AIMC Topic: Protein Interaction Maps

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MEG-PPIS: a fast protein-protein interaction site prediction method based on multi-scale graph information and equivariant graph neural network.

Bioinformatics (Oxford, England)
MOTIVATION: Protein-protein interaction sites (PPIS) are crucial for deciphering protein action mechanisms and related medical research, which is the key issue in protein action research. Recent studies have shown that graph neural networks have achi...

ASD2023: towards the integrating landscapes of allosteric knowledgebase.

Nucleic acids research
Allosteric regulation, induced by perturbations at an allosteric site topographically distinct from the orthosteric site, is one of the most direct and efficient ways to fine-tune macromolecular function. The Allosteric Database (ASD; accessible onli...

Integration of transcriptome and machine learning to identify the potential key genes and regulatory networks affecting drip loss in pork.

Journal of animal science
Low level of drip loss (DL) is an important quality characteristic of meat with high economic value. However, the key genes and regulatory networks contributing to DL in pork remain largely unknown. To accurately identify the key genes affecting DL i...

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...