Ruth Isserlin

The paper identifies four epithelial transcription states in pancreatic cancer and links their origins to early developmental processes.

The paper shows cell cycle duration influences gene expression and cell fate by acting as a transcriptional filter, supported by simulations and single-cell RNA-seq data.

RCy3 provides R access to Cytoscape's network biology tools, enabling reproducible workflows through automation and integration with existing packages.

This study uses single-cell transcriptomics to analyze aged mouse brains, identifying cell-type-specific aging signatures and highlighting molecular processes like ribosomal biogenesis.

netDx is a supervised patient classification framework that integrates diverse data types and provides interpretable results, showing high performance in cancer survival prediction.

Step-by-step protocol for interpreting omics gene lists via g:Profiler or GSEA enrichment testing, then grouping redundant enriched pathways into themes with Cytoscape Enrichment Map.

This paper introduces DNF, a computational framework that classifies new drugs by integrating structural, perturbation, and sensitivity data to infer drug relationships and taxonomies.