AIMC Topic: Computational Biology
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The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models.
PLoS computational biology
Jan 10, 2025
Complex deep learning models trained on very large datasets have become key enabling tools for current research in natural language processing and computer vision. By providing pre-trained models that can be fine-tuned for specific applications, they...
Identification of hub genes and immune-related pathways in acute myeloid leukemia: insights from bioinformatics and experimental validation.
Frontiers in immunology
Jan 10, 2025
BACKGROUND: This study aims to identify the hub genes and immune-related pathways in acute myeloid leukemia (AML) to provide new theories for immunotherapy.
Interpretable identification of cancer genes across biological networks via transformer-powered graph representation learning.
Nature biomedical engineering
Jan 9, 2025
Graph representation learning has been leveraged to identify cancer genes from biological networks. However, its applicability is limited by insufficient interpretability and generalizability under integrative network analysis. Here we report the dev...
Lessons from Deep Learning Structural Prediction of Multistate Multidomain Proteins-The Case Study of Coiled-Coil NOD-like Receptors.
International journal of molecular sciences
Jan 9, 2025
We test here the prediction capabilities of the new generation of deep learning predictors in the more challenging situation of multistate multidomain proteins by using as a case study a coiled-coil family of Nucleotide-binding Oligomerization Domain...
Eight quick tips for biologically and medically informed machine learning.
PLoS computational biology
Jan 9, 2025
Machine learning has become a powerful tool for computational analysis in the biomedical sciences, with its effectiveness significantly enhanced by integrating domain-specific knowledge. This integration has give rise to informed machine learning, in...
Multi-region infectious disease prediction modeling based on spatio-temporal graph neural network and the dynamic model.
PLoS computational biology
Jan 9, 2025
Human mobility between different regions is a major factor in large-scale outbreaks of infectious diseases. Deep learning models incorporating infectious disease transmission dynamics for predicting the spread of multi-regional outbreaks due to human...
Developing machine-learning-based amyloidogenicity predictors with Cross-Beta DB.
Alzheimer's & dementia : the journal of the Alzheimer's Association
Jan 8, 2025
INTRODUCTION: The importance of protein amyloidogenesis, associated with various diseases and functional roles, has driven the creation of computational predictors of amyloidogenicity. The accuracy of these predictors, particularly those utilizing ar...
Multi‑omics identification of a novel signature for serous ovarian carcinoma in the context of 3P medicine and based on twelve programmed cell death patterns: a multi-cohort machine learning study.
Molecular medicine (Cambridge, Mass.)
Jan 8, 2025
BACKGROUND: Predictive, preventive, and personalized medicine (PPPM/3PM) is a strategy aimed at improving the prognosis of cancer, and programmed cell death (PCD) is increasingly recognized as a potential target in cancer therapy and prognosis. Howev...
Deciphering hub genes and immune landscapes related to neutrophil extracellular traps in rheumatoid arthritis: insights from integrated bioinformatics analyses and experiments.
Frontiers in immunology
Jan 8, 2025
BACKGROUND: Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by synovial inflammation and progressive joint destruction. Neutrophil extracellular traps (NETs), a microreticular structure formed after neutrophil death, have rece...
Comprehensive bioinformatics analysis identifies metabolic and immune-related diagnostic biomarkers shared between diabetes and COPD using multi-omics and machine learning.
Frontiers in endocrinology
Jan 8, 2025
BACKGROUND: Diabetes and chronic obstructive pulmonary disease (COPD) are prominent global health challenges, each imposing significant burdens on affected individuals, healthcare systems, and society. However, the specific molecular mechanisms suppo...
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