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Integrated bioinformatics and experimental validation identifies CLIC6 as a novel tumor suppressor regulating NF-κB signaling and immune microenvironment in nasopharyngeal carcinoma
<h4>Background</h4>Nasopharyngeal carcinoma (NPC) is an Epstein-Barr virus-associated malignancy. Tumor-associated macrophages play a pivotal role in NPC development, but molecular mechanisms remain unclear. This study aimed to identify M1 macrophage-associated hub genes and investigate their biological …
Read PDFDNAvi: integration, statistics, and visualization of cell-free DNA fragment traces
<h4>Summary</h4>DNAvi is a Python-based tool for rapid grouped analysis and visualization of cell-free DNA fragment size profiles directly from electrophoresis data, overcoming the need for sequencing in basic fragmentomic screenings. It enables normalization, statistical comparison, …
Read PDFEpitope-based vaccine of NiV targeting glycoprotein and fusion protein: an integrated immunoinformatics and bioinformatics approach
NiV is an ongoing infection that causes severe complications, and its frequent outbreaks make its treatment more complicated in terms of the proper therapeutic design. No viable vaccine candidate exists to combat NiV; however, efforts …
Read PDFTotal and engineered biosynthesis of cinatrins: inhibitors of phospholipase A<sub>2</sub> and squalene synthase
An alkyl citrate biosynthetic gene cluster (<i>ctr</i>) was identified from 47 members of the fungal family of Hypoxylaceae by genome mining. The <i>Hypomontagnella monticulosa</i> MUCL 54604 <i>ctr</i> cluster was deployed for the total biosynthesis of …
Read PDFResponse to: "best practices when benchmarking CATCH for the design of genome enrichment probes"
We clarify the design principles and evaluation choices underlying Syotti, a robust and scalable probe-design tool developed to support large, heterogeneous bacterial datasets with minimal parameter tuning. We highlight Syotti's ability to perform simultaneous large-scale …
Read PDFAccelign: a GPU-based library for accelerating pairwise sequence alignment
<h4>Background</h4>The continually increasing volume of sequence data results in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments based on dynamic programming is an important part in many bioinformatics pipelines and …
Read PDFDeepLMI: deep feature mining with a globally enhanced graph convolutional network for robust lncRNA-miRNA interaction prediction
<h4>Motivation</h4>Interactions between long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) play pivotal roles in gene regulation and disease progression, notably through mechanisms such as competitive miRNA sponging. Accurate identification of lncRNA-miRNA interactions is therefore essential for …
Read PDFPredicting Pathogenicity of <i>TSHR</i> Missense Variants of Uncertain Significance: An Integrative Computational Study
Pathogenic variants in the thyroid-stimulating hormone receptor gene (<i>TSHR</i>) contribute to a wide spectrum of thyroid dysfunctions, ranging from congenital hypothyroidism to thyrotropin resistance. With the advancement of bioinformatics algorithms for variant effect prediction, assessing …
Read PDFIntegrative analysis via bioinformatics and machine learning identifies SERPING1 as a biomarker candidate for major depressive disorder
BACKGROUND: Major Depressive Disorder (MDD) represents a grave mental affliction characterised by intricate pathological mechanisms and an elevated susceptibility to neurodegeneration. This study aims to integrate machine learning and bioinformatics analysis to identify potential biomarkers …
Read PDFUnderstanding practical barriers to the global adoption of environmental DNA (eDNA) methods, tools, and standards
OBJECTIVE: Environmental DNA (eDNA) is a rapidly emerging data source with the potential to support environmental monitoring and biodiversity conservation around the world. Current efforts to standardize eDNA methods and reporting are aimed at strengthening …
Read PDFCorrection: Minimum uncertainty as Bayesian network model selection principle
No abstract available.
Read PDFPEtab-GUI: a graphical user interface to create, edit, and inspect PEtab parameter estimation problems
<h4>Motivation</h4>Parameter estimation is a cornerstone of data-driven modeling in systems biology. Yet, constructing such problems in a reproducible and accessible manner remains challenging. The PEtab format has established itself as a powerful community standard to …
Read PDFAn integrative bioinformatics framework for functional annotation and prioritization of hypothetical proteins in Bacillus thuringiensis relevant to biological pest control
Bacillus thuringiensis is a widely used biological control agent whose genomes contain a substantial proportion of coding sequences annotated as hypothetical proteins, limiting functional interpretation and hindering their exploitation in biotechnology and genetic engineering. Here, …
Read PDFAmos Bairoch (1957–2025): pioneer of bioinformatics and founder of Swiss-Prot
No abstract available.
Read PDFEvolving the HDRUK Phenotype Library: Phenotype Creation and Editing
No abstract available.
Read PDFBuilding genomic data structures from compressed representations using prefix-free parsing
Advances in high-throughput sequencing have lowered the cost and complexity of genome sequencing, making it possible for the first time to assemble large pangenomic data sets for many species. These data sets, comprising thousands of …
Read PDFIntegrative bioinformatics approaches for early detection biomarkers in ovarian cancer
Ovarian cancer remains a major clinical challenge, largely because most patients present with advanced-stage disease. Early detection is essential for improving outcomes, yet current biomarkers such as CA-125 and HE4 have limited sensitivity in early-stage …
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