, Li J, Holmes EC✉, Li ZR✉, Shi M✉. Cell. 2024.
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Virome characterization of game animals in China reveals a spectrum of emerging pathogens.
He WT†, Hou X†, Zhao J†, Sun J, He H, Si W, Wang J, Jiang Z, Yan Z, Xing G, Lu M, Suchard MA, Ji X, Gong W, He B, Li J, Lemey P, Guo D, Tu C, Holmes EC✉, Shi M✉, Su S✉. Cell. 2022.
> Nat Rev Microbio news
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The diversity and evolutionary relationships of ticks and tick-borne bacteria collected in China.
Tian J†, Hou X†, Ge M, Xu H, Yu B, Liu J, Shao R, Holmes EC, Lei C✉, Shi M✉. Parasites & vectors. 2022.

Isolation and identification of a novel Phlebovirus, Hedi virus, from sandflies collected in China.
Xu Z†, Fan N†, Hou X†, Wang J, Fu S, Song J, Shi M✉, Liang G✉. Viruses. 2021. 

Infectome analysis of small mammals in Southern China reveals ecological associations and emerging threats from diverse pathogens.
Xin GY†, Wang DX†, Zhang X†, Cen QQ, Peng MW, Liao YQ, Wang J, Le SJ, Cheng JX, Wu WC, Hou X, Luo GY, Gou QY, Kong JB, Pan Z, Li DQ, Gan SP, Chen A, Zhao HL, Shi PB, Ren ZR, Zhao WQ, Liu JJ, Jia PH, Sun CY, Lin WQ, Wu J, Kuang GP, Chen JD, Li JH, Holmes EC, Deng ZQ✉, Shi M✉. bioRxiv. 2025.

Metagenomic analysis of individual mosquito viromes reveals the geographical patterns and drivers of viral diversity.
Pan YF†, Zhao H†, Gou QY†, Shi PB, Tian JH, Feng Y, Li K, Yang WH, Wu D, Tang G, Zhang B, Ren Z, Peng S, Luo GY, Le SJ, Xin GY, Wang J, Hou X, Peng MW, Kong JB, Chen XX, Yang CH, Mei SQ, Liao YQ, Cheng JX, Wang J, Chaolemen, Wu YH, Wang JB, An T, Huang X, Eden JS, Li J, Guo D, Liang G, Jin X, Holmes EC, Li B, Wang D,, Li J✉, Wu WC✉, Shi M✉. Nat Ecol Evol. 2024.

A total infectome approach to understand the etiology of infectious disease in pigs.
Huang X†, Wu W†, Tian X, Hou X, Cui X, Xiao Y, Jiao Q, Zhou P, Liu L, Shi W, Chen L, Sun Y, Yang Y, Chen J, Zhang G, Liu J, Holmes EC, Cai X, An T✉, Shi M✉. Microbiome. 2022.

Trafficked Malayan pangolins contain viral pathogens of humans.
Shi WF†, Shi M†, Que TC†, Cui XM†, Ye RZ†, Xia LY, Hou X, Zheng JJ, Jia N, Xie X, Wu WC, He MH, Wang HF, Wei YJ, Wu AQ, Zhang SF, Pan YS, Chen PY, Wang Q, Li SS, Zhong YL, Li YJ, Tan LH, Zhao L, Jiang JF✉, Hu YL✉, Cao WC✉. Nat Microbiol. 2022.

Total RNA sequencing of Phlebotomus chinensis sandflies in China revealed viral, bacterial, and eukaryotic microbes potentially pathogenic to humans.
Wang J†, Gou QY†, Luo GY†, Hou X, Liang G, Shi M✉. Emerg Microbes Infect. 2022.

Beta-Hydroxysteroid Dehydrogenase Genes in Orange-Spotted Grouper (Epinephelus coioides): Genome-Wide Identification and Expression Analysis During Sex Reversal.
Xiao L†, Guo Y†, Wang D, Zhao M, Hou X, Li S, Lin H, Zhang Y✉. Front Genet. 2020.