Yuan Gao
Professor
Email: gaoy (AT) big.ac.cn
Tel:
Email: gaoy (AT) big.ac.cn
Tel:
PROFESSIONAL EXPERIENCE
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
EDUCATION
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
RESEARCH INTERESTS
Functional metagenomics
Spatial trancriptomics
Long read sequencing data processing and analysis
SOFTWARE & TOOLS
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)
SELECTED PUBLICATIONS
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 Genetics, 2018, 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 J†, Gao 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.
OPEN POSITIONS IN LAB
Assistant/Associate Professor
Engineer
Postdoc Associates
PhD Students
Master Students