AIMC Topic: Computational Biology
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iEnhancer-DS: Attention-based improved densenet for identifying enhancers and their strength.
Computational biology and chemistry
May 5, 2025
Enhancers are short DNA fragments that enhance gene expression by binding to transcription factors. Accurately identifying enhancers and their strength is crucial for understanding gene regulation mechanisms. However, traditional enhancer sequencing ...
M-DeepAssembly: enhanced DeepAssembly based on multi-objective multi-domain protein conformation sampling.
BMC bioinformatics
May 5, 2025
BACKGROUND: Association and cooperation among structural domains play an important role in protein function and drug design. Despite remarkable advancements in highly accurate single-domain protein structure prediction through the collaborative effor...
Identification of disulfidptosis-related genes and subgroups in spinal cord injury.
Spinal cord
May 4, 2025
STUDY DESIGN: Bioinformatics analysis and experimental validation study.
Identification of pyroptosis-related gene S100A12 as a potential diagnostic biomarker for sepsis through bioinformatics analysis and machine learning.
Molecular immunology
May 2, 2025
Sepsis is a non-discriminatory inflammatory reaction that can result in a diverse array of organ dysfunctions, which can be fatal. Pyroptosis is a programmed mechanism of cell death that is distinguishable from apoptosis and other forms of cellular d...
Accurate identification and mechanistic evaluation of pathogenic missense variants with .
Proceedings of the National Academy of Sciences of the United States of America
May 2, 2025
Understanding the effects of missense mutations or single amino acid variants (SAVs) on protein function is crucial for elucidating the molecular basis of diseases/disorders and designing rational therapies. We introduce here , a machine learning too...
ProFun-SOM: Protein Function Prediction for Specific Ontology Based on Multiple Sequence Alignment Reconstruction.
IEEE transactions on neural networks and learning systems
May 2, 2025
Protein function prediction is crucial for understanding species evolution, including viral mutations. Gene ontology (GO) is a standardized representation framework for describing protein functions with annotated terms. Each ontology is a specific fu...
Integration of Bioinformatics and Machine Learning Strategies Identifies Ferroptosis and Immune Infiltration Signatures in Peri-Implantitis.
International journal of molecular sciences
May 1, 2025
Peri-implantitis (PI) is a chronic inflammatory disease that ultimately leads to the dysfunction and loss of implants with established osseointegration. Ferroptosis has been implicated in the progression of PI, but its precise mechanisms remain uncle...
Machine learning based identification of anoikis related gene classification patterns and immunoinfiltration characteristics in diabetic nephropathy.
Scientific reports
May 1, 2025
Anoikis and immune cell infiltration are pivotal factors in the pathophysiological mechanism of diabetic nephropathy (DN), yet a comprehensive understanding of the mechanism is lacking. This work aimed to pinpoint distinctive anoikis-related genes (A...
AdptDilatedGCN: Protein-ligand binding affinity prediction based on multi-scale interaction fusion mechanism and dilated GCN.
International journal of biological macromolecules
Apr 30, 2025
Predicting protein-ligand binding affinity is crucial for drug discovery. However, existing prediction methods often make insufficient use of the features of proteins and ligands, lack interactions between different information, and have difficulty i...
Massive experimental quantification allows interpretable deep learning of protein aggregation.
Science advances
Apr 30, 2025
Protein aggregation is a pathological hallmark of more than 50 human diseases and a major problem for biotechnology. Methods have been proposed to predict aggregation from sequence, but these have been trained and evaluated on small and biased experi...
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