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Large language models (LLMs) are evolving from passive predictors into agentic systems capable of planning, tool-use, and multimodal reasoning. This shift is especially consequential for biology, where complex, noisy, and multi-scale data require adaptive and …
Read PDFUnravelling the genomic blueprint of a reference laboratory strain of the yeast Saccharomyces cerevisiae 30 years ago opened a new era in understanding yeast biology. Since then, genomics has transformed our ability to study, adapt, …
Read PDF<h4>Background/aim</h4>Hepatocellular carcinoma (HCC) is a highly heterogeneous malignancy with poor prognosis due to drug resistance and recurrence. Tumor-associated macrophages (TAMs) are pivotal in the HCC tumor microenvironment, but their prognostic and therapeutic relevance remains incompletely …
Read PDF<h4>Background</h4>Monogenic disorders are a major cause of fetal structural anomalies. Most genetic diagnoses involve de novo, biallelic or X linked variants; however, inherited variants in autosomal dominant disease genes have been detected across multiple studies. …
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Read PDF<h4>Motivation</h4>Protein-protein interactions (PPIs) provide the skeleton for signaling pathways in the cell. Their experimental measurement, however, reveals only the existence of an interaction without any information on its functional roles. A key step in developing …
Read PDFBACKGROUND Acute lung injury (ALI) after liver transplantation (LT) is a critical complication negatively affecting transplant outcomes and patient survival. However, effective biomarkers for early diagnosis remain unidentified. This study aimed to identify hub biomarkers …
Read PDF<h4>Background</h4>Ionizing radiation (IR) induces profound bone marrow (BM) injury by disrupting hematopoietic stem cell (HSC) homeostasis, leading to acute myelosuppression and long-term hematopoietic dysfunction. Although transcriptome-wide analyses have advanced our understanding of radiation responses, the …
Read PDF<h4>Objective</h4>The purpose of this study is to identify hub genes associated with both osteoporosis (OP) and chronic kidney disease (CKD) through bioinformatics analysis, and to explore the potential pathogenetic mechanisms in OP and CKD through …
Read PDFTo date, no effective chelation therapy exists to remove cadmium (Cd) from the kidneys, a condition that increases the risk of cadmium-induced chronic kidney disease among humans. consequently, it is vital to prevent kidney damage …
Read PDF<h4>Motivation</h4>Experimentally generated drug-induced transcriptomic signatures are valuable resources to infer candidate drugs for unseen transcriptomes. The Connectivity Map (CMap) includes over 720 000 compound-induced signatures and has been widely used in drug repurposing. However, the …
Read PDF<h4>Motivation</h4>Longitudinal microbiome studies (LMS) are increasingly common but have analytic challenges including nonindependent data requiring mixed-effects models. Furthermore, large amounts of data motivate exploratory analysis to identify factors related to outcome variables. Although change analysis …
Read PDFWhole-genome sequencing (WGS) has become a valuable tool for bacterial typing and resistome analysis. However, most existing antibiotic resistance databases and bioinformatics tools are not useful for <i>P. aeruginosa</i> resistome profiling as they fail to …
Read PDF<h4>Objectives</h4>Sinonasal inverted papilloma is a locally aggressive epithelial lesion with a relatively high recurrence rate, yet the molecular basis of its proliferative behaviour remains incompletely understood. This study investigated the clinical relevance of secreted phosphoprotein …
Read PDFModern crop varieties may exert reduced influence on their microbiome compared to their progenitors, as plant-microbe interactions were not targeted during breeding. Moreover, formerly beneficial microbiome functions might no longer be relevant in modern agricultural …
Read PDFDespite widespread vaccination, pertussis resurgence persists due to waning immunity and emerging resistant strains in <i>Bordetella pertussis</i>. This study employs a pangenomics-driven reverse vaccinology approach to identify novel vaccine candidates. Analyzing 160 genomes revealed a …
Read PDF<h4>Motivation</h4>Machine-generated or synthetic data is a valuable resource for training artificial intelligence algorithms, evaluating rare workflows, and sharing data under stricter data legislations. However, current statistical and deep learning methods struggle with large data volumes, …
Read PDF<h4>Introduction</h4>Alternative models are tools to replace and reduce the number of animals used in biomedical sciences, for either research or tests of industrial products. Several new alternative models have been developed in the most diverse …
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