It is of considerable interest to detect somatic mutations in paired tumor and normal sequencing data. A number of callers that are based on statistical or machine learning approaches have been developed to detect somatic small variants. However, the...
An interaction between pharmacological agents can trigger unexpected adverse events. Capturing richer and more comprehensive information about drug-drug interactions (DDIs) is one of the key tasks in public health and drug development. Recently, seve...
BACKGROUND: Determining drug-disease associations is an integral part in the process of drug development. However, the identification of drug-disease associations through wet experiments is costly and inefficient. Hence, the development of efficient ...
In order to extract useful information from a huge amount of biological data nowadays, simple and convenient tools are urgently needed for data analysis and modeling. In this paper, an automatic data mining tool, termed as ABCModeller (Automatic Bina...
MOTIVATION: The functional changes of the genes, RNAs and proteins will eventually be reflected in the metabolic level. Increasing number of researchers have researched mechanism, biomarkers and targeted drugs by metabolites. However, compared with o...
DNA/RNA motif mining is the foundation of gene function research. The DNA/RNA motif mining plays an extremely important role in identifying the DNA- or RNA-protein binding site, which helps to understand the mechanism of gene regulation and managemen...
Deep generative models can be trained to represent the joint distribution of data, such as measurements of single nucleotide polymorphisms (SNPs) from several individuals. Subsequently, synthetic observations are obtained by drawing from this distrib...
SUMMARY: Population studies such as genome-wide association study have identified a variety of genomic variants associated with human diseases. To further understand potential mechanisms of disease variants, recent statistical methods associate funct...
BACKGROUND:: In a pandemic situation (e.g., COVID-19), the most important issue is to select patients at risk of high mortality at an early stage and to provide appropriate treatments. However, a few studies applied the model to predict in-hospital m...
MOTIVATION: Mapping distal regulatory elements, such as enhancers, is a cornerstone for elucidating how genetic variations may influence diseases. Previous enhancer-prediction methods have used either unsupervised approaches or supervised methods wit...
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