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PLAID: ultrafast single-sample gene set enrichment scoring
<h4>Summary</h4>In recent years, computational methods have emerged that calculate enrichment of gene signatures within individual samples. These signatures offer critical insights into the coordinated activity of functionally related genes, proteins or metabolites, enabling the identification …
Read PDFDeciphering the potential pathogenic mechanisms of 3-BHA in ovarian cancer through integrated bioinformatics and machine learning strategies
Ovarian cancer (OC) remains a malignancy characterized by obscure risk factors and unfavorable prognosis. While 3-tert-butyl-4-hydroxyanisole (3-BHA) is suspected of exerting toxic effects on ovarian health, the precise molecular mechanisms underlying its impact remain elucidated. …
Read PDFBioAgents: Bridging the gap in bioinformatics analysis with multi-agent systems
Developing end-to-end bioinformatics workflows is challenging, demanding deep expertise in both genomics and computational techniques. While large language models (LLMs) provide some assistance, they often lack the nuanced guidance required for complex bioinformatics tasks, and …
Read PDFThe Small Molecule Compound Eupalinolide B Ameliorates Depressive Behaviors and Neuropathic Pain in Mice With Spared Nerve Injury: Integrating Network Pharmacology, Molecular Docking, Bioinformatics, Molecular Dynamics Simulation and Experimental Verification
<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 PDFCausal knowledge graph analysis identifies adverse drug effects
<h4>Motivation</h4>Knowledge graphs and structural causal models have each proven valuable for organizing biomedical knowledge and estimating causal effects, but remain largely disconnected: knowledge graphs encode qualitative relationships focusing on facts and deductive reasoning without formal …
Read PDFIntegrated bioinformatics analysis and experimental validation reveal Pevonedistat as a promising therapeutic agent modulating the CRL4-DTL-p21/p53 axis in nasopharyngeal carcinoma
BACKGROUND: Nasopharyngeal carcinoma (NPC) continues to represent a significant therapeutic challenge. Despite the substantial success of radiotherapy, chemotherapy, and immunotherapy, their effectiveness remains limited in recurrent or advanced NPC. Hence, the urgent identification of new …
Read PDFIntegrated bioinformatics analysis of molecular signatures and therapeutic targets in early sepsis
<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 PDFA bioinformatics analysis of the PIEZO channel interaction network and the genes related to glycometabolic reprogramming and mitochondrial oxidative phosphorylation in the progression of prostatic hyperplasia
<h4>Background</h4>Prostatic hyperplasia is a common condition among aging males characterized by excessive prostate cell proliferation, and while it is a benign process, it involves significant metabolic reprogramming and immune infiltration-features typically associated with malignant tumors. …
Read PDFscRegulate: single-cell regulatory-embedded variational inference of transcription factor activity from gene expression
<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 PDFCalibrating tissue level PDE models of ligand dynamics using single cell and spatial transcriptomics data
Many 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 PDFRoBep: a region-oriented deep learning model for B-cell epitope prediction
<h4>Motivation</h4>Accurate in silico identification of B-cell epitope residues is crucial for antibody design and structure-guided vaccine development. Although recent protein language models and structure-aware methods can capture spatial information of tertiary structure when generating residue …
Read PDFSISTEM: simulation of tumor evolution, metastasis, and DNA-seq data under genotype-driven selection
<h4>Summary</h4>SISTEM is a software package and mathematical framework for simulating tumor evolution and cell migrations at single-cell resolution. Unlike existing frameworks which simulate cancer cell populations under the neutral coalescent or using simple birth-death models, …
Read PDFMicrobial dynamics in primary and refractory apical periodontitis: Next-generation 16S rRNA sequencing reveals selective shifts and reduced diversity
<h4>Context</h4>Apical periodontitis (AP) is an inflammatory condition caused by root canal infection. Primary AP (PAP) arises from untreated necrotic pulp and is typically polymicrobial, whereas persistent or refractory AP (RAP) occurs after root canal treatment …
Read PDFMitochondrial Metabolic Biomarkers in Periodontitis: Discovery and Clinical Validation
<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 PDFThe potential involvement of FABP4 in rheumatoid arthritis-associated osteoporosis: a comprehensive bioinformatics analysis and experimental validation
<h4>Objective</h4>This study investigates the role and underlying mechanism of FABP4 in RA secondary OP by examining its correlation with the condition.<h4>Methods</h4>DEGs related to RA and OP were identified using GEO datasets (GSE17755 and GSE230665), focusing …
Read PDFListeria Genome Identification Using DNABERT Embedding With LightGBM and SHAP-Based Explainable Classification
Prompt and accurate identification of Listeria monocytogenes at the whole-genome level is essential for food safety surveillance and outbreak prevention, yet existing culture-based, PCR, and next-generation sequencing (NGS) workflows are either slow, labor-intensive, or rely …
Read PDFUnleashing potential: assessing Africa's readiness for the data science revolution to impact health
Data Science can revolutionize biomedical sciences, and ultimately, health. However, this relies on core elements, including computing infrastructure, data science skills, and well-curated contextually relevant data, which are limited in low- and middle-income countries. Many …
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