Jiangning Song

Summary

Affiliation: Monash University
Location: Melbourne, Australia
Summary:
structural bioinformatics, integrative systems biology, machine learning, data mining
Grants:
NHMRC, ARC, JSPS, Chinese Academy of Sciences
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Publications

  1. ncbi request reprint Exploring synonymous codon usage preferences of disulfide-bonded and non-disulfide bonded cysteines in the E. coli genome
    Jiangning Song
    Advanced Computational Modelling Centre, The University of Queensland, Brisbane, QLD 4072, Australia
    J Theor Biol 241:390-401. 2006
  2. ncbi request reprint Bioinformatic approaches for predicting substrates of proteases
    Jiangning Song
    Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
    J Bioinform Comput Biol 9:149-78. 2011
  3. ncbi request reprint PredCSF: an integrated feature-based approach for predicting conotoxin superfamily
    Yong Xian Fan
    Department of Automation, Shanghai Jiaotong University, Shanghai, China
    Protein Pept Lett 18:261-7. 2011
  4. doi request reprint EGM: encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomes
    Khalid Mahmood
    Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
    Bioinformatics 26:2076-84. 2010
  5. pmc APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility
    Jun Feng Xia
    Intelligent Computing Laboratory, Hefei Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, Anhui 230031, China
    BMC Bioinformatics 11:174. 2010
  6. doi request reprint Cascleave: towards more accurate prediction of caspase substrate cleavage sites
    Jiangning Song
    Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
    Bioinformatics 26:752-60. 2010
  7. pmc Prodepth: predict residue depth by support vector regression approach from protein sequences only
    Jiangning Song
    Department of Biochemistry and Molecular Biology, Monash University, Clayton, Melbourne, Victoria, Australia
    PLoS ONE 4:e7072. 2009
  8. doi request reprint Production of octenyl succinic anhydride-modified waxy corn starch and its characterization
    Zhiqiang Liu
    Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, People s Republic of China
    J Agric Food Chem 56:11499-506. 2008
  9. doi request reprint HSEpred: predict half-sphere exposure from protein sequences
    Jiangning Song
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Bioinformatics 24:1489-97. 2008
  10. ncbi request reprint Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure
    Jiangning Song
    Advanced Computational Modelling Centre, The University of Queensland, Brisbane, QLD 4072, Australia
    Bioinformatics 23:3147-54. 2007

Collaborators

Detail Information

Publications17

  1. ncbi request reprint Exploring synonymous codon usage preferences of disulfide-bonded and non-disulfide bonded cysteines in the E. coli genome
    Jiangning Song
    Advanced Computational Modelling Centre, The University of Queensland, Brisbane, QLD 4072, Australia
    J Theor Biol 241:390-401. 2006
    ..The approach presented in this paper can also be utilized as a complementary computational method and be applicable to analyse the synonymous codon usages in other model organisms...
  2. ncbi request reprint Bioinformatic approaches for predicting substrates of proteases
    Jiangning Song
    Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
    J Bioinform Comput Biol 9:149-78. 2011
    ..We also provide some suggestions about how future studies might further improve the accuracy of protease substrate specificity prediction...
  3. ncbi request reprint PredCSF: an integrated feature-based approach for predicting conotoxin superfamily
    Yong Xian Fan
    Department of Automation, Shanghai Jiaotong University, Shanghai, China
    Protein Pept Lett 18:261-7. 2011
    ..PredCSF is expected to be a powerful tool for in silico identification of novel conotonxins and is freely available for academic use at http://www.csbio.sjtu.edu.cn/bioinf/PredCSF...
  4. doi request reprint EGM: encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomes
    Khalid Mahmood
    Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
    Bioinformatics 26:2076-84. 2010
    ..Such an insight is particularly useful, for example, in the transfer of experimental results between different experimental systems such as Drosophila and mammals...
  5. pmc APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility
    Jun Feng Xia
    Intelligent Computing Laboratory, Hefei Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, Anhui 230031, China
    BMC Bioinformatics 11:174. 2010
    ..Therefore, reliable and efficient computational methods for identifying hot spots are greatly desired and urgently required...
  6. doi request reprint Cascleave: towards more accurate prediction of caspase substrate cleavage sites
    Jiangning Song
    Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
    Bioinformatics 26:752-60. 2010
    ..Accordingly, systematic computational screening studies of caspase substrate cleavage sites may provide insight into the substrate specificity of caspases and further facilitating the discovery of putative novel substrates...
  7. pmc Prodepth: predict residue depth by support vector regression approach from protein sequences only
    Jiangning Song
    Department of Biochemistry and Molecular Biology, Monash University, Clayton, Melbourne, Victoria, Australia
    PLoS ONE 4:e7072. 2009
    ..We also discuss the potential implications of this new structural parameter in the field of protein structure prediction and homology modeling. This method might prove to be a powerful tool for sequence analysis...
  8. doi request reprint Production of octenyl succinic anhydride-modified waxy corn starch and its characterization
    Zhiqiang Liu
    Institute of Bioengineering, Zhejiang University of Technology, Hangzhou, People s Republic of China
    J Agric Food Chem 56:11499-506. 2008
    ..The characteristics of modified waxy corn starch including infrared spectrum, scanning electron microscopy, and pasting property were tested and emulsification capacity of the OSA-modified starch were evaluated as well...
  9. doi request reprint HSEpred: predict half-sphere exposure from protein sequences
    Jiangning Song
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Bioinformatics 24:1489-97. 2008
    ..However, currently there is no existing method for the prediction of HSE measures from sequence data...
  10. ncbi request reprint Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure
    Jiangning Song
    Advanced Computational Modelling Centre, The University of Queensland, Brisbane, QLD 4072, Australia
    Bioinformatics 23:3147-54. 2007
    ..Therefore, there is a great need to develop computational methods capable of accurately predicting disulfide connectivity patterns in proteins that could have potentially important applications...
  11. pmc Predicting residue-wise contact orders in proteins by support vector regression
    Jiangning Song
    Advanced Computational Modelling Centre, The University of Queensland, Brisbane QLD 4072, Australia
    BMC Bioinformatics 7:425. 2006
    ..Accurately predicting RWCO values could have many important applications in protein three-dimensional structure prediction and protein folding rate prediction, and give deep insights into protein sequence-structure relationships...
  12. pmc Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information
    Jiangning Song
    Advanced Computational Modelling Centre, The University of Queensland, Brisbane QLD 4072, Australia
    BMC Bioinformatics 7:124. 2006
    ..Accurate prediction of proline cis/trans isomerization in proteins would have many important applications towards the understanding of protein structure and function...
  13. pmc FunSAV: predicting the functional effect of single amino acid variants using a two-stage random forest model
    Mingjun Wang
    National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
    PLoS ONE 7:e43847. 2012
    ..The sourcecodes of FunSAV and the datasets can be downloaded at http://sunflower.kuicr.kyoto-u.ac.jp/sjn/FunSAV...
  14. pmc Conditional random field approach to prediction of protein-protein interactions using domain information
    Morihiro Hayashida
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, Japan
    BMC Syst Biol 5:S8. 2011
    ..Several studies have shown that such mutual information is useful for identifying contact residues in interacting proteins...
  15. pmc Structural propensities of human ubiquitination sites: accessibility, centrality and local conformation
    Yuan Zhou
    State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
    PLoS ONE 8:e83167. 2013
    ..Therefore, the hypothesis about the structural level of the ubiquitination site selection mechanism has been substantially approved. ..
  16. pmc PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites
    Jiangning Song
    Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
    PLoS ONE 7:e50300. 2012
    ..It is freely available at http://lightning.med.monash.edu.au/PROSPER/...
  17. pmc TANGLE: two-level support vector regression approach for protein backbone torsion angle prediction from primary sequences
    Jiangning Song
    Department of Biochemistry and Molecular Biology, Faculty of Medicine, Monash University, Melbourne, Victoria, Australia
    PLoS ONE 7:e30361. 2012
    ..TANGLE is freely accessible at http://sunflower.kuicr.kyoto-u.ac.jp/~sjn/TANGLE/...