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Research Output 2004 2019

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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

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
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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
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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., 2019, (Accepted/In press) In : Briefings in Bioinformatics. 15 p., bby079.

Research output: Contribution to journalArticleResearchpeer-review

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

Li, P., 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., 30 Sep 2019, (Accepted/In press) In : Bioinformatics. 9 p., btz721.

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

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., 24 Apr 2019, (Accepted/In press) In : Briefings in Bioinformatics. 11 p., bbz041.

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

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., 8 Aug 2019, (Accepted/In press) In : Bioinformatics. 8 p., btz629.

Research output: Contribution to journalArticleResearchpeer-review

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
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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., 4 Jun 2019, (Accepted/In press) In : Briefings in Bioinformatics. 11 p., bbz050.

Research output: Contribution to journalArticleResearchpeer-review

Open Access

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
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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

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

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

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

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., 2018, (Accepted/In press) In : Briefings in Bioinformatics. 14 p., bby107.

Research output: Contribution to journalArticleResearchpeer-review

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

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

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
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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
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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
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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

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., 4 Oct 2018, (Accepted/In press) In : Briefings in Bioinformatics. 24 p., bby089.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Open Access
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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

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
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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

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

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
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Structural Principles Analysis of Host-Pathogen Protein-Protein Interactions: A Structural Bioinformatics Survey

Chen, H., Guo, W., Shen, J., Wang, L. & Song, J., 16 Mar 2018, In : IEEE Access. 6, p. 11760-11771 12 p.

Research output: Contribution to journalArticleResearchpeer-review

Taxonomic landscape of the dark proteomes: whole-proteome scale interplay between structural darkness, intrinsic disorder, and crystallization propensity

Hu, G., Wang, K., Song, J., Uversky, V. N. & Kurgan, L., 1 Nov 2018, In : Proteomics. 18, 21-22, 1800243.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Toward more accurate prediction of caspase cleavage sites: A comprehensive review of current methods, tools and features

Bao, Y., Marini, S., Tamura, T., Kamada, M., Maegawa, S., Hosokawa, H., Song, J. & Akutsu, T., 31 May 2018, (Accepted/In press) In : Briefings in Bioinformatics. 16 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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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., 2018, (Accepted/In press) In : Briefings in Bioinformatics. 17 p., bby077.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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2017

Antimicrobial susceptibility and mechanisms of fosfomycin resistance in extended-spectrum β-lactamase-producing Escherichia coli strains from urinary tract infections in Wenzhou, China

Bi, W., Li, B., Song, J., Hong, Y., Zhang, X., Liu, H., Lu, H., Zhou, T. & Cao, J., 1 Jul 2017, In : International Journal of Antimicrobial Agents. 50, 1, p. 29-34 6 p.

Research output: Contribution to journalArticleResearchpeer-review

Computing Minimum Reaction Modifications in a Boolean Metabolic Network

Tamura, T., Lu, W., Song, J. & Akutsu, T., 24 Nov 2017, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 15, 6, p. 1853-1862 10 p.

Research output: Contribution to journalArticleResearchpeer-review

HIVed, a knowledgebase for differentially expressed human genes and proteins during HIV infection, replication and latency

Li, C., Ramarathinam, S. H., Revote, J., Khoury, G., Song, J. & Purcell, A. W., 30 Mar 2017, In : Scientific Reports. 7, 45509.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Knowledge-Transfer learning for prediction of matrix metalloprotease substrate-cleavage sites

Wang, Y., Song, J., Marquez-Lago, T., Leier, A., Li, C., Lithgow, T., Webb, G. I. & Shen, H-B., 1 Dec 2017, In : Scientific Reports. 7, 1, 5755.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Metalexplorer, a bioinformatics tool for the improved prediction of eight types of metal-binding sites using a random forest algorithm with two-step feature selection

Song, J., Li, C., Zheng, C., Revote, J., Zhang, Z. & Webb, G. I., 2017, In : Current Bioinformatics. 12, 6, p. 480-489 10 p.

Research output: Contribution to journalArticleResearchpeer-review

PAnDE: Averaged n-dependence estimators for positive unlabeled learning

Li, F., Song, J., Li, C., Akutsu, T. & Zhang, Y., Sep 2017, In : ICIC Express Letters, Part B: Applications. 8, 9, p. 1287-1297 11 p.

Research output: Contribution to journalArticleResearchpeer-review

PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection

Song, J., Wang, H., Wang, J., Leier, A., Marquez-Lago, T., Yang, B., Zhang, Z., Akutsu, T., Webb, G. I. & Daly, R. J., 1 Dec 2017, In : Scientific Reports. 7, 1, 19 p., 6862.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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POSSUM: A bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles

Wang, J., Yang, B., Revote, J., Leier, A., Marquez-Lago, T. T., Webb, G., Song, J., Chou, K-C. & Lithgow, T., 1 Jan 2017, In : Bioinformatics. 33, 17, p. 2756-2758 3 p.

Research output: Contribution to journalArticleResearchpeer-review

Reductive evolution in outer membrane protein biogenesis has not compromised cell surface complexity in Helicobacter pylori

Webb, C. T., Chandrapala, D., Oslan, S. N., Bamert, R. S., Grinter, R. D., Dunstan, R. A., Gorrell, R. J., Song, J., Strugnell, R. A., Lithgow, T. & Kwok, T., 1 Dec 2017, In : MicrobiologyOpen. 6, 6, 17 p., e00513.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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SecretEPDB: A comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems

An, Y., Wang, J., Li, C., Revote, J., Zhang, Y., Naderer, T., Hayashida, M., Akutsu, T., Webb, G. I., Lithgow, T. & Song, J., 23 Jan 2017, In : Scientific Reports. 7, 10 p., 41031.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Staged heterogeneity learning to identify conformational B-cell epitopes from antigen sequences

Ren, J., Song, J., Ellis, J. & Li, J., 14 Mar 2017, In : BMC Genomics. 18, Suppl 2, 13 p., 113.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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Structure-based engineering of a pectate lyase with improved specific activity for ramie degumming

Zhou, Z., Liu, Y., Chang, Z., Wang, H., Leier, A., Marquez-Lago, T. T., Ma, Y., Li, J. & Song, J., Apr 2017, In : Applied Microbiology and Biotechnology. 101, 7, p. 2919-2929 11 p.

Research output: Contribution to journalArticleResearchpeer-review

2016

A highly conserved aspartic acid residue of the chitosanase from Bacillus sp. TS is involved in the substrate binding

Zhou, Z., Zhao, S., Liu, Y., Chang, Z., Ma, Y., Li, J. & Song, J., 1 Nov 2016, In : Applied Biochemistry and Biotechnology - Part A Enzyme Engineering and Biotechnology. 180, 6, p. 1167-1179 13 p.

Research output: Contribution to journalArticleResearchpeer-review

A neural network learning approach for improving the prediction of residue depth based on sequence-derived features

Yan, R., Wang, X., Xu, W., Cai, W., Lin, H-J., Li, J. & Song, J., 2016, In : RSC Advances. 6, 72, p. 67729-67738 10 p.

Research output: Contribution to journalArticleResearchpeer-review