Daly RJ - Search Results

1

HEAL: an automated deep learning framework for cancer histopathology image analysis.

Wang Y, Coudray N, Zhao Y, Li F, Hu C, Zhang YZ, Imoto S, Tsirigos A, Webb GI, Daly RJ, Song J. Wang Y, et al. Among authors: daly rj. Bioinformatics. 2021 Nov 18;37(22):4291-4295. doi: 10.1093/bioinformatics/btab380. Bioinformatics. 2021. PMID: 34009289

2

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 GI, Daly RJ. Song J, et al. Among authors: daly rj. Sci Rep. 2017 Jul 31;7(1):6862. doi: 10.1038/s41598-017-07199-4. Sci Rep. 2017. PMID: 28761071 Free PMC article.

3

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 TT, Wang Y, Webb GI, Smith AI, Daly RJ, Chou KC, Song J. Chen Z, et al. Among authors: daly rj. Bioinformatics. 2018 Jul 15;34(14):2499-2502. doi: 10.1093/bioinformatics/bty140. Bioinformatics. 2018. PMID: 29528364 Free PMC article.

4

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 TT, Leier A, Akutsu T, Purcell AW, Ian Smith A, Lithgow T, Daly RJ, Song J, Chou KC. Li F, et al. Among authors: daly rj. Bioinformatics. 2018 Dec 15;34(24):4223-4231. doi: 10.1093/bioinformatics/bty522. Bioinformatics. 2018. PMID: 29947803 Free PMC article.

5

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: daly rj. Brief Bioinform. 2019 Nov 27;20(6):2150-2166. doi: 10.1093/bib/bby077. Brief Bioinform. 2019. PMID: 30184176 Free PMC article. Review.

6

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 RS, Rodgers SJ, Li F, Huang C, Schittenhelm RB, Chan H, Chheang C, Wu J, Brown KK, Mitchell CA, Simpson KJ, Daly RJ. Ma X, et al. Among authors: daly rj. Nat Commun. 2019 Jan 17;10(1):296. doi: 10.1038/s41467-018-08154-1. Nat Commun. 2019. PMID: 30655532 Free PMC article.

7

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

Lee RS, Zhang L, Berger A, Lawrence MG, Song J, Niranjan B, Davies RG, Lister NL, Sandhu SK, Rubin MA, Risbridger GP, Taylor RA, Rickman DS, Horvath LG, Daly RJ. Lee RS, et al. Among authors: daly rj. Neoplasia. 2019 Apr;21(4):389-400. doi: 10.1016/j.neo.2019.02.005. Epub 2019 Mar 20. Neoplasia. 2019. PMID: 30901730 Free PMC article.

8

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 TT, Leier A, Revote J, Zhu Y, Powell DR, Akutsu T, Webb GI, Chou KC, Smith AI, Daly RJ, Li J, Song J. Chen Z, et al. Among authors: daly rj. Brief Bioinform. 2020 May 21;21(3):1047-1057. doi: 10.1093/bib/bbz041. Brief Bioinform. 2020. PMID: 31067315

9

CRISPRi enables isoform-specific loss-of-function screens and identification of gastric cancer-specific isoform dependencies.

Davies R, Liu L, Taotao S, Tuano N, Chaturvedi R, Huang KK, Itman C, Mandoli A, Qamra A, Hu C, Powell D, Daly RJ, Tan P, Rosenbluh J. Davies R, et al. Among authors: daly rj. Genome Biol. 2021 Jan 26;22(1):47. doi: 10.1186/s13059-021-02266-6. Genome Biol. 2021. PMID: 33499898 Free PMC article.

10

iLearnPlus: a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization.

Chen Z, Zhao P, Li C, Li F, Xiang D, Chen YZ, Akutsu T, Daly RJ, Webb GI, Zhao Q, Kurgan L, Song J. Chen Z, et al. Among authors: daly rj. Nucleic Acids Res. 2021 Jun 4;49(10):e60. doi: 10.1093/nar/gkab122. Nucleic Acids Res. 2021. PMID: 33660783 Free PMC article.

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