AI Medical Compendium Topic:
Computational Biology

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Visualization Methods for DNA Sequences: A Review and Prospects.

Biomolecules
The efficient analysis and interpretation of biological sequence data remain major challenges in bioinformatics. Graphical representation, as an emerging and effective visualization technique, offers a more intuitive method for analyzing DNA sequence...

deepBBQ: A Deep Learning Approach to the Protein Backbone Reconstruction.

Biomolecules
Coarse-grained models have provided researchers with greatly improved computational efficiency in modeling structures and dynamics of biomacromolecules, but, to be practically useful, they need fast and accurate conversion methods back to the all-ato...

Human-like dissociations between confidence and accuracy in convolutional neural networks.

PLoS computational biology
Prior research has shown that manipulating stimulus energy by changing both stimulus contrast and variability results in confidence-accuracy dissociations in humans. Specifically, even when performance is matched, higher stimulus energy leads to high...

An experimental analysis of graph representation learning for Gene Ontology based protein function prediction.

PeerJ
Understanding protein function is crucial for deciphering biological systems and facilitating various biomedical applications. Computational methods for predicting Gene Ontology functions of proteins emerged in the 2000s to bridge the gap between the...

Identification of TXN and F5 as novel diagnostic gene biomarkers of the severe asthma based on bioinformatics and machine learning analysis.

Autoimmunity
Asthma poses a major threat to human health. The aim of this study was to identify genetic markers of severe asthma and analyze the relationship between key genes and immune infiltration. Differentially expressed genes (DEGs) were first screened by d...

Using bioinformatics and artificial intelligence to map the cyclin-dependent kinase 4/6 inhibitor biomarker landscape in breast cancer.

Future oncology (London, England)
A cyclin-dependent kinase 4/6 (CDK4/6) inhibitor combined with endocrine therapy is the standard-of-care for patients with hormone receptor-positive/human epidermal growth factor receptor 2-negative advanced breast cancer. However, not all patients r...

DeepBP: Ensemble deep learning strategy for bioactive peptide prediction.

BMC bioinformatics
BACKGROUND: Bioactive peptides are important bioactive molecules composed of short-chain amino acids that play various crucial roles in the body, such as regulating physiological processes and promoting immune responses and antibacterial effects. Due...

B cell epitope prediction by capturing spatial clustering property of the epitopes using graph attention network.

Scientific reports
Knowledge of B cell epitopes is critical to vaccine design, diagnostics, and therapeutics. As experimental validation for epitopes is time-consuming and costly, many in silico tools have been developed to computationally predict the B cell epitopes. ...

Analyzing immune cell infiltrates in skeletal muscle of infantile-onset Pompe disease using bioinformatics and machine learning.

Scientific reports
Pompe disease, a severe lysosomal storage disorder, is marked by heart problems, muscle weakness, and respiratory difficulties. This study aimed to identify novel markers for infantile-onset Pompe disease by analyzing key genes and immune cells infil...