AIMC Topic: Phosphorylation
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A novel strategy to uncover specific GO terms/phosphorylation pathways in phosphoproteomic data in Arabidopsis thaliana.
BMC plant biology
Dec 14, 2021
BACKGROUND: Proteins are the workforce of the cell and their phosphorylation status tailors specific responses efficiently. One of the main challenges of phosphoproteomic approaches is to deconvolute biological processes that specifically respond to ...
Deep-Learning-Derived Evaluation Metrics Enable Effective Benchmarking of Computational Tools for Phosphopeptide Identification.
Molecular & cellular proteomics : MCP
Nov 1, 2021
Tandem mass spectrometry (MS/MS)-based phosphoproteomics is a powerful technology for global phosphorylation analysis. However, applying four computational pipelines to a typical mass spectrometry (MS)-based phosphoproteomic dataset from a human canc...
Non-invasive diagnostic tool for Parkinson's disease by sebum RNA profile with machine learning.
Scientific reports
Sep 20, 2021
Parkinson's disease (PD) is a progressive neurodegenerative disease presenting with motor and non-motor symptoms, including skin disorders (seborrheic dermatitis, bullous pemphigoid, and rosacea), skin pathological changes (decreased nerve endings an...
PARROT is a flexible recurrent neural network framework for analysis of large protein datasets.
eLife
Sep 17, 2021
The rise of high-throughput experiments has transformed how scientists approach biological questions. The ubiquity of large-scale assays that can test thousands of samples in a day has necessitated the development of new computational approaches to i...
A deep learning based approach for prediction of Chlamydomonas reinhardtii phosphorylation sites.
Scientific reports
Jun 15, 2021
Protein phosphorylation, which is one of the most important post-translational modifications (PTMs), is involved in regulating myriad cellular processes. Herein, we present a novel deep learning based approach for organism-specific protein phosphoryl...
Predicting phosphorylation sites using machine learning by integrating the sequence, structure, and functional information of proteins.
Journal of translational medicine
May 24, 2021
BACKGROUND: Post-translational modification (PTM) is a biological process that alters proteins and is therefore involved in the regulation of various cellular activities and pathogenesis. Protein phosphorylation is an essential process and one of the...
Application of deep learning to understand resilience to Alzheimer's disease pathology.
Brain pathology (Zurich, Switzerland)
May 19, 2021
People who have Alzheimer's disease neuropathologic change (ADNC) typically associated with dementia but not the associated cognitive decline can be considered to be "resilient" to the effects of ADNC. We have previously reported lower neocortical le...
iPhosH-PseAAC: Identify Phosphohistidine Sites in Proteins by Blending Statistical Moments and Position Relative Features According to the Chou's 5-Step Rule and General Pseudo Amino Acid Composition.
IEEE/ACM transactions on computational biology and bioinformatics
Apr 6, 2021
Protein phosphorylation is one of the key mechanism in prokaryotes and eukaryotes and is responsible for various biological functions such as protein degradation, intracellular localization, the multitude of cellular processes, molecular association,...
DeepPSP: A Global-Local Information-Based Deep Neural Network for the Prediction of Protein Phosphorylation Sites.
Journal of proteome research
Nov 26, 2020
Identification of phosphorylation sites is an important step in the function study and drug design of proteins. In recent years, there have been increasing applications of the computational method in the identification of phosphorylation sites becaus...
In vitro and in silico genetic toxicity screening of flavor compounds and other ingredients in tobacco products with emphasis on ENDS.
Journal of applied toxicology : JAT
Jul 13, 2020
Electronic nicotine delivery systems (ENDS) are regulated tobacco products and often contain flavor compounds. Given the concern of increased use and the appeal of ENDS by young people, evaluating the potential of flavors to induce DNA damage is impo...
Histones
Electronic Nicotine Delivery Systems
Consumer Product Safety
Flavoring Agents
Quantitative Structure-Activity Relationship
Mutagenicity Tests
Rats
Animals
Flow Cytometry
Humans
Models, Molecular
Cell Line
Risk Assessment
Machine Learning
DNA Damage
Phosphorylation
Tumor Suppressor Protein p53
Mice
Biomarkers
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