Personal profile
Author IDs
ORCID iD: 0000-0001-7218-429X
Scopus Author ID: 56007009300
Google Scholar Profile: BaWTpXcAAAAJ
Impact
Qualifications (Brief)
BSc Physics (Tianjin), PhD Computational Biology (Hong Kong)
Biography
Dr. 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, Dr. 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.
Dr. 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.
Position(s) Available
Positions for PhD students are available for 2025/2026 admission. Advanced programming skills (Python/Perl and R) and proficient Linux operation are needed for all candidates. Strong computational and statistical skills/knowledge are needed (especially bachelor/master degree in statistics, mathematics, philosophy, or physics). A master's degree with GPA>85% for 211 universities or GPA>80% for 985 universities is required.
To apply for a PhD position in Jun's lab, please send your research interest and your C.V. to: [email protected]
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
Expertise related to UN Sustainable Development Goals
In 2015, UN member states agreed to 17 global Sustainable Development Goals (SDGs) to end poverty, protect the planet and ensure prosperity for all. This person’s work contributes towards the following SDG(s):
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SDG 2 Zero Hunger -
SDG 3 Good Health and Well-being -
SDG 6 Clean Water and Sanitation -
SDG 7 Affordable and Clean Energy -
SDG 11 Sustainable Cities and Communities -
SDG 15 Life on Land -
SDG 16 Peace, Justice and Strong Institutions
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Collaborations from the last five years
Research output
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Generalized biological foundation model with unified nucleic acid and protein language
He, Y., Fang, P., Shan, Y., Pan, Y., Wei, Y., Chen, Y., Chen, Y., Liu, Y., Zeng, Z., Zhou, Z., Zhu, F., Holmes, E. C., Ye, J., Li, J., Shu, Y., Shi, M. & Li, Z., 18 Jun 2025, In: Nature Machine Intelligence. 7, 6, p. 942-953Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile12 Link opens in a new tab Citations (Scopus)17 Downloads (CityUHK Scholars) -
Resistant starch intake facilitates weight loss in humans by reshaping the gut microbiota
Li, H. (Co-first Author), Zhang, L. (Co-first Author), Li, J. (Co-first Author), Wu, Q. (Co-first Author), Qian, L., He, J., Ni, Y., Kovatcheva-Datchary, P., Yuan, R., Liu, S., Shen, L., Zhang, M., Sheng, B., Li, P., Kang, K., Wu, L., Fang, Q., Long, X., Wang, X. & Li, Y. & 9 others, , Mar 2024, In: Nature Metabolism. 6, 3, p. 578–597Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile164 Link opens in a new tab Citations (Scopus)177 Downloads (CityUHK Scholars) -
Probiotics Bifidobacterium lactis M8 and Lactobacillus rhamnosus M9 prevent high blood pressure via modulating the gut microbiota composition and host metabolic products
Zhang, Y. (Co-first Author), Zheng, T. (Co-first Author), Ma, D., Shi, P., Zhang, H., LI, J. & Sun, Z., Nov 2023, In: mSystems. 8, 6, e00331-23.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile26 Link opens in a new tab Citations (Scopus)56 Downloads (CityUHK Scholars) -
Mechanistic insights into zearalenone-accelerated colorectal cancer in mice using integrative multi-omics approaches
Lo, E. K. K. (Co-first Author), Wang, X. (Co-first Author), Lee, P.-K., Wong, H.-C., Lee, J.C.-Y., Gómez-Gallego, C., Zhao, D., El-Nezami, H. & Li, J., 2023, In: Computational and Structural Biotechnology Journal. 21, p. 1785-1796Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
Open AccessFile22 Link opens in a new tab Citations (Scopus)83 Downloads (CityUHK Scholars) -
Transformer neural network to predict and interpret pregnancy loss from activity data in Holstein dairy cows
Lin, D., Kenéz, Á., McArt, J. A. A. & Li, J., Feb 2023, In: Computers and Electronics in Agriculture. 205, 107638.Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
17 Link opens in a new tab Citations (Scopus)
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YCRG-ExtU-Lead: Improved Metabolic Network Reconstruction and Metabolite Profiles Prediction using Complete and Strain-resolved Microbial Genomes
ZHANG, E. L. (Main Project Coordinator [External]) & LI, J. (Principal Investigator / Project Coordinator)
30/06/24 → …
Project: Research
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YCRG-ExtU-Lead: Interception the Mitochondrial-to-Nuclear Communication for Treatment of Vascular Inflammation and Atherosclerosis
TIAN, X. (Main Project Coordinator [External]) & LI, J. (Principal Investigator / Project Coordinator)
1/06/24 → …
Project: Research
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HMRF: Improve Subclassification and Risk Assessment of Myelodysplastic Syndromes Using Deep-learning Models Incorporating Genomic Information
LI, J. (Principal Investigator / Project Coordinator)
1/07/23 → …
Project: Research
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HMRF: A System-Level and Multidimensional Quantification and Prediction of SARS-CoV-2 Infection in Animals: Are There Implications for Control of Human Infections?
LI, J. (Principal Investigator / Project Coordinator), BARRS, V. R. D. (Co-Investigator), Beatty, J. (Co-Investigator), CHEN, S. (Co-Investigator), GO, Y. Y. (Co-Investigator), MAGOURAS, I. (Co-Investigator), PEIRIS, J. S. M. (Co-Investigator), PFEIFFER, D. U. (Co-Investigator) & Shi, M. (Co-Investigator)
1/10/20 → 7/10/24
Project: Research
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SZGov-SRI: 肠道菌群对妊娠糖尿病形成的潜在影响：一个多组学系统性研究
LI, J. (Principal Investigator / Project Coordinator)
22/05/20 → 31/05/23
Project: Research
Press/Media
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Health and medical research funding for three Covid-19 projects
BARRS, V. R. D., LI, J., MAGOURAS, I. & YUAN, H.-Y. S.
12/01/21
4 items of Media coverage
Press/Media: Press / Media
Supervised Students
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Mr. Junsheng HE, 何俊笙
- Department of Infectious Diseases and Public Health - Research Assistant
Person: Doctor of Philosophy (Student), Research Assistant
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