AIMC Topic: Computational Biology

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Analyses of the mechanism and therapeutic targets of senescence related genes in ischemic stroke with multi-omics approach.

Scientific reports Jul 18, 2025
Ischemic stroke (IS) affects 11 million people annually, posing substantial clinical and economic burdens. Current therapies remain limited by time sensitivity and variable efficacy, necessitating novel biomarkers. We developed a multi-omics framewor...
Biomarkers Aging Gene Expression Profiling Humans Ischemic Stroke Gene Expression Regulation Cyclooxygenase 2 Computational Biology Multiomics Signal Transduction Transcriptome Gene Regulatory Networks
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Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings.

Nature communications Jul 18, 2025
Single-cell spatial transcriptomics can provide subcellular resolution for a deep understanding of molecular mechanisms. However, accurate segmentation and annotation remain a major challenge that limits downstream analysis. Current machine learning ...
Single-Cell Analysis Computational Biology Molecular Sequence Annotation Gene Expression Profiling Transcriptome Deep Learning Humans Algorithms Animals
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Computational protein design: Advancing biotechnology through in silico engineering.

Progress in biophysics and molecular biology Jul 17, 2025
Currently, computational protein design (CPD) is a disruptive force in biotechnology, changing the paradigm by which proteins are engineered for many applications. In this article, the evolution of CPD has been tracked from its initial forays in the ...
Proteins Biotechnology Protein Engineering Humans Computer Simulation Computational Biology
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Sceptic: pseudotime analysis for time-series single-cell sequencing and imaging data.

Genome biology Jul 17, 2025
Several computational methods have been developed to construct single-cell pseudotime embeddings for extracting the temporal order of transcriptional cell states from time-series scRNA-seq datasets. However, existing methods suffer from low predictiv...
Algorithms Single-Cell Analysis Image Processing, Computer-Assisted Computational Biology Sequence Analysis, RNA Support Vector Machine Humans
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Hybrid classical and quantum computing for enhanced glioma tumor classification using TCGA data.

Scientific reports Jul 17, 2025
Gliomas are the most prevalent malignant primary brain tumors and present diagnostic challenges due to varying survival rates and treatment responses between low-grade gliomas (LGGs) and high-grade gliomas (HGGs). Accurate classification is crucial f...
Biomarkers, Tumor Brain Neoplasms Computational Biology Humans Algorithms Glioma Quantum Theory
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Shared pathogenic mechanisms linking obesity and idiopathic pulmonary fibrosis revealed by bioinformatics and in vivo validation.

Scientific reports Jul 17, 2025
Previous studies have suggested a potential correlation between obesity and idiopathic pulmonary fibrosis (IPF). This study aimed to elucidate pathogenic pathways connecting obesity and IPF and identify diagnostic biomarkers for obesity-related pulmo...
Diet, High-Fat Gene Expression Profiling Protein Interaction Maps Humans Gene Regulatory Networks Machine Learning Mice Idiopathic Pulmonary Fibrosis Animals Computational Biology Male Mice, Inbred C57BL Disease Models, Animal Obesity Molecular Docking Simulation
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Identification of CTSK as a TLR-related critical biomarker in liver cirrhosis via integrative bioinformatics and pathological characterization.

Scientific reports Jul 17, 2025
Liver cirrhosis (LC) is a common chronic disease worldwide with a poor prognosis, and its pathogenesis has not been fully elucidated. Toll-like receptors (TLRs) are crucial in LC progression. Here, we identified TLR-related genes, providing novel ins...
Humans Biomarkers Signal Transduction Gene Expression Regulation Toll-Like Receptors Molecular Docking Simulation Gene Expression Profiling Gene Regulatory Networks Computational Biology Liver Cirrhosis
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Cross-attention graph neural networks for inferring gene regulatory networks with skewed degree distribution.

BMC bioinformatics Jul 16, 2025
BACKGROUND: Inferring Gene Regulatory Networks (GRNs) from gene expression data is a pivotal challenge in systems biology. Most existing methods fail to consider the skewed degree distribution of genes, complicating the application of directed graph ...
Computational Biology Software Humans Databases, Genetic Algorithms Neural Networks, Computer Graph Neural Networks Gene Regulatory Networks
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A comprehensive machine learning for high throughput Tuberculosis sequence analysis, functional annotation, and visualization.

Scientific reports Jul 16, 2025
With human guidance, computers now use machine learning (ML) in artificial intelligence (AI) to learn from data, detect trends, and make predictions. Software can adapt and improve with new information. Imaging scans leverage pattern recognition to p...
Support Vector Machine Tuberculosis Mycobacterium tuberculosis Molecular Sequence Annotation Machine Learning Algorithms Computational Biology Humans
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In Silico tool for predicting, designing and scanning IL-2 inducing peptides.

Scientific reports Jul 16, 2025
Interleukin-2 (IL-2) based immunotherapy has been approved for treating certain types of cancer, as IL-2 plays a crucial role in regulating the immune system. In this study, we developed a method for predicting IL-2-inducing peptides. Our method was ...
Computational Biology Interleukin-2 Peptides Deep Learning Humans Machine Learning Computer Simulation
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