Jian Qun Chen

Summary

Affiliation: Nanjing University
Country: China

Publications

  1. pmc Optimal codon identities in bacteria: implications from the conflicting results of two different methods
    Bin Wang
    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, China
    PLoS ONE 6:e22714. 2011
  2. pmc Important role of indels in somatic mutations of human cancer genes
    Haiwang Yang
    State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing 210093, China
    BMC Med Genet 11:128. 2010
  3. pmc Highly asymmetric rice genomes
    Jing Ding
    State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing, China
    BMC Genomics 8:154. 2007
  4. doi request reprint Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes
    Dacheng Tian
    State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing 210093, China
    Nature 455:105-8. 2008
  5. doi request reprint Unique evolutionary pattern of numbers of gramineous NBS-LRR genes
    Jing Li
    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
    Mol Genet Genomics 283:427-38. 2010
  6. pmc Rapidly evolving R genes in diverse grass species confer resistance to rice blast disease
    Sihai Yang
    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
    Proc Natl Acad Sci U S A 110:18572-7. 2013
  7. ncbi request reprint Genetic variation of NBS-LRR class resistance genes in rice lines
    Sihai Yang
    State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing 210093, China
    Theor Appl Genet 116:165-77. 2008
  8. doi request reprint Loss/retention and evolution of NBS-encoding genes upon whole genome triplication of Brassica rapa
    Ping Wu
    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, China Electronic address
    Gene 540:54-61. 2014
  9. pmc Insight into the evolution of the histidine triad protein (HTP) family in Streptococcus
    Zhu Qing Shao
    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, China
    PLoS ONE 8:e60116. 2013
  10. doi request reprint Non-random arrangement of synonymous codons in archaea coding sequences
    Yan mei Zhang
    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, 210093, China
    Genomics 101:362-7. 2013

Collaborators

Detail Information

Publications25

  1. pmc Optimal codon identities in bacteria: implications from the conflicting results of two different methods
    Bin Wang
    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, China
    PLoS ONE 6:e22714. 2011
    ..For all above reasons, we conclude that real optimal codons actually do not track the genomic GC content, and correlation method is misleading in identifying optimal codons and better be avoided...
  2. pmc Important role of indels in somatic mutations of human cancer genes
    Haiwang Yang
    State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing 210093, China
    BMC Med Genet 11:128. 2010
    ..More and more cancer related genes are found to have accumulated somatic mutations. However, little has been reported about mutational patterns of insertions/deletions (indels) in these genes...
  3. pmc Highly asymmetric rice genomes
    Jing Ding
    State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing, China
    BMC Genomics 8:154. 2007
    ..var. 93-11 provide an opportunity to systematically investigate the extent of the gene repertoire polymorphism, even though the genomic data of 93-11 derived from whole-short-gun sequencing is not yet as complete as that of Nipponbare...
  4. doi request reprint Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes
    Dacheng Tian
    State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing 210093, China
    Nature 455:105-8. 2008
    ..The consistency of these patterns within and between species suggests that indel-associated substitution is a general mutational mechanism...
  5. doi request reprint Unique evolutionary pattern of numbers of gramineous NBS-LRR genes
    Jing Li
    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210093, China
    Mol Genet Genomics 283:427-38. 2010
    ..In addition, the small proportion of conserved NBSs suggests that the loss of NBSs may be a general tendency in grass species...
  6. pmc Rapidly evolving R genes in diverse grass species confer resistance to rice blast disease
    Sihai Yang
    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
    Proc Natl Acad Sci U S A 110:18572-7. 2013
    ..Our results open avenues for R-gene identification that will help to elucidate R-gene vs. effector mechanisms and may yield new sources of durable pathogen resistance. ..
  7. ncbi request reprint Genetic variation of NBS-LRR class resistance genes in rice lines
    Sihai Yang
    State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing 210093, China
    Theor Appl Genet 116:165-77. 2008
    ..Our results also suggested that R-genes were under strong selection, which shaped R-gene variation patterns...
  8. doi request reprint Loss/retention and evolution of NBS-encoding genes upon whole genome triplication of Brassica rapa
    Ping Wu
    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, China Electronic address
    Gene 540:54-61. 2014
    ..The evolution of genes is more likely determined by the property of each gene family, and the whole genome triplication provided only a specific condition. ..
  9. pmc Insight into the evolution of the histidine triad protein (HTP) family in Streptococcus
    Zhu Qing Shao
    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, China
    PLoS ONE 8:e60116. 2013
    ..Specifically, the regions outside the HTP domains are under strong positive selection. This distinct evolutionary pattern likely helped Streptococcus to easily escape from recognition by host immunity...
  10. doi request reprint Non-random arrangement of synonymous codons in archaea coding sequences
    Yan mei Zhang
    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, 210093, China
    Genomics 101:362-7. 2013
    ....
  11. doi request reprint Codon usage bias and determining forces in green plant mitochondrial genomes
    Bin Wang
    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
    J Integr Plant Biol 53:324-34. 2011
    ..Such differences, together with previous reports based on the chloroplast data, suggests that after plants colonized the land, their codon usages in organellar genomes are more reluctant to be shaped by selection force...
  12. ncbi request reprint Unique pattern of R-gene variation within populations in Arabidopsis
    Jing Ding
    State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing 210093, China
    Mol Genet Genomics 277:619-29. 2007
    ..Consequently, the shared-polymorphism became recyclable for new R-genes, as the corresponding avirulence re-emerges in pathogen populations...
  13. pmc A primary survey on bryophyte species reveals two novel classes of nucleotide-binding site (NBS) genes
    Jia Yu Xue
    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, China
    PLoS ONE 7:e36700. 2012
    ..The presence of specific introns highlights the chimerical structures of HNL, PNL and TNL genes, and implies their possible origin via exon-shuffling during the quick lineage separation processes of early land plants...
  14. pmc Synonymous codon ordering: a subtle but prevalent strategy of bacteria to improve translational efficiency
    Zhu Qing Shao
    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, China
    PLoS ONE 7:e33547. 2012
    ..Such a phenomenon of co-tRNA codons pairing bias (CTCPB) is also found in some other eukaryotes but it is not known whether it occurs in prokaryotes...
  15. doi request reprint Tracing the origin and evolutionary history of plant nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes
    Jia Xing Yue
    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
    New Phytol 193:1049-63. 2012
    ....
  16. pmc Unique evolutionary mechanism in R-genes under the presence/absence polymorphism in Arabidopsis thaliana
    Jingdan Shen
    State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, China
    Genetics 172:1243-50. 2006
    ..031-0.103). Our results suggest that R-P/A loci evolved differently from other R-gene loci and that balancing selection plays an important role in molecular evolution of R-P/A...
  17. doi request reprint Recent duplications dominate NBS-encoding gene expansion in two woody species
    Sihai Yang
    State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing, China
    Mol Genet Genomics 280:187-98. 2008
    ..Non-TIR-NBS-encoding genes were poly- or paraphyletic, i.e. genes from three or more plant species were nested in different clades, suggesting different evolutionary patterns between these two gene types...
  18. doi request reprint Complex mutation and weak selection together determined the codon usage bias in bryophyte mitochondrial genomes
    Bin Wang
    State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing 210093, China
    J Integr Plant Biol 52:1100-8. 2010
    ..In summary, complex mutation and weak selection together determined the codon usages in bryophyte mitochondrial genomes...
  19. pmc Great majority of recombination events in Arabidopsis are gene conversion events
    Sihai Yang
    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
    Proc Natl Acad Sci U S A 109:20992-7. 2012
    ..Finally, our analysis reveals recombination hot spots and unexpectedly high recombination rates near centromeres. This may be responsible for the previously unexplained pattern of high genetic diversity near Arabidopsis centromeres...
  20. doi request reprint Increased complexity of gene structure and base composition in vertebrates
    Ying Wu
    State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, China
    J Genet Genomics 38:297-305. 2011
    ....
  21. pmc Patterns of exon-intron architecture variation of genes in eukaryotic genomes
    Liucun Zhu
    State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing 210093, PR China
    BMC Genomics 10:47. 2009
    ..Several studies have investigated the variations of intron length, GC content, ordinal position in a gene and divergence. However, there is little study about the structural variation of exons and introns...
  22. doi request reprint Relative evolutionary rates of NBS-encoding genes revealed by soybean segmental duplication
    Xiaohui Zhang
    State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
    Mol Genet Genomics 285:79-90. 2011
    ..It is important to determine the exact relative evolutionary rates of TNL, non-TNL, and non-NBS genes in order to understand how fast the host plant can adjust its response to rapidly evolving pathogens in a coevolutionary context...
  23. ncbi request reprint [A genome-wide analysis of P450 gene family in waterflea (Daphnia pulex)]
    Yun Hua Zhang
    School of Life Science, Nanjing University, Nanjing 210093
    Fen Zi Xi Bao Sheng Wu Xue Bao 42:53-60. 2009
    ..5% of genes in which positive selections were detected. Moreover, twenty motifs were identified, there in to, 5 motifs existed in over 90% of P450 genes...
  24. doi request reprint Variation in the ratio of nucleotide substitution and indel rates across genomes in mammals and bacteria
    Jian Qun Chen
    State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing, China
    Mol Biol Evol 26:1523-31. 2009
    ..Indels, therefore, may play a nontrivial role in controlling differences in genetic variation and divergence across functional regions of a genome...
  25. ncbi request reprint [Monitoring of pollen-mediated gene flow from transgenic Bt cotton]
    Chang Yong Wang
    School of Life Sciences, Nanjing University, Nanjing 210093, China
    Ying Yong Sheng Tai Xue Bao 18:801-6. 2007
    ..01), and FGF generally tended to decrease with increasing distance from the Bt cotton plot, with a frequency of 2.0% at the farthest distance of 25 m...