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Computational Biology

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Caps-ac4C: An effective computational framework for identifying N4-acetylcytidine sites in human mRNA based on deep learning.

Journal of molecular biology
N4-acetylcytidine (ac4C) is a crucial post-transcriptional modification in human mRNA, involving the acetylation of the nitrogen atom at the fourth position of cytidine. This modification, catalyzed by N-acetyltransferases such as NAT10, is primarily...

Modern machine learning methods for protein property prediction.

Current opinion in structural biology
Recent progress and development of artificial intelligence and machine learning (AI/ML) techniques have enabled addressing complex biomolecular problems. AI/ML models learn the underlying distribution of data they are trained on and when exposed to n...

Alzheimer's disease: an integrative bioinformatics and machine learning analysis reveals glutamine metabolism-associated gene biomarkers.

BMC pharmacology & toxicology
BACKGROUND: Alzheimer's disease (AD), a hallmark of age-related cognitive decline, is defined by its unique neuropathology. Metabolic dysregulation, particularly involving glutamine (Gln) metabolism, has emerged as a critical but underexplored aspect...

Identification of biomarkers associated with coronary artery disease and non-alcoholic fatty liver disease by bioinformatics analysis and machine learning.

Scientific reports
The constantly emerging evidence indicates a close association between coronary artery disease (CAD) and non-alcoholic fatty liver disease (NAFLD). However, the exact mechanisms underlying their mutual relationship remain undefined. This study aims t...

Identification of ubiquitination-related key biomarkers and immune infiltration in Crohn's disease by bioinformatics analysis and machine learning.

Scientific reports
Crohn's disease (CD) is a chronic inflammatory bowel disease with an unknown etiology. Ubiquitination plays a significant role in the pathogenesis of CD. This study aimed to explore the functional roles of ubiquitination-related genes in CD. Differen...

Human-like face pareidolia emerges in deep neural networks optimized for face and object recognition.

PLoS computational biology
The human visual system possesses a remarkable ability to detect and process faces across diverse contexts, including the phenomenon of face pareidolia--seeing faces in inanimate objects. Despite extensive research, it remains unclear why the visual ...

Identification and validation of key autophagy-related genes in lupus nephritis by bioinformatics and machine learning.

PloS one
INTRODUCTION: Lupus nephritis (LN) is one of the most frequent and serious organic manifestations of systemic lupus erythematosus (SLE). Autophagy, a new form of programmed cell death, has been implicated in a variety of renal diseases, but the relat...

HDN-DDI: a novel framework for predicting drug-drug interactions using hierarchical molecular graphs and enhanced dual-view representation learning.

BMC bioinformatics
BACKGROUND: Drug-drug interactions (DDIs) especially antagonistic ones present significant risks to patient safety, underscoring the urgent need for reliable prediction methods. Recently, substructure-based DDI prediction has garnered much attention ...

Identification of Novel Biomarkers for Ischemic Stroke Through Integrated Bioinformatics Analysis and Machine Learning.

Journal of molecular neuroscience : MN
Ischemic stroke leads to permanent damage to the affected brain tissue, with strict time constraints for effective treatment. Predictive biomarkers demonstrate great potential in the clinical diagnosis of ischemic stroke, significantly enhancing the ...

Exploiting the similarity of dissimilarities for biomedical applications and enhanced machine learning.

PLoS computational biology
The "similarity of dissimilarities" is an emerging paradigm in biomedical science with significant implications for protein function prediction, machine learning (ML), and personalized medicine. In protein function prediction, recognizing dissimilari...