Durfee, L. A., Lyon, N., Seo, K., & Huibregtse, J. M. (2010). The ISG15 conjugation system broadly targets newly synthesized proteins: implications for the antiviral function of ISG15. Molecular cell, 38(5), 722–732.
Dastur, A., Beaudenon, S., Kelley, M., Krug, R. M., & Huibregtse, J. M. (2006). Herc5, an interferon-induced HECT E3 enzyme, is required for conjugation of ISG15 in human cells. The Journal of biological chemistry, 281(7), 4334–4338.
Kim, W., Bennett, E. J., Huttlin, E. L., Guo, A., Li, J., Possemato, A., Sowa, M. E., Rad, R., Rush, J., Comb, M. J., Harper, J. W., & Gygi, S. P. (2011). Systematic and quantitative assessment of the ubiquitin-modified proteome. Molecular cell, 44(2), 325–340.
Fulzele, A., & Bennett, E. J. (2018). Ubiquitin diGLY Proteomics as an Approach to Identify and Quantify the Ubiquitin-Modified Proteome. Methods in molecular biology (Clifton, N.J.), 1844, 363–384.
Jacquet, S., Pontier, D., & Etienne, L. (2020). Rapid Evolution of HERC6 and Duplication of a Chimeric HERC5/6 Gene in Rodents and Bats Suggest an Overlooked Role of HERCs in Mammalian Immunity. Frontiers in immunology, 11, 605270.
Kawashima, S., Pokarowski, P., Pokarowska, M., Kolinski, A., Katayama, T., and Kanehisa, M.; AAindex: amino acid index database, progress report 2008. Nucleic Acids Res. 36, D202-D205 (2008).
Andreatta, M., Alvarez, B., & Nielsen, M. (2017). GibbsCluster: unsupervised clustering and alignment of peptide sequences. Nucleic acids research, 45(W1), W458–W463. https://doi.org/10.1093/nar/gkx248
Chandra, A., Sharma, A., Dehzangi, A., Ranganathan, S., Jokhan, A., Chou, K. C., & Tsunoda, T. (2018). PhoglyStruct: Prediction of phosphoglycerylated lysine residues using structural properties of amino acids. Scientific reports, 8(1), 17923.
Heffernan, R., Paliwal, K., Lyons, J., Singh, J., Yang, Y., & Zhou, Y. (2018). Single-sequence-based prediction of protein secondary structures and solvent accessibility by deep whole-sequence learning. Journal of computational chemistry, 39(26), 2210–2216.
McKinney, W., & others. (2010). Data structures for statistical computing in python. In Proceedings of the 9th Python in Science Conference (Vol. 445, pp. 51–56).
Hunter, J. D. (2007). Matplotlib: A 2D graphics environment. Computing in Science & Engineering, 9(3), 90–95.
Waskom, M., Botvinnik, Olga;Kane, Drew, Hobson, Paul, Lukauskas, Saulius, Gemperline, David C, … Qalieh, Adel. (2017). mwaskom/seaborn: v0.8.1 (September 2017). Zenodo.
Scikit-learn: Machine Learning in Python, Pedregosa et al., JMLR 12, pp. 2825-2830, 2011.
Harris, C. R., Millman, K. J., van der Walt, S. J., Gommers, R., Virtanen, P., Cournapeau, D., … Oliphant, T. E. (2020). Array programming with NumPy. Nature, 585, 357–362.
Virtanen, P., Gommers, R., Oliphant, T. E., Haberland, M., Reddy, T., Cournapeau, D., … SciPy 1.0 Contributors. (2020). SciPy 1.0: Fundamental Algorithms for Scientific Computing in Python. Nature Methods, 17, 261–272.
https://github.com/tkonopka/umap
https://towardsdatascience.com/hyperparameter-tuning-the-random-forest-in-python-using-scikit-learn-28d2aa77dd74
https://sinyi-chou.github.io/python-sklearn-precision-recall/
https://stackoverflow.com/questions/25009284/how-to-plot-roc-curve-in-python
Saethang, T., Payne, D. M., Avihingsanon, Y., & Pisitkun, T. (2016). A machine learning strategy for predicting localization of post-translational modification sites in protein-protein interacting regions. BMC bioinformatics, 17(1), 307.
Wang, C., Tan, X., Tang, D., Gou, Y., Han, C., Ning, W., Lin, S., Zhang, W., Chen, M., Peng, D., & Xue, Y. (2022). GPS-Uber: a hybrid-learning framework for prediction of general and E3-specific lysine ubiquitination sites. Briefings in bioinformatics, 23(2), bbab574.
Gareau, J. R., & Lima, C. D. (2010). The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition. Nature reviews. Molecular cell biology, 11(12), 861–871. https://doi.org/10.1038/nrm3011
Yang, S. H., Galanis, A., Witty, J., & Sharrocks, A. D. (2006). An extended consensus motif enhances the specificity of substrate modification by SUMO. The EMBO journal, 25(21), 5083–5093.
Zhang, Y., Thery, F., Wu, N. C., Luhmann, E. K., Dussurget, O., Foecke, M., Bredow, C., Jiménez-Fernández, D., Leandro, K., Beling, A., Knobeloch, K. P., Impens, F., Cossart, P., & Radoshevich, L. (2019). The in vivo ISGylome links ISG15 to metabolic pathways and autophagy upon Listeria monocytogenes infection. Nature communications, 10(1), 5383.
Zhu, C., Li, J., Tian, C., Qin, M., Wang, Z., Shi, B., Qu, G., Wu, C., & Nan, Y. (2021). Proteomic Analysis of ISGylation in Immortalized Porcine Alveolar Macrophage Cell Lines Induced by Type I Interferon. Vaccines, 9(2), 164.