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We thank MD Kazim Okan Dolu for their interest in our published work and for the opportunity to clarify several points regarding software versioning, benchmark independence, secondary-structure generation, binding-free-energy terminology, and negative-control design. We acknowledge …
Read PDFMetaNetX (https://www.metanetx.org/) is a comprehensive resource for the reconciliation and integration of metabolic information across diverse biochemical databases. The 2025 update significantly enhances chemical and reaction coverage, incorporating new data and refining chemical structure computation …
Read PDF<h4>Motivation</h4>Enzymes are proteins that catalyze specific biochemical reactions in cells. Enzyme Commission (EC) numbers are used to annotate enzymes in a four-level hierarchy that classifies enzymes based on the specific chemical reactions they catalyze. Accurate …
Read PDF<h4>Motivation</h4>Nanopores are cutting-edge interdisciplinary tools that can analyze biomolecules at the single-molecule level for many applications, e.g. DNA sequencing. Efforts are underway to extend nanopores to proteomics, including the development of machine learning algorithms for …
Read PDFCancer remains a major global health challenge, with substantial morbidity and mortality worldwide. Advances in genomic and proteomic biomarker discovery have transformed cancer diagnosis, prognosis, and treatment selection. The evolution from early serological markers such …
Read PDF<b>Background/Objectives</b>: Mitochondrial DNA (mtDNA) is an important resource for understanding human ancestry, population diversity, and the molecular mechanisms of mitochondrial diseases. However, analyzing mtDNA thoroughly often requires advanced bioinformatics skills and command-line knowledge. To address …
Read PDF<h4>Motivation</h4>Interactions among long noncoding RNAs, circular RNAs, microRNAs, and messenger RNAs form complex gene expression regulatory networks, which are of great significance for the diagnosis, prevention, and treatment of complex diseases. Although existing computational methods …
Read PDFThe aim of the present study was to thoroughly examine the mechanism of action underlying the therapeutic efficacy of <i>Psoralea corylifolia</i> in the management of vitiligo, using a comprehensive approach integrating bioinformatics prediction with empirical …
Read PDFThis paper offers a methodological critique of the study by AlShurman et al. that examined whether COVID-19 vaccine hesitancy (VH) and COVID-19-related factors interact to influence booster dose uptake among university students in Canada from …
Read PDFStanford type A aortic dissection (TAAD) is a life-threatening cardiovascular condition associated with high mortality. Ferroptosis has been implicated in TAAD pathogenesis, but comprehensive analyses and experimental validation of ferroptosis-related driver genes (FRDGs) remain limited. …
Read PDF<h4>Objective and background</h4>Postmenopausal osteoporosis (PMOP) significantly increases the risk of fragility fractures and has substantial negative effects on patients. Accumulating evidence suggests that the pathogenesis of PMOP is associated with ferroptosis. In this study, we …
Read PDF<h4>Background</h4>Quantitative structure-activity relationship (QSAR) models are central to computer-aided drug discovery and predictive toxicology, but practical adoption is often impeded by ad-hoc tooling, inconsistent validation protocols, and poor reproducibility.<h4>Objective</h4>We introduce ProQSAR, a modular, reproducible workbench …
Read PDF<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 PDFOvarian 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 PDFDeveloping 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 PDF<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 …
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