AIMC Topic: Computational Biology
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The role and machine learning analysis of mitochondrial autophagy-related gene expression in lung adenocarcinoma.
Frontiers in immunology
Apr 17, 2025
OBJECTIVE: Lung adenocarcinoma (LUAD) continues to be a primary cause of cancer-related mortality globally, highlighting the urgent need for novel insights finto its molecular mechanisms. This study aims to investigate the relationship between gene e...
An integrated bioinformatics and machine learning approach to identifying biomarkers connecting parkinson's disease with purine metabolism-related genes.
BMC neurology
Apr 16, 2025
BACKGROUND: Parkinson's disease (PD), a prevalent neurodegenerative disorder in the aging population, poses significant challenges in unraveling its pathogenesis and progression. A key area of investigation is the disruption of oncological metabolic ...
TRAPT: a multi-stage fused deep learning framework for predicting transcriptional regulators based on large-scale epigenomic data.
Nature communications
Apr 16, 2025
It is challenging to identify regulatory transcriptional regulators (TRs), which control gene expression via regulatory elements and epigenomic signals, in context-specific studies on the onset and progression of diseases. The use of large-scale mult...
Emerging frontiers in protein structure prediction following the AlphaFold revolution.
Journal of the Royal Society, Interface
Apr 16, 2025
Models of protein structures enable molecular understanding of biological processes. Current protein structure prediction tools lie at the interface of biology, chemistry and computer science. Millions of protein structure models have been generated ...
Optimizing lipocalin sequence classification with ensemble deep learning models.
PloS one
Apr 16, 2025
Deep learning (DL) has become a powerful tool for the recognition and classification of biological sequences. However, conventional single-architecture models often struggle with suboptimal predictive performance and high computational costs. To addr...
Identifying potential risk genes for clear cell renal cell carcinoma with deep reinforcement learning.
Nature communications
Apr 15, 2025
Clear cell renal cell carcinoma (ccRCC) is the most prevalent type of renal cell carcinoma. However, our understanding of ccRCC risk genes remains limited. This gap in knowledge poses challenges to the effective diagnosis and treatment of ccRCC. To a...
Identification of aging-related biomarkers for intervertebral disc degeneration in whole blood samples based on bioinformatics and machine learning.
Frontiers in immunology
Apr 15, 2025
INTRODUCTION: Aging is characterized by gradual structural and functional changes in the body over time, with intervertebral disc degeneration (IVDD) representing a key manifestation of spinal aging and a major contributor to low back pain (LBP).
Deep learning tools predict variants in disordered regions with lower sensitivity.
BMC genomics
Apr 12, 2025
BACKGROUND: The recent AI breakthrough of AlphaFold2 has revolutionized 3D protein structural modeling, proving crucial for protein design and variant effects prediction. However, intrinsically disordered regions-known for their lack of well-defined ...
Identification of M1 macrophage infiltration-related genes for immunotherapy in Her2-positive breast cancer based on bioinformatics analysis and machine learning.
Scientific reports
Apr 11, 2025
Over the past several decades, there has been a significant increase in the number of breast cancer patients. Among the four subtypes of breast cancer, Her2-positive breast cancer is one of the most aggressive breast cancers. In this study, we screen...
Predicting viral host codon fitness and path shifting through tree-based learning on codon usage biases and genomic characteristics.
Scientific reports
Apr 10, 2025
Viral codon fitness (VCF) of the host and the VCF shifting has seldom been studied under quantitative measurements, although they could be concepts vital to understand pathogen epidemiology. This study demonstrates that the relative synonymous codon ...
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