Dr. Jun LI

Assistant Professor
BSc Physics (Tianjin), PhD Computational Biology (Hong Kong)
Office Address
Room 1B-406, 4/F, Block 1, To Yuen Building, 31 To Yuen Street, City University of Hong Kong
Office Tel
Office Fax

Dr Jun Li joined City University of Hong Kong in February 2018 as an Assistant Professor in Bioinformatics.

He graduated from Tianjin University with a bachelor degree in physics and then joined Beijing Genomics Institute (BGI) in Beijing in 2003. In BGI, he was trained as a bioinformatician and served as senior project leader for over 3 years, leading a team focused on comparative genomics, evolution and population genetics.

He received his PhD degree from the University of Hong Kong (HKU) in 2013 under the supervision of Prof. Frederick Leung, working in the fields of comparative genomics/transcriptomics for viruses and bacteria. Afterwards, he joined the lab of Dr. Gianni Panagiotou as a postdoctoral researcher at HKU and the Hans Knoll Institute in Germany, studying the microbiome from human, animal and various other environments.

Dr Li is interested in developing mathematical models and using computational skills in the analysis of multi-omics, structural and phenotypic data to understand the intrinsic nature of the biological processes and dynamics, especially in the field of health-related microbiome and drug development.

  • Antibiotic resistance and pathogenesis in human, animal and environmental samples
  • Disease-related microbiome
  • Microbial interactions and dynamics
  • Big data mining with multi-omics and metadata
  • Structural biology and antibiotic developing

Please click here to access his Google Scholar profile.

Personal Website:

(*co-first author, ^corresponding author)

Heshiki, Y., Dissanayake, T., Zheng, T., Kang, K., Yueqiong, N., Xu, Z., … Li, J.^ (2017). Toward a Metagenomic Understanding on the Bacterial Composition and Resistome in Hong Kong Banknotes. Frontiers in Microbiology, 8, 632.

Mang Shi, Xian-Dan Lin, Jun-Hua Tian, Liang-Jun Chen, Xiao Chen, Ci-Xiu Li, Xin-Cheng Qin, Li J., Jian-Ping Cao, John-Sebastian Eden, Jan Buchmann, Wen Wang, Jianguo Xu, Edward C Holmes, Yong-Zhen Zhang. (2017) Redefining the invertebrate RNA virosphere. Nature, 2017, 540, 539–543. doi:10.1038/nature20167

Y. Ni, V.H.Y. Wong, W.C.S. Tai, Li J., W.Y. Wong, M.M.L. Lee, F.L.Y. Fong, H. El-Nezami, G. Panagiotou (2017). A metagenomic study of the preventive effect of Lactobacillus rhamnosus GG on intestinal polyp formation in ApcMin/+ mice. Journal of Applied Microbiology, 15 February 2017.

Y. Ni, Li J., G. Panagiotou. COMAN: a web server for Comprehensive Metatranscriptomics Analysis. BMC Genomics. 2016. 17(1):622. doi: 10.1186/s12864-016-2964-z

Li J., C. Ying Ju Sung, N. Lee, Y. Ni, J. Pihlajamäki, G. Panagiotou*, H. El-Nezami. Probiotics modulated gut microbiota suppresses hepatocellular carcinoma growth in mice. PNAS. 2016.

Y. Ni, Li J., G. Panagiotou. A Molecular-Level Landscape of Diet-Gut Microbiome Interactions: Towards Dietary Interventions Targeting Bacterial Genes. mBIO. 2015 vol. 6 no. 6 e01263-15. doi: 10.1128/mBio.01263-15

Kang K., Li J., Lim BL. & Panagiotou G. (2015). MESSI: metabolic engineering target selection and best strain identification tool. Database (Oxford). 2015 Aug 8.

Li J., Wong, C. F., Wong, M.T, Huang H. & Leung, F. C. (2014). Modularized evolution during the creation and expansion of pan-genomes in archaeal methanogens. Genome Biology and Evolution, 2014. doi: 10.1093/gbe/evu259

Westergaard D, Li J., Jensen K, Kouskoumvekaki I, Panagiotou G. (2014). Exploring mechanisms of diet-colon cancer associations through candidate molecular interaction networks. BMC genomics. 2014 May 17;15:380. doi: 10.1186/1471-2164-15-380.

Li J, Jiang J, Leung FC. (2012). 6-10× pyrosequencing is a practical approach for whole prokaryote genome studies. Gene. 2012 Feb 15;494(1):57-64. doi: 10.1016/j.gene.2011.11.051

Jiang J.*, Li J. *, Kwan HS, Au CH, Law PT, Li L, Kam KM, Ling JM, Leung FC. (2012). A cost-effective and universal strategy for complete prokaryotic genomic sequencing proposed by computer simulation. BMC Res Notes. 2012 Jan 31;5(1):80.

Zhang Zhang, Li J, Peng Cui, Feng Ding, Ang Li, Jeffrey P Townsend and Jun Yu, (2012). Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance. BMC bioinformatics. 2012, 13:43.

Cai, S.*, Li J.*, Wong, M.T., Jiao, P., Fan, H., Liu, D., Liao, M., Jiang, J., Shi, M., Lam, T.T.-Y., Ren, T., Leung, F.C.-C. (2010). Genetic characterization and evolutionary analysis of 4 Newcastle disease virus isolate full genomes from waterbirds in South China during 2003-2007, Veterinary Microbiology (2010), doi:10.1016/j.vetmic.2011.04.014

Ruiqiang Li, Wei Fan, Geng Tian, Hongmei Zhu, Lin He, Jing Cai, Quanfei Huang, Qingle Cai1, Bo Li, Yinqi Bai, Zhihe Zhang, Yaping Zhang, Wen Wang, Jun Li, … , Jian Wang & Jun Wang. (2010). The sequence and de novo assembly of the giant panda genome. Nature 463, 311-317. doi:10.1038/nature08696

Li, J., Zhang Z., Van S., Yu, J., Wong, G.K. and Wang, J. Correlation between Ka/Ks and Ks is related to substitution model and evolutionary lineage. (2009) Journal of Molecular Evolution. 68(4):414-23. doi: 10.1007/s00239-009-9222-9.

Jun Wang, Ruiqiang Li, Yingrui Li, Xiaodong Fang, Binxiao Feng and Li, J. (2008) Genome resequencing and identification of variations by Illumina Genome Analyzer Reads. Protocol Exchange. doi:10.1038/nprot.2008.238

Zhang, Z.*, Li, J.*., Wang, J., Wong, G.K. and Yu, J. (2006) KaKs_Calculator: Calculating Ka and Ks through Model Selection and Model Averaging. Genomics Proteomics Bioinformatics. 4(4):259-263. DOI: 10.1016/S1672-0229(07)60007-2

Zhang, Z.*, Li, J.*., and Yu, J. (2006) Computing Ka and Ks with a consideration of unequal transitional substitutions. BMC Evol Biol, 6, 44.

L. Liu*, Li, J.*, X. Tian, D. Ren and J. Lin (2005). Information Theory in Prediction of Cleavage Sites of Signal Peptides. Protein and Peptide Letters 12: 339-442.

Yu, J. J. Wang W.... Li, J. … H. Yang. (2005). The Genomes of Oryza sativa: a history of duplications. PLoS Biol 3: e38.

X, J., X, Q., Li, J., P, G., and Z,Z. (2005). Survey of long terminal repeat retrotransposons of domesticated silkworm (Bombyx mori). Insect Biochem Mol Biol 35: 921-929.

Qingyou Xia, Zeyang Zhou, … Li, J., ..., Jian Wang, Gane Ka-Shu Wong, and Huanming Yang. (2004). A Draft Sequence for the Genome of the Domesticated Silkworm (Bombyx mori) Science 10 December 2004 306: 1937-1940.