AIMC Topic: Computational Biology
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Identification and validation of hub genes related to neutrophil extracellular traps-mediated cell damage and immune recruitment during abdominal aortic aneurysm.
Scientific reports
Aug 7, 2025
Previous research has shown that the formation of Neutrophil Extracellular Traps (NETs), mediated by neutrophils, leads to an increase in inflammatory cell response and cellular tissue damage during Abdominal Aortic Aneurysm (AAA). Building on this f...
Network-based approach identifies key genes associated with tumor heterogeneity in HPV positive and negative head and neck cancer patients.
Scientific reports
Aug 7, 2025
Head and Neck Squamous Cell Carcinoma (HNSCC) is the seventh most prevalent cancer worldwide and is classified as human papillomavirus (HPV) positive or negative. Substantial heterogeneity has been observed in the two groups, posing a significant cli...
In-depth bioinformatics analysis uncovers the crosstalk genes and immune interactions among diagnostic markers linked to natural killer cells in patients with cirrhosis and sepsis.
Clinical and experimental medicine
Aug 6, 2025
Patients with cirrhosis face an elevated risk of developing sepsis, leading to an escalating mortality rate. This study focuses on the link between natural killer (NK) cells, cirrhosis, and sepsis. Our goal is to identify NK cell-related genes that c...
Bag-of-words is competitive with sum-of-embeddings language-inspired representations on protein inference.
PloS one
Aug 6, 2025
Inferring protein function is a fundamental and long-standing problem in biology. Laboratory experiments in this field are often expensive, and therefore large-scale computational protein inference from readily available amino acid sequences is neede...
PreMode predicts mode-of-action of missense variants by deep graph representation learning of protein sequence and structural context.
Nature communications
Aug 5, 2025
Accurate prediction of the functional impact of missense variants is important for disease gene discovery, clinical genetic diagnostics, therapeutic strategies, and protein engineering. Previous efforts have focused on predicting a binary pathogenici...
A computational framework for inferring species dynamics and interactions with applications in microbiota ecology.
NPJ systems biology and applications
Aug 5, 2025
We present MBPert, a generic computational framework for inferring species interactions and predicting dynamics in time-evolving ecosystems from perturbation and time-series data. In this work, we contextualize the framework in microbial ecosystem mo...
Bioinformatics analysis of Rho-signal transduction genes in postmenopausal osteoporosis and periodontitis.
Scientific reports
Aug 5, 2025
Postmenopausal osteoporosis (PMOP) increases the risk of periodontitis (PD), yet the shared mechanisms remain unclear. Rho-signal transduction genes may play a role due to their involvement in bone remodeling. This study aimed to explore Rho-related ...
varCADD: large sets of standing genetic variation enable genome-wide pathogenicity prediction.
Genome medicine
Aug 4, 2025
BACKGROUND: Machine learning and artificial intelligence are increasingly being applied to identify phenotypically causal genetic variation. These data-driven methods require comprehensive training sets to deliver reliable results. However, large unb...
Semi-supervised contrastive learning variational autoencoder Integrating single-cell multimodal mosaic datasets.
BMC bioinformatics
Aug 4, 2025
As single-cell sequencing technology became widely used, scientists found that single-modality data alone could not fully meet the research needs of complex biological systems. To address this issue, researchers began simultaneously collect multi-mod...
Prediction of protein-protein interaction based on interaction-specific learning and hierarchical information.
BMC biology
Aug 4, 2025
BACKGROUND: Prediction of protein-protein interactions (PPIs) is fundamental for identifying drug targets and understanding cellular processes. The rapid growth of PPI studies necessitates the development of efficient and accurate tools for automated...
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