Dr Jiangning Song - Researcher Profile

Biography

Jiangning works in the Faculty of Medicine, Nursing & Health Sciences at Monash University as an NHMRC Peter Doherty Fellow.

Keywords

Bioinformatics, Systems biology, Structural genomics, Machine learning and data mining, Systems Biology, Machine learning, Data mining, Structural genomics

Qualifications

CERTIFICATE OF PHD DEGREE - BIOINFORMATICS

Institution: Jiangnan University/Wuxi China

Year awarded: 2005

BIOTECHNOLOGY

Institution: Jiangnan University/Wuxi China

Year awarded: 2000

Publications

Book Chapters

Song, J., Matthews, A., Reboul, C.F., Kaiserman, D., Pike, R.N., Bird, P.I., Whisstock, J.C., 2011, Predicting serpin/protease interactions, in Methods in Enzymology, Volume 501: Serpin Structure and Evolution, eds James C Whisstock and Philip I Bird, Academic Press, USA, pp. 237-273.

Journal Articles

Zhu, Y., Song, J., Xu, Z., Sun, J., Zhang, Y., Liu, Y., Ma, Y., 2013, Development of thermodynamic optimum searching (TOS) to improve the prediction accuracy of flux balance analysis, Biotechnology And Bioengineering [P], vol 110, issue 3, John Wiley & Sons Inc, USA, pp. 914-923.

Xu, H., Li, X., Zhang, Z., Song, J., 2013, Identifying Coevolution Between Amino Acid Residues in Protein Families: Advances in the Improvement and Evaluation of Correlated Mutation Algorithms, Current Bioinformatics [P], vol 8, issue 2, Bentham Science Publishers Ltd, The Netherlands, pp. 148-160.

Fan, Y., Song, J., Xu, C., Shen, H., 2013, Predicting Protein N-Terminal Signal Peptides Using Position-Specific Amino Acid Propensities and Conditional Random Fields, Current Bioinformatics [P], vol 8, issue 2, Bentham Science Publishers Ltd, The Netherlands, pp. 183-192.

Wang, M., Sun, Z., Akutsu, T., Song, J., 2013, Recent Advances in Predicting Functional Impact of Single Amino Acid Polymorphisms: A Review of Useful Features, Computational Methods and Available Tools, Current Bioinformatics [P], vol 8, issue 2, Bentham Science Publishers Ltd, The Netherlands, pp. 161-176.

Zheng, C., Wang, M., Takemoto, K., Akutsu, T., Zhang, Z., Song, J., 2012, An integrative computational framework based on a two-step random forest algorithm improves prediction of zinc-binding sites in proteins, PLoS ONE [P], vol 7, issue 11 (Art. No.: e49716), Public Library of Science, USA, pp. 1-15.

Zhou, Y., Zhou, Y.S., He, F., Song, J., Zhang, Z., 2012, Can simple codon pair usage predict protein-protein interaction?, Molecular Biosystems [P], vol 8, issue 5, Royal Society of Chemistry Publications, UK, pp. 1396-1404.

Li, X., Zhang, Z., Song, J., 2012, Computational enzyme design approaches with significant biological outcomes: progress and challenges, Computational and Structural Biotechnology Journal [E], vol 2, issue 3 (Art. No.:e201209007), Research Network of Computational and Structural Biotechnology, Denmark, pp. 1-12.

Mahmood, K., Webb, G.I., Song, J., Whisstock, J.C., Konagurthu, A.S., 2012, Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs, Nucleic Acids Research [P], vol 40, issue 6 (Art. ID: e44), Oxford University Press, UK, pp. 1-11.

Wang, Y., Xu, K., Song, J., Zhao, X., 2012, Exploring drug combinations in genetic interaction network, BMC Bioinformatics [P], vol 13, issue Suppl 7 (S7), BioMed Central Ltd, UK, pp. 1-7.

Wang, M., Zhao, X., Takemoto, K., Xu, H., Akutsu, T., Song, J., 2012, FunSAV: predicting the functional effect of single amino acid variants using a two-stage random forest model, PLoS ONE [P], vol 7, issue 8 (Art. ID: e43847), Public Library of Science, USA, pp. 1-14.

Han, L., Zhang, Y., Song, J., Liu, M.S., Zhang, Z., 2012, Identification of catalytic residues using a novel feature that integrates the microenvironment and geometrical location properties of residues, PLoS ONE [P], vol 7, issue 7 (Art. ID: :e41370), Public Library of Science, USA, pp. 1-13.

Wang, H., Li, J., Liu, L., Li, X., Jia, D., Du, G., Chen, J., Song, J., 2012, Increased production of alkaline polygalacturonate lyase in the recombinant Pichia pastoris by controlling cell concentration during continuous culture, Bioresource Technology [P], vol 124, Elsevier BV, Netherlands, pp. 338-346.

Tian, T., Song, J., 2012, Mathematical modelling of the MAP kinase pathway using proteomic datasets, PLoS ONE [P], vol 7, issue 8, Public Library of Science, San Francisco USA, pp. 1-12.

Song, J., Tan, H., Perry, A.J., Akutsu, T., Webb, G.I., Whisstock, J.C., Pike, R.N., 2012, PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites, PLoS ONE [P], vol 7, issue 11 (Art. No.: e50300), Public Library of Science, USA, pp. 1-23.

Qu, X., Zhang, X., Yao, J., Song, J., Nikolic-Paterson, D.J., Li, J., 2012, Resolvins E1 and D1 inhibit interstitial fibrosis in the obstructed kidney via inhibition of local fibroblast proliferation, Journal Of Pathology [P], vol 228, issue 4, John Wiley & Sons Ltd, UK, pp. 506-519.

Song, J., Tan, H., Wang, M., Webb, G.I., Akutsu, T., 2012, TANGLE: Two-level support vector regression approach for protein backbone torsion angle prediction from primary sequences, PLoS ONE [P], vol 7, issue 2 (Art. ID: e30361), Public Library of Science, USA, pp. 1-16.

Xu, K., Song, J., Zhao, X., 2012, The drug cocktail network, BMC Systems Biology [P], vol 6, issue Suppl 1: S5, BioMed Central Ltd, UK, pp. 1-12.

Song, J., Tan, H., Boyd, S.E., Shen, H., Mahmood, K., Webb, G., Akutsu, T., Whisstock, J., Pike, R., 2011, Bioinformatic approaches for predicting substrates of proteases, Journal of Bioinformatics and Computational Biology [P], vol 9, issue 1, Imperial College Press, UK, pp. 149-178.

Hayashida, M., Kamada, M., Song, J., Akutsu, T., 2011, Conditional random field approach to prediction of protein-protein interactions using domain information, BMC Systems Biology [P], vol 5, issue Suppl 1 (Art. No: S8), BioMed Central Ltd, UK, pp. 1-9.

Fan, Y., Song, J., Kong, X., Shen, H., 2011, PredCSF: An integrated feature-based approach for predicting conotoxin superfamily, Protein and Peptide Letters [P], vol 18, issue 3, Bentham Science Publishing Ltd, UAE, pp. 261-267.

Wang, X., Chen, Z., Wang, C., Yan, R., Zhang, Z., Song, J., 2011, Predicting residue-residue contacts and helix-helix interactions in transmembrane proteins using an integrative feature-based random forest approach, PLoS ONE [P], vol 6, issue 10 (art. No: e26767), Public Library of Science, USA, pp. 1-11.

Xia, J., Zhao, X., Song, J., Huang, D., 2010, APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility, BMC Bioinformatics [P], vol 11, issue 174, BioMed Central Ltd, UK, pp. 1-14.

Song, J., Tan, H., Shen, H., Mahmood, K., Boyd, S.E., Webb, G., Akutsu, T., Whisstock, J., 2010, Cascleave: towards more accurate prediction of caspase substrate cleavage sites, Bioinformatics [P], vol 26, issue 6, Oxford University Press, UK & USA, pp. 752-760.

Mahmood, K., Konagurthu, A.S., Song, J., Buckle, A.M., Webb, G.I., Whisstock, J.C., 2010, EGM: Encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomes, Bioinformatics [P], vol 26, issue 17, Oxford University Press, UK, USA, pp. 2076-2084.

Zhu, L., Yang, J., Song, J., Chou, K.-., Shen, H.-., 2010, Improving the accuracy of predicting disulfide connectivity by feature selection, Journal Of Computational Chemistry [P], vol 31, issue 7, John Wiley & Sons, Inc., USA, pp. 1478-1485.

Song, J., Takemoto, K., Shen, H., Tan, H., Gromiha, M.M., Akutsu, T., 2010, Prediction of protein folding rates from structural topology and complex network properties, IPSJ Transactions on Bioinformatics [E], vol 3, Information Processing Society of Japan, Japan, pp. 40-53.

Shen, H., Song, J., Chou, K., 2009, Prediction of protein folding rates from primary sequence by fusing multiple sequential features, Journal of Biomedical Science and Engineering [P], vol 2, Scientific Research Publishing, Inc., USA, pp. 136-143.

Song, J., Tan, H., Mahmood, K., Law, R.H.P., Buckle, A.M., Webb, G., Akutsu, T., Whisstock, J., 2009, Prodepth: Predict residue depth by support vector regression approach from protein sequences only, PLoS ONE [P], vol 4, issue 9 (e7072), Public Library of Science, USA, pp. 1-14.

Song, J., Tan, H., Takemoto, K., Akutsu, T., 2008, HSEpred: Predict half-sphere exposure from protein sequences, Bioinformatics [P], vol 24, issue 13, Oxford University Press, Oxford UK, pp. 1489-1497.

Liu, Z., Li, Y., Cui, F., Ping, L., Song, J., Ravee, Y., Jin, L., Xue, Y., Xu, J., Li, G., Wang, Y., Zheng, Y., 2008, Production of octenyl succinic anhydride-modified waxy corn starch and its characterization, Journal of Agricultural and Food Chemistry [P], vol 56, issue 23, American Chemical Society, USA, pp. 11499-11506.

Song, J., Yuan, Z., Huber, T., Burrage, K., Tan, H., 2007, Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure, Bioinformatics [P], vol 23, issue 23, Oxford University Press, UK & USA, pp. 3147-3154.

Song, J., Wang, M., Burrage, K., 2006, Exploring synonymous codon usage preferences of disulfide-bonded and non-disulfide bonded cysteines in the E. coli genome, Journal Of Theoretical Biology [P], vol 241, issue 2, Academic Press, UK, pp. 390-401.

Song, J., Burrage, K., 2006, Predicting residue-wise contact orders in proteins by support vector regression, BMC Bioinformatics [P], vol 7, issue 425, BioMed Central Ltd, UK, pp. 1-15.

Song, J., Burrage, K., Yuan, Z., Huber, T., 2006, Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information, BMC Bioinformatics [P], vol 7, issue 124, BioMed Central Ltd, UK, pp. 1-13.

Wang, M., Song, J., Xu, W., Li, W., 2004, A novel method of analyzing proline synonymous codons in E. coli, FEBS Letters [P], vol 576, issue 3, Elsevier BV, The Netherlands, Denmark, pp. 336-338.

Song, J., Li, W., Xu, W., 2004, Cooperativity of the oxidization of cysteines in globular proteins, Journal Of Theoretical Biology [P], vol 231, issue 1, Academic Press, UK, pp. 85-95.

Song, J., Wang, M., Li, W., Xu, W., 2004, Prediction of the disulfide-bonding state of cysteines in proteins based on dipeptide composition, Biochemical And Biophysical Research Communications [P], vol 318, issue 1, Academic Press, USA, pp. 142-147.

Conference Proceedings

Hayashida, M., Kamada, M., Song, J., Akutsu, T., 2012, Predicting Protein-RNA Residue-base Contacts Using Two-dimensional Conditional Random Field, 2012 IEEE 6th International Conference on Systems Biology (ISB), Curran Associates Inc, USA, pp. 152-157.

Hayashida, M., Kamada, M., Song, J., Akutsu, T., 2012, Predicting protein-RNA residue-base contacts using two-dimensional conditional random field, 2012 IEEE 6th International Conference on Systems Biology, ISB 2012, 18 August 2012 to 20 August 2012, Institute of Electrical and Electronics Engineers (IEEE), USA, pp. 152-157.

Kamada, M., Hayashida, M., Song, J., Akutsu, T., 2011, Discriminative random field approach to prediction of protein residue contacts, 2011 IEEE Conference on Systems Biology (ISB), 2-4 September 2011, IEEE, China, pp. 285-291.

Xu, K., Hu, F., Song, J., Zhao, X., 2011, Exploring drug combinations in a drug-cocktail network, 2011 IEEE Conference on Systems Biology (ISB), 2-4 September 2011, IEEE, China, pp. 393-398.

Wang, M., Shen, H., Akutsu, T., Song, J., 2011, Predicting functional impact of single amino acid polymorphisms by integrating sequence and structural features, 2011 IEEE Conference on Systems Biology 2011, 2-4 September 2011, IEEE, China, pp. 18-26.

Xu, K., Song, J., Zhao, X., 2010, A Network Biology Approach to Understand Combination of Drugs, The 4th International Conference on Computational Systems Biology (ISB2010), IEEE, China, pp. 347-354.

Hayashida, M., Kamada, M., Song, J., Akutsu, T., 2010, Conditional Random Field Approach to Prediction of Protein-Protein Interactions Using Mutual Information Between Domains, The 4th International Conference on Computational Systems Biology (ISB2010), IEEE, China, pp. 276-284.

Postgraduate Research Supervisions

Current Supervision

Program of Study:

(DOCTORATE BY RESEARCH).

Thesis Title:

A Bioinformatics study of protein folding aggregation and disease.

Supervisors:

Buckle, A (Main), Song, J (Associate).