Song J - Search Results

1

T4SEfinder: a bioinformatics tool for genome-scale prediction of bacterial type IV secreted effectors using pre-trained protein language model.

Zhang Y, Zhang Y, Xiong Y, Wang H, Deng Z, Song J, Ou HY. Zhang Y, et al. Among authors: song j. Brief Bioinform. 2022 Jan 17;23(1):bbab420. doi: 10.1093/bib/bbab420. Brief Bioinform. 2022. PMID: 34657153

2

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 GI, Song J, Lithgow T. An Y, et al. Among authors: song j. Brief Bioinform. 2018 Jan 1;19(1):148-161. doi: 10.1093/bib/bbw100. Brief Bioinform. 2018. PMID: 27777222

3

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 GI, Lithgow T, Song J. An Y, et al. Among authors: song j. Sci Rep. 2017 Jan 23;7:41031. doi: 10.1038/srep41031. Sci Rep. 2017. PMID: 28112271 Free PMC article.

4

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

Wang H, Feng L, Webb GI, Kurgan L, Song J, Lin D. Wang H, et al. Among authors: song j. Brief Bioinform. 2018 Sep 28;19(5):838-852. doi: 10.1093/bib/bbx018. Brief Bioinform. 2018. PMID: 28334201 Free PMC article. Review.

5

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 GI, Strugnell RA, Song J, Lithgow T. Wang J, et al. Among authors: song j. Brief Bioinform. 2019 May 21;20(3):931-951. doi: 10.1093/bib/bbx164. Brief Bioinform. 2019. PMID: 29186295 Free PMC article.

6

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

Wang J, Yang B, Leier A, Marquez-Lago TT, Hayashida M, Rocker A, Zhang Y, Akutsu T, Chou KC, Strugnell RA, Song J, Lithgow T. Wang J, et al. Among authors: song j. Bioinformatics. 2018 Aug 1;34(15):2546-2555. doi: 10.1093/bioinformatics/bty155. Bioinformatics. 2018. PMID: 29547915 Free PMC article.

7

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. Wei L, et al. Among authors: song j. Bioinformatics. 2018 Dec 1;34(23):4007-4016. doi: 10.1093/bioinformatics/bty451. Bioinformatics. 2018. PMID: 29868903 Free PMC article.

8

iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites.

Song J, Wang Y, Li F, Akutsu T, Rawlings ND, Webb GI, Chou KC. Song J, et al. Brief Bioinform. 2019 Mar 25;20(2):638-658. doi: 10.1093/bib/bby028. Brief Bioinform. 2019. PMID: 29897410 Free PMC article. Review.

9

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 TT, Leier A, Rawlings ND, Haffari G, Revote J, Akutsu T, Chou KC, Purcell AW, Pike RN, Webb GI, Ian Smith A, Lithgow T, Daly RJ, Whisstock JC, Song J. Li F, et al. Among authors: song j. Brief Bioinform. 2019 Nov 27;20(6):2150-2166. doi: 10.1093/bib/bby077. Brief Bioinform. 2019. PMID: 30184176 Free PMC article. Review.

10

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 GI, Xu D, Smith AI, Li L, Chou KC, Song J. Chen Z, et al. Among authors: song j. Brief Bioinform. 2019 Nov 27;20(6):2267-2290. doi: 10.1093/bib/bby089. Brief Bioinform. 2019. PMID: 30285084 Free PMC article. Review.

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