Dr. Xuan Li is engaged in applied research in computational and systems biology. We also serve as a bioinformatics core to provide analytical support to other research groups at Institute of Plant Physiology and Ecology, CAS.

The major interests for  Dr Li's group include: 

1) Functional genomics and transcriptomics of plant and animal models;

2) Systems biology study of RNA editing and splicing; 

3) mGWAS and metabolic study of plants and  natural products.  

1988   B. S. in Biology

Peking University, Beijing,China

1996   Ph. D. in Biochemistry and Molecular Biology

St.  Louis University, St. Louis, Missouri

2002   Master of Engineering in Computer Science

North  Carolina State University, Raleigh, North Carolina

Dr. Xuan Li acquired his bachelor degree in Biology from Peking University in 1988, and Ph.D degree in biochemistry from St. Louis University in 1996. He received postdoctoral training at Duke University from 1997 to 2000. He also obtained a master of engineering degree in computer science from North Carolina State University. From 2001 to 2008, he was working as Scientist, Bioinformatician, and Informatics Consultant at Curagen, GSK, and SCBIT. In 2009, he joined Institute of Plant Physiology and Ecology, where he has performed research and trained graduate students in bioinformatics and computational biology.  His research interests are focused in the following areas: 1) Functional genomics and transcriptomics of model organisms; 2) Systems biology study of RNA editing and splicing; and 3) mGWAS and metabolic study of plants and  natural products. 

Shen F^#, Wu X^#, Shi L, Zhang H, Chen Y, Qi X, Wang Z*, and Li X*. Transcriptomic and metabolic flux analyses reveal shift of metabolic patterns during rice grain development. BMC Systems Biology 2018; 12(Suppl 4):47.

Jing X^#, Xie B^#, Chen L, Zhang N, Jiang Y, Qin H, Wang H, Hao P*, Yang S*, Li X*. Implementation of the CRISPR-Cas13a system in fission yeast and its repurposing for precise RNA editing. Nucleic Acids Res 2018; doi: 10.1093/nar/gky433.

Huang Y, Cao Y, Li J, Liu Y, Zhong W, Li X*, Chen C*, Hao P*. A survey on cellular RNA editing activity in response to Candida albicans infections. BMC Genomics 2018; 19(Suppl 1):43.

Cao Y, Cao R, Huang Y, Zhou H, Liu Y, Li X*, Zhong W*, Hao P*. A comprehensive study on cellular RNA editing activity in response to infections with different subtypes of influenza A viruses. BMC Genomics 2018; 19(Suppl 1):925.

Lv C^#, Wu X^#, Wang X, Su J, Zeng H, Zhao J, Lin S, Liu R, Li H*, Li X*, Zhang W*. The gene expression profiles in response to 102 traditional Chinese medicine (TCM) components: a general template for research on TCMs. Scientific Reports 2017; 7:352.

Chen P^#, Jing X^#, Liao B, Zhu Y, Xu J, Liu R, Zhao Y, and Li X*. BioNano map resource for Oryza sativa ssp. japonica and indica and its application in rice genome sequence correction and gap filling. Molecular Plant 2017; 10, 895–898.

Kong Y, Xu P, Jing X, Chen L, Li L*, Li X*. Decipher the ancestry of the plant-specific LBD gene family. BMC Genomics 2017; 18(Suppl 1):951.

Zhu Y^#, Chen L^#, Zhang C, Hao P, Jing X* and Li X*. Global transcriptome analysis reveals extensive gene remodeling, alternative splicing and differential transcription profiles in nonseed vascular plant Selaginella moellendorffii. BMC Genomics 2017; 18(Suppl 1):1042.

Yu Y, Zhou H, Kong Y, Pan B, Chen L, Wang H, Hao P* and Li X*. The landscape of A-to-I RNA editome is shaped by both positive and purifying selection. PLoS Genetics 2016; 12(7): e1006191.

 Zhu Y#, Chen L#, Zhang C, Hao P, Jing X* and Li X*. Global transcriptome analysis reveals extensive gene remodeling, alternative splicing and differential transcription profiles in nonseed vascular plant Selaginella moellendorffii. BMC Genomics 2016 (Accepted).

 Zhao Q-Y*, Gratten J, Restuadi R, and Li X*. Mapping and differential expression analysis from short-read RNA-Seq data in model organisms. Quantitative Biology 2016; 4(1): 22-35.

 Li X* , Kong Y, Zhao Q-Y, Li Y-Y, and Hao P*. De novo assembly of transcriptome from next-generation sequencing data. Quantitative Biology 2016; 4(2): 94-105. 

Kong Y, Zhou H, Yu Y, Chen L, Hao P*, Li X*. The evolutionary landscape of intergenic trans-splicing events in insects. Nature Communications 2015; 6:8734.

Di Z, Yu Y, Wu Y, Hao P, He Y, Zhao H, Li Y, Zhao G, Li X*, Li W*, Cao Z*. Genome-wide analysis of homeobox genes from Mesobuthus martensii reveals Hox gene duplication in scorpions. Insect Biochem Mol Biol 2015; 61:25-33.

Chen J, Wu X-T, Xu Y-Q, Zhong Y, Li Y-X, Chen J-K, Li X* and Nan P*. Global transcriptome analysis profiles metabolic pathways in traditional herb Astragalus membranaceus Bge. var. mongolicus (Bge.) Hsiao. BMC Genomics 2015; 16(Suppl 7):S15.

Li C-F, Zhu Y, Yu Y, Zhao Q-Y, Wang S-J, Wang X-C, Yao M-Z, Luo D, Li X*, Chen L*, Yang Y-J*. Global transcriptome and gene regulation network for secondary metabolite biosynthesis of tea plant (Camellia sinensis). BMC Genomics 2015; 16:560.

Xing M-Q, Zhang Y-J, Zhou S-R, Hu W-Y, Wu X-T, Ye Y-J, Wu X-X, Xiao Y-P, Li X, Xue H-W*. Global Analysis Reveals the Crucial Roles of DNA Methylation during Rice Seed Development. Plant Physiology 2015; 168: 1417–1432.

Song X, Wei H, Chen W, Zhao Y, Yang S, Li X, Luo D, Zhang H, Feng X*. Development of INDEL Markers for Genetic Mapping Based on Whole-Genome Re-sequencing in Soybean. G3 (Bethesda) 2015; 5:2793-2799.

Xu P, Kong Y, Song D, Huang C, Li X, Li L*. Conservation and functional influence of alternative splicing in wood formation of Populus and Eucalyptus. BMC Genomics 2014; 15:780,

Cao Z, Yu Y, Wu Y, Hao P, Di Z, He Y, ... Xing X, Zhao G, Li X*, Li Y*, Li W*. The genome of Mesobuthus martensii reveals a unique adaptation model of arthropods. Nature Communications 2013;4:2602.

Pan B, Sheng J, Sun W, Zhao Y, Hao P*, Li X*. OrysPSSP: a comparative platform for small secreted proteins from rice and other plants. Nucleic Acids Research 2013; 41(D1):D1192-8.

Wang XC, Zhao QY, Ma CL, Zhang ZH, Cao HL, Kong YM, Yue C, Hao XY, Chen L, Ma JQ, Jin JQ, Li X*, Yang YJ*. Global transcriptome profiles of Camellia sinensis during cold acclimation. BMC Genomics 2013, 14:415.

Xu P, Kong Y, Li X, Li L*. Identification of molecular processes needed for vascular formation through transcriptome analysis of different vascular systems. BMC Genomics 2013;14:217.

Yu S, Zheng L, Li Y, Li C, Ma C, Yu Y, Li X, Hao P*. Causal co-expression method with module analysis to screen drugs with specific target. Gene 2013; 518(1):145-51.

Ma L-X, Wang Y-J, Wang J-F*, Li X and Hao P*. Expression Sensitivity Analysis of Human Disease Related Genes. BioMed Research International 2013; DOI: 10.1155/2013/637424.

Hu Y, Lu S, Song Z, Wang W, Hao P, Li J, Zhang X, Yen HL, Shi B, Li T, Guan W, Xu L, Liu Y, Wang S, Zhang X, Tian D, Zhu Z, He J, Huang K, Chen H, Zheng L, Li X, Ping J, Kang B, Xi X, Zha L, Li Y, Zhang Z, Peiris M*, Yuan Z*. Association between adverse clinical outcome in human disease caused by novel influenza A H7N9 virus and sustained viral shedding and emergence of antiviral resistance. Lancet 2013; 381(9885):2273-9.

Zhang XW, Jia LJ, Zhang Y, Jiang G, Li X, Zhang D, and Tang WH*. In planta stage-specific fungal gene profiling elucidates the molecular strategies of Fusarium graminearum growing inside wheat coleoptiles. Plant Cell 2012; 24(12): 5159-76.

Wang Y, Yu Y, Pan B, Hao P, Li Y, Shao Z, Xu X* and Li X*. Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome. BMC Systems Biology 2012; 6 (Suppl 3):S2.

Yu S, Zheng L, Yu Y, Li Y, Wang Y, Ma C, Li Y, Li X* and Hao P*. A cross-species analysis method to analyze animal models’ similarity to human’s disease state. BMC Systems Biology 2012; 6(Suppl 3):S18.

Ping J, Wang Y, Yu Y, Li YX, Li X*, Hao P*. A comparative analysis of tissue gene expression data from high-throughput studies. Chinese Science Bulletin 2012; 57(22): 2920-2927.

Shao W, Zhao Q-Y, Wang XY, Xu X-Y, Tang Q, Li M, Li X* and Xu Y-Z*. Alternative splicing and trans-splicing events revealed by analysis of the Bombyx mori transcriptome. RNA 2012; 18(7):1395-407.

Chen Y, Liu F, Yang B, Lu A, Wang S, Wang J, Ling QZ, Li X, Beerntsen BT, Ling E*. Specific amino acids affecting Drosophila melanogaster prophenoloxidase activity in vitro. Dev Comp Immunol 2012; 38(1):88-97.

Wang J-F*, Hao P, Li Y-X, Dai J-L, Li X. Exploration of conformational transition in the aryl-binding site of human FXa using molecular dynamics simulations. J Mol Model 2012;18(6):2717-25.

Zhao Q-Y, Wang Y, Kong Y-M, Luo D, Li X* and Hao P*. Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics 2011; 12(Suppl 14):S2.

Li Y, Tu K, Zheng S, Wang J, Li Y-X, Hao P, Li X*. Association of feature gene expression with structural fingerprints of chemical compounds. J Bioinform Comput Biol 2011;9(4):503-19

Zhong Y, Chang X, Cao X, Zhang Y, Zheng H-J, Zhu Y-Z, Cai C-S, Li Y-Y, Zhao G-P, Wang S-Y, Li Y-X*, Zeng R*, Li X*, Guo X-K*. Comparative Proteogenomic Analysis of the Leptospira interrogans Virulence Attenuated Strain IPAV against the Pathogenic Strain 56601. Cell Res 2011;21(8):1210-29.

Hao P, Zheng H, Yu Y, Ding G, Gu W, Chen S, Yu Z, Ren S, Oda M, Konno T, Wang S, Li X*, Ji Z-S* and Zhao G*. Complete sequencing and pan-genomic analysis of Lactobacillus delbrueckii subsp. bulgaricus reveal its genetic basis for industrial yogurt production. PLoS One 2011; 6(1):e15964.

Yu Y, Xu T, Yu Y, Hao P*, Li X*. Association of tissue lineage and gene expression: conservatively and differentially expressed genes define common and special functions of tissues. BMC Bioinformatics 2010; 11(Suppl 11):S1.

Xu T, Yu Y, Yu T, Yu Y, Hao P*, Li X*. Revealing parasite influence in metabolic pathways in Apicomplexa infected patients. BMC Bioinformatics 2010; 11(Suppl 11):S13.

The major interests of Dr Xuan Li are focused in three areas:  

1) Functional genomics and transcriptomics of plant and animal models;

2) Systems biology study of RNA editing and splicing; 

3) mGWAS and metabolic study of plants and  natural products. 

已指导学生

潘伯虎  博士研究生  071005-微生物学  

孔艺萌  博士研究生  071005-微生物学  

周红霞  博士研究生  071005-微生物学  

陈萍  博士研究生  071005-微生物学  

解冰冉  博士研究生  071005-微生物学  

陈龙现  博士研究生  071005-微生物学  

李雪童  博士研究生  071005-微生物学  

李佳  硕士研究生  071005-微生物学  

秦航  博士研究生  071005-微生物学  

江涛  硕士研究生  085238-生物工程  

现指导学生

张梦杰  博士研究生  071005-微生物学  

周辉  博士研究生  071005-微生物学  

龚洁  硕士研究生  071005-微生物学  

张牛冰  博士研究生  071005-微生物学  

周小娟  博士研究生  071005-微生物学  

程香  硕士研究生  071005-微生物学  

时晗  博士研究生  071005-微生物学  

郝陈惠  硕士研究生  071005-微生物学