Shiheng Tao

Summary

Affiliation: Northwest A and F University
Country: China

Publications

  1. pmc Patterns of insertion and deletion in Mammalian genomes
    Yanhui Fan
    Bioinformatics Center, College of Life Science, Northwest A and F University, Yangling, Shaanxi 712100, China
    Curr Genomics 8:370-8. 2007
  2. pmc A meta-analysis of the association between the hOGG1 Ser326Cys polymorphism and the risk of esophageal squamous cell carcinoma
    Junjie Zhang
    College of Life Science, Northwest A and F University, Yangling, Shaanxi, China
    PLoS ONE 8:e65742. 2013
  3. pmc A comparison and evaluation of five biclustering algorithms by quantifying goodness of biclusters for gene expression data
    Li Li
    State Key Laboratory of Crop Stress Biology in Arid Areas and College of Sciences, Northwest A and F University, Yangling, Shaanxi, 712100, China
    BioData Min 5:8. 2012
  4. pmc Statistical distributions of optimal global alignment scores of random protein sequences
    Hongxia Pang
    School of Life Science, Northwest A and F University, Yangling, Shaanxi, China
    BMC Bioinformatics 6:257. 2005
  5. pmc A new computational strategy for predicting essential genes
    Jian Cheng
    College of Life Science, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A and F University, Yangling, Shaanxi, China
    BMC Genomics 14:910. 2013
  6. pmc Deciphering the rules by which dynamics of mRNA secondary structure affect translation efficiency in Saccharomyces cerevisiae
    Yuanhui Mao
    College of life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A and F University, Yangling, Shaanxi 712100, China, Bioinformatics Center, Northwest A and F University, Yangling, Shaanxi 712100, China and College of Enology, Northwest A and F University, Yangling, Shaanxi 712100, China
    Nucleic Acids Res 42:4813-22. 2014
  7. pmc Number variation of high stability regions is correlated with gene functions
    Yuanhui Mao
    College of life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A and F University, Yangling, Shaanxi, China
    Genome Biol Evol 5:484-93. 2013
  8. pmc Vertebrate paralogous MEF2 genes: origin, conservation, and evolution
    Wenwu Wu
    College of Life Science, Northwest A and F University, Yangling, Shaanxi, China
    PLoS ONE 6:e17334. 2011
  9. pmc Training set selection for the prediction of essential genes
    Jian Cheng
    College of life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A and F University, Yangling, Shaanxi, China Bioinformatics Center, Northwest A and F University, Yangling, Shaanxi, China
    PLoS ONE 9:e86805. 2014
  10. doi request reprint Characteristics of the CArG-SRF binding context in mammalian genomes
    Wenwu Wu
    College of Life Science, Northwest A and F University, 712100, Yangling, Shaanxi, China
    Mamm Genome 21:104-13. 2010

Collaborators

Detail Information

Publications24

  1. pmc Patterns of insertion and deletion in Mammalian genomes
    Yanhui Fan
    Bioinformatics Center, College of Life Science, Northwest A and F University, Yangling, Shaanxi 712100, China
    Curr Genomics 8:370-8. 2007
    ..The frequencies of both insertions and deletions can be described well by power law...
  2. pmc A meta-analysis of the association between the hOGG1 Ser326Cys polymorphism and the risk of esophageal squamous cell carcinoma
    Junjie Zhang
    College of Life Science, Northwest A and F University, Yangling, Shaanxi, China
    PLoS ONE 8:e65742. 2013
    ..However, the published findings are inconsistent. We therefore performed a meta-analysis to derive a more precise estimation of the association between the hOGG1 Ser326Cys polymorphism and ESCC risk...
  3. pmc A comparison and evaluation of five biclustering algorithms by quantifying goodness of biclusters for gene expression data
    Li Li
    State Key Laboratory of Crop Stress Biology in Arid Areas and College of Sciences, Northwest A and F University, Yangling, Shaanxi, 712100, China
    BioData Min 5:8. 2012
    ..abstract:..
  4. pmc Statistical distributions of optimal global alignment scores of random protein sequences
    Hongxia Pang
    School of Life Science, Northwest A and F University, Yangling, Shaanxi, China
    BMC Bioinformatics 6:257. 2005
    ..So far the statistical distribution function underlying the optimal global alignments has not been completely determined...
  5. pmc A new computational strategy for predicting essential genes
    Jian Cheng
    College of Life Science, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A and F University, Yangling, Shaanxi, China
    BMC Genomics 14:910. 2013
    ..Several computational models have recently been developed to integrate gene features and used as alternatives to transfer gene essentiality annotations between organisms...
  6. pmc Deciphering the rules by which dynamics of mRNA secondary structure affect translation efficiency in Saccharomyces cerevisiae
    Yuanhui Mao
    College of life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A and F University, Yangling, Shaanxi 712100, China, Bioinformatics Center, Northwest A and F University, Yangling, Shaanxi 712100, China and College of Enology, Northwest A and F University, Yangling, Shaanxi 712100, China
    Nucleic Acids Res 42:4813-22. 2014
    ..Together, these findings reveal how the dynamics of mRNA secondary structure coupling with codon usage affect translation efficiency. ..
  7. pmc Number variation of high stability regions is correlated with gene functions
    Yuanhui Mao
    College of life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A and F University, Yangling, Shaanxi, China
    Genome Biol Evol 5:484-93. 2013
    ..In addition, essential genes exhibited higher HSR density than nonessential genes. Overall, our study presented the previously unappreciated correlation between the number variation of HSRs and cellular processes...
  8. pmc Vertebrate paralogous MEF2 genes: origin, conservation, and evolution
    Wenwu Wu
    College of Life Science, Northwest A and F University, Yangling, Shaanxi, China
    PLoS ONE 6:e17334. 2011
    ....
  9. pmc Training set selection for the prediction of essential genes
    Jian Cheng
    College of life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A and F University, Yangling, Shaanxi, China Bioinformatics Center, Northwest A and F University, Yangling, Shaanxi, China
    PLoS ONE 9:e86805. 2014
    ..Thus, our results provide empirical guidance on training set selection for the identification of essential genes on a genome-wide scale. ..
  10. doi request reprint Characteristics of the CArG-SRF binding context in mammalian genomes
    Wenwu Wu
    College of Life Science, Northwest A and F University, 712100, Yangling, Shaanxi, China
    Mamm Genome 21:104-13. 2010
    ..This is a significant step toward understanding the mechanism of transcriptional regulation of SRF-dependent genes...
  11. pmc Neighbor preferences of amino acids and context-dependent effects of amino acid substitutions in human, mouse, and dog
    Mingchuan Fu
    College of life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A and F University, Yangling 712100, China
    Int J Mol Sci 15:15963-80. 2014
    ..Our findings may improve secondary structure prediction algorithms and protein design; moreover, this study provided useful information to develop empirical models of protein evolution that consider dependence between residues. ..
  12. pmc The influence of deleterious mutations on adaptation in asexual populations
    Xiaoqian Jiang
    Bioinformatics Center, College of Life Science, Northwest A and F University, Yangling, Shaanxi, China
    PLoS ONE 6:e27757. 2011
    ..And interestingly, the lowest adaptation rate occurs for a moderate value of selection coefficient of deleterious mutations...
  13. pmc Evolution of the F-box gene family in Euarchontoglires: gene number variation and selection patterns
    Ailan Wang
    State Key Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A and F University, Yangling, Shaanxi, China Bioinformatics Center, Northwest A and F University, Yangling, Shaanxi, China
    PLoS ONE 9:e94899. 2014
    ....
  14. pmc Genome-wide analysis of selective constraints on high stability regions of mRNA reveals multiple compensatory mutations in Escherichia coli
    Yuanhui Mao
    College of life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A and F University, Yangling, Shaanxi, China Bioinformatics Center, Northwest A and F University, Yangling, Shaanxi, China
    PLoS ONE 8:e73299. 2013
    ..Overall, these results suggest a significant role of local structural stability as a selective force operating on mRNA, which furthers our understanding of the constraints imposed on protein-coding RNAs. ..
  15. pmc Coevolution in RNA molecules driven by selective constraints: evidence from 5S rRNA
    Nan Cheng
    StateKey Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A and F University, Yangling, People s Republic of China
    PLoS ONE 7:e44376. 2012
    ..In conclusion, our results indicate that sequence coevolution is a direct result of maintaining optimal structural and functional integrity...
  16. doi request reprint Universally increased mRNA stability downstream of the translation initiation site in eukaryotes and prokaryotes
    Yuanhui Mao
    State Key Laboratory of Crop Stress Biology in Arid Areas and College of Life Sciences, Northwest A and F University, Yangling, Shaanxi 712100, China
    Gene 517:230-5. 2013
    ..Overall, our results revealed a previously unappreciated correlation between structural stability and protein localization...
  17. pmc Impacts of mutation effects and population size on mutation rate in asexual populations: a simulation study
    Xiaoqian Jiang
    Bioinformatics Center, Northwest A and F University, Yangling, Shaanxi 712100, China
    BMC Evol Biol 10:298. 2010
    ..The aim of the present study was to use computer simulations to investigate how natural selection adjusts mutation rate among asexually reproducing subpopulations with different mutation rates...
  18. pmc Patterns of nucleotides that flank substitutions in human orthologous genes
    Lei Ma
    Bioinformatics Centre, Northwest A and F University, Yangling, Shaanxi, 712100, China
    BMC Genomics 11:416. 2010
    ..The effect of context on mutagenesis should be revealed in the usage of nucleotides that flank substitutions. Relative entropy (also known as Kullback-Leibler divergence) is useful for finding unusual patterns in biological sequences...
  19. pmc Physiologically Shrinking the Solution Space of a Saccharomyces cerevisiae Genome-Scale Model Suggests the Role of the Metabolic Network in Shaping Gene Expression Noise
    Baofang Chi
    College of Enology, Northwest A and F University, Yangling, Shaanxi, China Bioinformatics Center, Northwest A and F University, Yangling, Shaanxi, China
    PLoS ONE 10:e0139590. 2015
    ..Altogether, this study proposes a new approach in shrinking the solution space of a genome-scale model, of which sampling provides new insights into gene expression noise. ..
  20. pmc Influences of dominance and evolution of sex in finite diploid populations
    Yujun Chang
    State Key Laboratory of Crop Stress Biology for Arid Areas, Bioinformatics Center, College of Life Sciences, Northwest A and F University, Yangling, Shaanxi, China
    PLoS ONE 10:e0128459. 2015
    ..Overall, these results illustrate that the existence of dominance is an important mechanism that affects the evolution of sex. ..
  21. pmc Genome-wide identification and evolution of HECT genes in soybean
    Xianwen Meng
    College of life Sciences and State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A and F University, Yangling 712100, China
    Int J Mol Sci 16:8517-35. 2015
    ..In summary, this work provides useful information on which further functional studies of soybean HECT genes can be based. ..
  22. pmc Codon Usage in Signal Sequences Affects Protein Expression and Secretion Using Baculovirus/Insect Cell Expression System
    Yalan Wang
    College of Life Sciences, Northwest A and F University, Yangling, Shaanxi 712100, P R China
    PLoS ONE 10:e0145887. 2015
    ....
  23. doi request reprint Conservation and evolution in and among SRF- and MEF2-type MADS domains and their binding sites
    Wenwu Wu
    College of Life Science, Northwest A and F University, Yangling, Shaanxi, China
    Mol Biol Evol 28:501-11. 2011
    ....
  24. doi request reprint Large-scale information entropy analysis of important sites in mature and precursor miRNA sequences
    Jiangfeng Du
    Bioinformatics Center, Northwest Science and Technology University of Agriculture, Yangling, 712100, China
    Sci China C Life Sci 52:771-9. 2009
    ..Those results provided another perspective for understanding more about the primary structure of pre-miRNA...