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Sepsis is a life-threatening organ malfunction induced by the host's abnormal reaction to infection. Sepsis can induce cellular senescence, thereby exacerbating tissue damage and organ dysfunction. However, the key biomarkers of cellular senescence and the …
Read PDF<h4>Motivation</h4>Differentiable programming frameworks like PyTorch and JAX revolutionized biological modeling. A foremost merit is that multiple components programmed separately can be put together so that the parameters are jointly optimized. Despite its proven value in …
Read PDFDNA N-gram analysis methodologies have been successfully deployed to provide a wide range of elegant solutions to a variety of complex problems in bioinformatics, such as sequence alignment, DNA barcoding, the identification of functional gene …
Read PDF<h4>Summary</h4>Omics profiling has proven of great use for unbiased and comprehensive identification of key features that define biological phenotypes and underlie medical conditions. While each omics profile assists characterization of specific molecular components relevant for …
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Read PDFTuberculosis remains a major global health problem due to the emergence of drug-resistant strains of <i>Mycobacterium tuberculosis</i>. <i>Mycobacterium tuberculosis</i> DprE1, a key enzyme involved in cell wall biosynthesis, was targeted to identify potential anti-tuberculosis agents. …
Read PDF<h4>Motivation</h4>Proteins play a crucial role in biological systems, and accurate protein sequence prediction is essential for applications such as drug discovery. Existing inverse folding models primarily rely on protein backbone structure information, overlooking the biochemical …
Read PDF<h4>Summary</h4>Designing mRNA coding sequences (CDSs) for vaccine development requires co-optimizing secondary structure stability and codon usage, which are typically measured by minimum free energy (MFE) and codon adaptation index (CAI), respectively. To address this challenge, …
Read PDF<h4>Motivation</h4>Transcription factors (TFs) and their target genes form regulatory networks that control gene expression and influence diverse biological processes and disease outcomes. Although multiple computational methods and curated databases have been developed to identify TF-target …
Read PDF<h4>Motivation</h4>Aligning sequencing reads to reference genomes is a fundamental task in bioinformatics. Aligners can be classified as lossy or lossless: lossy aligners prioritize speed by reporting only one or a few high-scoring alignments, whereas lossless …
Read PDF<h4>Motivation</h4>Integrating omics data analysis with publicly available databases is crucial for unravelling complex biological mechanisms. However, this integration process is often intricate and time-consuming due to the diversity and complexity of the data involved. Achieving …
Read PDF<h4>Introduction</h4>Mothers' milk is the optimal source of nutrition for infants. When unavailable, pasteurized donor human milk (PDHM) is the recommended alternative, particularly for premature neonates at a risk of food insecurity. However, processing methods, such …
Read PDFBioinformatics and systems biology strategies for managing cancer and Alzheimer's disease. Key concepts include multi-omics data, computational modeling, network analysis, and nanotechnology. Translational applications cover diagnostics, prognostics, and therapeutics. Arrows suggest a circular process between …
Read PDF<h4>Introduction</h4>Exon 11 and exon 14 of BRCA1, a tumor suppressor gene, are known to be mutated in various cancers.<h4>Methodology</h4>We screened 24 samples (13 from patients with acute myeloid leukemia and 11 from normal controls) using …
Read PDF<h4>Objective</h4>This study aims to explore the potential molecular mechanisms by which di (2-ethylhexyl) phthalate (DEHP) exposure induces pulmonary arterial hypertension (PAH).<h4>Methods</h4>We conducted differential expression analysis on multiple genomics datasets to pinpoint PAH-associated genes. Subsequently, an …
Read PDF<h4>Background</h4>Chronic kidney disease (CKD) is a serious global health problem with increasing incidence. Ferroptosis plays a crucial role in kidney diseases, but limited studies have elucidated the mechanism and role of ferroptosis in CKD.<h4>Methods</h4>CKD data …
Read PDF<h4>Objective</h4>To systematically review the pleiotropic roles of Cathepsin K (CTSK) beyond classical bone resorption, elucidating its critical function in regulating extracellular matrix (ECM) dynamics and epithelial-mesenchymal transition (EMT) across diverse pathological systems.<h4>Methods</h4>A comprehensive analysis was …
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