教师基本信息：
姓名：崔杰
职称：研究员
职务：研究组长
电子邮箱：jiecui@fudan.edu.cn
办公地点：湾谷科技园A1座附楼-401
办公电话：021-52888262
个人网页/课题组主页：https://orcid.org/0000-0001-8176-9951
研究方向：病原演化、病毒组
个人简介：
崔杰博士，复旦大学感染与健康研究院研究员，博士生导师。2011年博士毕业于华东师范大学。曾在宾夕法尼亚州立大学、悉尼大学、新加坡国立大学从事博士后研究。2016-2023年任中国科学院研究员及研究组长，2023年至今任复旦大学研究员及研究组长。崔杰博士主要从事病原演化、病毒组研究领域，为中国科学院百人计划入选者，为爱思唯尔中国高被引学者，入选全球前2%顶尖科学家榜单。迄今为止，已在国际核心期刊上发表SCI论文74余篇，总引用13000 余次，H因子为33。研究成果受到国内外同行的高度关注，多次被 Nature、Science、F1000等选为研究亮点。崔杰博士的团队围绕病原进化过程中的基础问题，病毒学、基因组流行病学、进化生物学、生物信息学、群体遗传学等多学科方法和手段追溯病原演化历程，探索病原跨物种传播机制，探索病毒圈的起源和演化，指导病原追踪、检测、宿主抗感染、抗病毒研究，开发病毒分子标识物，有望用于重大感染性疾病的追踪、诊断和早期预警。
授课情况：病原生物信息学
招生专业：微生物学
科研项目：重点研发计划、重大传染病专项、自然基金面上项目
代表性论文和论著：
1. Wang X, Chen Y, Cui J*. (2023) Identification of Cartilaginous Fish Endogenous Foamy Virus Rooting to Vertebrate Counterparts. J Virol. 18:e0181622.
2. Wang J, Ren M, Yu J, Hu M, Wang X, Ma W, Jiang X*, Cui J*. (2022) Single- cell RNA sequencing highlights the functional role of human endogenous retroviruses in gallbladder cancer. EBioMedicine 85:104319.
3. Zhang YY, Chen Y, Wei X, Cui J*. (2022) Viromes in marine ecosystems reveal remarkable invertebrate RNA virus diversity. Sci China Life Sci. 65:426-437.
4. Zhang YY, Liao ME, Wu F, Chen Y, Song Y, Sun Q, Jiang S, Huang H, Cui J*. (2021) Comparative study of the Malacostraca viromes between deep sea and shallow water. Sci Bull. 66:2458-2461.
5. He G, Ming L, L X, Song Y, Tang L, Ma M, Cui J*, Wang T*. (2021) Genetically divergent highly pathogenic avian influenza A(H5N8) viruses in wild birds, eastern China. Emerg Infect Dis. 27:2940-2943.
6. Chen Y, Zhang YY, Wei X, Cui J*. (2021) Multiple infiltration and cross- species transmission of foamy viruses across Paleozoic to Cenozoic era. J Virol. 92:e0048421.
7. Song Y, Li X, Wei X, Cui J*. (2021) Human Endogenous Retroviruses as Biomedicine Markers. Virol Sin. 36:852-858.
8. Tang X, Wu C, Li X, Song Y, Yao X, Wu X, Duan Y, Zhang H, Wang Y, Qian Z, Cui J*, Lu J*. (2020) On the origin and continuing evolution of SARS-CoV-2. Natl Sci Rev. 7:1012-1023.
9. Wei X, Li X, Cui J*. (2020) Evolutionary perspectives on novel coronaviruses identified in pneumonia cases in China. Natl Sci Rev. 7:239-242.
10. Li X, Song Y, Wong G, Cui J*. (2020) Bat origin of a new human coronavirus: there and back again. Sci China Life Sci. 63:461-462.
11. Chen Y, Wei X, Zhang G, Holmes EC, Cui J*. (2019) Identification and evolution of avian endogenous foamy viruses. Virus Evol. 5:vez049.
12. Wei X, Chen Y, Duan G, Holmes EC, Cui J*. (2019) A reptilian endogenous foamy virus sheds light on the early evolution of retroviruses. Virus Evol. 5:vez001.
13. Cui J, Li F, Shi ZL*. (2019) Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol. 17:181-192.
14. Wei X, Cui J*. (2018) Why were so few people infected with H7N9 influenza A viruses in China from late 2017 to 2018? Sci China Life Sci. 61:1442-1444.
15. Wei X, Chen M, Cui J*. (2017) Bayesian evolutionary analysis for emerging infectious disease: an exemplified application for H7N9 avian influenza viruses. Sci China Life Sci. 60:1392-1395.
16. Hu B, Zeng LP, Yang XL, Ge XY, Zhang W, Li B, Xie JZ, Shen XR, Zhang YZ, Wang N, Luo DS, Zheng XS, Wang MN, Daszak P, Wang LF, Cui J*, Shi ZL*. (2017) Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus. PLoS Pathog. 13:e1006698.
17. Du Y, Chen M, Yang J, Jia Y, Han S, Holmes EC, Cui J*. (2017) Molecular evolution and emergence of H5N6 avian influenza virus in central China. J Virol. 91:e00143-17.
18. Cui J*, Zhao W, Huang Z, Jarvis ED, Gilbert M, Walker PJ, Holmes EC, Zhang G*. (2014) Low frequency of paleoviral infiltration across the avian phylogeny. Genome Biol. 15:539.
19. Cui J, Schlub TE, Holmes EC. (2014). An allometric relationship between the genome length and virion volume of viruses. J Virol. 88:6403-6410.
20. Nielsen ACY, Gyhrs ML, Holmes EC, Cui J*. (2012). Co-circulation and persistence of genetically distinct Saffold viruses, Denmark. Emerg Infect Dis. 18:1694-1696.
21. Cui J, Holmes EC. (2012). Endogenous hepadnaviruses in the genome of the budgerigar (Melopsittacusundulatus) and the evolution of avian hepadnaviruses. J Virol. 86:7688-7691.
22. Cui J, Holmes EC. (2012). Endogenous lentiviruses in the ferret genome. J Virol. 86:3383-3385.
23. Cui J, Tachedjian M, Wang L, Tachedjian G, Wang LF, Zhang S. (2012). Discovery of retroviral homologs in bats: implications for the origin of mammalian gammaretroviruses. J Virol. 86:4288-4293.
24. Cui J*, Tachedjian G, Tachedjian M, Holmes EC, Zhang S, Wang LF. (2012). Identification of diverse groups of endogenous gammaretroviruses in mega and microbats. J Gen Virol. 93:2037-2045.
25. Cui J, Holmes EC. (2012). Evidence for an endogenous papillomavirus-like element in the platypus genome. J Gen Virol. 93:1362-1366.
26. Cui J, Pan YH, Zhang Y, Jones G, Zhang S. (2011). Progressive pseudogenization: vitamin C synthesis and its loss in bats. Mol Biol Evol. 28:1025-1031.
27. Cui J, Han N, Streicker D, Li G, Tang X, Shi Z, Hu Z, Zhao G, Fontanet A, Guan Y, Wang L, Jones G, Field HE, Daszak P, Zhang S. (2007). Evolutionary relationships between bat coronaviruses and their hosts. Emerg Infect Dis. 13:1526-1532.
Basic information：
Name：Jie Cui
Title：Professor
Position：Research group leader
E-mail：jiecui@fudan.edu.cn
Office location：Bay Valley Science Park, Block A1 Annex-401
Office phone：021-52888262
Personal web：https://orcid.org/0000-0001-8176-9951
Research direction：Virus evolution, virome
Personal profile：
Dr. Jie Cui is a research group leader and doctoral supervisor at the Institute of Infection and Health Research, Fudan University. He graduated from East China Normal University in 2011. He did postdoctoral research at Penn State University, the University of Sydney, and the National University of Singapore. From 2016 to 2023, he has been a professor and research group leader of the Chinese Academy of Sciences and a professor and research group leader of Fudan University since 2023. Dr. Jie Cui is mainly engaged in the field of pathogen evolution and virome research. He was selected by the Chinese Academy of Sciences 100 Talent Program, named as the most cited scholar of Elsevier China, and selected as one of the top 2% of the world's top scientists. So far, more than 74 SCI papers have been published in peer-reviewed journals, with a total of more than 13,000 citations, and the H-factor is 33. His research results have been highly concerned by domestic and foreign peers, and have been selected as research highlights by Nature, Science, F1000, etc. Dr. Cui's team focuses on the basic problems in the process of pathogen evolution, tracing the evolution of pathogens by using multidisciplinary methods such as virology, genomic epidemiology, evolutionary biology, bioinformatics, and population genetics, exploring the mechanism of pathogen cross-species transmission, exploring the origin and evolution of the virosphere, and guiding pathogen tracking, detection, and host anti-infection and anti-virus research. The development of viral molecular markers is expected to be used in the tracking, diagnosis, and early warning of infectious diseases.
Lectures：Pathogen bioinformatics
Admission major：Microbiology
Research projects：MOST, NSFC
Publications：
1. Wang X, Chen Y, Cui J*. (2023) Identification of Cartilaginous Fish Endogenous Foamy Virus Rooting to Vertebrate Counterparts. J Virol. 18:e0181622.
2. Wang J, Ren M, Yu J, Hu M, Wang X, Ma W, Jiang X*, Cui J*. (2022) Single- cell RNA sequencing highlights the functional role of human endogenous retroviruses in gallbladder cancer. EBioMedicine 85:104319.
3. Zhang YY, Chen Y, Wei X, Cui J*. (2022) Viromes in marine ecosystems reveal remarkable invertebrate RNA virus diversity. Sci China Life Sci. 65:426-437.
4. Zhang YY, Liao ME, Wu F, Chen Y, Song Y, Sun Q, Jiang S, Huang H, Cui J*. (2021) Comparative study of the Malacostraca viromes between deep sea and shallow water. Sci Bull. 66:2458-2461.
5. He G, Ming L, L X, Song Y, Tang L, Ma M, Cui J*, Wang T*. (2021) Genetically divergent highly pathogenic avian influenza A(H5N8) viruses in wild birds, eastern China. Emerg Infect Dis. 27:2940-2943.
6. Chen Y, Zhang YY, Wei X, Cui J*. (2021) Multiple infiltration and cross- species transmission of foamy viruses across Paleozoic to Cenozoic era. J Virol. 92:e0048421.
7. Song Y, Li X, Wei X, Cui J*. (2021) Human Endogenous Retroviruses as Biomedicine Markers. Virol Sin. 36:852-858.
8. Tang X, Wu C, Li X, Song Y, Yao X, Wu X, Duan Y, Zhang H, Wang Y, Qian Z, Cui J*, Lu J*. (2020) On the origin and continuing evolution of SARS-CoV-2. Natl Sci Rev. 7:1012-1023.
9. Wei X, Li X, Cui J*. (2020) Evolutionary perspectives on novel coronaviruses identified in pneumonia cases in China. Natl Sci Rev. 7:239-242.
10. Li X, Song Y, Wong G, Cui J*. (2020) Bat origin of a new human coronavirus: there and back again. Sci China Life Sci. 63:461-462.
11. Chen Y, Wei X, Zhang G, Holmes EC, Cui J*. (2019) Identification and evolution of avian endogenous foamy viruses. Virus Evol. 5:vez049.
12. Wei X, Chen Y, Duan G, Holmes EC, Cui J*. (2019) A reptilian endogenous foamy virus sheds light on the early evolution of retroviruses. Virus Evol. 5:vez001.
13. Cui J, Li F, Shi ZL*. (2019) Origin and evolution of pathogenic coronaviruses. Nat Rev Microbiol. 17:181-192.
14. Wei X, Cui J*. (2018) Why were so few people infected with H7N9 influenza A viruses in China from late 2017 to 2018? Sci China Life Sci. 61:1442-1444.
15. Wei X, Chen M, Cui J*. (2017) Bayesian evolutionary analysis for emerging infectious disease: an exemplified application for H7N9 avian influenza viruses. Sci China Life Sci. 60:1392-1395.
16. Hu B, Zeng LP, Yang XL, Ge XY, Zhang W, Li B, Xie JZ, Shen XR, Zhang YZ, Wang N, Luo DS, Zheng XS, Wang MN, Daszak P, Wang LF, Cui J*, Shi ZL*. (2017) Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus. PLoS Pathog. 13:e1006698.
17. Du Y, Chen M, Yang J, Jia Y, Han S, Holmes EC, Cui J*. (2017) Molecular evolution and emergence of H5N6 avian influenza virus in central China. J Virol. 91:e00143-17.
18. Cui J*, Zhao W, Huang Z, Jarvis ED, Gilbert M, Walker PJ, Holmes EC, Zhang G*. (2014) Low frequency of paleoviral infiltration across the avian phylogeny. Genome Biol. 15:539.
19. Cui J, Schlub TE, Holmes EC. (2014). An allometric relationship between the genome length and virion volume of viruses. J Virol. 88:6403-6410.
20. Nielsen ACY, Gyhrs ML, Holmes EC, Cui J*. (2012). Co-circulation and persistence of genetically distinct Saffold viruses, Denmark. Emerg Infect Dis. 18:1694-1696.
21. Cui J, Holmes EC. (2012). Endogenous hepadnaviruses in the genome of the budgerigar (Melopsittacusundulatus) and the evolution of avian hepadnaviruses. J Virol. 86:7688-7691.
22. Cui J, Holmes EC. (2012). Endogenous lentiviruses in the ferret genome. J Virol. 86:3383-3385.
23. Cui J, Tachedjian M, Wang L, Tachedjian G, Wang LF, Zhang S. (2012). Discovery of retroviral homologs in bats: implications for the origin of mammalian gammaretroviruses. J Virol. 86:4288-4293.
24. Cui J*, Tachedjian G, Tachedjian M, Holmes EC, Zhang S, Wang LF. (2012). Identification of diverse groups of endogenous gammaretroviruses in mega and microbats. J Gen Virol. 93:2037-2045.
25. Cui J, Holmes EC. (2012). Evidence for an endogenous papillomavirus-like element in the platypus genome. J Gen Virol. 93:1362-1366.
26. Cui J, Pan YH, Zhang Y, Jones G, Zhang S. (2011). Progressive pseudogenization: vitamin C synthesis and its loss in bats. Mol Biol Evol. 28:1025-1031.
27. Cui J, Han N, Streicker D, Li G, Tang X, Shi Z, Hu Z, Zhao G, Fontanet A, Guan Y, Wang L, Jones G, Field HE, Daszak P, Zhang S. (2007). Evolutionary relationships between bat coronaviruses and their hosts. Emerg Infect Dis. 13:1526-1532.