Prof. LI Jun joined City University of Hong Kong in February 2018 as an Assistant Professor in Bioinformatics. He is also affiliated with the Department of Data Science, School of Computing.
He graduated from Tianjin University with a bachelor's degree in physics. In 2014, he received his PhD degree from the University of Hong Kong (HKU), where he worked in the fields of comparative -omics evolution for viruses and bacteria. Following his PhD, Prof. Li joined the lab of Dr. Gianni Panagiotou as a postdoctoral researcher at HKU and the Hans Knoll Institute in Germany, investigating the microbiome from human, animal, and other environments using the techniques of bioinformatics, biostatistics, and systems biology.
Prof. Li is interested in developing statistical models and using computational skills in the analysis of multi-omics, structural and phenotypic data to understand the intrinsic/mathematical nature of the biological processes, the complex, adaptive and evolving systems, especially in the field of health-related and environmental microbiome. Additionally, he is devoted to the investigation of other health-related issues, disease prediction and prognosis, and fundamental biological processes based on machine learning and data mining techniques.
Research Interests/Areas
- Disease-related microbiome and environmental microbiome
- Biodiversity and conservation
- Metabolic disorders and effective interventional methods
- Microbial interactions and dynamics
- Self-assembly and complex systems
- Disease prediction and prognosis based on AI
- Artificial intelligence in -omics
Please click here to access his Google Scholar profile.
Personal Website: https://www.junli-group.org
(*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. doi.org/10.3389/fmicb.2017.00632
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. doi.org/10.1111/jam.13386
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. https://doi.org/10.1073/pnas.1518189113
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. https://doi.org/10.1093/database/bav076
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. doi.org/10.1186/1756-0500-5-80
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. doi.org/10.1186/1471-2105-13-43
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. doi.org/10.1186/1471-2148-6-44
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. doi.org/10.2174/0929866053765644
Yu, J. J. Wang W.... Li, J. … H. Yang. (2005). The Genomes of Oryza sativa: a history of duplications. PLoS Biol 3: e38. doi.org/10.1371/journal.pbio.0030038
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. doi.org/10.1016/j.ibmb.2005.03.014
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. doi.org/10.1126/science.1102210