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Name:
 Fangqing Zhao
Subject:
 Omics technology and artificial intelligence
Tel/Fax:
 +86-10-84504172  / 
E-mail:
 zhfq@ioz.ac.cn
Address:
 Lincui East Road, Bldg #1, Institute of Genetics and Developmental Biology, Chaoyang District, Beijing 100101
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Resume:

Fangqing Zhao, Professor and principal investigator. He has successively received the National Science Fund for Excellent Young Scholars of China (2017), Beijing NSF Outstanding Scholarship Award (2018), National Science Fund for Distinguished Young Scholars of China (2020), and was appointed as a Distinguished Professor by the Chinese Academy of Sciences in 2022. He currently serves as the Deputy Director of the Research Department of BIOLS and Director of the Genomic Informatics Branch of the Chinese Society of Bioinformatics. Dr. Zhao is mainly devoted to establishing efficient algorithm models and experimental techniques, exploring the composition and dynamics of the human microbiome and non-coding RNA, with the aim of deciphering their relationships with human health and disease. He has served as Associate Editor or Editorial Board Member for more than 10 academic journals, including Briefings in Bioinformatics, Science Bulletin, Science China Life Sciences, Genomics, Proteomics & Bioinformatics, Journal of Genetics and Genomics, mLife, etc.

Dr. Zhao has published more than 80 corresponding author papers in journals such as Cell, Gut, Nature Biotechnology, Nature Methods, Nature Computational Science, and Nature Communications. His papers have been cited over 12,000 times (H-index 48), with more than ten papers being recognized as highly cited according to ESI. He has received the "Outstanding Supervisor Award of the Chinese Academy of Sciences" for six consecutive years (2017 to 2023), and twice received the "Chinese Academy of Sciences University Leadership Award," the "Zhu Liyuehua Outstanding Teacher Award of the Chinese Academy of Sciences," and the "BHP Outstanding Mentor Award of the Chinese Academy of Sciences." He has mentored seven graduate students who have received the "President's Award of the Chinese Academy of Sciences" and the "Outstanding Doctoral Thesis of the Chinese Academy of Sciences." Currently, he is responsible for projects such as the Chief Scientist of the National Key R&D Program, the National Natural Science Foundation for Distinguished Young Scholars and Key Projects.

Research Interests:

1. Gut microbiome and human health

Integrating genomics, computational biology, and systems biology approaches to study the composition and dynamics of the human gut microbiome, as well as the interactions between microbes and hosts.

2. Circular noncoding RNAs

Establish statistical models and algorithms for circular RNA recognition, quantification, transcript assembly, alternative splicing identification, and functional annotation, providing methodological tools for unraveling their biogenesis mechanisms and functions.

3. Single-cell and spatial omics

Based on microfluidics and deep learning technologies, establish new methods for single cell and spatial transcriptomics/proteomics/metabolomics, uncovering the spatial heterogeneity of cells and functions, and gaining a deeper understanding of the impact of the gut microbiota and its metabolites on the host.

Awards and Honors:

Professional Activities:

Research Grants:

Selected Publications:
  1. He R, Zhu J, Ji P* & Zhao F*. SEVtras delineates small extracellular vesicles at droplet resolution from single-cell transcriptomes. Nature Methods, 2024, 21:259-266.
  2. Zhou T, Xiao L, Zuo Z* & Zhao F*. MAMI: a comprehensive database of mother-infant microbiome and probiotic resources. Nucleic Acids Research, 2024, 52:D738-D746.
  3. Li Z, Zhang B, Wang N, Zuo Z, Wei H & Zhao F*. A novel peptide protects against diet-induced obesity by suppressing appetite and modulating the gut microbiota. Gut, 2023,72:686-698.
  4. Hou L, Zhang J* & Zhao F*. Full-length circular RNA profiling by nanopore sequencing and CIRI-long. Nature Protocols, 2023, 18:1795-1813.
  5. Xiao L & Zhao F*. Microbial transmission, colonization and succession: from pregnancy to infancy. Gut, 2023, 72: 772-786.
  6. He R, Li P, Wang J, Cui B, Zhang F & Zhao F*. The interplay of gut microbiota between donors and recipients determines the efficacy of fecal microbiota transplantation. Gut Microbes, 2022, 14(1):e2100197.
  7. Xiao L, Zhang F & Zhao F*. Large-scale microbiome data integration enables robust biomarker identification. Nature Computational Science, 2022, 2: 307-316.
  8. Wu W, Zhang J, Cao X, Cai Z & Zhao F*. Exploring the cellular landscape of circular RNAs using full-length single-cell RNA sequencing. Nature Communications, 2022, 13(1):3242.
  9. Yang J, Hou L, Wang J, Xiao L, Zhang J, Yin N, Yao S, Cheng K, Zhang W, Shi Z, Wang J, Jiang H, Huang N, You Y, Lin M, Shang R, Wei Y*, Zhao Y* & Zhao F*. Unfavourable intrauterine environment contributes to abnormal gut microbiome and metabolome in twins. Gut, 2022, 71:2451-2462.
  10. Chen S, Cao X, Zhang J, Wu W, Zhang B & Zhao F*. circVAMP3 drives CAPRIN1 phase separation and inhibits hepatocellular carcinoma by suppressing c-Myc translation. Advanced Science, 2022, 9(8):e2103817.
  11. Yu Y, Zhang B, Ji P, Zuo Z, Huang Y, Wang N, Liu C, Liu SJ & Zhao F*. Changes to gut amino acid transporters and microbiome associated with increased E/I ratio in Chd8+/- mouse model of ASD-like behavior. Nature Communications, 2022, 13(1):1151.
  12. Zhang J, Hou L, Zuo Z, Zhang X, Xue Y & Zhao F*. Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long. Nature Biotechnology, 2021, 39:836-845.
  13. Xiao L, Wang J, Zheng J, Li X & Zhao F*. Deterministic transition of enterotypes shapes the infant gut microbiome at an early age. Genome Biology, 2021, 22:243.
  14. Wang J, Li Z, Ma X, Du L, Jia Z, Cui X, Yu L, Xiao L, Zhang B, Fan H & Zhao F*. Translocation of vaginal microbiota is involved in impairment and protection of uterine health. Nature Communications, 2021, 12:4191.
  15. Jia N, Wang J, Shi W, Du L, Sun Y, et al., Tick Genome and Microbiome Consortium, Zhao F* & Cao WC*. Large-scale comparative analyses of tick genomes elucidate their genetic diversity and vector capacities. Cell, 2020, 182(5):1328-1340
  16. Zhang J, Chen S, Yang J & Zhao F*. Accurate quantification of circular RNAs identifies extensive circular isoform switching events. Nature Communications, 2020, 11:90.
  17. Wu W, Ji P & Zhao F*. CircAltas: An integrated resource of one million highly confident circular RNAs from 1,070 transcriptomes of vertebrates. Genome Biology, 2020, 21:101.
  18. Wang J, Jia Z, Zhang B, Peng L & Zhao F*. Tracing the accumulation of in vivo human oral microbiota elucidates microbial community dynamics at the gateway to the GI tract. Gut, 2020, 69:1355-1356.
  19. Ji P, Wu W, Chen S, et al, Zhao F*. Expanded expression landscape and prioritization of circular RNAs in mammals. Cell Reports, 2019, 26 (12), 3444-3460.
  20. Wang J, Zheng J, Shi W, Du N, Xu X, Zhang Y, Ji P, Zhang F, Jia Z, Wang Y, Zheng Z, Zhang H & Zhao F*. Dysbiosis of maternal and neonatal microbiota associated with gestational diabetes mellitus. Gut, 2018, 67:1614-1625.