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The potential impact of exosomal miR-484 on post-myocardial infarction angiogenesis using bioinformatics and experimental verification
OBJECTIVE: 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 PDFComprehensive evaluation of ACMG/AMP-based variant classification tools
<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 PDFMigrasome and cancer - from cellular to clinical perspectives
Migrasomes, 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 PDFONYX: an alignment-free biological sex inference from high-throughput sequencing data
Biological 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 PDFRemoving array-specific batch effects in GWAS mega-analyses by applying a two-step imputation workflow
<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 PDFA Multiomics and Bioinformatics Analysis of the Role and Mechanism of <i>CNKSR1</i> in Ovarian Cancer Progression
This 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 PDFImpact of genotype and soil fertility on wheat rhizosphere microbiota under the trans-gangetic plain
The effects of genotypes (HD3086 and PBW343) and soil physicochemical properties on the wheat rhizospheric bacterial communities along the trans Indo-Gangetic plains were studied. The trans-Indo-Gangetic Plains of India are one of the areas in …
Read PDFSULF1 and EPB41L3: Potential Biomarkers of Acute Myocardial Infarction and the Vascular Inflammatory Milieu
<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 PDFggplotAgent: a self-debugging multi-modal agent for robust and reproducible scientific visualization
<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 PDFApple pomace and hempseed cake can reduce methane intensity (CH₄/DMI) and alter the rumen microbiome in dairy cows: a shotgun metagenomic approach
<h4>Background</h4>With growing attention to environmental impacts, the dairy sector is increasingly focused on implementing strategies that lower methane emissions and enhance sustainability while maintaining productivity and economic viability. Utilizing agro-industrial by-products as alternative feed ingredients …
Read PDFeMZed 3: flexible and interactive development of scalable LC-MS/MS data analysis workflows in python
<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 PDFFAD: a comprehensive database merging information about food allergens
Food 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 PDFTranscriptional and epigenetic regulation of Ca<sup>2+</sup>-signaling genes in hepatitis B-derived hepatocellular carcinoma and their association with the cancer hallmarks
<h4>Motivation</h4>Dysregulation of Ca<sup>2+</sup>-signaling genes has been shown in some types of cancer; however, it is virtually unknown in hepatitis B-derived hepatocellular carcinoma (HBV-HCC). Here, we evaluate the transcriptional and epigenetic regulation of Ca<sup>2+</sup>-signaling genes in …
Read PDFBenchmarking methods for measuring biosynthetic gene cluster similarity and determination of gene cluster families
<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: human spaceflight platform for analysis and research-an integrative omics database for space health
H-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 PDFGenomeDepot: data management system for microbial comparative genomics
<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 PDFMorphoGrad: A MATLAB toolbox for simulating steady-state morphogen gradients under cell-to-cell variability
Studying 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 PDFChart builder: an interactive tool for user driven data visualization in the electron microscopy data bank
The 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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