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The present study aimed to investigate the functional role and molecular mechanisms of long intergenic non‑protein coding RNA 1117 (LINC01117) in lung adenocarcinoma (LUAD). Bioinformatics analysis was performed to assess the expression level and prognostic …
Read PDF<h4>Motivation</h4>Citation is central to scholarly communication, enabling researchers to navigate rapidly expanding literature and identify relevant prior work. Yet the 'reasoning' behind why a particular paper is cited is often implicit or opaque. Although academic …
Read PDF<h4>Objective</h4>This study investigates the role of the protocadherin-1 (PCDH1) gene in pancreatic cancer metastasis, focusing on its influence on the epithelial-mesenchymal transition (EMT) process and the NF-κB signaling pathway.<h4>Methods</h4>Clinical specimens from pancreatic cancer patients were …
Read PDFOBJECTIVE: This study aimed to investigate the effect of miRNAs differentially expressed in serum exosomes on endothelial cells after myocardial infarction. DESIGN & METHODS: Specific pathogen-free male Sprague–Dawley rats with acute myocardial infarction (AMI) were …
Read PDF<h4>Motivation</h4>The American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines represent the gold standard for clinical variant interpretation. Despite the widespread adoption of ACMG/AMP guidelines, a comprehensive comparison of the software tools …
Read PDFMigrasomes, a newly discovered class of extracellular organelles, have emerged as pivotal mediators of intercellular communication, signaling gradient establishment, and organelle homeostasis. Their unique biogenesis—arising from retraction fibers of migrating cells—positions them as critical regulators …
Read PDFBiological sex inference from genomic data is important in population genomics, conservation biology, and forensic science, yet many existing approaches depend on sequence alignment or species-specific markers and may therefore be limited in their transferability …
Read PDF<h4>Summary</h4>Combining genetic data from different genotyping arrays (mega-analysis) increases statistical power but introduces array-specific batch effects that may bias results. This project developed a two-step genotype imputation workflow addressing this bias in studies using multiple …
Read PDFThis study aims to utilize multiomics and bioinformatics techniques to investigate the expression of the connection enzyme inhibitor Ras1 1 (CNKSR1) in ovarian cancer (OC) and its mechanism of action in the processes of tumor …
Read PDF<h4>Background and objective</h4>Coronary endothelial dysfunction is considered one of the key pathological components in acute myocardial infarction (AMI). This study aimed to explore the expression patterns and potential significance of the differentially expressed genes SULF1 …
Read PDF<h4>Motivation</h4>Creating publication-quality visualizations is essential for bioinformatics but remains a bottleneck for researchers with limited coding expertise. While Large Language Models (LLMs) are proficient at generating code, they often fail in practice due to library …
Read PDF<h4>Summary</h4>Liquid chromatography-mass spectrometry (LC-MS/MS) data analysis requires adaptable software solutions to meet diverse analytical needs. We present eMZed 3, a modern Python framework for flexible and interactive analysis of LC-MS/MS data. eMZed 3 enables users …
Read PDFFood allergies represent a significant and growing global challenge. However, researchers and risk assessors still lack a dedicated and comprehensive resource that centralizes food allergen information. As a result, obtaining the necessary structural, biochemical, and …
Read PDF<h4>Motivation</h4>Natural products are often produced by a set of biosynthetic enzymes that are encoded by genes clustered together in the producer's genome, referred to as a biosynthetic gene cluster (BGC). The ability to compare and …
Read PDFH-SPAR DB is a comprehensive database designed to support space health research by providing a unified platform for data integration, analysis, and interpretation. The database simplifies the complex workflows associated with spaceflight-related biology studies by …
Read PDF<h4>Summary</h4>GenomeDepot is an open-source web-based platform for annotation, management, and comparative analysis of microbial genomic sequences and associated data including ortholog families, protein domains, operons, regulatory interactions, strain taxonomy, and sample metadata. GenomeDepot supports rapid …
Read PDFStudying morphogen gradient-based tissue patterning in silico while accounting for biological variability remains challenging. Here, we present a MATLAB-based protocol for simulating steady-state morphogen gradients in one- and two-dimensional tissues with cell-to-cell variability in model …
Read PDFThe cryogenic sample-electron microscopy (cryoEM) field has generated significant amounts of 3D Electron Microscopy (3DEM) volumetric data and associated metadata, now comprehensively archived in the Electron Microscopy Data Bank (EMDB - www.emdatabank.org) and the Electron …
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