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The Lipid Interactome: an interactive and open access platform for exploring cellular lipid-protein interactions
<h4>Summary</h4>Lipid-protein interactions play essential roles in cellular signaling and membrane dynamics, yet their systematic characterization has long been hindered by the inherent biochemical properties of lipids. Recent advances in functionalized lipid probes-equipped with photoactivatable crosslinkers, …
Read PDFUncovering the Independent Role of Lipid Peroxidation in Osteoporosis Through an Integrated Bibliometric and Bioinformatics Analysis
<h4>Objective</h4>This study, utilising bibliometric analysis combined with bioinformatics approaches, systematically analysed research trends in the fields of osteoporosis (OP) and autophagy (ATG) over the past two decades, with a focus on the emerging frontier of …
Read PDFUnraveling gene interaction networks in colorectal cancer and inflammatory bowel disease via a novel hybrid radial basis function network
Colorectal cancer (CRC) is a significant global health challenge, closely linked with inflammatory bowel disease (IBD). Understanding the genetic and molecular underpinnings of CRC and its association with IBD is critical for early diagnosis and …
Read PDFThe mechanism of fibronectin 1 promoting papillary thyroid cancer progression by regulating anoikis resistance
Background: Papillary thyroid cancer is a common head and neck malignancy with a globally rising incidence. While most patients attain favorable prognosis following standard treatment, a subset develops recurrence and metastasis—two key factors that compromise …
Read PDFThe Orexin System Modulates Stress-Induced Alcohol Preference and Reinstatement in Adolescents: Bioinformatics and Experimental Evidence
Underage drinking has become a global public health concern. One of the major causes of underage drinking is stress. The orexin system has been reported to be involved in both alcohol addiction and stress. However, …
Read PDFIntegrative Metabolic-Flux Platform for Analysis, Contextualization, and Targeting (IMPACT): bridging untargeted and targeted flux analysis
<h4>Summary</h4>The "Integrative Metabolic-Flux Platform for Analysis, Contextualization, and Targeting" (IMPACT) is a comprehensive, fully modular platform designed for both targeted and untargeted metabolomics analysis in stable-isotope labeling experiments. It facilitates the accurate calculation of mass …
Read PDFrMAP 2.0: a modular, reproducible, and scalable WDL-Cromwell-Docker workflow for genomic analysis of ESKAPEE pathogens
<h4>Motivation</h4>Antimicrobial resistance surveillance in ESKAPEE pathogens (<i>Enterococcus faecium</i>, <i>Staphylococcus aureus</i>, <i>Klebsiella pneumoniae</i>, <i>Acinetobacter baumannii</i>, <i>Pseudomonas aeruginosa</i>, <i>Enterobacter</i> spp., and <i>Escherichia coli</i>) requires reproducible, portable whole-genome analysis that public health laboratories including those operating under data-sovereignty …
Read PDFGOFlowLLM-curating miRNA literature with large language models and flowcharts
<h4>Motivation</h4>The exponential growth of non-coding RNA research-with over 230 000 papers published since 2000-has created an urgent knowledge management crisis in molecular biology. Despite their crucial regulatory roles, microRNAs (miRNAs) face a significant curation bottleneck, …
Read PDFPseudoChecker2 and PseudoViz: automation and visualization of gene loss in the Genome Era
<h4>Summary</h4>High-fidelity genome assemblies provide unprecedented opportunities to decipher mechanisms of molecular evolution and phenotype landscapes. Here, we present PseudoChecker2, a command-line version of the web-tool PseudoChecker with expanded functions. It identifies gene loss via drastic …
Read PDFViral Diseases Explorer: a webtool to identify viral disease information derived from multiple LLMs
<h4>Motivation</h4>With nearly 266,500 viruses cataloged currently at NCBI and increasing by the day, identifying the diseases they cause, and the affected hosts remains challenging. Hence the motivation for undertaking this study.<h4>Results</h4>Utilizing the AI-powered tools, we …
Read PDFSecreted Peptidome Profiling of Human Dental Pulp Stem Cells-Conditioned Medium During Odontogenic Differentiation
<h4>Introduction and aims</h4>Odontogenic differentiation of human dental pulp stem cells (hDPSCs) is critical for pulp repair. This study aims to characterise the secretory peptidome of human dental pulp stem cells (hDPSCs) during odontogenic differentiation, thereby …
Read PDFTargeted gene sequencing and bioinformatics analysis of a patient with gallbladder adenosquamous carcinoma: a case report
<h4>Introduction</h4>Gallbladder adenosquamous carcinoma (GBASC) is an uncommon, highly aggressive neoplasm characterized by the coexistence of both glandular and squamous cells. Representing fewer than 5% of gallbladder malignancies, GBASC demonstrates a more aggressive behavior and has …
Read PDFQTLNetwork-MP: integrative mapping of additive, epistatic, and G × E effects for complex traits in multiparent advanced generation intercross populations
Quantitative trait locus (QTL) mapping is a powerful approach to uncover the genetic architecture of complex traits. Traditional biparental populations, though widely used, offer limited genetic diversity and resolution, making them less effective for robust …
Read PDFImpact of miR-146a-3p rs2910164 polymorphism on peri-implantitis susceptibility and target gene-mediated inflammatory responses
<h4>Objectives</h4>This study investigated the association between miR-146a-3p rs2910164 polymorphism and peri-implantitis (PI) susceptibility in the Han Chinese population, as well as the potential mechanisms underlying PI progression.<h4>Material and methods</h4>183 PI patients and 219 individuals with …
Read PDFTransformer-based operon prediction using textual representations of gene pairs
<h4>Motivation</h4>Operons are fundamental units of gene regulation in bacteria and can provide valuable insights into genome organization, co-expression, and functional relationships between genes. Computational prediction of operons can support downstream analyses such as pathway reconstruction, …
Read PDFAn Integrative Variant Scoring Function for Finding Novel Genes Associated with Ovarian and Thyroid Cancer
We devised a quantitative scoring function to assess the cumulative effects of somatic nonsynonymous single-nucleotide variants (SNVs) on protein-coding genes in patients with ovarian cancer (OvCa) and thyroid cancer (ThCa). The goal is to find …
Read PDFImproving biomedical entity linking with generative relevance feedback
<h4>Motivation</h4>Biomedical Entity Linking (BEL) maps mentions in biomedical text to standardized identifiers, enabling structured data integration and downstream knowledge discovery. However, current BEL systems remain fundamentally constrained by the recall of the initial candidate pool, …
Read PDFCorrection: Evaluation of ctDNA-guided adjuvant therapy de-escalation in head and neck squamous cell carcinoma: a comparative cohort study
[This corrects the article DOI: 10.3389/fimmu.2025.1576042.].
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