Curriculum vitae:
1994-1998 China Agricultural University Plant pathology B.S.
2000-2005 Pecking University Bioinformatic Ph.D.
2005-2007 Institute of Botany, CAS PostDoc
2007-2009 The University of Arizona PostDoc
2009-2014 The University of Texas at Austin PostDoc
2016-Present Institute of Genetics and Developmental Biology, CAS associate researcher
Research direction and interest:
Bioinformatics
List of published articles:
1. Shi XL, Cui F, Han XY, He YL, Zhao L, Zhang N, Zhu HD, Liu ZX, Ma B, Zheng SS et al: Comparative genomic and transcriptomic analyses uncover the molecular basis of high nitrogen use efficiency in the wheat cultivar Kenong 9204. Molecular Plant 2022, 15(9):1440-1456
2. Ling HQ, Ma B, Shi XL, Liu H, Dong LL, Sun H, Cao YH, Gao Q, Zheng SS, Li Y et al: Genome sequence of the progenitor of wheat A subgenome Triticum urartu. Nature 2018, 557(7705):424-428.
3. Shi XL, Ling HQ: Current advances in genome sequencing of common wheat and its ancestral species. Crop Journal 2018, 6(1):15-21.
4. 史晓黎，何伊琳，凌宏清：小麦A基因组测序与进化研究进展. 遗传 2019，41(9): 836-844.
5. Si YQ, Zheng SS, Niu JQ, Tian SQ, Gu MJ, Lu Q, He YL, Zhang J, Shi XL, Li YW, Ling HQ: Ne2, a typical CC-NBS-LRR-type gene, is responsible for hybrid necrosis in wheat. New Phytologist 2021, 232(1):279-289.
6. Si YQ, Zheng SS, Niu JQ, Tian SQ, Shi XL, He YL, Li YW, Ling HQ: Fine mapping of hybrid necrosis gene Ne1 in common wheat (Triticum aestivum L.). Theoretical and Applied Genetics 2021, 134:2603-2611
7. Shi XL, Zhang CQ, Ko DK, Chen ZJ: Genome-Wide Dosage-Dependent and -Independent Regulation Contributes to Gene Expression and Evolutionary Novelty in Plant Polyploids. Molecular Biology Evolution 2015, 32(9):2351-2366.
8. Shi XL, Ng DWK, Zhang CQ, Comai L, Ye WX, Chen ZJ: Cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids. Nature Communications 2012, 3.
9. Kirkbride RC, Yu HH, Nah G, Zhang CQ, Shi XL, Chen ZJ: An Epigenetic Role for Disrupted Paternal Gene Expression in Postzygotic Seed Abortion in Arabidopsis Interspecific Hybrids. Molecular Plant 2015, 8(12):1766-1775.
10. Miller M, Song QX, Shi XL, Juenger TE, Chen ZJ: Natural variation in timing of stress-responsive gene expression predicts heterosis in intraspecific hybrids of Arabidopsis. Nature Communications 2015, 6.
11. Guan XY, Lee JJ, Pang MX, Shi XL, Stelly DM, Chen ZJ: Activation of Arabidopsis Seed Hair Development by Cotton Fiber-Related Genes. Plos One 2011, 6(7).
12. Shi XL, Wang XY, Li Z, Zhu QH, Yang J, Ge S, Luo JC: Evidence that natural selection is the primary cause of the guanine-cytosine content variation in rice genes. Journal of Integrative Plant Biology 2007, 49(9):1393-1399.
13. Shi XL, Wang XY, Li Z, Zhu QH, Tang W, Ge S, Luo JC: Nucleotide substitution pattern in rice paralogues: implication for negative correlation between the synonymous substitution rate and codon usage bias. Gene 2006, 376(2):199-206.
14. Wang XY, Shi XL, Li Z, Zhu QH, Kong L, Tang W, Ge S, Luo JC: Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice. BMC Bioinformatics 2006, 7:447.
15. Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C et al: The Genomes of Oryza sativa: a history of duplications. PLoS Biology 2005, 3(2):e38.
16. Wang XY, Shi XL, Hao BL, Ge S, Luo JC: Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytologist 2005, 165(3):937-946.
17. Wang XY, Shi XL, Hao BL: The tRNA and rRNA genes in the Oryza sativa genome. Yi Chuan Xue Bao 2004, 31(9):871-877.
18. Wang XY, Shi XL, Hao BL: The transfer RNA genes in Oryza sativa L. ssp. indica. Sci China C Life Sci 2002, 45(5):504-511.
19. Guan XY, Pang MX, Nah G, Shi XL, Ye WX, Stelly DM, Chen ZJ: miR828 and miR858 regulate homoeologous MYB2 gene functions in Arabidopsis trichome and cotton fibre development. Nature Communications 2014, 5.
20. Ng DWK, Shi XL, Nah G, Chen ZJ: High-throughput RNA-seq for allelic or locus-specific expression analysis in Arabidopsis-related species, hybrids, and allotetraploids. Methods Molecular Biology 2014, 1112:33-48.
21. Shi XL, Xie HM, Zhang SY, Hao BL: Decomposition and reconstruction of protein sequences: The Problem of Uniqueness and Factorizable Language. Journal of the Korean Physical Society 2007, 50:6.
