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<h4>Motivation</h4>Unique molecular identifiers (UMIs) are widely used in next-generation sequencing to enable accurate molecular counting and error correction. However, challenges remain in accurately collapsing UMI clusters, especially when read counts are low or sparse read …
Read PDFBioinformatics is a key part of modern biomedical research that helps scientists understand complex biological systems with great accuracy [...].
Read PDFThis study aims to reveal drug targets for sepsis: an association study integrating Mendelian randomization (MR), expression quantitative trait loci, protein quantitative trait loci, and protein-protein interaction networks. We identified 43 druggable proteins associated with …
Read PDF<h4>Summary</h4>Uniparental disomies (UPDs) are copy-neutral chromosomal alterations that occur when both copies of a chromosome pair (entire or segmental) come from one parent. UPDs, including isodisomies (identical parental chromosome) and heterodisomies (two different homologs from …
Read PDFAcute pancreatitis (AP) is a common and rapidly progressing disease of the digestive system. The occurrence of coagulation dysfunction is closely related to the severity of AP. Therefore, this study aims to explore the correlation …
Read PDFMalignant melanoma is an aggressive skin cancer with increasing incidence and poor prognosis after metastasis. Identifying key molecular drivers of melanoma progression is critical for developing novel therapeutic strategies. Therefore, in the present study, differential …
Read PDF<h4>Motivation</h4>Understanding chemical reactions requires bridging fine-grained molecular edits with broader semantic context. Reaction mechanisms are determined not only by local atom-bond transformations but also by the global reaction class. However, most existing approaches treat these …
Read PDFIn recent years, artificial intelligence (AI) has increasingly influenced daily life and scientific research. Traditionally, AI-related courses have targeted computer science majors, while systematic instructional opportunities for early-stage undergraduates from non-computing backgrounds remain limited. To …
Read PDFWe discuss the drawbacks of using homogeneity and completeness, statistics defined for the evaluation of clustering accuracy, for evaluating plasmid binning tools accuracy, motivated by the recently published paper "Circling in on plasmids: benchmarking plasmid …
Read PDF<h4>Motivation</h4>Genome-scale metabolic network (GSMN) models enable flux-based metabolite fate discovery, metabolic engineering, drug target identification, and multi-omics integration. However, programming requirements, architectural complexity, and limited visualization support impede its adoption by the broader scientific community. …
Read PDF<h4>Motivation</h4>Spatial omics data provides unprecedented insights into disease biology, yet its complexity introduces significant challenges in data analysis. Comprehensive analysis requires frameworks that integrate diverse modalities and enable joint processing of multiple datasets and corresponding …
Read PDF<h4>Background and aim</h4>COPD is a common respiratory disease characterized by progressive airflow restriction that severely affects patients' quality of life and leads to significant mortality rates worldwide. This study aims to strengthen the early diagnosis …
Read PDFIQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelihood. Here, we present IQ-TREE version 3, the third major release of the software. IQ-TREE 3 significantly extends version …
Read PDF<h4>Motivation</h4>The increasing prevalence of antibiotic-resistant bacteria has intensified the demand for novel antimicrobial agents. Antimicrobial peptides (AMPs) have emerged as promising alternatives, yet their identification or classification remains challenging due to the lack of multi-perspective …
Read PDF<h4>Motivation</h4>Epistasis, or genetic interaction, plays a crucial role in shaping complex traits and has been increasingly recognized for its widespread influence in genetic architectures. While epistasis detection has been extensively evaluated in case-control studies, its …
Read PDFMetabarcoding of environmental and ancient environmental DNA (eDNA and sedaDNA) is a powerful approach for studying and monitoring marine communities. However, its effectiveness is limited by the availability of comprehensive and well-curated reference databases, particularly …
Read PDF<h4>Purpose</h4>In this study, we evaluated 90 bioinformatics pipelines using RNA-Seq datasets from Rats, Zebrafish and Mice. The analysis was conducted in the context of weak signals, including exposure to metallic particles (tungsten), low-dose radiation or …
Read PDFModern sequencing and high-throughput profiling technologies [...].
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