近年来，率先开展青藏高原野生动物微生物研究，提出反向病原学理论，即改变应对传染病的被动局面，发现、分离和研究新的微生物，评估潜在的公共卫生意义，预防可能发生的新发传染病。已经发现、命名和发表40余种新的细菌，其中4个新细菌具有潜在医学意义。 发现并发表了一些新的病毒，如喜马拉雅型蜱传脑炎病毒、新型小双节RNA病毒等。合作发现新型甲肝病毒、荆门病毒，以及未知病毒若干等。创立细菌宏分类学方法。1996年获国家自然科学基金杰出青年基金，1997年获国家科技进步二等奖，2001年获何梁何利奖，发表SCI论文200余篇，包括JAMA、 Lancet、Nature、Clinical Infectious Disease、Emerging Infectious Diseases等著名期刊。

近年来承担的科研和咨询项目：

1. 中国工程院战略研究与咨询项目：人类传染病第三次重大转变发展趋势预测

及应对策略研究，350万，2022-2023（负责，南开大学为课题承担单位）

2. 中国医学科学院创新单元：发现新细菌

3. 中国工程院咨询项目“新型冠状病毒等野生动物源新发传染病防控策略”。2020年4月-9月（负责）。

4. 国家自然科学基金委重大项目 “动物源性病原体及其对人致病性”。2013-2017（负责）。

5. 中国工程院和国家自然科学基金委联合资助的重大咨询项目“我国未来传染病和发现新病原战略研究”2016-1017（负责）

6. 中国工程院重大咨询课题“全民健康与医药卫生事业国家发展战略研究 课题三 新型国家预防医学体系建立研究报告”（负责）2014-2016

7. 中国工程院“中国工程科技2035发展战略研究”“医药卫生领域课题”（负责人之一）2015-2017

8. 中国工程院重大咨询项目“我国医药卫生人才培养战略研究”子课题“我国公共卫生人才培养战略研究”（负责）2016-2018.

科技杂志任职：

1. Emerging Microbial Infection, Associate Editor

2. Frontier of Medicine, Member of editorial Board

3. 微生物学报副主编

4. 中国人兽共患病学报副主编

5. 疾病监测主编

6. 首都公共卫生杂志  主编

7. 中国公共卫生杂志主编

8. Editor-in-Chief, Journal of Biosafety and Biosecurity

部分论文：

1. Xu, J. (2019). Reverse microbial etiology: A research field for predicting and preventing emerging infectious diseases caused by an unknown microorganism. Journal of Biosafety and Biosequrity 1(1): 19-21.

2. Luo, X. L., S. Lu, D. Jin, J. Yang, S. S. Wu and J. Xu (2018). Marmota himalayana in the Qinghai-Tibetan plateau as a special host for bi-segmented and unsegmented picobirnaviruses. Emerg Microbes Infect 7(1): 20.

3. Dai X, Shang G, Lu S, Yang J, Xu J (2018) A new subtype of eastern tick-borne encephalitis virus discovered in Qinghai-Tibet Plateau, China. Emerg Microbes Infect 7:74

4. Du P, Zheng H, Zhou J, Lan R, Ye C, Jing H, Jin D, Cui Z, Bai X, Liang J, Liu J, Xu L, Zhang W, Chen C, Xu J (2017) Detection of Multiple Parallel Transmission Outbreak of Streptococcus suis Human Infection by Use of Genome Epidemiology, China, 2005. Emerg Infect Dis 23:204-211

5. Guo WP, Lin XD, Wang W, Tian JH, Cong ML, Zhang HL, Wang MR, Zhou RH, Wang JB, Li MH, Xu J, Holmes EC, Zhang YZ (2013) Phylogeny and origins of hantaviruses harbored by bats, insectivores, and rodents. PLoS Pathog 9:e1003159

6. Li CX, Shi M, Tian JH, Lin XD, Kang YJ, Chen LJ, Qin XC, Xu J, Holmes EC, Zhang YZ (2015) Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses. Elife.

7. Li K, Lin XD, Wang W, Shi M, Guo WP, Zhang XH, Xing JG, He JR, Wang K, Li MH, Cao JH, Jiang ML, Holmes EC, Zhang YZ (2015) Isolation and characterization of a novel arenavirus harbored by Rodents and Shrews in Zhejiang province, China. Virology 476:37-42。

8. Liu Q, Xu W, Lu S, Jiang J, Zhou J, Shao Z, Liu X, Xu L, Xiong Y, Zheng H, Jin S, Jiang H, Cao W, Xu J (2018) Landscape of emerging and re-emerging infectious diseases in China: impact of ecology, climate, and behavior. Front Med 12:3-22

9. Lu S, Jin D, Wu S, Yang J, Lan R, Bai X, Liu S, Meng Q, Yuan X, Zhou J, Pu J, Chen Q, Dai H, Hu Y, Xiong Y, Ye C, Xu J (2016) Insights into the evolution of pathogenicity of Escherichia coli from genomic analysis of intestinal E. coli of Marmota himalayana in Qinghai-Tibet plateau of China. Emerg Microbes Infect 5:e122

10. Meng X, Lu S, Yang J, Jin D, Wang X, Bai X, Wen Y, Wang Y, Niu L, Ye C, Rossello-Mora R, Xu J (2017) Metataxonomics reveal vultures as a reservoir for Clostridium perfringens. Emerg Microbes Infect 6:e9

11. Qin XC, Shi M, Tian JH, Lin XD, Gao DY, He JR, Wang JB, Li CX, Kang YJ, Yu B, Zhou DJ, Xu J, Plyusnin A, Holmes EC, Zhang YZ (2014) A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors. Proc Natl Acad Sci U S A 111:6744-6749

12. Rohde H, Qin J, Cui Y, Li D, Loman NJ, Hentschke M, Chen W, Pu F, Peng Y, Li J, Xi F, Li S, Li Y, Zhang Z, Yang X, Zhao M, Wang P, Guan Y, Cen Z, Zhao X, Christner M, Kobbe R, Loos S, Oh J, Yang L, Danchin A, Gao GF, Song Y, Li Y, Yang H, Wang J, Xu J, Pallen MJ, Wang J, Aepfelbacher M, Yang R, Consortium EcOHGAC-S (2011) Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4. N Engl J Med 365:718-724

13. Shao Z, Li W, Ren J, Liang X, Xu L, Diao B, Li M, Lu M, Ren H, Cui Z, Zhu B, Dai Z, Zhang L, Chen X, Kan B, Xu J (2006) Identification of a new Neisseria meningitidis serogroup C clone from Anhui province, China. Lancet 367:419-423

14. Shi M, Lin XD, Vasilakis N, Tian JH, Li CX, Chen LJ, Eastwood G, Diao XN, Chen MH, Chen X, Qin XC, Widen SG, Wood TG, Tesh RB, Xu J, Holmes EC, Zhang YZ (2015) Divergent Viruses Discovered in Arthropods and Vertebrates Revise the Evolutionary History of the Flaviviridae and Related Viruses. J Virol 90:659-669

15. Shi M, Lin XD, Tian JH, Chen LJ, Chen X, Li CX, Qin XC, Li J, Cao JP, Eden JS, Buchmann J, Wang W, Xu J, Holmes EC, Zhang YZ (2016) Redefining the invertebrate RNA virosphere. Nature 540:539-543

16. Sun Q, Knirel YA, Wang J, Luo X, Senchenkova SN, Lan R, Shashkov AS, Xu J (2014) Serotype-converting bacteriophage SfII encodes an acyltransferase protein that mediates 6-O-acetylation of GlcNAc in Shigella flexneri O-antigens, conferring on the host a novel O-antigen epitope. J Bacteriol 196:3656-3666

17. Xu J, Lu S, Wang H, Chen C (2013) Reducing exposure to avian influenza H7N9. Lancet 381:1815-1816

18. Xu L, Stige LC, Chan KS, Zhou J, Yang J, Sang S, Wang M, Yang Z, Yan Z, Jiang T, Lu L, Yue Y, Liu X, Lin H, Xu J, Liu Q, Stenseth NC (2017) Climate variation drives dengue dynamics. Proc Natl Acad Sci U S A 114:113-118

19. Ye C, Zhu X, Jing H, Du H, Segura M, Zheng H, Kan B, Wang L, Bai X, Zhou Y, Cui Z, Zhang S, Jin D, Sun N, Luo X, Zhang J, Gong Z, Wang X, Wang L, Sun H, Li Z, Sun Q, Liu H, Dong B, Ke C, Yuan H, Wang H, Tian K, Wang Y, Gottschalk M, Xu J (2006) Streptococcus suis sequence type 7 outbreak, Sichuan, China. Emerg Infect Dis 12:1203-1208

20. Ye C, Bai X, Zhang J, Jing H, Zheng H, Du H, Cui Z, Zhang S, Jin D, Xu Y, Xiong Y, Zhao A, Luo X, Sun Q, Gottschalk M, Xu J (2008) Spread of Streptococcus suis sequence type 7, China. Emerg Infect Dis 14:787-791

21. Ye C, Zheng H, Zhang J, Jing H, Wang L, Xiong Y, Wang W, Zhou Z, Sun Q, Luo X, Du H, Gottschalk M, Xu J (2009) Clinical, experimental, and genomic differences between intermediately pathogenic, highly pathogenic, and epidemic Streptococcus suis. J Infect Dis 199:97-107

22. Yu H, Jing H, Chen Z, Zheng H, Zhu X, Wang H, Wang S, Liu L, Zu R, Luo L, Xiang N, Liu H, Liu X, Shu Y, Lee SS, Chuang SK, Wang Y, Xu J, Yang W, Streptococcus suis study g (2006) Human Streptococcus suis outbreak, Sichuan, China. Emerg Infect Dis 12:914-920

23. Yu JM, Li LL, Zhang CY, Lu S, Ao YY, Gao HC, Xie ZP, Xie GC, Sun XM, Pang LL, Xu JG, Lipkin WI, Duan ZJ (2016) A novel hepatovirus identified in wild woodchuck Marmota himalayana. Sci Rep 6:22361

24. Zhang L, Liu Y, Ni D, Li Q, Yu Y, Yu XJ, Wan K, Li D, Liang G, Jiang X, Jing H, Run J, Luan M, Fu X, Zhang J, Yang W, Wang Y, Dumler JS, Feng Z, Ren J, Xu J (2008) Nosocomial transmission of human granulocytic anaplasmosis in China. JAMA 300:2263-2270

25. Zhang N, Lan R, Sun Q, Wang J, Wang Y, Zhang J, Yu D, Hu W, Hu S, Dai H, Du P, Wang H, Xu J (2014) Genomic portrait of the evolution and epidemic spread of a recently emerged multidrug-resistant Shigella flexneri clone in China. J Clin Microbiol 52:1119-1126

26. Zhang YZ, Zhou DJ, Xiong Y, Chen XP, He YW, Sun Q, Yu B, Li J, Dai YA, Tian JH, Qin XC, Jin D, Cui Z, Luo XL, Li W, Lu S, Wang W, Peng JS, Guo WP, Li MH, Li ZJ, Zhang S, Chen C, Wang Y, de Jong MD, Xu J (2011) Hemorrhagic fever caused by a novel tick-borne Bunyavirus in Huaiyangshan, China. Zhonghua Liu Xing Bing Xue Za Zhi 32:209-220

27. Zhang YZ, He YW, Dai YA, Xiong Y, Zheng H, Zhou DJ, Li J, Sun Q, Luo XL, Cheng YL, Qin XC, Tian JH, Chen XP, Yu B, Jin D, Guo WP, Li W, Wang W, Peng JS, Zhang GB, Zhang S, Chen XM, Wang Y, Li MH, Li Z, Lu S, Ye C, de Jong MD, Xu J (2012) Hemorrhagic fever caused by a novel Bunyavirus in China: pathogenesis and correlates of fatal outcome. Clin Infect Dis 54:527-533

28. Zhang YZ, Zhou DJ, Qin XC, Tian JH, Xiong Y, Wang JB, Chen XP, Gao DY, He YW, Jin D, Sun Q, Guo WP, Wang W, Yu B, Li J, Dai YA, Li W, Peng JS, Zhang GB, Zhang S, Chen XM, Wang Y, Li MH, Lu X, Ye C, de Jong MD, Xu J (2012) The ecology, genetic diversity, and phylogeny of Huaiyangshan virus in China. J Virol 86:2864-2868

29. Zhang YZ, Xu J (2016) The emergence and cross species transmission of newly discovered tick-borne Bunyavirus in China. Curr Opin Virol 16:126-131.

30. Ren SX, Fu G, Jiang XG, Zeng R, Miao YG, Xu H, Zhang YX, Xiong H, Lu G, Lu LF, Jiang HQ, Jia J, Tu YF, Jiang JX, Gu WY, Zhang YQ, Cai Z, Sheng HH, Yin HF, Zhang Y, Zhu GF, Wan M, Huang HL, Qian Z, Wang SY, Ma W, Yao ZJ, Shen Y, Qiang BQ, Xia QC, Guo XK, Danchin A, Saint Girons I, Somerville RL, Wen YM, Shi MH, Chen Z, Xu JG, Zhao GP (2003) . Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing. Nature 422:888-893