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Low back pain caused by intervertebral disc degeneration (IVDD), a common orthopedic disease in middle-aged and elderly populations, burdens patients' quality of life and work capacity. IVDD is closely associated with nucleus pulposus cell apoptosis …
Read PDF<h4>Background</h4>Esophageal squamous cell carcinoma (ESCC) is a highly aggressive cancer with a poor prognosis, and its molecular mechanisms remain unclear. Our previous research identified the signal sequence receptor subunit delta (SSR4) of the TRAP complex …
Read PDFThe field of causal discovery has advanced considerably over the past three decades, in terms of perspectives, computational methods, and foundational concepts. Nevertheless, their application to biological systems that are commonly found in nature (i.e. …
Read PDFOrganisations are challenged when meeting the computational requirements of large-scale bioinformatics analyses using their own resources. Cloud computing has democratised large-scale resources, and to reduce the barriers of working with large-scale compute, leading cloud vendors …
Read PDF<h4>Background</h4>Pathological upstaging (PU) of clear cell renal cell carcinoma (ccRCC) from clinical cT1 to pT3 stage often requires conversion from partial to radical nephrectomy. Preoperative PU prediction lacks objective, precise methods, hindering surgical decision-making.<h4>Methods</h4>We developed …
Read PDF<h4>Background</h4>The Myelin Basic Protein (MBP) gene is essential for myelin sheath formation in the central nervous system. Coding and noncoding single-nucleotide polymorphisms (SNPs) can impair the protein structure and function, contributing to demyelinating diseases exemplified …
Read PDF<h4>Motivation</h4>Protein language models (PLMs) have emerged as pivotal tools for protein representation, enabling significant advances in structure-function prediction and computational biology. However, current PLMs predominantly rely on fine-grained amino acid sequences as input, treating individual …
Read PDFMajor depressive disorder (MDD) is a highly prevalent and debilitating condition in patients undergoing long-term hemodialysis (HD), severely impairing quality of life and imposing a substantial economic burden. Despite the clinical significance of this frequent …
Read PDFBACKGROUND: QStrain is an integrated resource platform designed to facilitate viral genome analysis and the rational design of nucleic acid therapeutics. RESULTS: The system integrates reference-guided multiple sequence alignment of high-risk viral pathogens, including Severe …
Read PDF<h4>Purpose</h4>To investigate the complement-modulating mechanisms of Ginkgo biloba extract (EGb 761) in dry age-related macular degeneration (dry AMD) through an integrative approach combining bioinformatics, molecular docking, and molecular dynamics (MD) simulations.<h4>Methods</h4>Bioinformatics analysis was used to …
Read PDF<h4>Background</h4>Endometriosis (EMs) is a chronic inflammatory disease characterized by ectopic endometrial growth. This study aimed to identify and analyze potential signatures of pyroptosis-related genes in EMs.<h4>Methods</h4>We conducted a comprehensive bioinformatics analysis using transcriptomic datasets from …
Read PDF<h4>Motivation</h4>Biocuration is the integration of biological information databases for the enhancement of research. Curation of these databases is challenged by the exponential growth of scientific data and literature. Integration of machine learning and artificial intelligence …
Read PDF<h4>Motivation</h4>Cell-cell interactions (CCIs) are fundamental to multicellular organisms and play crucial roles in diverse biological processes and disease mechanisms. Understanding CCIs is vital for deciphering disease pathogenesis and developing therapeutic strategies. Although numerous computational methods …
Read PDF<h4>Motivations</h4>Electroencephalography (EEG) is a non-invasive method that records brain electrical activity from scalp electrodes, offering millisecond temporal resolution but limited spatial detail due to sparse sensor layouts.<h4>Results</h4>We present DiBiMa-EEGSR, a bidirectional Mamba-2 diffusion framework for …
Read PDF<h4>Motivation</h4>Recombinant protein expression can be a limiting step in the production of protein reagents for drug discovery and other biotechnology applications. We introduce RP3Net (Recombinant Protein Production Prediction Network), an AI model of small-scale heterologous …
Read PDF<h4>Summary</h4>We present Alignoth, a lightweight command line application that generates self-contained portable HTML reports of DNA sequencing read alignment pileups and additionally supports export to static formats such as PNG, SVG, and PDF as well …
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