General

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 several first-author papers published on top journals such as Nature Methods, Science AdvancesTrends in Genetics, Nature Communications and Genome Biology, which have more than 1,000 citations according to Google Scholar. In 2021, Dr. GAO set up his current laboratory in BIG. 

Research Areas

Computational genomics, metagenomics and transcriptomics

Publications

(1) Role of Dietary Fiber in the Recovery of the Human Gut Microbiome and its Metabolome, Cell host & microbe, 2021
(2) isoCirc catalogs full-length circular RNA isoforms in human transcriptomes, NATURE COMMUNICATIONS, 2021
(3) Computational Strategies for Exploring Circular RNAs, TRENDS IN GENETICS, 2018
(4) Circular RNA identification based on multiple seed matching, BRIEFINGS IN BIOINFORMATICS, 2018
(5) Quantifying and comparing bacterial growth dynamics in multiple metagenomic samples, NATURE METHODS, 2018
(6) Phage-bacteria interaction network in human oral microbiome, ENVIRONMENTAL MICROBIOLOGY, 2016
(7) Comprehensive identification of internal structure and alternative splicing events in circular RNAs, NATURE COMMUNICATIONS, 2016
(8) CIRI: an efficient and unbiased algorithm for de novo circular RNA identification, GENOME BIOLOGY, 2015

Research Interests

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. 

The recent research of Dr. GAO Yuan focused on development of computational methods for omics data, including several widely used algorithms in transcriptomics and metagenomics: 1) a de novo algorithm for sensitive and specific detection of circular RNAs, CIRI/CIRI2; 2) an algorithm for detecting internal structure and alternative splicing events for circular RNAs, CIRI-AS; 3) a reference-free algorithm for quantifying and comparing bacterial growth dynamics from multiple metagenomic samples, DEMIC. 

Students

现指导学生

郑鑫  硕士研究生  0710Z1-基因组学  

胡文奥  硕士研究生  0710J3-生物信息学  

周子菡  博士研究生  0710J3-生物信息学