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Artificial intelligence (AI)-driven graduate education and research in pharmacology and pharmaceutical sciences (AIPPS) aims to address the rapidly-growing role of AI and machine learning (ML) applications in biomedical sciences. This review provides perspectives on why …
Read PDFBACKGROUND: Accurate prediction of protein complex structures remains a significant challenge, particularly when stoichiometry information is unavailable. In the recent Critical Assessment of Structure Prediction Round XVI (CASP16), the “Phase 0” challenge was introduced to …
Read PDFThis study aimed to elucidate the core therapeutic targets and mechanisms of action of rosehip extract (FRLE) in IgA nephropathy (IgAN) by integrating bioinformatics, machine learning, and computational simulation techniques to simultaneously analyze the therapeutic …
Read PDFBACKGROUND: Continuous traits evolution of a group of taxa that are correlated through a phylogenetic tree is commonly modelled using parametric stochastic differential equations to represent deterministic change of traits through time, while incorporating noises …
Read PDF<h4>Summary</h4>Recent advances in long-read sequencing and genome assembly techniques have enabled the generation of high-quality assemblies, often comprising megabase-scale sequences that span entire chromosomes. This results in longer but fewer sequences per genome, which affects …
Read PDFThis response addresses the comments raised by Dr. Epain and colleagues in their Letter to the Editor titled 'On using clustering statistics for assessing plasmid binning tools accuracy' in response to our paper 'Circling in …
Read PDF<h4>Motivation</h4>DNA damage response (DDR) is essential for maintaining genome stability and preventing tumorigenesis. While protein-coding DDR genes have been extensively investigated, long non-coding RNAs (lncRNAs) remain relatively understudied despite the growing evidence of their involvement …
Read PDF<h4>Motivation</h4>Protein-protein interactions (PPIs) are central to cellular functions, and predicting mutation-induced changes in binding affinity (ΔΔG) remains challenging. Although existing computational methods integrate sequence- and structure-derived features and thus implicitly capture certain sequence-structure relationships, they …
Read PDFAntimicrobial resistance in <i>Escherichia coli (E. coli</i>) is a major public health concern globally, driven by increased resistance to commonly used antimicrobial agents such as β-lactams and fluoroquinolones. The main goal of our research is …
Read PDF<h4>Summary</h4>The biological function of proteins is often driven by "invisible" excited states-transient, low-population conformations that remain undetectable by conventional structural methods. Chemical Exchange Saturation Transfer (CEST) NMR spectroscopy is a powerful technique for characterizing these …
Read PDFUnmapped sequencing reads in livestock often contain valuable information about pathogens but are typically discarded. We analyzed blood-derived DNA and RNA from chickens and pigs kept under high- and low-biosecurity conditions, focusing on unmapped reads. …
Read PDF<h4>Motivation</h4>Accurate prediction of protein function is essential for elucidating molecular mechanisms and advancing biological and therapeutic discovery. Yet experimental annotation lags far behind the rapid growth of protein sequence data. Computational approaches address this gap …
Read PDF<h4>Motivation</h4>Hydrogen/deuterium exchange-mass spectrometry (HX-MS) is a rapidly expanding technique used to investigate protein conformational ensembles. The growing popularity and utility of HX-MS has driven the development of diverse instrumentation and software, resulting in inconsistent, non-standardized …
Read PDF<h4>Motivation</h4>Integrated analysis across biological databases is becoming increasingly important in life science research, leading many public databases to adopt Semantic Web technologies, also known as knowledge graphs. However, biological data possesses inherently complex and diverse …
Read PDF<h4>Background</h4>Childhood asthma (CA), a chronic inflammatory disorder of the airways, and childhood obesity (CO), characterized by low-grade systemic inflammation, frequently coexist. This study seeks to elucidate shared biological mechanisms underlying CA and CO and to …
Read PDFIron-sulfur (Fe-S) clusters are ubiquitous cofactors in metalloproteins, supporting essential biological functions such as electron transfer, enzymatic catalysis, and metabolic regulation. Despite their importance, large-scale identification of Fe-S proteins remains challenging due to limitations of …
Read PDFOsteoporosis (OP) is a chronic systemic skeletal disorder that predominantly affects the elderly. It is characterized by an imbalance in bone homeostasis, reduced bone mass, microarchitectural deterioration of bone tissue, and increased bone fragility, ultimately …
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