A Review of Machine Learning and Algorithmic Methods for Protein Phosphorylation Site Prediction

F Esmaili, M Pourmirzaei, S Ramazi… - Genomics …, 2023 - academic.oup.com
Post-translational modifications (PTMs) have key roles in extending the functional diversity
of proteins and, as a result, regulating diverse cellular processes in prokaryotic and …

Emerging trends in post-translational modification: Shedding light on Glioblastoma multiforme

S Kumari, R Gupta, RK Ambasta, P Kumar - Biochimica et Biophysica Acta …, 2023 - Elsevier
Recent multi-omics studies, including proteomics, transcriptomics, genomics, and
metabolomics have revealed the critical role of post-translational modifications (PTMs) in the …

Predicting protein phosphorylation sites in soybean using interpretable deep tabular learning network

E Khalili, S Ramazi, F Ghanati… - Briefings in …, 2022 - academic.oup.com
Phosphorylation of proteins is one of the most significant post-translational modifications
(PTMs) and plays a crucial role in plant functionality due to its impact on signaling, gene …

Evaluating machine learning-powered classification algorithms which utilize variants in the GCKR gene to predict metabolic syndrome: Tehran Cardio-metabolic …

M Akbarzadeh, N Alipour, H Moheimani… - Journal of Translational …, 2022 - Springer
Abstract Background Metabolic syndrome (MetS) is a prevalent multifactorial disorder that
can increase the risk of developing diabetes, cardiovascular diseases, and cancer. We …

Deep learning in phosphoproteomics: methods and application in cancer drug discovery

N Varshney, AK Mishra - Proteomes, 2023 - mdpi.com
Protein phosphorylation is a key post-translational modification (PTM) that is a central
regulatory mechanism of many cellular signaling pathways. Several protein kinases and …

Comprehensive analysis of the lysine succinylome in fish oil-treated prostate cancer cells

Y Jiang, C He, H Ye, Q Xu, X Chen… - Life Science …, 2023 - life-science-alliance.org
Prostate cancer (PCa) poses a significant health threat to males, and research has shown
that fish oil (FO) can impede PCa progression by activating multiple mitochondria-related …

A hybrid feature extraction scheme for efficient malonylation site prediction

AG Sorkhi, J Pirgazi, V Ghasemi - Scientific Reports, 2022 - nature.com
Lysine malonylation is one of the most important post-translational modifications (PTMs). It
affects the functionality of cells. Malonylation site prediction in proteins can unfold the …

Holistic similarity-based prediction of phosphorylation sites for understudied kinases

R Ma, S Li, L Parisi, W Li, HD Huang… - Briefings in …, 2023 - academic.oup.com
Phosphorylation is an essential mechanism for regulating protein activities. Determining
kinase-specific phosphorylation sites by experiments involves time-consuming and …

Comparative phosphoproteomics of neuro-2a cells under insulin resistance reveals new molecular signatures of Alzheimer's disease

D Kim, YS Jo, HS Jo, S Bae, YW Kwon, YS Oh… - International Journal of …, 2022 - mdpi.com
Insulin in the brain is a well-known critical factor in neuro-development and regulation of
adult neurogenesis in the hippocampus. The abnormality of brain insulin signaling is …

Machine learning-based approaches for ubiquitination site prediction in human proteins

M Pourmirzaei, S Ramazi, F Esmaili… - BMC …, 2023 - Springer
Protein ubiquitination is a critical post-translational modification (PTMs) involved in
numerous cellular processes. Identifying ubiquitination sites (Ubi-sites) on proteins offers …