UNLABELLED: Gene prioritization refers to a family of computational techniques for inferring disease genes through a set of training genes and carefully chosen similarity criteria. Test genes are scored based on their average similarity to the traini...
SUMMARY: Disease ontology (DO) annotates human genes in the context of disease. DO is important annotation in translating molecular findings from high-throughput data to clinical relevance. DOSE is an R package providing semantic similarity computati...
As the amount of genome information increases rapidly, there is a correspondingly greater need for methods that provide accurate and automated annotation of gene function. For example, many high-throughput technologies--e.g., next-generation sequenci...
This paper considers microarray gene expression data clustering using a novel two stage meta-heuristic algorithm based on the concept of α-planes in general type-2 fuzzy sets. The main aim of this research is to present a powerful data clustering app...
Statistical methods in medical research
Oct 14, 2012
Since its first publication in 2003, the Gene Set Enrichment Analysis method, based on the Kolmogorov-Smirnov statistic, has been heavily used, modified, and also questioned. Recently a simplified approach using a one-sample t-test score to assess en...
SUMMARY: Currently available and frequently used tools for annotating antibiotic resistance genes (ARGs) in genomes and metagenomes provide results using inconsistent nomenclature. This makes the comparison of different ARG annotation outputs challen...
Database : the journal of biological databases and curation
Mar 21, 2025
Ontologies are widely used in databases to standardize data, improving data quality, integration, and ease of comparison. Within ontologies tailored to diverse use cases, post-composing user-defined terms reconciles the demands for standardization on...
Accurate prediction of pathogenic variants in human disease-associated genes would have a profound effect on clinical decision-making; however, it remains a significant challenge due to the overwhelming number of these variants. We propose graph neur...
The rapid advancement of next-generation sequencing (NGS) technology and the expanding availability of NGS datasets have led to a significant surge in biomedical research. To better understand the molecular processes, underlying cancer and to support...
MOTIVATION: Enabling clinicians and researchers to directly interact with global genomic data resources by removing technological barriers is vital for medical genomics. AskBeacon enables large language models (LLMs) to be applied to securely shared ...