MOTIVATION: Ontologies contain formal and structured information about a domain and are widely used in bioinformatics for annotation and integration of data. Several methods use ontologies to provide background knowledge in machine learning tasks, wh...
Mathematical biosciences and engineering : MBE
37161227
OBJECTIVE: Quantification of disease-disease association (DDA) enables the understanding of disease relationships for discovering disease progression and finding comorbidity. For effective DDA strength calculation, there is a need to address the main...
MOTIVATION: The rapid accumulation of high-throughput sequence data demands the development of effective and efficient data-driven computational methods to functionally annotate proteins. However, most current approaches used for functional annotatio...
Journal of cellular and molecular medicine
37494129
Ulcerative colitis (UC) is one of the high-risk pathogenic factors for colorectal cancer (CRC). However, the shared gene and signalling mechanisms between UC and CRC remain unclear. The goal of this study was to delve more into the probable causal re...
Recently, there has been a growing interest in the development of pharmacological interventions targeting ageing, as well as in the use of machine learning for analysing ageing-related data. In this work, we use machine learning methods to analyse da...
MOTIVATION: The number and size of computational models in biology have drastically increased over the past years and continue to grow. Modeled networks are becoming more complex, and reconstructing them from the beginning in an exchangeable and repr...
As applications of the gene ontology (GO) increase rapidly in the biomedical field, quality auditing of it is becoming more and more important. Existing auditing methods are mostly based on rules, observed patterns or hypotheses. In this study, we pr...
BACKGROUND: Although Deep Neural Networks (DDNs) have been successful in predicting the efficacy of cancer drugs, the lack of explainability in their decision-making process is a significant challenge. Previous research proposed mimicking the Gene On...
Protein function annotation is one of the most important research topics for revealing the essence of life at molecular level in the post-genome era. Current research shows that integrating multisource data can effectively improve the performance of ...
Single-cell RNA-sequencing (scRNA-seq) allows for obtaining genomic and transcriptomic profiles of individual cells. That data make it possible to characterize tissues at the cell level. In this context, one of the main analyses exploiting scRNA-seq ...