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2020

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

3 Citations (Scopus)

FastEE: fast Ensembles of Elastic Distances for time series classification

Tan, C. W., Petitjean, F. & Webb, G. I., Jan 2020, In : Data Mining and Knowledge Discovery. 34, 1, p. 231-272 42 p.

Research output: Contribution to journalArticleResearchpeer-review

PCA-based drift and shift quantification framework for multidimensional data

Goldenberg, I. & Webb, G. I., 6 Feb 2020, (Accepted/In press) In : Knowledge and Information Systems. 20 p.

Research output: Contribution to journalArticleResearchpeer-review

2019

Adaptive online extreme learning machine by regulating forgetting factor by concept drift map

Yu, H. & Webb, G. I., 28 May 2019, In : Neurocomputing. p. 141-153 13 p.

Research output: Contribution to journalArticleResearchpeer-review

1 Citation (Scopus)

A novel selective naïve Bayes algorithm

Chen, S., Webb, G. I., Liu, L. & Ma, X., 16 Dec 2019, (Accepted/In press) In : Knowledge-Based Systems. 12 p., 105361.

Research output: Contribution to journalArticleResearchpeer-review

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

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

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

14 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

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15 Citations (Scopus)

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

Proximity Forest: an effective and scalable distance-based classifier for time series

Lucas, B., Shifaz, A., Pelletier, C., O’Neill, L., Zaidi, N., Goethals, B., Petitjean, F. & Webb, G. I., May 2019, In : Data Mining and Knowledge Discovery. 33, 3, p. 607-635 29 p.

Research output: Contribution to journalArticleResearchpeer-review

7 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

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1 Citation (Scopus)

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

9 Citations (Scopus)

Temporal Convolutional Neural Network for the classification of satellite image time series

Pelletier, C., Webb, G. I. & Petitjean, F., 4 Mar 2019, In : Remote Sensing. 11, 5, 25 p., 523.

Research output: Contribution to journalArticleResearchpeer-review

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12 Citations (Scopus)

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

14 Citations (Scopus)
2018

Accurate parameter estimation for Bayesian network classifiers using hierarchical Dirichlet processes

Petitjean, F., Buntine, W., Webb, G. I. & Zaidi, N., Sep 2018, In : Machine Learning. 107, 8-10, p. 1303-1331 29 p.

Research output: Contribution to journalArticleResearchpeer-review

6 Citations (Scopus)

Analyzing concept drift and shift from sample data

Webb, G. I., Lee, L. K., Goethals, B. & Petitjean, F., Sep 2018, In : Data Mining and Knowledge Discovery. 32, 5, p. 1179-1199 21 p.

Research output: Contribution to journalArticleResearchpeer-review

10 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

17 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

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8 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

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67 Citations (Scopus)

Mining significant crisp-fuzzy spatial association rules

Shi, W., Zhang, A. & Webb, G. I., 2018, In : International Journal of Geographical Information Science. 32, 6, p. 1247-1270 24 p.

Research output: Contribution to journalArticleResearchpeer-review

2 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

73 Citations (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

49 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

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1 Citation (Scopus)

Survey of distance measures for quantifying concept drift and shift in numeric data

Goldenberg, I. & Webb, G. I., Sep 2018, In : Knowledge and Information Systems. 60, 2, p. 591-615 25 p.

Research output: Contribution to journalArticleResearchpeer-review

1 Citation (Scopus)
2017

Designing a more efficient, effective and safe Medical Emergency Team (MET) service using data analysis

Bergmeir, C., Bilgrami, I., Bain, C., Webb, G. I., Orosz, J. & Pilcher, D., 1 Dec 2017, In : PLoS ONE. 12, 12, 13 p., e0188688.

Research output: Contribution to journalArticleResearchpeer-review

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4 Citations (Scopus)

Efficient parameter learning of Bayesian network classifiers

Zaidi, N. A., Webb, G. I., Carman, M., Petitjean, F., Buntine, W., Hynes, M. & De Sterck, H., 2017, In : Machine Learning. 106, 9-10, p. 1289-1329 41 p.

Research output: Contribution to journalArticleResearchpeer-review

6 Citations (Scopus)

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

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8 Citations (Scopus)

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

4 Citations (Scopus)

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

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22 Citations (Scopus)

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

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54 Citations (Scopus)

Sample-based attribute selective An DE for large data

Chen, S., Martinez, A. M., Webb, G. I. & Wang, L., 1 Jan 2017, In : IEEE Transactions on Knowledge and Data Engineering. 29, 1, p. 172-185 14 p., 7565579.

Research output: Contribution to journalArticleResearchpeer-review

6 Citations (Scopus)

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

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15 Citations (Scopus)

Selective AnDE for large data learning: A low-bias memory constrained approach

Chen, S., Martínez, A. M., Webb, G. I. & Wang, L., Feb 2017, In : Knowledge and Information Systems. 50, 2, p. 475-503 29 p.

Research output: Contribution to journalArticleResearchpeer-review

7 Citations (Scopus)

SimUSF: An efficient and effective similarity measure that is invariant to violations of the interval scale assumption

Fernando, T. L. & Webb, G. I., Jan 2017, In : Data Mining and Knowledge Discovery. 31, 1, p. 264-286 23 p.

Research output: Contribution to journalArticleResearchpeer-review

3 Citations (Scopus)
2016

ALRn: Accelerated higher-order logistic regression

Zaidi, N. A., Webb, G. I., Carman, M. J., Petitjean, F. & Cerquides, J., 1 Sep 2016, In : Machine Learning. 104, 2-3, p. 151-194 44 p.

Research output: Contribution to journalArticleResearchpeer-review

10 Citations (Scopus)

Characterizing concept drift

Webb, G. I., Hyde, R., Cao, H., Nguyen, H-L. & Petitjean, F., 1 Jul 2016, In : Data Mining and Knowledge Discovery. 30, 4, p. 964-994 31 p.

Research output: Contribution to journalArticleResearchpeer-review

70 Citations (Scopus)

Crysalis: An integrated server for computational analysis and design of protein crystallization

Wang, H., Feng, L., Zhang, Z., Webb, G. I., Lin, D. & Song, J., 24 Feb 2016, In : Scientific Reports. 6, 14 p., 21383.

Research output: Contribution to journalArticleResearchpeer-review

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19 Citations (Scopus)

Faster and more accurate classification of time series by exploiting a novel dynamic time warping averaging algorithm

Petitjean, F., Forestier, G., Webb, G. I., Nicholson, A. E., Chen, Y. & Keogh, E., 2016, In : Knowledge and Information Systems. 47, 1, p. 1 - 26 26 p.

Research output: Contribution to journalArticleResearchpeer-review

52 Citations (Scopus)

GlycoMinestruct: A new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features

Li, F., Li, C., Revote, J., Zhang, Y., Webb, G. I., Li, J., Song, J. & Lithgow, T., 6 Oct 2016, In : Scientific Reports. 6, 16 p., 34595.

Research output: Contribution to journalArticleResearchpeer-review

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25 Citations (Scopus)

Mining significant association rules from uncertain data

Zhang, A., Shi, W. & Webb, G. I., 1 Jul 2016, In : Data Mining and Knowledge Discovery. 30, 4, p. 928-963 36 p.

Research output: Contribution to journalArticleResearchpeer-review

7 Citations (Scopus)

Periscope: Quantitative prediction of soluble protein expression in the periplasm of Escherichia coli

Chang, C. C. H., Li, C., Webb, G. I., Tey, B., Song, J. & Ramanan, R. N., 2 Mar 2016, In : Scientific Reports. 6, 11 p., 21844.

Research output: Contribution to journalArticleResearchpeer-review

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10 Citations (Scopus)

Scalable learning of Bayesian network classifiers

Martínez, A. M., Webb, G. I., Chen, S. & Zaidi, N. A., 2016, In : Journal of Machine Learning Research. 17, 44, p. 1-35 35 p.

Research output: Contribution to journalArticleResearchpeer-review

19 Citations (Scopus)

Skopus: Mining top-k sequential patterns under leverage

Petitjean, F., Li, T., Tatti, N. & Webb, G. I., 1 Sep 2016, In : Data Mining and Knowledge Discovery. 30, 5, p. 1086-1111 26 p.

Research output: Contribution to journalArticleResearchpeer-review

16 Citations (Scopus)

Smoothing a rugged protein folding landscape by sequence-based redesign

Porebski, B. T., Keleher, S., Hollins, J. J., Nickson, A. A., Marijanovic, E. M., Borg, N. A., Costa, M. G. S., Pearce, M. A., Dai, W., Zhu, L., Irving, J. A., Hoke, D. E., Kass, I., Whisstock, J. C., Bottomley, S. P., Webb, G. I., McGowan, S. & Buckle, A. M., 26 Sep 2016, In : Scientific Reports. 6, 14 p., 33958.

Research output: Contribution to journalArticleResearchpeer-review

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10 Citations (Scopus)
2015

GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome

Li, F., Li, C., Wang, M., Webb, G. I., Zhang, Y., Whisstock, J. C. & Song, J., 2015, In : Bioinformatics. 31, 9, p. 1411 - 1419 9 p.

Research output: Contribution to journalArticleResearchpeer-review

60 Citations (Scopus)

Structural and dynamic properties that govern the stability of an engineered fibronectin type III domain

Porebski, B. T., Nickson, A., Hoke, D. E., Hunter, M. R., Zhu, L., McGowan, S., Webb, G. I. & Buckle, A. M., 2015, In : Protein Engineering Design and Selection. 28, 3, p. 67-78 12 p.

Research output: Contribution to journalArticleResearchpeer-review

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18 Citations (Scopus)
2014

Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features

Liu, Y., Wang, M., Wang, H., Tan, H., Zhang, Z., Webb, G. I. & Song, J., 2014, In : Scientific Reports. 4, (Art. No.: 5765), p. 1 - 12 12 p.

Research output: Contribution to journalArticleResearchpeer-review

Open Access
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49 Citations (Scopus)