Abstract Motivation: Experiments such as ChIP-chip, ChIP-seq, ChIP-PET and DamID (the
four methods referred herein as ChIP-X) are used to profile the binding of transcription …

There are many thousands of hereditary diseases in humans, each of which has a specific
combination of phenotypic features, but computational analysis of phenotypic data has been …

In plants, flavonoids are important secondary metabolites that contribute to the nutritional
quality of many foods. Apple is a popular and frequently consumed food because of its high …

Background The purpose of gene set enrichment analysis (GSEA) is to find general trends in
the huge lists of genes or proteins generated by many functional genomics techniques and …

The interpretation of data-driven experiments in genomics often involves a search for
biological categories that are enriched for the responder genes identified by the …

Motivation: Controlled vocabularies such as the Medical Subject Headings (MeSH)
thesaurus and the Gene Ontology (GO) provide an efficient way of accessing and organizing …

Parts-based representations, such as non-negative matrix factorization and topic modeling,
have been used to identify structure from single-cell sequencing data sets, in particular …

According to the World Health Organization (WHO), gastric cancer (GC) is the fourth leading
cause of tumor-related mortality globally and one of the most prevalent malignant tumors. To …

A goal of genomics is to understand the relationships between biological processes.
Pathways contribute to functional interplay within biological processes through complex but …

In high-throughput studies of diseases, terms enriched with disease-related genes based on
Gene Ontology (GO) are routinely found. However, most current algorithms used to find …