Jiangning Song

Summary

Affiliation: Monash University
Country: Australia

Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. doi request reprint Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets
    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 300308, Department of Computer Science, School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia, Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan and ARC Centre of Excellence for Structural and Functional Microbial Genomics, Monash University, Melbourne, Victoria 3800, Australia
    Bioinformatics 30:71-80. 2014
  6. 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
  7. pmc Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs
    Khalid Mahmood
    Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia
    Nucleic Acids Res 40:e44. 2012
  8. doi request reprint Predicting serpin/protease interactions
    Jiangning Song
    Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
    Methods Enzymol 501:237-73. 2011
  9. 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
  10. pmc KinetochoreDB: a comprehensive online resource for the kinetochore and its related proteins
    Chen Li
    Infection and Immunity Program, Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Faculty of Medicine, Monash University, Melbourne, Victoria, 3800, Australia
    Database (Oxford) 2016:. 2016

Collaborators

Detail Information

Publications13

  1. 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...
  2. 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...
  3. 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/...
  4. 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...
  5. doi request reprint Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets
    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 300308, Department of Computer Science, School of Electronics and Information Engineering, Tongji University, Shanghai 201804, China, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia, Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan and ARC Centre of Excellence for Structural and Functional Microbial Genomics, Monash University, Melbourne, Victoria 3800, Australia
    Bioinformatics 30:71-80. 2014
    ..Accordingly, systematic bioinformatics studies of known cleavage sites may provide important insights into their substrate specificity and facilitate the discovery of novel substrates...
  6. 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/...
  7. pmc Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs
    Khalid Mahmood
    Department of Biochemistry and Molecular Biology, Monash University, VIC 3800, Australia
    Nucleic Acids Res 40:e44. 2012
    ..med.monash.edu.au/∼kmahmood/afree. EGM2, complete ortholog assignment pipeline (including afree and the iterative graph matching method) available from http://vbc.med.monash.edu.au/∼kmahmood/EGM2...
  8. doi request reprint Predicting serpin/protease interactions
    Jiangning Song
    Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
    Methods Enzymol 501:237-73. 2011
    ..The method described here could also be applied to other proteases for more generalized substrate specificity analysis and substrate discovery...
  9. 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...
  10. pmc KinetochoreDB: a comprehensive online resource for the kinetochore and its related proteins
    Chen Li
    Infection and Immunity Program, Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Faculty of Medicine, Monash University, Melbourne, Victoria, 3800, Australia
    Database (Oxford) 2016:. 2016
    ..Database URL: http://lightning.med.monash.edu/kinetochoreDB2/...
  11. doi request reprint GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome
    Fuyi Li
    College of Information Engineering, Northwest A and F University, Yangling 712100, China, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia, National Engineering Laboratory for Industrial Enzymes and Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China, Centre for Research in Intelligent Systems, Faculty of Information Technology, Monash University, Melbourne, VIC 3800, Australia and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC 3800, Australia
    Bioinformatics 31:1411-9. 2015
    ..Thus, bioinformatics approaches that can predict the glycan occupancy at specific sequons in protein sequences would be useful for understanding and utilizing this important PTM...
  12. pmc Mathematical modelling of the MAP kinase pathway using proteomic datasets
    Tianhai Tian
    School of Mathematical Sciences, Faculty of Science, Monash University, Clayton, Victoria, Australia
    PLoS ONE 7:e42230. 2012
    ....
  13. ncbi request reprint Inference Method for Developing Mathematical Models of Cell Signaling Pathways Using Proteomic Datasets
    Tianhai Tian
    School of Mathematical Sciences, Faculty of Science, Monash University, Clayton, Vic, 3800, Australia
    Methods Mol Biol 1526:329-344. 2017
    ....