Education

Ph.D., Institute National des Sciences Appliquées (INSA)

Current position

Professor, School of Life Sciences, Nanjing University, China

Publications

1. Zhang, X., Yang, S., Wang, J., Jia, Y., Huang, J., Tan, S., Zhong, Y., Wang, L., Gu, L., Chen, J. Q., Pan, Q., Bergelson, J. and Tian, D. (2015). A genome-wide survey reveals abundant rice blast R genes in resistant cultivars. Plant J 84(1): 20-28.
   
2. Yang, S., Wang, L., Huang, J., Zhang, X., Yuan, Y., Chen, J. Q., Hurst, L. D. and Tian, D. (2015). Parent-progeny sequencing indicates higher mutation rates in heterozygotes. Nature 523(7561): 463-467.
   
3. Zhou, G. C., Shao, Z. Q., Ma, F. F., Wu, P., Wu, X. Y., Xie, Z. Y., Yu, D. Y., Cheng, H., Liu, Z. H., Jiang, Z. F., Chen, Q. S., Wang, B. and Chen, J. Q. (2015). The evolution of soybean mosaic virus: An updated analysis by obtaining 18 new genomic sequences of Chinese strains/isolates. Virus Res 208: 189-198.
   
4. Zhang, Y. M., Shao, Z. Q., Wang, Q., Hang, Y. Y., Xue, J. Y., Wang, B. and Chen, J. Q. (2015). Uncovering the dynamic evolution of nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes in Brassicaceae. J Integr Plant Biol.
   
5. Liu, H., Zhang, X., Huang, J., Chen, J. Q., Tian, D., Hurst, L. D. and Yang, S. (2015). Causes and consequences of crossing-over evidenced via a high-resolution recombinational landscape of the honey bee. Genome Biol 16: 15.
   
6. Sun, X., Pang, H., Li, M., Chen, J. and Hang, Y. (2014). Tracing the origin and evolution of plant TIR-encoding genes. Gene 546(2): 408-416.
   
7. Shao, Z. Q., Zhang, Y. M., Hang, Y. Y., Xue, J. Y., Zhou, G. C., Wu, P., Wu, X. Y., Wu, X. Z., Wang, Q., Wang, B. and Chen, J. Q. (2014). Long-term evolution of nucleotide-binding site-leucine-rich repeat genes: understanding gained from and beyond the legume family. Plant Physiol 166(1): 217-234.
   
8. Wu, P., Shao, Z. Q., Wu, X. Z., Wang, Q., Wang, B., Chen, J. Q., Hang, Y. Y. and Xue, J. Y. (2014). Loss/retention and evolution of NBS-encoding genes upon whole genome triplication of Brassica rapa. Gene 540(1): 54-61.
   
9. Amborella Genome, P. (2013). The Amborella genome and the evolution of flowering plants. Science 342(6165): 1241089.
   
10. Yang, S., Li, J., Zhang, X., Zhang, Q., Huang, J., Chen, J. Q., Hartl, D. L. and Tian, D. (2013). Rapidly evolving R genes in diverse grass species confer resistance to rice blast disease. Proc Natl Acad Sci U S A 110(46): 18572-18577.
    
11. Shao, Z. Q., Zhang, Y. M., Pan, X. Z., Wang, B. and Chen, J. Q. (2013). Insight into the evolution of the histidine triad protein (HTP) family in Streptococcus. PLoS One 8(3): e60116.
    
12. Zhang, L., Hou, D., Chen, X., Li, D., Zhu, L., Zhang, Y., Li, J., Bian, Z., Liang, X., Cai, X., Yin, Y., Wang, C., Zhang, T., Zhu, D., Zhang, D., Xu, J., Chen, Q., Ba, Y., Liu, J., Wang, Q., Chen, J., Wang, J., Wang, M., Zhang, Q., Zhang, J., Zen, K. and Zhang, C. Y. (2012). Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA. Cell Res 22(1): 107-126.
    
13. Yang, S., Yuan, Y., Wang, L., Li, J., Wang, W., Liu, H., Chen, J. Q., Hurst, L. D. and Tian, D. (2012). Great majority of recombination events in Arabidopsis are gene conversion events. Proc Natl Acad Sci U S A 109(51): 20992-20997.
    
14. Xue, J. Y., Wang, Y., Wu, P., Wang, Q., Yang, L. T., Pan, X. H., Wang, B. and Chen, J. Q. (2012). A primary survey on bryophyte species reveals two novel classes of nucleotide-binding site (NBS) genes. PLoS One 7(5): e36700.
    
15. Shao, Z. Q., Zhang, Y. M., Feng, X. Y., Wang, B. and Chen, J. Q. (2012). Synonymous codon ordering: a subtle but prevalent strategy of bacteria to improve translational efficiency. PLoS One 7(3): e33547.
    
16. Yue, J. X., Meyers, B. C., Chen, J. Q., Tian, D. and Yang, S. (2012). Tracing the origin and evolutionary history of plant nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes. New Phytol 193(4): 1049-1063.
    
17. Wu, Y., Yuan, H., Tan, S., Chen, J. Q., Tian, D. and Yang, H. (2011). Increased complexity of gene structure and base composition in vertebrates. J Genet Genomics 38(7): 297-305.
    
18. Zhang, X., Feng, Y., Cheng, H., Tian, D., Yang, S. and Chen, J. Q. (2011). Relative evolutionary rates of NBS-encoding genes revealed by soybean segmental duplication. Mol Genet Genomics 285(1): 79-90.
    
19. Wang, B., Shao, Z. Q., Xu, Y., Liu, J., Liu, Y., Hang, Y. Y. and Chen, J. Q. (2011). Optimal codon identities in bacteria: implications from the conflicting results of two different methods. PLoS One 6(7): e22714.
    
20. Wang, B., Yuan, J., Liu, J., Jin, L. and Chen, J. Q. (2011). Codon usage bias and determining forces in green plant mitochondrial genomes. J Integr Plant Biol 53(4): 324-334.
    
21. Yang, H., Zhong, Y., Peng, C., Chen, J. Q. and Tian, D. (2010). Important role of indels in somatic mutations of human cancer genes. BMC Med Genet 11: 128.
    
22. Wang, B., Liu, J., Jin, L., Feng, X. Y. and Chen, J. Q. (2010). Complex mutation and weak selection together determined the codon usage bias in bryophyte mitochondrial genomes. J Integr Plant Biol 52(12): 1100-1108.
    
23. Li, J., Ding, J., Zhang, W., Zhang, Y., Tang, P., Chen, J. Q., Tian, D. and Yang, S. (2010). Unique evolutionary pattern of numbers of gramineous NBS-LRR genes. Mol Genet Genomics 283(5): 427-438.
    
24. Zhang, Y., Wang, J., Zhang, X., Chen, J. Q., Tian, D. and Yang, S. (2009). Genetic signature of rice domestication shown by a variety of genes. J Mol Evol 68(4): 393-402.
    
25. Chen, J. Q., Wu, Y., Yang, H., Bergelson, J., Kreitman, M. and Tian, D. (2009). Variation in the ratio of nucleotide substitution and indel rates across genomes in mammals and bacteria. Mol Biol Evol 26(7): 1523-1531.
    
26. Zhu, L., Zhang, Y., Zhang, W., Yang, S., Chen, J. Q. and Tian, D. (2009). Patterns of exon-intron architecture variation of genes in eukaryotic genomes. BMC Genomics 10: 47.
    
27. Deng, H., Yu, F., Chen, J., Zhao, Y., Xiang, J. and Lin, A. (2008). Phosphorylation of Bad at Thr-201 by JNK1 promotes glycolysis through activation of phosphofructokinase-1. J Biol Chem 283(30): 20754-20760.
    
28. Tian, D., Wang, Q., Zhang, P., Araki, H., Yang, S., Kreitman, M., Nagylaki, T., Hudson, R., Bergelson, J. and Chen, J. Q. (2008). Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes. Nature 455(7209): 105-108.
    
29. Sun, X., Zhang, Y., Yang, S., Chen, J. Q., Hohn, B. and Tian, D. (2008). Insertion DNA Promotes Ectopic Recombination during Meiosis in Arabidopsis. Mol Biol Evol 25(10): 2079-2083.
    
30. Yang, S., Zhang, X., Yue, J. X., Tian, D. and Chen, J. Q. (2008). Recent duplications dominate NBS-encoding gene expansion in two woody species. Mol Genet Genomics 280(3): 187-198.
    
31. Yang, S., Gu, T., Pan, C., Feng, Z., Ding, J., Hang, Y., Chen, J. Q. and Tian, D. (2008). Genetic variation of NBS-LRR class resistance genes in rice lines. Theor Appl Genet 116(2): 165-177.
    
32. Conservation, P. E. S. (2008). Phylogeny of Dioscorea sect. Stenophora based on chloroplast matK, rbcL and trnL-F sequences. Journal of Systematics and Evolution 46(3): 315-321.
    
33. Ding, J., Araki, H., Wang, Q., Zhang, P., Yang, S., Chen, J. Q. and Tian, D. (2007). Highly asymmetric rice genomes. BMC Genomics 8: 154.
    
34. Ding, J., Zhang, W., Jing, Z., Chen, J. Q. and Tian, D. (2007). Unique pattern of R-gene variation within populations in Arabidopsis. Mol Genet Genomics 277(6): 619-629.
    
35. Yang, S., Feng, Z., Zhang, X., Jiang, K., Jin, X., Hang, Y., Chen, J. Q. and Tian, D. (2006). Genome-wide investigation on the genetic variations of rice disease resistance genes. Plant Mol Biol 62(1-2): 181-193.
    
36. Shen, J., Araki, H., Chen, L., Chen, J. Q. and Tian, D. (2006). Unique evolutionary mechanism in R-genes under the presence/absence polymorphism in Arabidopsis thaliana. Genetics 172(2): 1243-1250.
    
37. Zhou, T., Wang, Y., Chen, J. Q., Araki, H., Jing, Z., Jiang, K., Shen, J. and Tian, D. (2004). Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes. Mol Genet Genomics 271(4): 402-415.
    
38. Zhang, Y., Zhang, D., Li, W., Chen, J., Peng, Y. and Cao, W. (2003). A novel real-time quantitative PCR method using attached universal template probe. Nucleic Acids Res 31(20): e123.
    
39. Tian, D., Traw, M. B., Chen, J. Q., Kreitman, M. and Bergelson, J. (2003). Fitness costs of R-gene-mediated resistance in Arabidopsis thaliana. Nature 423(6935): 74-77.