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The AlphaFold Protein Structure Database (AFDB; https://alphafold.ebi.ac.uk), developed by EMBL-EBI and Google DeepMind, provides open access to hundreds of millions of high-accuracy protein structure predictions, transforming research in structural biology and the wider life sciences. …
Read PDF<h4>Motivation</h4>Spatial transcriptomics (ST) enables the study of spatial heterogeneity in tissues. However, current methods struggle with large-scale, high-resolution data, leading to reduced efficiency and accuracy in detecting spatial domains. A scalable, precise solution is urgently …
Read PDF<h4>Background</h4>Neuropathic pain (NP) frequently co-occurs with depression (DP), exhibiting complex pathogenesis and limited clinical treatment options. This study aims to investigate the efficacy of Eupalinolide B (EB) in alleviating NP co-occurring with DP and its …
Read PDF<h4>Objective</h4>This study aimed to identify key molecular signatures and therapeutic targets in early sepsis through integrated bioinformatics analysis.<h4>Methods</h4>We analyzed three independent blood transcriptomic datasets (GSE95233, GSE137340, GSE57065) from the Gene Expression Omnibus. Differential expression, functional …
Read PDF<h4>Motivation</h4>Accurately inferring transcription factor (TF) activity from single-cell RNA sequencing (scRNA-seq) data remains a fundamental challenge in computational biology. While existing methods rely on statistical models, motif enrichment, or prior-based inference, they often depend on …
Read PDFMany physiological processes rely on cellular communication through ligand mediated signalling, where ligands secreted by cells diffuse through the extracellular space and bind to receptors to trigger downstream responses. Although reaction diffusion models capture these …
Read PDF<h4>Introduction and aims</h4>Mitochondrial metabolic dysregulation is associated with periodontitis (PD); however, related biomarkers remain unclear. In this study, we identified key mitochondrial metabolism-related biomarkers in PD through integrated bioinformatics technology.<h4>Methods</h4>Transcriptomic and single-cell RNA sequencing data …
Read PDFRNA-seq quantifies the abundance of transcripts within a biological sample and performs differential analysis between different conditions to reveal regulated gene signatures. Three challenges exist: (1) different analytical packages can often report different expression patterns …
Read PDF<h4>Motivation</h4>Life science databases include large collections of public transcriptome and large-scale structural data. The reuse and integration of these datasets may facilitate the identification of understudied genes and enable functional annotation across distantly related species, …
Read PDFLung adenocarcinoma (LUAD), the most common subtype of nonsmall cell lung cancer, exhibits substantial molecular heterogeneity, complicating subtype classification, progression assessment, and treatment decision-making. Advances in high-throughput sequencing enable multi-omics analysis to reveal cancer mechanisms …
Read PDF<h4>Motivation</h4>Targeted enrichment can offset the bias and depth requirements of random-primed second-strand synthesis in 3'-end RNA-seq by reallocating reads to transcripts of interest. We present PeakPrime, a reproducible Nextflow pipeline that (i) identifies high-coverage 3 …
Read PDF<h4>Motivation</h4>Single-cell RNA sequencing (scRNA-Seq) technology enables detailed exploration of gene expression at the individual cell level, crucial for annotating cell types and understanding cellular diversity. Traditional methods for cell type annotation often rely on marker …
Read PDFAneurysm progression is associated with complex molecular alterations that are insufficiently studied at transcriptomics level. An aneurysm is characterized as a bulge or a weak spot in a blood artery's wall that causes the vessel …
Read PDFDysregulation of signaling pathways contributes substantially to the initiation and progression of laryngeal squamous cell carcinoma (LSCC). This study aimed to elucidate the mTOR and S6 kinase (S6K) gene expression levels, clinical significance, interplay of …
Read PDF<h4>Motivation</h4>High-throughput multi-omics technologies produce increasingly large and heterogeneous datasets that are difficult to analyze without advanced computational expertise. Existing bioinformatics tools are often fragmented or limited to specific omics types, hindering reproducibility and accessibility. There …
Read PDFExpression Atlas (https://www.ebi.ac.uk/gxa/home) is EMBL-EBI's comprehensive knowledgebase for gene and protein expression across tissues, cell types, conditions, and multiple species. Since our last update, Expression Atlas has expanded substantially in both content and functionality, now …
Read PDFAtrial fibrillation (AF) is a common arrhythmia associated with immune dysregulation and complex molecular mechanisms. This observational bioinformatics study aimed to identify key genes involved in AF, explore their functional roles, and uncover potential therapeutic …
Read PDF<h4>Background</h4>With the rapid progress of molecular medicine, new target therapies for solid tumors have become available, leading to the creation of molecular tumor boards (MTBs) designated to evaluate potential individualized treatment options. Unlike other solid …
Read PDF<h4>Summary</h4>SCODE reconstructs gene regulatory networks from single-cell RNA sequencing (scRNA-seq) data using an ordinary differential equation (ODE) model, and has been successfully applied to a wide range of scRNA-seq datasets, including mouse, human, and plant …
Read PDF<h4>Motivation</h4>Long-read sequencing has made RNA isoform detection and characterization more accessible. While several bioinformatics tools have been developed to examine the data generated by these approaches, a major challenge in the field has been comparing …
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