Introduction
The recent research of Dr. GAO Yuan focused on development of computational methods for omics data, including several widely used tools in transcriptomics and metagenomics: 1) a de novo method for sensitive and specific detection of circular RNAs, CIRI/CIRI2; 2) a method for detecting internal structure and alternative splicing events for circular RNAs, CIRI-AS; 3) a reference-free method for quantifying and comparing bacterial growth dynamics from multiple metagenomic samples, DEMIC; and 4) a method for discovering and quantifying transcript isoforms from long-read RNA-seq data, ESPRESSO.
His lab is broadly interested in development and application of novel computational methods combined with latest sequencing technologies to solve various biological problems, which include but are not limited to the following areas. (1) Functional metagenomics. (2) Spatial transcriptomics. (3) Long read sequencing data processing and analysis.
Group leader
Dr. GAO Yuan is a professor at Beijing Institute of Genomics (BIG), CAS. Prior to his appointment at BIG, he completed his Ph.D. training with Dr. Fangqing Zhao at Beijing Institutes of Life Science, CAS, and his postdoctoral training with Dr. LI Hongzhe at University of Pennsylvania (UPENN) and with Dr. XING Yi at Childeren’s Hospital of Philadelphia (CHOP). Dr. GAO has an extensive publication record in recent years, including first-author or corresponding-author papers published on top journals such as Nature Methods, Science Advances, Trends in Genetics,Advanced Science, Nature Communications and Genome Biology, which have more than 2,400 citations according to Google Scholar. In 2021, Dr. GAO set up his current laboratory in BIG.
Selected Publications
（# Co-first author, *Corresponding author）
1.Zhou Z#, Zhang J#, Zheng X, Pan Z, Zhao F*, Gao Y*. CIRI-deep enables single-cell and spatial transcriptomic analysis of circular RNAs with deep learning [J]. Advanced Science, 2024, DOI: 10.1002/advs.202308115.
2. Gao Y, Li H*. Quantifying and comparing bacterial growth dynamics in multiple metagenomic samples [J]. Nature Methods, 2018, 15(12): 1041.
3. Gao Y#*, Wang F#, Wang F#, Kutschera E, Xu Y, Xie S, Wang Y, Kadash-Edmondson K, Lin L, Xing Y*. ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data [J]. Science Advances, 2023, 9(3), eabq5072.
4. Gao Y#, Wang J#, Zhao F*. CIRI: an efficient and unbiased algorithm for de novo circular RNA identification [J]. Genome Biology, 2015, 16(1): 4.
5. Gao Y#, Wang J#, Zheng Y#, Zhang J, Chen S & Zhao F*. Comprehensive identification of internal structure and alternative splicing events in circular RNAs [J]. Nature Communications, 2016, DOI: 10.1038/ncomms12060.
6. Gao Y, Zhao F*. Computational strategies for exploring circular RNAs [J]. Trends in Genetics, 2018, 34(5): 389-400.
7. Gao Y, Zhang J, Zhao F*. Circular RNA identification based on multiple seed matching [J]. Briefings in Bioinformatics, 2018, 19(5): 803-810.
8. Wang J#, Gao Y#, Zhao F*. Phage–bacteria interaction network in human oral microbiome [J]. Environmental Microbiology, 2016, 7(18): 2143-2158.
9. Zhou H#, Zhao H#, Zheng J, Gao Y, Zhang Y, Zhao F & Wang J*. CRISPRs provide broad and robust protection to oral microbial flora of gingival health against bacteriophage challenge [J]. Protein & Cell, 2015, 6(7):541-545.
10. Ye N#*, Zhang X#, Miao M#, Fan X#, Zheng Y, Xu D, Wang J, Zhou L, Wang D, Gao Y, Wang Y, Shi W, Ji P, Li D, Guan Z, Shao C, Zhuang Z, Gao Z, Qi J & Zhao F*. Saccharina genomes provide novel insight into kelp biology [J]. Nature Communications, 2015, 6: 6986.
11. Xin R#, Gao Y#, Gao Y, Wang R, Kadash-Edmondson K & Xing Y*. isoCirc catalogs full-length circular RNA isoforms in human transcriptomes [J]. Nature Communications, 2021, 12(1): 1-11.
12. Tanes C#, Bittinger K#, Gao Y, Friedman S E, Nessel L, RoyPaladhi U, Chau L, Panfen E, Fischbach M A, Braun J, Xavier R J, Clish C B, Li H, Bushman F D, Lewis J D* & Wu G D*. Role of dietary fiber in the recovery of the human gut microbiome and its metabolome [J]. Cell Host & Microbe, 2021, 29(3): 394-407. e5.
Awards and Honors
Excellent Doctoral Dissertation, Chinese Academy of Sciences (2017)
President Scholarship for Postgraduate Students, Chinese Academy of Sciences (2016)
