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<h4>Motivation</h4>The rational design of chemical compounds that bind to a desired protein target molecule is a major goal of drug discovery. Most current molecular docking but also fragment-based buildup or machine learning-based generative drug design …
Read PDF<h4>Motivation</h4>Advances in hardware have made molecular dynamics (MD) simulations of protein structures faster and more accessible to the scientific community. However, accurately estimating protein flexibility using MD remains computationally demanding, especially for large systems and …
Read PDFSequence-based typing is critical for microbial genomics, yet existing tools are often developed in isolation, leading to duplicated effort, inconsistent formats, and limited community participation. To address this, we developed camlhmp (https://github.com/rpetit3/camlhmp), a framework for …
Read PDF<h4>Introduction</h4>Thyroid cancer, the most prevalent endocrine malignancy globally, poses challenges owing to the limited understanding of its molecular drivers. Previous research has highlighted collagen genes, such as COL13A1 and COL23A1, as key players in thyroid …
Read PDFBridging the gap between learning algorithms and biological interpretation remains the central challenge of bioinformatics education. To move students beyond just learning code and acquire higher-order knowledge, educators face a complexity overload when attempting to …
Read PDF[This corrects the article DOI: 10.3389/fmed.2025.1427136.].
Read PDF<h4>Summary</h4>We propose a new algorithm, "interval hashing," which distinguishes identical k-mers arising from different repeat sequences, particularly in complex repeat arrays such as alpha satellite HORs. We implement this algorithm as a fork of minimap2, …
Read PDF<h4>Motivation</h4>Enrichment analysis across multiple databases often results in a high level of redundancy due to overlapping terms, complicating the interpretation of biological data. To address this, we developed SummArIzeR, an R package to cluster and …
Read PDF<h4>Motivation</h4>Chromosomal abnormalities, referred to as aneuploidies, occur in approximately 0.3% of live births. While the majority of aneuploidies in humans are incompatible with life, well-characterized exceptions include Down syndrome (47,+21), Patau syndrome (47,+13), Edwards syndrome …
Read PDFBACKGROUND: Familial hypercholesterolemia (FH) is a genetic disorder characterized by imbalances in lipid metabolism, markedly increasing cardiovascular risk. Identifying lipid metabolism-related biomarkers is essential for understanding FH pathogenesis and developing therapeutic strategies. METHODS: A comprehensive …
Read PDF<h4>Motivation</h4>Predicting the impact of missense mutations on protein structure and function is a fundamental challenge for cancer research and clinical applications. Despite all the computational advances and, more recently, the use of artificial intelligence (AI), …
Read PDF<h4>Motivation</h4>Predicting synergistic drug combinations for cancer therapies is vital but challenged by interaction complexity and vast combinatorial possibilities. To address this, we propose a novel ranking-based approach for drug synergy prediction. Our method builds upon …
Read PDF<h4>Motivation</h4>Traditional genome-wide association studies (GWAS) aim to uncover the genetic variants associated with a single phenotype of interest (typically a disease), and to elucidate its genotypic architecture. However, many of today's GWAS simultaneously measure multiple …
Read PDFBioinformatics is entering a new phase characterized by the integration of universal biological models and multi-agent systems to enable end-to-end scientific discoveries. This review argues that the next paradigm shift will go beyond traditional predictive …
Read PDFBACKGROUND: This study investigated the potential of endothelial progenitor cells (EPCs) as biomarkers for lung adenocarcinoma. METHODS: Blood samples were collected from 34 lung adenocarcinoma patients and 8 healthy controls at the Department of Tumor …
Read PDFEmerging evidence has implicated non-SMC condensin I complex subunit H (NCAPH) as a key regulator of mitosis and driver of tumorigenesis. However, its expression profiling and clinical relevance in endometrial cancer (EC) remain inadequately characterized. …
Read PDFObesity and metabolic dysfunction associated steatotic liver disease (MASLD) are interrelated metabolic disorders characterized by chronic inflammation, insulin resistance, and dyslipidemia. While both conditions are well recognized clinically, the molecular mechanisms underlying their frequent coexistence …
Read PDF<h4>Motivation</h4>The exponential growth of academic literature has presented unprecedented opportunities. However, it also underscores the need for advanced search methodologies to support efficient knowledge discovery. While effective for structured queries, traditional keyword-based search engines often …
Read PDF<h4>Purpose</h4>This study aimed to identify the academic stress experienced by medical students in basic medical science courses and analyze its underlying factors.<h4>Methods</h4>A survey was conducted among 228 students from a medical school in Seoul, South …
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