Accepting PhD Students

PhD projects

Bioinformatics, computational biology, machine learning, pattern recognition, biomedical big data

20042020

Research output per year

If you made any changes in Pure these will be visible here soon.

Research Output

Filter
Article
2020

Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features

Zhu, Y-H., Hu, J., Ge, F., Li, F., Song, J., Zhang, Y. & Yu, D-J., 20 May 2020, (Accepted/In press) In : Briefings in Bioinformatics. 14 p., bbaa076.

Research output: Contribution to journalArticleResearchpeer-review

A framework towards data analytics on host–pathogen protein–protein interactions

Chen, H., Shen, J., Wang, L. & Song, J., 20 Jan 2020, (Accepted/In press) In : Journal of Ambient Intelligence and Humanized Computing. 13 p.

Research output: Contribution to journalArticleResearchpeer-review

Comparative analysis and prediction of quorum-sensing peptides using feature representation learning and machine learning algorithms

Wei, L., Hu, J., Li, F., Song, J., Su, R. & Zou, Q., Jan 2020, In : Briefings in Bioinformatics. 21, 1, p. 106-119 14 p., bby107.

Research output: Contribution to journalArticleResearchpeer-review

Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework

Li, F., Chen, J., Ge, Z., Wen, Y., Yue, Y., Hayashida, M., Baggag, A., Bensmail, H. & Song, J., 4 May 2020, (Accepted/In press) In : Briefings in Bioinformatics. 15 p., bbaa049.

Research output: Contribution to journalArticleResearchpeer-review

DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites

Li, F., Chen, J., Leier, A., Marquez-Lago, T., Liu, Q., Wang, Y., Revote, J., Smith, A. I., Akutsu, T., Webb, G. I., Kurgan, L. & Song, J., 15 Feb 2020, In : Bioinformatics. 36, 4, p. 1057-1065 9 p.

Research output: Contribution to journalArticleResearchpeer-review

5 Citations (Scopus)

DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites

Liu, Q., Chen, J., Wang, Y., Li, S., Jia, C., Song, J. & Li, F., 2020, (Accepted/In press) In : Briefings in Bioinformatics. 14 p., bbaa124.

Research output: Contribution to journalArticleResearchpeer-review

DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy

Xie, R., Li, J., Wang, J., Dai, W., Leier, A., Marquez-Lago, T. T., Akutsu, T., Lithgow, T., Song, J. & Zhang, Y., 22 May 2020, (Accepted/In press) In : Briefings in Bioinformatics. 15 p., bbaa125.

Research output: Contribution to journalArticleResearchpeer-review

iLearn: an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data

Chen, Z., Zhao, P., Li, F., Marquez-Lago, T. T., Leier, A., Revote, J., Zhu, Y., Powell, D. R., Akutsu, T., Webb, G. I., Chou, K-C., Smith, A. I., Daly, R. J., Li, J. & Song, J., 21 May 2020, In : Briefings in Bioinformatics. 21, 3, p. 1047-1057 11 p., bbz041.

Research output: Contribution to journalArticleResearchpeer-review

14 Citations (Scopus)

Inspector: a lysine succinylation predictor based on edited nearest-neighbor undersampling and adaptive synthetic oversampling

Zhu, Y., Jia, C., Li, F. & Song, J., 15 Mar 2020, In : Analytical Biochemistry. 593, 10 p., 113592.

Research output: Contribution to journalArticleResearchpeer-review

Pan-transcriptomic analysis identified common differentially expressed genes of Acinetobacter baumannii in response to polymyxin treatments

Li, M., Aye, S. M., Ahmed, M. U., Han, M-L., Li, C., Song, J., Boyce, J. D., Powell, D. R., Azad, M. A. K., Velkov, T., Zhu, Y. & Li, J., 22 May 2020, (Accepted/In press) In : Molecular Omics. 12 p.

Research output: Contribution to journalArticleResearchpeer-review

PASSION: an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs

Jia, C., Bi, Y., Chen, J., Leier, A., Li, F. & Song, J., 22 May 2020, (Accepted/In press) In : Bioinformatics. 7 p., btaa522.

Research output: Contribution to journalArticleResearchpeer-review

PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins

Zhang, Y., Yu, S., Xie, R., Li, J., Leier, A., Marquez-Lago, T. T., Akutsu, T., Smith, A. I., Ge, Z., Wang, J., Lithgow, T. & Song, J., 1 Feb 2020, In : Bioinformatics. 36, 3, p. 704-712 9 p.

Research output: Contribution to journalArticleResearchpeer-review

2 Citations (Scopus)

Pippin: A random forest-based method for identifying presynaptic and postsynaptic neurotoxins

Li, P., Zhang, H., Zhao, X., Jia, C., Li, F. & Song, J., 5 May 2020, In : Journal of Bioinformatics and Computational Biology. 18, 2, 21 p., 2050008.

Research output: Contribution to journalArticleResearchpeer-review

PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact

Li, F., Fan, C., Marquez-Lago, T. T., Leier, A., Revote, J., Jia, C., Zhu, Y., Smith, A. I., Webb, G. I., Liu, Q., Wei, L., Li, J. & Song, J., 21 May 2020, In : Briefings in Bioinformatics. 21, 3, p. 1069-1079 11 p.

Research output: Contribution to journalArticleResearchpeer-review

3 Citations (Scopus)

Procleave: Predicting protease-specific substrate cleavage sites by combining sequence and structural information

Li, F., Leier, A., Liu, Q., Wang, Y., Xiang, D., Akutsu, T., Webb, G. I., Smith, A. I., Marquez-Lago, T., Li, J. & Song, J., 12 May 2020, (Accepted/In press) In : Genomics Proteomics Bioinformatics. 13 p.

Research output: Contribution to journalArticleResearchpeer-review

PROSPECT: A web server for predicting protein histidine phosphorylation sites

Chen, Z., Zhao, P., Li, F., Leier, A., Marquez-Lago, T. T., Webb, G. I., Baggag, A., Bensmail, H. & Song, J., 2020, In : Journal of Bioinformatics and Computational Biology. 18, 3, 17 p., 2050018.

Research output: Contribution to journalArticleResearchpeer-review

Systematic evaluation of machine learning methods for identifying human-pathogen protein-protein interactions

Chen, H., Li, F., Wang, L., Jin, Y., Chi, C-H., Kurgan, L., Song, J. & Shen, J., 27 May 2020, (Accepted/In press) In : Briefings in Bioinformatics. 21 p., bbaa068.

Research output: Contribution to journalArticleResearchpeer-review

The YEATS Domain Histone Crotonylation Readers Control Virulence-Related Biology of a Major Human Pathogen

Wang, Q., Verma, J., Vidan, N., Wang, Y., Tucey, T. M., Lo, T. L., Harrison, P. F., See, M., Swaminathan, A., Kuchler, K., Tscherner, M., Song, J., Powell, D. R., Sopta, M., Beilharz, T. H. & Traven, A., 21 Apr 2020, In : Cell Reports. 31, 3, 16 p., 107528.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
2019

Bastion3: A two-layer ensemble predictor of type III secreted effectors

Wang, J., Li, J., Yang, B., Xie, R., Marquez-Lago, T. T., Leier, A., Hayashida, M., Akutsu, T., Zhang, Y., Chou, K-C., Selkrig, J., Zhou, T., Song, J. & Lithgow, T., 1 Jun 2019, In : Bioinformatics. 35, 12, p. 2017-2028 12 p., bty914.

Research output: Contribution to journalArticleResearchpeer-review

14 Citations (Scopus)

Characterization of the ERG-regulated Kinome in Prostate Cancer Identifies TNIK as a Potential Therapeutic Target

Lee, R. S., Zhang, L., Berger, A., Lawrence, M. G., Song, J., Niranjan, B., Davies, R. G., Lister, N. L., Sandhu, S. K., Rubin, M. A., Risbridger, G. P., Taylor, R. A., Rickman, D. S., Horvath, L. G. & Daly, R. J., 1 Apr 2019, In : Neoplasia. 21, 4, p. 389-400 12 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
1 Citation (Scopus)

Characterization of the Src-regulated kinome identifies SGK1 as a key mediator of Src-induced transformation

Ma, X., Zhang, L., Song, J., Nguyen, E., Lee, R. S., Rodgers, S. J., Li, F., Huang, C., Schittenhelm, R. B., Chan, H., Chheang, C., Wu, J., Brown, K. K., Mitchell, C. A., Simpson, K. J. & Daly, R. J., 17 Jan 2019, In : Nature Communications. 10, 1, 16 p., 296.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
3 Citations (Scopus)

Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences

Chen, Z., Zhao, P., Li, F., Wang, Y., Smith, A. I., Webb, G. I., Akutsu, T., Baggag, A., Bensmail, H. & Song, J., 11 Nov 2019, (Accepted/In press) In : Briefings in Bioinformatics. 21 p., bbz112.

Research output: Contribution to journalArticleResearchpeer-review

Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework

Zhang, Y., Xie, R., Wang, J., Leier, A., Marquez-Lago, T. T., Akutsu, T., Webb, G. I., Chou, K-C. & Song, J., Nov 2019, In : Briefings in Bioinformatics. 20, 6, p. 2185-2199 15 p.

Research output: Contribution to journalArticleResearchpeer-review

Deep learning with evolutionary and genomic profiles for identifying cancer subtypes

Lin, C. Y., Ruan, P., Li, R., Yang, J. M., See, S., Song, J. & Akutsu, T., 27 Jun 2019, In : Journal of Bioinformatics and Computational Biology. 17, 3, 15 p., 1940005.

Research output: Contribution to journalArticleResearchpeer-review

2 Citations (Scopus)

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Brown, P., RELISH Consortium & Zhou, Y., 29 Oct 2019, In : Database: the Journal of Biological Databases and Curation. 2019, 66 p., baz085.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File

Large-scale comparative assessment of computational predictors for lysine post-translational modification sites

Chen, Z., Liu, X., Li, F., Li, C., Marquez-Lago, T., Leier, A., Akutsu, T., Webb, G. I., Xu, D., Smith, A. I., Li, L., Chou, K. C. & Song, J., Nov 2019, In : Briefings in Bioinformatics. 20, 6, p. 2267-2290 24 p., bby089.

Research output: Contribution to journalArticleResearchpeer-review

MULTiPly: a novel multi-layer predictor for discovering general and specific types of promoters

Zhang, M., Li, F., Marquez-Lago, T. T., Leier, A., Fan, C., Kwoh, C. K., Chou, K-C., Song, J. & Jia, C., 1 Sep 2019, In : Bioinformatics. 35, 17, p. 2957-2965 9 p., btz016.

Research output: Contribution to journalArticleResearchpeer-review

27 Citations (Scopus)

Positive-unlabelled learning of glycosylation sites in the human proteome

Li, F., Zhang, Y., Purcell, A. W., Webb, G. I., Chou, K-C., Lithgow, T., Li, C. & Song, J., 6 Mar 2019, In : BMC Bioinformatics. 20, 1, 17 p., 112.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
18 Citations (Scopus)
Open Access
4 Citations (Scopus)

SIMLIN: a bioinformatics tool for prediction of S-sulphenylation in the human proteome based on multi-stage ensemble-learning models

Wang, X., Li, C., Li, F., Sharma, V. S., Song, J. & Webb, G. I., 21 Nov 2019, In : BMC Bioinformatics. 20, 1, 12 p., 602.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File

Synergistic Combination of Polymyxin B and Enrofloxacin Induced Metabolic Perturbations in Extensive Drug-resistant Pseudomonas aeruginosa

Lin, Y-W., Han, M-L., Zhao, J., Zhu, Y., Rao, G., Forrest, A., Song, J., Kaye, K. S., Hertzog, P., Purcell, A., Creek, D., Zhou, T. Q., Velkov, T. & Li, J., 3 Oct 2019, In : Frontiers in Pharmacology. 10, 11 p., 1146.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File

Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches

Wang, J., Yang, B., An, Y., Marquez-Lago, T., Leier, A., Wilksch, J., Hong, Q., Zhang, Y., Hayashida, M., Akutsu, T., Webb, G. I., Strugnell, R. A., Song, J. & Lithgow, T., 21 May 2019, In : Briefings in Bioinformatics. 20, 3, p. 931-951 21 p.

Research output: Contribution to journalArticleResearchpeer-review

13 Citations (Scopus)

The flagellotropic bacteriophage YSD1 targets Salmonella Typhi with a Chi-like protein tail fibre

Dunstan, R. A., Pickard, D., Dougan, S., Goulding, D., Cormie, C., Hardy, J., Li, F., Grinter, R., Harcourt, K., Yu, L., Song, J., Schreiber, F., Choudhary, J., Clare, S., Coulibaly, F., Strugnell, R. A., Dougan, G. & Lithgow, T., Dec 2019, In : Molecular Microbiology. 112, 6, p. 1831-1846 16 p.

Research output: Contribution to journalArticleResearchpeer-review

Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods

Li, F., Wang, Y., Li, C., Marquez-Lago, T. T., Leier, A., Rawlings, N. D., Haffari, G., Revote, J., Akutsu, T., Chou, K-C., Purcell, A. W., Pike, R. N., Webb, G. I., Smith, A. I., Lithgow, T., Daly, R. J., Whisstock, J. C. & Song, J., 27 Nov 2019, In : Briefings in Bioinformatics. 20, 6, p. 2150-2166 17 p.

Research output: Contribution to journalArticleResearchpeer-review

2018

ACPred-FL: a sequence-based predictor using effective feature representation to improve the prediction of anti-cancer peptides

Wei, L., Zhou, C., Chen, H., Song, J. & Su, R., 1 Dec 2018, In : Bioinformatics. 34, 23, p. 4007-4016 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access

A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands

Faridi, P., Li, C., Ramarathinam, S. H., Vivian, J. P., Illing, P. T., Mifsud, N. A., Ayala, R., Song, J., Gearing, L. J., Hertzog, P. J., Ternette, N., Rossjohn, J., Croft, N. P. & Purcell, A. W., 12 Oct 2018, In : Science Immunology. 3, 28, 12 p., eaar3947.

Research output: Contribution to journalArticleResearchpeer-review

33 Citations (Scopus)

Bastion6: A bioinformatics approach for accurate prediction of type VI secreted effectors

Wang, J., Yang, B., Leier, A., Marquez-Lago, T., Hayashida, M., Rocker, A., Zhang, Y., Akutsu, T., Chou, K-C., Strugnell, R. A., Song, J. & Lithgow, T., 1 Jan 2018, In : Bioinformatics. 34, 15, p. 2546-2555 10 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
41 Citations (Scopus)

Characteristic and mechanism of immobilization effect of Staphylococcus aureus on human spermatozoa

Li, J., Li, B., Song, J., Liu, H., Bi, W., Dong, G. & Zhou, T., 1 Jun 2018, In : Microbial Pathogenesis. 119, p. 28-34 7 p.

Research output: Contribution to journalArticleResearchpeer-review

1 Citation (Scopus)

Comparative analysis of phosphoethanolamine transferases involved in polymyxin resistance across 10 clinically relevant Gram-negative bacteria

Huang, J., Zhu, Y., Han, M., Li, M., Song, J., Velkov, T., Li, C. & Li, J., 1 Apr 2018, In : International Journal of Antimicrobial Agents. 51, 4, p. 586-593 8 p.

Research output: Contribution to journalArticleResearchpeer-review

6 Citations (Scopus)

Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI

An, Y., Wang, J., Li, C., Leier, A., Marquez-Lago, T., Wilksch, J., Zhang, Y., Webb, G. I., Song, J. & Lithgow, T., 1 Jan 2018, In : Briefings in Bioinformatics. 19, 1, p. 148-161 14 p., bbw100.

Research output: Contribution to journalArticleResearchpeer-review

23 Citations (Scopus)

Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity

Wang, H., Feng, L., Webb, G. I., Kurgan, L., Song, J. & Lin, D., 28 Sep 2018, In : Briefings in Bioinformatics. 19, 5, p. 838-852 15 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
8 Citations (Scopus)

FusC, a member of the M16 protease family acquired by bacteria for iron piracy against plants

Grinter, R., Hay, I. D., Song, J., Wang, J., Teng, D., Dhanesakaran, V., Wilksch, J. J., Davies, M. R., Littler, D., Beckham, S. A., Henderson, I. R., Strugnell, R. A., Dougan, G. & Lithgow, T., 2 Aug 2018, In : PLoS Biology. 16, 8, 21 p., e2006026.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
3 Citations (Scopus)

Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa

Zhu, Y., Czauderna, T., Zhao, J., Klapperstueck, M., Mahamad Maifiah, M. H. B., Han, M-L., Lu, J., Sommer, B., Velkov, T., Lithgow, T., Song, J., Schreiber, F. & Li, J., 1 Apr 2018, In : GigaScience. 7, 4, 18 p., giy021.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
9 Citations (Scopus)

iFeature: a python package and web server for features extraction and selection from protein and peptide sequences

Chen, Z., Zhao, P., Li, F., Leier, A., Marquez-Lago, T., Wang, Y., Webb, G. I., Smith, A. I., Daly, R. J., Chou, K-C. & Song, J., 15 Jul 2018, In : Bioinformatics. 34, 14, p. 2499-2502 4 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
88 Citations (Scopus)
Open Access
File
6 Citations (Scopus)

PREvaIL, an integrative approach for inferring catalytic residues using sequence, structural, and network features in a machine-learning framework

Song, J., Li, F., Takemoto, K., Haffari, G., Akutsu, T., Chou, K. C. & Webb, G. I., 14 Apr 2018, In : Journal of Theoretical Biology. 443, p. 125-137 13 p.

Research output: Contribution to journalArticleResearchpeer-review

80 Citations (Scopus)

ProBAPred: Inferring protein-protein binding affinity by incorporating protein sequence and structural features

Lu, B., Li, C., Chen, Q. & Song, J., 29 Jun 2018, In : Journal of Bioinformatics and Computational Biology. 16, 4, 18 p., 1850011.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
1 Citation (Scopus)

PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy

Song, J., Li, F., Leier, A., Marquez-Lago, T., Akutsu, T., Haffari, G., Chou, K-C., Webb, G. I. B. & Pike, R. N., 15 Feb 2018, In : Bioinformatics. 34, 4, p. 684-687 4 p.

Research output: Contribution to journalArticleResearchpeer-review

62 Citations (Scopus)

Quokka: A comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome

Li, F., Li, C., Marquez-Lago, T. T., Leier, A., Akutsu, T., Purcell, A. W., Smith, A. I., Lithgow, T., Daly, R. J., Song, J. & Chou, K-C., 15 Dec 2018, In : Bioinformatics. 34, 24, p. 4223-4231 9 p., bty522.

Research output: Contribution to journalArticleResearchpeer-review

56 Citations (Scopus)

Structural Capacitance in Protein Evolution and Human Diseases

Li, C., Clark, L. V. T., Zhang, R., Porebski, B. T., McCoey, J. M., Borg, N. A., Webb, G. I., Kass, I., Buckle, M., Song, J., Woolfson, A. & Buckle, A. M., 14 Sep 2018, In : Journal of Molecular Biology. 430, 18, p. 3200-3217 18 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
File
1 Citation (Scopus)