The gut microbiome modulates immune and metabolic health. Human microbiome data are
biased toward industrialized populations, limiting our understanding of non-industrialized …

Motivation Gene set enrichment analysis (GSEA) is a commonly used algorithm for
characterizing gene expression changes. However, the currently available tools used to …

Millions of transcriptome samples were generated by the Library of Integrated Network-
based Cellular Signatures (LINCS) program. When these data are processed into …

Integrating gene expression across tissues and cell types is crucial for understanding the
coordinated biological mechanisms that drive disease and characterize homoeostasis …

Breast cancer remains a significant health challenge with complex molecular mechanisms.
While many studies have explored genetic markers in breast carcinogenesis, few have …

Chemical modulation of proteins enables a mechanistic understanding of biology and
represents the foundation of most therapeutics. However, despite decades of research, 80 …

Tissue damage and repair are hallmarks of inflammation. Despite a wealth of information on
the mechanisms that govern tissue damage, mechanistic insight into how inflammation …

Advances in single-cell technology have enabled the measurement of cell-resolved
molecular states across a variety of cell lines and tissues under a plethora of genetic …

To infer the biological meaning from transcriptome data, it is useful to focus on genes that
are regulated by the same regulator, ie, regulons. Unfortunately, current gene set …

Osteosarcoma (OS) mortality stems from lung metastases. Matrix metalloproteinases
(MMPs) facilitate metastatic dissemination by degrading extracellular matrix components …