Yuan Gao


Email: gaoy (AT) big.ac.cn



  • Professor, Beijing Institute of Genomics, Chinese Academy of Sciences, China, 2021−Present

  • Postdoctoral Associate, Department of Pathology, Children’s Hospital of Philadelphia, USA, 2018-2021

  • Postdoctoral Associate, Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, USA, 2016-2018


  • Ph.D. in Genetics, University of Chinese Academy of Sciences UCAS, China, 2016

  • M.S. in Marine Pharmacology, Institute of Oceanology, Chinese Academy of Sciences, China, 2009

  • B.S. in Biological Science, Ocean University of China, China, 2006


  • Functional metagenomics

  • Spatial trancriptomics

  • Long read sequencing data processing and analysis


  • CIRI/CIRI2 (de novo detection of circular RNA back-splice junction)

  • CIRI-AS (Internal structure and alternative splicing detection within circular RNAs)

  • CRISPR_network (phage–bacteria infection network reconstruction from CRISPR arrays)

  • DEMIC (Bacterial growth rate comparison in multiple metagenomic samples)

  • ESPRESSO (Discovery and quantification of transcript isoforms from long-read RNA-seq data)

  • SPIRIT (Consensus sequences from rolling circle amplification libraries)


1.    Gao Y, Li H*. Quantifying and comparing bacterial growth dynamics in multiple metagenomic samples [J]. Nature Methods, 2018, 15(12): 1041.

2.    Gao Y*†, Wang F†, Wang R†, Kutschera E, Xu Y, Xie S, Wang Y, Kadash-Edmondson KE, Lin L, and 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.

3.    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. (citation>800) 

4.    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.

5.    Gao Y, Zhao F*. Computational strategies for exploring circular RNAs [J]. Trends in Genetics2018, 34(5): 389-400.

6.    Gao Y, Zhang J, Zhao F*. Circular RNA identification based on multiple seed matching [J]. Briefings in Bioinformatics, 2018, 19(5): 803-810.

7.    Wang JGao Y, Zhao F*. Phage–bacteria interaction network in human oral microbiome [J]. Environmental Microbiology, 2016, 7(18): 2143-2158. 

8.    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.

9.    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.

10.    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.


  • Assistant/Associate Professor

  • Engineer

  • Postdoc Associates

  • PhD Students

  • Master Students