AIMC Topic: Computational Biology
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Prediction of circRNA-Disease Associations via Graph Isomorphism Transformer and Dual-Stream Neural Predictor.
Biomolecules
Feb 6, 2025
Circular RNAs (circRNAs) have attracted increasing attention for their roles in human diseases, making the prediction of circRNA-disease associations (CDAs) a critical research area for advancing disease diagnosis and treatment. However, traditional ...
Protein ligand structure prediction: From empirical to deep learning approaches.
Current opinion in structural biology
Feb 5, 2025
Protein-ligand structure prediction methods, aiming to predict the three-dimensional complex structure and binding energy of a compound and target protein, are essential in many structure-based drug discovery pipelines, including virtual screening an...
Ontology-based expansion of virtual gene panels to improve diagnostic efficiency for rare genetic diseases.
BMC medical informatics and decision making
Feb 5, 2025
BACKGROUND: Virtual Gene Panels (VGP) comprising disease-associated causal genes are utilized in the diagnosis of rare genetic diseases to evaluate candidate genes identified by whole-genome and whole-exome sequencing. VGPs generated by the PanelApp ...
Learning Phenotype Associated Signature in Spatial Transcriptomics with PASSAGE.
Small methods
Feb 4, 2025
Spatially resolved transcriptomics (SRT) is poised to advance the understanding of cellular organization within complex tissues under various physiological and pathological conditions at unprecedented resolution. Despite the development of numerous c...
Identification of biomarkers associated with macrophage polarization in diabetic cardiomyopathy based on bioinformatics and machine learning approaches.
Life sciences
Feb 4, 2025
BACKGROUND: Numerous studies have investigated the role of macrophages in the pathogenesis of diabetic cardiomyopathy (DCM); however, the underlying mechanisms remain unclear.
Decoding the cytokine code for heart failure based on bioinformatics, machine learning and Bayesian networks.
Biochimica et biophysica acta. Molecular basis of disease
Feb 4, 2025
BACKGROUND: Despite maximal pharmacological treatment guided by clinical guidelines, the prognosis of heart failure (HF) remains poor, posing a significant public health burden. This necessitates uncovering novel pathological and cardioprotective pat...
Identifying potential signatures of immune cells in hepatocellular carcinoma using integrative bioinformatics approaches and machine-learning strategies.
Immunologic research
Feb 4, 2025
Hepatocellular carcinoma (HCC) is a malignant tumor regulated by the immune system. Immunotherapy using checkpoint inhibitors has shown encouraging outcomes in a subset of HCC patients. The main challenges in checkpoint immunotherapy for HCC are to e...
PmiProPred: A novel method towards plant miRNA promoter prediction based on CNN-Transformer network and convolutional block attention mechanism.
International journal of biological macromolecules
Feb 3, 2025
It is crucial to understand the transcription mechanisms of miRNAs, especially considering the presence of peptides encoded by miRNAs. Since promoters function as the switch for gene transcription, precisely identifying these regions is essential for...
Contrastive-learning of language embedding and biological features for cross modality encoding and effector prediction.
Nature communications
Feb 3, 2025
Identifying and characterizing virulence proteins secreted by Gram-negative bacteria are fundamental for deciphering microbial pathogenicity as well as aiding the development of therapeutic strategies. Effector predictors utilizing pre-trained protei...
ERNIE-ac4C: A Novel Deep Learning Model for Effectively Predicting N4-acetylcytidine Sites.
Journal of molecular biology
Feb 1, 2025
RNA modifications are known to play a critical role in gene regulation and cellular processes. Specifically, N4-acetylcytidine (ac4C) modification has emerged as a significant marker involved in mRNA translation efficiency, stability, and various dis...
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