Our understanding of gene expression has changed dramatically over the past decade,
largely catalysed by technological developments. High-throughput experiments …

Transcription factors (TFs) regulate the expression of genes at the transcriptional level.
Modification of TF activity dynamically alters the transcriptome, which leads to metabolic and …

Motivation: Well-annotated gene sets representing the universe of the biological processes
are critical for meaningful and insightful interpretation of large-scale genomic data. The …

Motivation: The continued progress in develo** technological platforms, availability of
many published experimental datasets, as well as different statistical methods to analyze …

Genomic experiments produce multiple views of biological systems, among them are DNA
sequence and copy number variation, and mRNA and protein abundance. Understanding …

Inferring potential drug indications, for either novel or approved drugs, is a key step in drug
development. Previous computational methods in this domain have focused on either drug …

A decade ago, the Gene Expression Omnibus (GEO) database was established at the
National Center for Biotechnology Information (NCBI). The original objective of GEO was to …

Research in several fields now requires the analysis of datasets in which multiple high-
dimensional types of data are available for a common set of objects. In particular, The …

Reprogramming of cellular metabolism is an emerging hallmark of neoplastic
transformation. However, it is not known how the expression of metabolic genes in tumors …

Motivation: Describing biological sample variables with ontologies is complex due to the
cross-domain nature of experiments. Ontologies provide annotation solutions; however, for …