AIMC Topic: Autophagy
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Rapid 3D phenotypic analysis of neurons and organoids using data-driven cell segmentation-free machine learning.
PLoS computational biology
Feb 22, 2021
Phenotypic profiling of large three-dimensional microscopy data sets has not been widely adopted due to the challenges posed by cell segmentation and feature selection. The computational demands of automated processing further limit analysis of hard-...
Using Reactome to build an autophagy mechanism knowledgebase.
Autophagy
Jun 2, 2020
The 21st century has revealed much about the fundamental cellular process of autophagy. Autophagy controls the catabolism and recycling of various cellular components both as a constitutive process and as a response to stress and foreign material inv...
A Multi-Omics Interpretable Machine Learning Model Reveals Modes of Action of Small Molecules.
Scientific reports
Jan 22, 2020
High-throughput screening and gene signature analyses frequently identify lead therapeutic compounds with unknown modes of action (MoAs), and the resulting uncertainties can lead to the failure of clinical trials. We developed an approach for uncover...
Machine learning with autophagy-related proteins for discriminating renal cell carcinoma subtypes.
Scientific reports
Jan 20, 2020
Machine learning techniques have been previously applied for classification of tumors based largely on morphological features of tumor cells recognized in H&E images. Here, we tested the possibility of using numeric data acquired from software-based ...
DeepPhagy: a deep learning framework for quantitatively measuring autophagy activity in .
Autophagy
Jun 20, 2019
Seeing is believing. The direct observation of GFP-Atg8 vacuolar delivery under confocal microscopy is one of the most useful end-point measurements for monitoring yeast macroautophagy/autophagy. However, manually labelling individual cells from larg...
Degradation of TRPML1 in Neurons Reduces Neuron Survival in Transient Global Cerebral Ischemia.
Oxidative medicine and cellular longevity
Dec 18, 2018
Postcardiac arrest syndrome yields poor neurological outcomes, but the mechanisms underlying this condition remain poorly understood. Autophagy plays an important role in neuronal apoptosis induced by ischemia. However, whether autophagy is involved ...
Exploring autophagy with Gene Ontology.
Autophagy
Feb 17, 2018
Autophagy is a fundamental cellular process that is well conserved among eukaryotes. It is one of the strategies that cells use to catabolize substances in a controlled way. Autophagy is used for recycling cellular components, responding to cellular ...
Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes.
Database : the journal of biological databases and curation
Dec 26, 2016
We previously reported a paradigm for large-scale phylogenomic analysis of gene families that takes advantage of the large corpus of experimentally supported Gene Ontology (GO) annotations. This 'GO Phylogenetic Annotation' approach integrates GO ann...
Structure-based artificial intelligence-aided design of MYC-targeting degradation drugs for cancer therapy.
Biochemical and biophysical research communications
Jun 20, 2025
The MYC protein is an oncoprotein that plays a crucial role in various cancers. Although its significance has been well recognized in research, the development of drugs targeting MYC remains relatively slow. In this study, we developed a novel MYC pe...
Autophagy-related gene SQSTM1 predicts the prognosis of hepatocellular carcinoma.
Computers in biology and medicine
Jun 1, 2025
BACKGROUND: The relationship between autophagy and the progression of hepatocellular carcinoma (HCC) is notably substantial, yet the underlying mechanisms remain incompletely elucidated. Our objective is to construct a predictive model, thereby provi...
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