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<h4>Objective</h4>Genome-wide association studies have identified shared genetic risk loci between schizophrenia (SCZ) and multiple sclerosis (MS), suggesting overlapping biological mechanisms despite distinct clinical presentations. Here, we aimed to characterize the biological plausibility of <i>KIF21B</i> as …
Read PDF<h4>Background</h4>Osteoarthritis has become a global health challenge due to its complex pathologic mechanisms. Spliceosome-associated factor 2 (SYF2) has been reported in tumors and neurological diseases, but not in studies of osteoarthritis. We employed single-cell sequencing …
Read PDFEarly detection of melanoma is essential for improving patient outcomes. This research aimed to identify upregulated gene expression in peripheral blood mononuclear cells (PBMCs) induced by secretory factors derived from melanoma cells. These gene alterations …
Read PDFNonobstructive azoospermia (NOA) is one of the most severe types of male infertility. Amino acid metabolism (AAM) is strongly associated with various diseases. This study intended to identify biomarkers related to AAM in NOA. Biomarkers …
Read PDF<h4>Motivation</h4>Accurate cancer subtyping is critically important for cancer treatment due to significant molecular heterogeneity. While existing methods with multi-omics integration have achieved some success in cancer subtype identification by leveraging the rich information provided by …
Read PDFLarge language models (LLMs) have recently been adopted to assist in the interpretation of human genomic variants. However, general-purpose LLMs can produce incorrect outputs (commonly termed 'hallucinations'), particularly on specialized queries, raising concerns about their …
Read PDF<h4>Motivation</h4>Malaria, caused by Plasmodium parasites, imposes a significant public health burden. While Plasmodium falciparum remains the primary target of elimination strategies due to its high mortality rate, lesser-known species such as P. malariae, P. vivax, …
Read PDF<h4>Background</h4>Neighborhood characteristics can affect aging and health. We tested the effects of neighborhood deprivation on deficit accumulation frailty scores in a prospective cohort of breast cancer survivors vs control individuals aged 60 to 98 years.<h4>Methods</h4>Newly …
Read PDF<h4>Motivation</h4>Gene expression plays a crucial role in cell function, and enhancers can regulate gene expression precisely. Therefore, accurate prediction of enhancers is particularly critical. However, existing prediction methods have low accuracy or rely on fixed …
Read PDF<h4>Motivation</h4>Predicting linear B-cell epitopes remains a major challenge in immunoinformatics, particularly for rapidly evolving viruses such as Influenza A. Many existing predictors rely on heterogeneous training datasets, poorly defined negative samples, or low-interpretability models, which …
Read PDFThe COVID-19 pandemic revealed critical gaps in preparedness and response capacities globally. These gaps were evident in the Middle East and North Africa (MENA) region, as the region faces unique challenges due to ongoing humanitarian …
Read PDF<h4>Summary</h4>The Random Circuit Perturbation (RACIPE) algorithm enables the exploration of the dynamical behaviors of gene regulatory circuits (GRCs) by simulating an ensemble of differential equation models via randomization of kinetic parameters. Here, we release sRACIPE …
Read PDFLarge-scale artificial intelligence (AI) models can mine potential patterns from massive amounts of data and provide more accurate analyses. This capability has enabled its gradual application in various areas of bioinformatics. However, few reviews have …
Read PDF<h4>Motivation</h4>MicroRNAs (miRNAs) are small non-coding RNAs, typically 18-24 nucleotides in length, that play a pivotal role in RNA silencing and the post-transcriptional regulation of gene expression by targeting messenger RNAs (mRNAs). Dysregulation of these miRNAs …
Read PDF<h4>Motivation</h4>Substitution matrices like BLOSUM62 model the likelihood of replacement of amino acids in evolution. Substitution matrices are used in protein sequence alignment tasks. Since the introduction of BLOSUM62 over three decades ago, many matrices have …
Read PDF<h4>Motivation</h4>Large language models (LLMs) are rapidly becoming indispensable across the life‑sciences spectrum, from literature mining through clinical decision support to experimental design. Yet, in single‑cell RNA‑sequencing (scRNA‑seq) analysis, most LLM‑enabled tools remain opaque: they output …
Read PDF<b>Background:</b> The coronary no-reflow phenomenon remains a major obstacle to optimal outcomes after primary percutaneous coronary intervention. Its mechanisms are multifactorial and not fully clarified, with genetic components increasingly recognized as important contributors. This study …
Read PDF<h4>Motivation</h4>Minimal residual disease (MRD) assessment has become a powerful tool in modern cancer management, offering early, actionable insights across diverse malignancies and often anticipating clinical events traditionally used to gauge therapeutic response. Beyond quantifying residual …
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