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Protein Interaction Maps

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scGraph2Vec: a deep generative model for gene embedding augmented by graph neural network and single-cell omics data.

GigaScience
BACKGROUND: Exploring the cellular processes of genes from the aspects of biological networks is of great interest to understanding the properties of complex diseases and biological systems. Biological networks, such as protein-protein interaction ne...

Machine Learning Identify Ferroptosis-Related Genes as Potential Diagnostic Biomarkers for Gastric Intestinal Metaplasia.

Technology in cancer research & treatment
BACKGROUND: Gastric intestinal metaplasia(GIM) is an independent risk factor for GC, however, its pathogenesis is still unclear. Ferroptosis is a new type of programmed cell death, which may be involved in the process of GIM. The purpose of this stud...

hdWGCNA and Cellular Communication Identify Active NK Cell Subtypes in Alzheimer's Disease and Screen for Diagnostic Markers through Machine Learning.

Current Alzheimer research
BACKGROUND: Alzheimer's disease (AD) is a recognized complex and severe neurodegenerative disorder, presenting a significant challenge to global health. Its hallmark pathological features include the deposition of β-amyloid plaques and the formation ...

A Strategy based on Bioinformatics and Machine Learning Algorithms Reveals Potential Mechanisms of Shelian Capsule against Hepatocellular Carcinoma.

Current pharmaceutical design
BACKGROUND: Hepatocellular carcinoma (HCC) is a prevalent and life-threatening form of cancer, with Shelian Capsule (SLC), a traditional Chinese medicine (TCM) formulation, being recommended for clinical treatment. However, the mechanisms underlying ...

Evidence from Machine Learning, Diagnostic Hub Genes in Sepsis and Diagnostic Models based on Xgboost Models, Novel Molecular Models for the Diagnosis of Sepsis.

Current medicinal chemistry
BACKGROUND: Systemic multi-organ dysfunction resulting from dysregulated immune responses in the host triggered by microbial infection or other factors is a major cause of death in sepsis, and secretory pathways play an important role in it.

Graph-DTI: A New Model for Drug-target Interaction Prediction Based on Heterogenous Network Graph Embedding.

Current computer-aided drug design
BACKGROUND: In this study, we aimed to develop a new end-to-end learning model called Graph-Drug-Target Interaction (DTI), which integrates various types of information in the heterogeneous network data, and to explore automatic learning of the topol...

Ensemble-GNN: federated ensemble learning with graph neural networks for disease module discovery and classification.

Bioinformatics (Oxford, England)
SUMMARY: Federated learning enables collaboration in medicine, where data is scattered across multiple centers without the need to aggregate the data in a central cloud. While, in general, machine learning models can be applied to a wide range of dat...

HNetGO: protein function prediction via heterogeneous network transformer.

Briefings in bioinformatics
Protein function annotation is one of the most important research topics for revealing the essence of life at molecular level in the post-genome era. Current research shows that integrating multisource data can effectively improve the performance of ...

ActivePPI: quantifying protein-protein interaction network activity with Markov random fields.

Bioinformatics (Oxford, England)
MOTIVATION: Protein-protein interactions (PPI) are crucial components of the biomolecular networks that enable cells to function. Biological experiments have identified a large number of PPI, and these interactions are stored in knowledge bases. Howe...

AFTGAN: prediction of multi-type PPI based on attention free transformer and graph attention network.

Bioinformatics (Oxford, England)
MOTIVATION: Protein-protein interaction (PPI) networks and transcriptional regulatory networks are critical in regulating cells and their signaling. A thorough understanding of PPIs can provide more insights into cellular physiology at normal and dis...