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Professor Huang, Shi  portrait
Faculty Staff
Professor Huang, Shi
PhD (University of Chinese Academy of Sciences)
General Information
Assistant Professor in Microbiology
Applied Oral Sciences & Community Dental Care
Phone Number
2859 0572
Research profile
Research Theme
Microbiome Innovation
Areas of Research Expertise
Metagenomics method development
Human microbiome association with chronic diseases
Adaptive co-evolution of probiotics and native gut microbiome
Machine learning applications in microbiome data
Advanced Sorting
  1. Ren Lihui, Liu Shuang, Huang Shi, Wang Qi, Lu Yuan, Song Jiaojian, Guo Jinjia. Identification of microplastics using a convolutional neural network based on micro-Raman spectroscopy, Talanta 2023; 260 doi:10.1016/j.talanta.2023.124611
  2. Sun Z, Huang S, Zhu P, Lam T, Zhao H, Lv J, Zhang R, Zhou L, Niu Q, Wang X, Zhang M, Jing G, Bao Z, Liu J, Wang S, Xu J. Species-resolved sequencing of low-biomass or degraded microbiomes using 2bRAD-M, Genome Biology 2022; 23: article no. 36-article no. 36 doi:10.1186/s13059-021-02576-9
  3. Chen Y, Li J, Zhang Y, Zhang M, Sun Z, Jing G, Huang S, Su X. Parallel-Meta Suite: Interactive and rapid microbiome data analysis on multiple platforms, iMeta 2022; 1(1): article no. e1-article no. e1 doi:10.1002/imt2.1
  4. JIang S, Chen D, Ma C, Liu H, Huang S, Zhang J. Establishing a novel inflammatory bowel disease prediction model based on gene markers identified from single nucleotide variants of the intestinal microbiota, iMeta 2022; e40-e40 doi:10.1002/imt2.40
  5. Zhu Q, Huang S, Gonzalez A, McGrath I, McDonald D, Haiminen N, Armstrong G, Vazquez-Baeza Y, Yu J, Kuczynski J, Sepich-Poore GD, Swafford AD, Das P, Shaffer JP, Lejzerowicz F, Belda-Ferre P, Havulinna AS, Meric G, Niiranen T, Lahti L, Salomaa V, Kim HC, Jain M, Inouye M, Gilbert JA, Knight R. Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy, mSystems 2022; e0016722-e0016722 doi:10.1128/msystems.00167-22
  6. Zhu Qiyun, Hou Qiangchuan, Huang Shi, Ou Qianying, Huo Dongxue, Vázquez-Baeza Yoshiki, Cen Chaoping, Cantu Victor, Estaki Mehrbod, Chang Haibo, Belda-Ferre Pedro, Kim Ho Cheol, Chen Kaining, Knight Rob, Zhang Jiachao. Correction to: Compositional and genetic alterations in Graves’ disease gut microbiome reveal specific diagnostic biomarkers, ISME Journal 2022; 16(4): 1201-1201 doi:10.1038/s41396-021-01040-7
  7. Huang S, He T, Yue F, Xu X, Wang L, Zhu P, Teng F, Sun Z, Liu X, Jing G, Su X, Jin L, Liu J, Xu J. Longitudinal Multi-omics and Microbiome Meta-analysis Identify an Asymptomatic Gingival State That Links Gingivitis, Periodontitis, and Aging, mBio 2021; 12(2): article no. e03281-20-article no. e03281-20 doi:10.1128/mBio.03281-20
  8. Liu Wenjun, Sun Zheng, Ma Chen, Zhang Jiachao, Ma Chen Chen, Zhao Yinqi, Wei Hong, Huang Shi, Zhang Heping. Exposure to soil environments during earlier life stages is distinguishable in the gut microbiome of adult mice, Gut Microbes 2021; 13(1): article no. 1830699-article no. 1830699 doi:10.1080/19490976.2020.1830699
  9. Sun Zheng, Huang Shi, Zhang Meng, Zhu Qiyun, Haiminen Niina, Carrieri Anna Paola, Vázquez-Baeza Yoshiki, Parida Laxmi, Kim Ho Cheol, Knight Rob, Liu Yang Yu. Challenges in benchmarking metagenomic profilers, Nature Methods 2021; 18(6): 618-626 doi:10.1038/s41592-021-01141-3
  10. Zhang Ying, Huang Shi, Jia Songbo, Sun Zheng, Li Shanshan, Li Fan, Zhang Lijuan, Lu Jie, Tan Kaixuan, Teng Fei, Yang Fang. The predictive power of saliva electrolytes exceeds that of saliva microbiomes in diagnosing early childhood caries, Journal of Oral Microbiology 2021; 13(1): article no. 1921486-article no. 1921486 doi:10.1080/20002297.2021.1921486
  11. Jiang Lingjing, Haiminen Niina, Carrieri Anna Paola, Huang Shi, Vázquez-Baeza Yoshiki, Parida Laxmi, Kim Ho Cheol, Swafford Austin D., Knight Rob, Natarajan Loki. Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data, Biometrics 2021; doi:10.1111/biom.13481
  12. Zhu Qiyun, Hou Qiangchuan, Huang Shi, Ou Qianying, Huo Dongxue, Vázquez-Baeza Yoshiki, Cen Chaoping, Cantu Victor, Estaki Mehrbod, Chang Haibo, Belda-Ferre Pedro, Kim Ho Cheol, Chen Kaining, Knight Rob, Zhang Jiachao. Compositional and genetic alterations in Graves’ disease gut microbiome reveal specific diagnostic biomarkers, ISME Journal 2021; 15(11): 3399-3411 doi:10.1038/s41396-021-01016-7
  13. Marotz Clarisse, Belda-Ferre Pedro, Ali Farhana, Das Promi, Huang Shi, Cantrell Kalen, Jiang Lingjing, Martino Cameron, Diner Rachel E., Rahman Gibraan, McDonald Daniel, Armstrong George, Kodera Sho, Donato Sonya, Ecklu-Mensah Gertrude, Gottel Neil, Salas Garcia Mariana C., Chiang Leslie Y., Salido Rodolfo A., Shaffer Justin P., Bryant Mac Kenzie, Sanders Karenina, Humphrey Greg, Ackermann Gail, Haiminen Niina, Beck Kristen L., Kim Ho Cheol, Carrieri Anna Paola, Parida Laxmi, Vázquez-Baeza Yoshiki, Torriani Francesca J., Knight Rob, Gilbert Jack, Sweeney Daniel A., Allard Sarah M.. SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment, Microbiome 2021; 9(1): article no. 132-article no. 132 doi:10.1186/s40168-021-01083-0
  14. Li Shanshan, Huang Shi, Guo Yi, Zhang Ying, Zhang Lijuan, Li Fan, Tan Kaixuan, Lu Jie, Chen Zhenggang, Guo Qingyuan, Tang Yongping, Teng Fei, Yang Fang. Geographic Variation Did Not Affect the Predictive Power of Salivary Microbiota for Caries in Children With Mixed Dentition, Frontiers in Cellular and Infection Microbiology 2021; 11: article no. 680288-article no. 680288 doi:10.3389/fcimb.2021.680288
  15. Ma Chenchen, Zhang Chengcheng, Chen Denghui, Jiang Shuaiming, Shen Siyuan, Huo Dongxue, Huang Shi, Zhai Qixiao, Zhang Jiachao. Probiotic consumption influences universal adaptive mutations in indigenous human and mouse gut microbiota, Communications Biology 2021; 4(1): article no. 1198-article no. 1198 doi:10.1038/s42003-021-02724-8
  16. Huang Shi, Jiang Shuaiming, Huo Dongxue, Allaband Celeste, Estaki Mehrbod, Cantu Victor, Belda-Ferre Pedro, Vázquez-Baeza Yoshiki, Zhu Qiyun, Ma Chenchen, Li Congfa, Zarrinpar Amir, Liu Yang Yu, Knight Rob, Zhang Jiachao. Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome, Microbiome 2021; 9(1): article no. 151-article no. 151 doi:10.1186/s40168-021-01102-0
  17. He Tao, Huang Shi, Yue Feng, Wang Lijiang, Liu Jiquan, Xu Jian. A randomized, controlled comparison of a stannous-containing dentifrice for reducing gingival bleeding and balancing the oral microbiome relative to a positive control, American journal of dentistry 2021; 34(4): 222-227
  18. He Yuehui, Huang Shi, Zhang Peng, Ji Yuetong, Xu Jian. Intra-ramanome correlation analysis unveils metabolite conversion network from an isogenic population of cells, mBio 2021; 12(4): article no. e01470-21-article no. e01470-21 doi:10.1128/mBio.01470-21
  19. Armstrong George, Cantrell Kalen, Huang Shi, McDonald Daniel, Haiminen Niina, Carrieri Anna Paola, Zhu Qiyun, Gonzalez Antonio, McGrath Imran, Beck Kristen L., Hakim Daniel, Havulinna Aki S., Méric Guillaume, Niiranen Teemu, Lahti Leo, Salomaa Veikko, Jain Mohit, Inouye Michael, Swafford Austin D., Kim Ho Cheol, Parida Laxmi, Vázquez-Baeza Yoshiki, Knight Rob. Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes, Genome research 2021; 31(11): 2131-2137 doi:10.1101/gr.275777.121
  20. Ma Chenchen, Wasti Sanjeev, Huang Shi, Zhang Zeng, Mishra Rajeev, Jiang Shuaiming, You Zhengkai, Wu Yixuan, Chang Haibo, Wang Yuanyuan, Huo Dongxue, Li Congfa, Sun Zhihong, Sun Zheng, Zhang Jiachao. The gut microbiome stability is altered by probiotic ingestion and improved by the continuous supplementation of galactooligosaccharide, Gut Microbes 2020; 12(1): article no. 1785252-article no. 1785252 doi:10.1080/19490976.2020.1785252
  21. Ji Wenyan, Jiang Ting, Sun Zheng, Teng Fei, Ma Chenchen, Huang Shi, Yan Suhua. The Enhanced Pharmacological Effects of Modified Traditional Chinese Medicine in Attenuation of Atherosclerosis Is Driven by Modulation of Gut Microbiota, Frontiers in Pharmacology 2020; 11: article no. 546589-article no. 546589 doi:10.3389/fphar.2020.546589
  22. Ma Chenchen, Guo Hongyang, Chang Haibo, Huang Shi, Jiang Shuaiming, Huo Dongxue, Zhang Jiachao, Zhu Xiaopeng. The effects of exopolysaccharides and exopolysaccharide-producing Lactobacillus on the intestinal microbiome of zebrafish (Danio rerio), BMC Microbiology 2020; 20(1): article no. 300-article no. 300 doi:10.1186/s12866-020-01990-6
  23. Su Xiaoquan, Jing Gongchao, Sun Zheng, Liu Lu, Xu Zhenjiang, McDonald Daniel, Wang Zengbin, Wang Honglei, Gonzalez Antonio, Zhang Yufeng, Huang Shi, Huttley Gavin, Knight Rob, Xu Jian. Multiple-disease detection and classification across cohorts via microbiome search, mSystems 2020; 5(2): article no. e00150-20-article no. e00150-20 doi:10.1128/mSystems.00150-20
  24. Huang Shi, Haiminen Niina, Carrieri Anna Paola, Hu Rebecca, Jiang Lingjing, Parida Laxmi, Russell Baylee, Allaband Celeste, Zarrinpar Amir, Vázquez-Baeza Yoshiki, Belda-Ferre Pedro, Zhou Hongwei, Kim Ho Cheol, Swafford Austin D., Knight Rob, Xu Zhenjiang Zech. Human skin, oral, and gut microbiomes predict chronological age, mSystems 2020; 5(1): article no. e00630-19-article no. e00630-19 doi:10.1128/mSystems.00630-19
  25. Sun Zheng, Huang Shi, Zhu Pengfei, Yue Feng, Zhao Helen, Yang Ming, Niu Yueqing, Jing Gongchao, Su Xiaoquan, Li Huiying, Callewaert Chris, Knight Rob, Liu Jiquan, Smith Ed, Wei Karl, Xu Jian. A microbiome-based index for assessing skin health and treatment effects for atopic dermatitis in children, mSystems 2019; 4(4): article no. e00293-19-article no. e00293-19 doi:10.1128/mSystems.00293-19
  26. Xu Zhenjiang Zech, Amir Amnon, Sanders Jon, Zhu Qiyun, Morton James T., Bletz Molly C., Tripathi Anupriya, Huang Shi, McDonald Daniel, Jiang Lingjing, Knight Rob. Calour: an Interactive, Microbe-Centric Analysis Tool, mSystems 2019; 4(1): article no. e00269-18-article no. e00269-18 doi:10.1128/MSYSTEMS.00269-18
  27. de la Cuesta-Zuluaga Jacobo, Kelley Scott T., Chen Yingfeng, Escobar Juan S., Mueller Noel T., Ley Ruth E., McDonald Daniel, Huang Shi, Swafford Austin D., Knight Rob, Thackray Varykina G.. Age- And sex-dependent patterns of gut microbial diversity in human adults, mSystems 2019; 4(4): article no. e00261-19-article no. e00261-19 doi:10.1128/mSystems.00261-19
  28. Xiaoquan Su, Jing Gongchao, McDonald Daniel, Wang Honglei, Wang Zengbin, Gonzalez Antonio, Sun Zheng, Huang Shi, Navas Jose, Knight Rob, Xu Jian. Reply to Sun et al., “Identifying composition novelty in microbiome studies: Improvement of prediction accuracy”, mBio 2019; 10(4): article no. e01234-19-article no. e01234-19 doi:10.1128/mBio.01234-19
  29. Zhu Qiyun, Mai Uyen, Pfeiffer Wayne, Janssen Stefan, Asnicar Francesco, Sanders Jon G., Belda-Ferre Pedro, Al-Ghalith Gabriel A., Kopylova Evguenia, McDonald Daniel, Kosciolek Tomasz, Yin John B., Huang Shi, Salam Nimaichand, Jiao Jian Yu, Wu Zijun, Xu Zhenjiang Z., Cantrell Kalen, Yang Yimeng, Sayyari Erfan, Rabiee Maryam, Morton James T., Podell Sheila, Knights Dan, Li Wen Jun, Huttenhower Curtis, Segata Nicola, Smarr Larry, Mirarab Siavash, Knight Rob. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea, Nature Communications 2019; 10(1): article no. 5477-article no. 5477 doi:10.1038/s41467-019-13443-4
  30. Sun Tong Zheng, Teng Fei, Jia Song Bo, Tang Yong Ping, Jiang Ming, Huang Shi, Yuan Xiao, Li Xiao Lan, Yang Fang. 与重症低龄儿童龋病相关的唾液微生物群落研究, 华西口腔医学杂志 2018; 36(2): 150-155 doi:10.7518/hxkq.2018.02.007
  31. Xian Peng, Xuedong Zhou, Xin Xu, Yuqing Li, Yan Li, Jiyao Li, Xiaoquan Su, Shi Huang, Jian Xu, Ga Liao. The Oral Microbiome Bank of China, International Journal of Oral Science 2018; 10(2): article no. 16-article no. 16 doi:10.1038/s41368-018-0018-x
  32. Su Xiaoquan, Jing Gongchao, McDonald Daniel, Wang Honglei, Wang Zengbin, Gonzalez Antonio, Sun Zheng, Huang Shi, Navas Jose, Knight Rob, Xu Jian. Identifying and predicting novelty in microbiome studies, mBio 2018; 9(6): article no. e02099-18-article no. e02099-18 doi:10.1128/mBio.02099-18
  33. Teng Fei, Darveekaran Nair Sree Sankar, Zhu Pengfei, Li Shanshan, Huang Shi, Li Xiaolan, Xu Jian, Yang Fang. Impact of DNA extraction method and targeted 16S-rRNA hypervariable region on oral microbiota profiling, Scientific Reports 2018; 8(1): article no. 16321-article no. 16321 doi:10.1038/s41598-018-34294-x
  34. Ma Chen, Sun Zheng, Zeng Benhua, Huang Shi, Zhao Jie, Zhang Yong, Su Xiaoquan, Xu Jian, Wei Hong, Zhang Heping. Cow-to-mouse fecal transplantations suggest intestinal microbiome as one cause of mastitis, Microbiome 2018; 6(1): article no. 200-article no. 200 doi:10.1186/s40168-018-0578-1
  35. Su Lijuan, Yang Lele, Huang Shi, Li Yan, Su Xiaoquan, Wang Fengqin, Bo Cunpei, Wang En Tao, Song Andong. Variation in the Gut Microbiota of Termites (Tsaitermes ampliceps) Against Different Diets, Applied Biochemistry and Biotechnology 2017; 181(1): 32-47 doi:10.1007/s12010-016-2197-2
  36. Xu Jian, Ma Bo, Su Xiaoquan, Huang Shi, Xu Xin, Zhou Xuedong, Huang Wei E., Knight Rob. Emerging Trends for Microbiome Analysis: From Single-Cell Functional Imaging to Microbiome Big Data, Engineering 2017; 3(1): 66-70 doi:10.1016/J.ENG.2017.01.020
  37. Jing Gongchao, Sun Zheng, Wang Honglei, Gong Yanhai, Huang Shi, Ning Kang, Xu Jian, Su Xiaoquan. Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities, Scientific Reports 2017; 7: article no. 40371-article no. 40371 doi:10.1038/srep40371
  38. Zheng Xin, He Jinzhi, Wang Lin, Zhou Shuangshuang, Peng Xian, Huang Shi, Zheng Liwei, Cheng Lei, Hao Yuqing, Li Jiyao, Xu Jian, Xu Xin, Zhou Xuedong. Ecological Effect of Arginine on Oral Microbiota, Scientific Reports 2017; 7(1): article no. 7206-article no. 7206 doi:10.1038/s41598-017-07042-w
  39. Tao Yifan, Wang Yun, Huang Shi, Zhu Pengfei, Huang Wei E., Ling Junqi, Xu Jian. Metabolic-Activity-Based Assessment of Antimicrobial Effects by D2O-Labeled Single-Cell Raman Microspectroscopy, Analytical Chemistry 2017; 89(7): 4108-4115 doi:10.1021/acs.analchem.6b05051
  40. He Yuehui, Zhang Peng, Huang Shi, Wang Tingting, Ji Yuetong, Xu Jian. Label-free, simultaneous quantification of starch, protein and triacylglycerol in single microalgal cells, Biotechnology for Biofuels 2017; 10(1): article no. 275-article no. 275 doi:10.1186/s13068-017-0967-x
  41. Gao Pengfei, Ma Chen, Sun Zheng, Wang Lifeng, Huang Shi, Su Xiaoquan, Xu Jian, Zhang Heping. Feed-additive probiotics accelerate yet antibiotics delay intestinal microbiota maturation in broiler chicken, Microbiome 2017; 5(1): article no. 91-article no. 91 doi:10.1186/s40168-017-0315-1
  42. Su Li Juan, Yang Le Le, Huang Shi, Su Xiao Quan, Li Yan, Wang Feng Qin, Wang En Tao, Kang Ning, Xu Jian, Song An Dong. Comparative gut microbiomes of four species representing the higher and the lower termites, Journal of Insect Science 2016; 16(1): article no. 97-article no. 97 doi:10.1093/jisesa/iew081
  43. Wang Ying, Su Lijuan, Huang Shi, Bo Cunpei, Yang Sen, Li Yan, Wang Fengqin, Xie Hui, Xu Jian, Song Andong. Diversity and resilience of the wood-feeding higher termite Mironasutitermes shangchengensis gut microbiota in response to temporal and diet variations, Ecology and Evolution 2016; 6(22): 8235-8242 doi:10.1002/ece3.2497
  44. Wang Qintao, Lu Yandu, Xin Yi, Wei Li, Huang Shi, Xu Jian. Genome editing of model oleaginous microalgae Nannochloropsis spp. by CRISPR/Cas9, Plant Journal 2016; 88(6): 1071-1081 doi:10.1111/tpj.13307
  45. Teng Fei, He Tao, Huang Shi, Bo Cun Pei, Li Zhen, Chang Jin Lan, Liu Ji Quan, Charbonneau Duane, Xu Jian, Li Rui, Ling Jun Qi. Cetylpyridinium Chloride Mouth Rinses Alleviate Experimental Gingivitis by Inhibiting Dental Plaque Maturation, International Journal of Oral Science 2016; 8(3): 182-190 doi:10.1038/ijos.2016.18
  46. Huang Shi, Li Zhen, He Tao, Bo Cunpei, Chang Jinlan, Li Lin, He Yanyan, Liu Jiquan, Charbonneau Duane, Li Rui, Xu Jian. Microbiota-based Signature of Gingivitis Treatments: A Randomized Study, Scientific Reports 2016; 6: article no. 24705-article no. 24705 doi:10.1038/srep24705
  47. Guo Zhuang, Zhang Jiachao, Wang Zhanli, Ang Kay Ying, Huang Shi, Hou Qiangchuan, Su Xiaoquan, Qiao Jianmin, Zheng Yi, Wang Lifeng, Koh Eileen, Danliang Ho, Xu Jian, Lee Yuan Kun, Zhang Heping. Intestinal Microbiota Distinguish Gout Patients from Healthy Humans, Scientific Reports 2016; 6: article no. 20602-article no. 20602 doi:10.1038/srep20602
  48. Fan Jianhua, Ning Kang, Zeng Xiaowei, Luo Yuanchan, Wang Dongmei, Hu Jianqiang, Li Jing, Xu Hui, Huang Jianke, Wan Minxi, Wang Weiliang, Zhang Daojing, Shen Guomin, Run Conglin, Liao Junjie, Fang Lei, Huang Shi, Jing Xiaoyan, Su Xiaoquan, Wang Anhui, Bai Lili, Hu Zanmin, Xu Jian, Li Yuanguang. Genomic foundation of starch-to-lipid switch in oleaginous chlorella spp., Plant Physiology 2015; 169(4): 2444-2461 doi:10.1104/pp.15.01174
  49. Zhang Dayi, Berry James P., Zhu Di, Wang Yun, Chen Yin, Jiang Bo, Huang Shi, Langford Harry, Li Guanghe, Davison Paul A., Xu Jian, Aries Eric, Huang Wei E.. Magnetic nanoparticle-mediated isolation of functional bacteria in a complex microbial community, ISME Journal 2015; 9(3): 603-614 doi:10.1038/ismej.2014.161
  50. Sheng Rong, Qin Hongling, O’Donnell Anthony G., Huang Shi, Wu Jinshui, Wei Wenxue. Bacterial succession in paddy soils derived from different parent materials, Journal of Soils and Sediments 2015; 15(4): 982-992 doi:10.1007/s11368-014-1058-2
  51. Teng Fei, Yang Fang, Huang Shi, Bo Cunpei, Xu Zhenjiang Zech, Amir Amnon, Knight Rob, Ling Junqi, Xu Jian. Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota, Cell Host and Microbe 2015; 18(3): 296-306 doi:10.1016/j.chom.2015.08.005
  52. Su Xiaoquan, Wang Xiaojun, Jing Gongchao, Huang Shi, Xu Jian, Ning Kang. Application of Meta-Mesh on the analysis of microbial communities from human associated-habitats, Quantitative Biology 2015; 3(1): 4-18 doi:10.1007/s40484-015-0040-3
  53. Su Xiaoquan, Hu Jianqiang, Huang Shi, Ning Kang. Rapid comparison and correlation analysis among massive number of microbial community samples based on MDV data model, Scientific Reports 2014; 4: article no. 6393-article no. 6393 doi:10.1038/srep06393
  54. Xu Yuan, Teng Fei, Huang Shi, Lin Zhengmei, Yuan Xiao, Zeng Xiaowei, Yang Fang. Changes of saliva microbiota in nasopharyngeal carcinoma patients under chemoradiation therapy, Archives of Oral Biology 2014; 59(2): 176-186 doi:10.1016/j.archoralbio.2013.10.011
  55. Wang Tingting, Ji Yuetong, Wang Yun, Jia Jing, Li Jing, Huang Shi, Han Danxiang, Hu Qiang, Huang Wei E., Xu Jian. Quantitative dynamics of triacylglycerol accumulation in microalgae populations at single-cell resolution revealed by Raman microspectroscopy, Biotechnology for Biofuels 2014; 7(1): article no. 58-article no. 58 doi:10.1186/1754-6834-7-58
  56. Li Jing, Han Danxiang, Wang Dongmei, Ning Kang, Jia Jing, Wei Li, Jing Xiaoyan, Huang Shi, Chen Jie, Li Yantao, Hu Qiang, Xu Jian. Choreography of transcriptomes and lipidomes of Nannochloropsis reveals the mechanisms of oil synthesis in microalgae, Plant Cell 2014; 26(4): 1645-1665 doi:10.1105/tpc.113.121418
  57. Huang Shi, Li Rui, Zeng Xiaowei, He Tao, Zhao Helen, Chang Alice, Bo Cunpei, Chen Jie, Yang Fang, Knight Rob, Liu Jiquan, Davis Catherine, Xu Jian. Predictive modeling of gingivitis severity and susceptibility via oral microbiota, ISME Journal 2014; 8(9): 1768-1780 doi:10.1038/ismej.2014.32
  58. Yang F., Huang S., he T., Catrenich C., Teng F., bo C., Chen J., Liu J., li J., Song Y., Li R., Xu J.. Microbial Basis of Oral Malodor Development in Humans, Journal of Dental Research 2013; 92(12): 1106-1112 doi:10.1177/0022034513507065
  59. Wang Yun, Chen Yin, Zhou Qian, Huang Shi, Ning Kang, Xu Jian, Kalin Robert M., Rolfe Stephen, Huang Wei E.. A Culture-Independent Approach to Unravel Uncultured Bacteria and Functional Genes in a Complex Microbial Community, PLoS ONE 2012; 7(10): article no. e47530-article no. e47530 doi:10.1371/journal.pone.0047530
  60. Huang Shi, Yang Fang, Zeng Xiaowei, Chen Jie, Li Rui, Wen Ting, Li Chun, Wei Wei, Liu Jiquan, Chen Lan, Davis Catherine, Xu Jian. Preliminary characterization of the oral microbiota of Chinese adults with and without gingivitis, BMC Oral Health 2011; 11(1): article no. 33-article no. 33 doi:10.1186/1472-6831-11-33
Conference Paper
  1. Huang Shi, Zhang Yufeng, Liu Jiang, Wang Xiuping, Zhou Lisa, Wang Shi. IDDF2023-ABS-0267 Strain-resolved taxonomic profiling and functional prediction of human microbiota using Strain2bFunc, International Digestive Disease Forum (10/06/2023-11/06/2023, Hong Kong) 2023; A120-A123 doi:10.1136/gutjnl-2023-IDDF.106
  2. Li Xiaoxu, Huang Shi, Yu Jun, Wang Quanxi, Wu Shuangxiu. Improvement of hydrogen production of Chlamydomonas reinhardtii by co-cultivation with isolated bacteria, International Journal of Hydrogen Energy 2013; 38(25): 10779-10787 doi:10.1016/j.ijhydene.2013.02.102
  1. 2023: Editor. mSystems.
  2. 2022: Youth editor. iMeta.
  3. 2022: Youth editor. The Innovation.
  4. 2022: Associate Editor. Frontiers in Cellular and Infection Microbiology.
Knowledge Exchange
  1. 10 July 2023: Huang Shi. Seminar: "The spatiotemporal dynamics of oral microbiome and its impact on oral and gastrointestinal diseases" delivered by Prof. Xu, Zech Zhenjiang from Nanchang Univ, China .
  2. 22 February 2023: Huang Shi. Seminar: "Small molecules from the oral microbiome" delivered by Dr. Tang Xiaoyu from Shenzhen Bay Lab, China.
  1. Project Title: Discovering Microbial Features for Oral Cancer Diagnosis and Prediction
    Grant Type: Health and Medical Research Fund 2021
    Funding Year: 2022
    Amount: HKD1499864
    Principal Investigator: Professor Huang, Shi
    Co-principal investigator(s): Dr Liu Pei, Professor Su Yuxiong, Professor Khoo Ui Soon Co-investigator(s): Dr Koohimoghadam Mohamad
  2. Project Title: ASM Microbe 2023
    Grant Type: Conference Support for Teaching Staff
    Funding Year: 2022
    Amount: HKD16500
    Principal Investigator: Dr Huang, Shi
  3. Project Title: Discovering Microbial Features for Oral Cancer Diagnosis and Prediction
    Grant Type: Seed Fund for Basic Research for New Staff
    Funding Year: 2021
    Amount: HKD150000
    Principal Investigator: Dr Huang, Shi
    Co-investigator(s): Dr Koohi-Moghadam Hongzhe, Dr Liu Pei, Professor Su Yuxiong, Professor Khoo Ui Soon
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