Mamie HUI
Margaret IP
Christopher KC LAI
Rita WY NG
Zigui CHEN
Jessie LIANG
Siaw Shi BOON
Yun Kit YEOH
Chiu Yeung CHAN
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Faculty > Zigui CHEN
Personal information
Name Zigui CHEN
Academic / Professional Qualifications Ph.D
Academic title & affiliations Assistant Professor
Email zigui.chen@cuhk.edu.hk
Current Appointments
(Including honorary appointments)
  • Assistant Professor, Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong
  • Member, Papillomaviridae Study Group of the International Committee on Taxonomy of Viruses (ICTV)
  • Scientific Advisor, Papillomavirus Episteme (PaVE), NIAID/NIH
ORCID iD iconorcid.org/0000-0002-8577-1298
Research interest
Microbial evolution and bioinformatics - Using big dataset and bioinformatics to elucidate the genomic diversity and community dynamics of human gut microbiome, mycobiome and virome.
Molecular genomics and epigenetics of human papillomaviruses - Using molecular evolution and in-vitro cell models to understand the carcinogenicity of human papillomaviruses in cervical cancer.
Carcinogenic potential of human microbes in cancers - Using meta-community theory and in-vitro cell models to investigate the clinical impact of human microbiota in head and neck squamous cell carcinoma and colorectal cancer.

Understanding evolution of disease-causing microorganisms is the foundation of what we know about genetic basis, gene origins, and the adaptation of pathogens to a changing environment. It helps us solve biological problems that impact our health. Our group devotes to the studies of human microbial and viral evolution, genomics and epigenetics using analytic tools of systems biology and advanced bioinformatics pipeline. We have collaborated with several scientists and made fruitful contributions to identifying the genetic heterogeneity of human papillomaviruses (HPVs) causing cervical cancer. With the quick facilitation of Next-Generation Sequencing (NGS) and big dataset analysis, we are expanding our research interests in the complex ecological community of human microbiome interacting with human cancers and disease outcomes. Our mission is to develop and apply evolutionary and bioinformatics approaches to characterize and interpret the host-pathogen causality.
Postgraduate students
Information for Postgraduate Study in Department of Microbiology
Research Experience
9/1997 – 7/2002 PhD Student
Laboratory of Protozoa, Ocean University of China
9/2002 – 7/2009 Research Associate
Department of Microbiology and Immunology, Albert Einstein College of Medicine, NY, USA
7/2009 – 5/2015 Instructor
Department of Pediatrics, Albert Einstein College of Medicine, NY, USA
Name of award Second prize of “National Nature Science Award”, China
Date 2004
Place Ocean University of China
Name of award First prize of “Nature Science Award” by the Education Ministry of China
Date 2001
Place Ocean University of China
Grant General Research Fund (GRF)
Project title Association between oral microbiome, HPV and human epigenetic events in head and neck squamous cell carcinoma
Project period :2018.1.1 - 2020.12.31
Amount awarded HK $1,187,382
Role Principle Investigator
Grant General Research Fund (GRF)
Project title Evolutionary dynamics and genetic basis of carcinogenicity of primate papillomaviruses
Project period 2017.1.1 – 2019.12.31
Amount awarded HK $1,081,888
Role Principle Investigator
Publications (Selected publications relevance to viruses and microbiota)
  1. Chen Z, Hui PC, Hui M, Yeoh YK, Wong PY, Chan MCW, Wong MCS, Ng SC, Chan FKL, Chan PKS. Impact of Preservation Method and 16S rRNA Hypervariable Region on Gut Microbiota Profiling. mSystems 2019;4(1) doi: 10.1128/mSystems.00271-18 [published Online First: 2019/03/06]
  2. Wong MCS, Vlantis AC, Liang M, Wong PY, Ho WCS, Boon SS, Sze RKH, Leung C, Chan PKS, Chen Z. Prevalence and Epidemiologic Profile of Oral Infection with Alpha, Beta, and Gamma Papillomaviruses in an Asian Chinese Population. J Infect Dis 2018;218(3):388-97. doi: 10.1093/infdis/jiy160 [published Online First: 2018/07/10]
  3. Van Doorslaer K, Chen Z, Bernard HU, Chan PKS, DeSalle R, Dillner J, Forslund O, Haga T, McBride AA, Villa LL, Burk RD, Ictv Report C. ICTV Virus Taxonomy Profile: Papillomaviridae. J Gen Virol 2018 doi: 10.1099/jgv.0.001105 [published Online First: 2018/06/22]
  4. Nakatsu G, Zhou H, Wu WKK, Wong SH, Coker OO, Dai Z, Li X, Szeto CH, Sugimura N, Lam TY, Yu AC, Wang X, Chen Z, Wong MC, Ng SC, Chan MTV, Chan PKS, Chan FKL, Sung JJ, Yu J. Alterations in Enteric Virome Are Associated With Colorectal Cancer and Survival Outcomes. Gastroenterology 2018;155(2):529-41 e5. doi: 10.1053/j.gastro.2018.04.018 [published Online First: 2018/04/25]
  5. Goldman DL, Chen Z, Shankar V, Tyberg M, Vicencio A, Burk R. Lower airway microbiota and mycobiota in children with severe asthma. J Allergy Clin Immunol 2018;141(2):808-11 e7. doi: 10.1016/j.jaci.2017.09.018 [published Online First: 2017/10/17]
  6. Dai Z, Coker OO, Nakatsu G, Wu WKK, Zhao L, Chen Z, Chan FKL, Kristiansen K, Sung JJY, Wong SH, Yu J. Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers. Microbiome 2018;6(1):70. doi: 10.1186/s40168-018-0451-2 [published Online First: 2018/04/13]
  7. Coker OO, Dai Z, Nie Y, Zhao G, Cao L, Nakatsu G, Wu WK, Wong SH, Chen Z, Sung JJY, Yu J. Mucosal microbiome dysbiosis in gastric carcinogenesis. Gut 2018;67(6):1024-32. doi: 10.1136/gutjnl-2017-314281 [published Online First: 2017/08/03]
  8. Chen Z, Yeoh YK, Hui M, Wong PY, Chan MCW, Ip M, Yu J, Burk RD, Chan FKL, Chan PKS. Diversity of macaque microbiota compared to the human counterparts. Scientific reports 2018;8(1):15573. doi: 10.1038/s41598-018-33950-6 [published Online First: 2018/10/24]
  9. Chen Z, Schiffman M, Herrero R, DeSalle R, Anastos K, Segondy M, Sahasrabuddhe VV, Gravitt PE, Hsing AW, Chan PKS, Burk RD. Classification and evolution of human papillomavirus genome variants: Alpha-5 (HPV26, 51, 69, 82), Alpha-6 (HPV30, 53, 56, 66), Alpha-11 (HPV34, 73), Alpha-13 (HPV54) and Alpha-3 (HPV61). Virology 2018;516:86-101. doi: 10.1016/j.virol.2018.01.002 [published Online First: 2018/01/15]
  10. Chen Z, DeSalle R, Schiffman M, Herrero R, Wood CE, Ruiz JC, Clifford GM, Chan PKS, Burk RD. Niche adaptation and viral transmission of human papillomaviruses from archaic hominins to modern humans. PLoS Pathog 2018;14(11):e1007352. doi: 10.1371/journal.ppat.1007352 [published Online First: 2018/11/02]
  11. Agalliu I, Chen Z, Wang T, Hayes RB, Freedman ND, Gapstur SM, Burk RD. Oral Alpha, Beta, and Gamma HPV Types and Risk of Incident Esophageal Cancer. Cancer Epidemiol Biomarkers Prev 2018 doi: 10.1158/1055-9965.EPI-18-0287 [published Online First: 2018/08/09]
  12. Mirabello L, Yeager M, Yu K, Clifford GM, Xiao Y, Zhu B, Cullen M, Boland JF, Wentzensen N, Nelson CW, Raine-Bennett T, Chen Z, Bass S, Song L, Yang Q, Steinberg M, Burdett L, Dean M, Roberson D, Mitchell J, Lorey T, Franceschi S, Castle PE, Walker J, Zuna R, Kreimer AR, Beachler DC, Hildesheim A, Gonzalez P, Porras C, Burk RD, Schiffman M. HPV16 E7 Genetic Conservation Is Critical to Carcinogenesis. Cell 2017;170(6):1164-74 e6. doi: 10.1016/j.cell.2017.08.001 [published Online First: 2017/09/09]
  13. Chen Z, Ho WCS, Boon SS, Law PTY, Chan MCW, DeSalle R, Burk RD, Chan PKS. Ancient Evolution and Dispersion of Human Papillomavirus 58 Variants. J Virol 2017;91(21) doi: 10.1128/JVI.01285-17 [published Online First: 2017/08/11]
  14. Cancer Genome Atlas Research Network. Integrated genomic and molecular characterization of cervical cancer. Nature 2017;543(7645):378-84. doi: 10.1038/nature21386 [published Online First: 2017/01/24]
  15. Mirabello L, Yeager M, Cullen M, Boland JF, Chen Z, Wentzensen N, Zhang X, Yu K, Yang Q, Mitchell J, Roberson D, Bass S, Xiao Y, Burdett L, Raine-Bennett T, Lorey T, Castle PE, Burk RD, Schiffman M. HPV16 Sublineage Associations With Histology-Specific Cancer Risk Using HPV Whole-Genome Sequences in 3200 Women. J Natl Cancer Inst 2016;108(9) doi: 10.1093/jnci/djw100 [published Online First: 2016/05/01]
  16. Jelen MM, Chen Z, Kocjan BJ, Hosnjak L, Burt FJ, Chan PK, Chouhy D, Combrinck CE, Estrade C, Fiander A, Garland SM, Giri AA, Gonzalez JV, Groning A, Hibbitts S, Luk TN, Marinic K, Matsukura T, Neumann A, Ostrbenk A, Picconi MA, Sagadin M, Sahli R, Seedat RY, Seme K, Severini A, Sinchi JL, Smahelova J, Tabrizi SN, Tachezy R, Tohme Faybush S, Uloza V, Uloziene I, Wong YW, Zidovec Lepej S, Burk RD, Poljak M. Global Genomic Diversity of Human Papillomavirus 11 Based on 433 Isolates and 78 Complete Genome Sequences. J Virol 2016;90(11):5503-13. doi: 10.1128/JVI.03149-15 [published Online First: 2016/04/01]
  17. Harari A, Chen Z, Rodriguez AC, Hildesheim A, Porras C, Herrero R, Wacholder S, Panagiotou OA, Befano B, Burk RD, Schiffman M, Costa Rica HPVVTG. Cross-protection of the Bivalent Human Papillomavirus (HPV) Vaccine Against Variants of Genetically Related High-Risk HPV Infections. J Infect Dis 2016;213(6):939-47. doi: 10.1093/infdis/jiv519 [published Online First: 2015/11/01]
  18. Agalliu I, Gapstur S, Chen Z, Wang T, Anderson RL, Teras L, Kreimer AR, Hayes RB, Freedman ND, Burk RD. Associations of Oral alpha-, beta-, and gamma-Human Papillomavirus Types With Risk of Incident Head and Neck Cancer. JAMA Oncol 2016 doi: 10.1001/jamaoncol.2015.5504 [published Online First: 2016/01/23]
  19. Mirabello L, Frimer M, Harari A, McAndrew T, Smith B, Chen Z, Wentzensen N, Wacholder S, Castle PE, Raine-Bennett T, Schiffman M, Burk RD. HPV16 methyl-haplotypes determined by a novel next-generation sequencing method are associated with cervical precancer. Int J Cancer 2015;136(4):E146-53. doi: 10.1002/ijc.29119 [published Online First: 2014/08/02]
  20. Chen Z, de Freitas LB, Burk RD. Evolution and classification of oncogenic human papillomavirus types and variants associated with cervical cancer. Methods Mol Biol 2015;1249:3-26. doi: 10.1007/978-1-4939-2013-6_1 [published Online First: 2014/10/29]
  21. Zhang C, Park JS, Grce M, Hibbitts S, Palefsky JM, Konno R, Smith-McCune KK, Giovannelli L, Chu TY, Picconi MA, Pina-Sanchez P, Settheetham-Ishida W, Coutlee F, De Marco F, Woo YL, Ho WC, Wong MC, Chirenje MZ, Magure T, Moscicki AB, Sabol I, Fiander AN, Chen Z, Chan MC, Cheung TH, Burk RD, Chan PK. Geographical distribution and risk association of human papillomavirus genotype 52-variant lineages. J Infect Dis 2014;210(10):1600-4. doi: 10.1093/infdis/jiu310 [published Online First: 2014/06/01]
  22. Jelen MM, Chen Z, Kocjan BJ, Burt FJ, Chan PK, Chouhy D, Combrinck CE, Coutlee F, Estrade C, Ferenczy A, Fiander A, Franco EL, Garland SM, Giri AA, Gonzalez JV, Groning A, Heidrich K, Hibbitts S, Hosnjak L, Luk TN, Marinic K, Matsukura T, Neumann A, Ostrbenk A, Picconi MA, Richardson H, Sagadin M, Sahli R, Seedat RY, Seme K, Severini A, Sinchi JL, Smahelova J, Tabrizi SN, Tachezy R, Tohme S, Uloza V, Vitkauskiene A, Wong YW, Zidovec Lepej S, Burk RD, Poljak M. Global genomic diversity of human papillomavirus 6 based on 724 isolates and 190 complete genome sequences. J Virol 2014;88(13):7307-16. doi: 10.1128/JVI.00621-14 [published Online First: 2014/04/18]
  23. Chen Z, Schiffman M, Herrero R, DeSalle R, Anastos K, Segondy M, Sahasrabuddhe VV, Gravitt PE, Hsing AW, Burk RD. Evolution and taxonomic classification of alphapapillomavirus 7 complete genomes: HPV18, HPV39, HPV45, HPV59, HPV68 and HPV70. PLoS ONE 2013;8(8):e72565. doi: 10.1371/journal.pone.0072565 [published Online First: 2013/08/27]
  24. Chan PK, Zhang C, Park JS, Smith-McCune KK, Palefsky JM, Giovannelli L, Coutlee F, Hibbitts S, Konno R, Settheetham-Ishida W, Chu TY, Ferrera A, Alejandra Picconi M, De Marco F, Woo YL, Raiol T, Pina-Sanchez P, Bae JH, Wong MC, Chirenje MZ, Magure T, Moscicki AB, Fiander AN, Capra G, Young Ki E, Tan Y, Chen Z, Burk RD, Chan MC, Cheung TH, Pim D, Banks L. Geographical distribution and oncogenic risk association of human papillomavirus type 58 E6 and E7 sequence variations. Int J Cancer 2013;132(11):2528-36. doi: 10.1002/ijc.27932 [published Online First: 2012/11/09]
  25. Burk RD, Harari A, Chen Z. Human papillomavirus genome variants. Virology 2013;445(1-2):232-43. doi: 10.1016/j.virol.2013.07.018 [published Online First: 2013/09/04]
  26. Smith B, Chen Z, Reimers L, van Doorslaer K, Schiffman M, Desalle R, Herrero R, Yu K, Wacholder S, Wang T, Burk RD. Sequence imputation of HPV16 genomes for genetic association studies. PLoS ONE 2011;6(6):e21375. doi: 10.1371/journal.pone.0021375 [published Online First: 2011/07/07]
  27. Chen Z, Schiffman M, Herrero R, Desalle R, Anastos K, Segondy M, Sahasrabuddhe VV, Gravitt PE, Hsing AW, Burk RD. Evolution and taxonomic classification of human papillomavirus 16 (HPV16)-related variant genomes: HPV31, HPV33, HPV35, HPV52, HPV58 and HPV67. PLoS ONE 2011;6(5):e20183. doi: 10.1371/journal.pone.0020183 [published Online First: 2011/06/16]
  28. Bottalico D, Chen Z, Dunne A, Ostoloza J, McKinney S, Sun C, Schlecht NF, Fatahzadeh M, Herrero R, Schiffman M, Burk RD. The oral cavity contains abundant known and novel human papillomaviruses from the Betapapillomavirus and Gammapapillomavirus genera. J Infect Dis 2011;204(5):787-92. doi: 10.1093/infdis/jir383 [published Online First: 2011/08/17]
  29. Schiffman M, Rodriguez AC, Chen Z, Wacholder S, Herrero R, Hildesheim A, Desalle R, Befano B, Yu K, Safaeian M, Sherman ME, Morales J, Guillen D, Alfaro M, Hutchinson M, Solomon D, Castle PE, Burk RD. A population-based prospective study of carcinogenic human papillomavirus variant lineages, viral persistence, and cervical neoplasia. Cancer Res 2010;70(8):3159-69. doi: 10.1158/0008-5472.CAN-09-4179 [published Online First: 2010/04/01]
  30. Bernard HU, Burk RD, Chen Z, van Doorslaer K, zur Hausen H, de Villiers EM. Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments. Virology 2010;401(1):70-9. doi: 10.1016/j.virol.2010.02.002 [published Online First: 2010/03/09]
  31. Chen Z, van Doorslaer K, DeSalle R, Wood CE, Kaplan JR, Wagner JD, Burk RD. Genomic diversity and interspecies host infection of alpha12 Macaca fascicularis papillomaviruses (MfPVs). Virology 2009;393(2):304-10. doi: 10.1016/j.virol.2009.07.012 [published Online First: 2009/09/01]
  32. Chen Z, DeSalle R, Schiffman M, Herrero R, Burk RD. Evolutionary dynamics of variant genomes of human papillomavirus types 18, 45, and 97. J Virol 2009;83(3):1443-55. doi: 10.1128/JVI.02068-08 [published Online First: 2008/11/28]
  33. Burk RD, Chen Z, Van Doorslaer K. Human papillomaviruses: genetic basis of carcinogenicity. Public Health Genomics 2009;12(5-6):281-90. doi: 10.1159/000214919 [published Online First: 2009/08/18]
  34. Wood CE, Chen Z, Cline JM, Miller BE, Burk RD. Characterization and experimental transmission of an oncogenic papillomavirus in female macaques. J Virol 2007;81(12):6339-45. doi: 10.1128/JVI.00233-07 [published Online First: 2007/04/13]
  35. Chen Z, Schiffman M, Herrero R, Desalle R, Burk RD. Human papillomavirus (HPV) types 101 and 103 isolated from cervicovaginal cells lack an E6 open reading frame (ORF) and are related to gamma-papillomaviruses. Virology 2007;360(2):447-53. doi: 10.1016/j.virol.2006.10.022 [published Online First: 2006/11/28]
  36. Chen Z, Schiffman M, Herrero R, Burk RD. Identification and characterization of two novel human papillomaviruses (HPVs) by overlapping PCR: HPV102 and HPV106. J Gen Virol 2007;88(Pt 11):2952-5. doi: 10.1099/vir.0.83178-0 [published Online First: 2007/10/20]
  37. Chen Z, Fu L, Herrero R, Schiffman M, Burk RD. Identification of a novel human papillomavirus (HPV97) related to HPV18 and HPV45. Int J Cancer 2007;121(1):193-8. doi: 10.1002/ijc.22632 [published Online First: 2007/03/14]
  38. Narechania A, Chen Z, DeSalle R, Burk RD. Phylogenetic incongruence among oncogenic genital alpha human papillomaviruses. J Virol 2005;79(24):15503-10. doi: 10.1128/JVI.79.24.15503-15510.2005 [published Online First: 2005/11/25]
  39. Chen Z, Terai M, Fu L, Herrero R, DeSalle R, Burk RD. Diversifying selection in human papillomavirus type 16 lineages based on complete genome analyses. J Virol 2005;79(11):7014-23. doi: 10.1128/JVI.79.11.7014-7023.2005 [published Online First: 2005/05/14]