Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide
experiments. Here we present a significant update to one of the tools in this domain called …

Profiling samples from patients, tissues, and cells with genomics, transcriptomics, epigenomics,
proteomics, and metabolomics ultimately produces lists of genes and proteins that need …

The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common
Fund program that catalogs how human cells globally respond to chemical, genetic, and …

We developed a model of 545 components (nodes) and 1259 interactions representing
signaling pathways and cellular machines in the hippocampal CA1 neuron. Using graph theory …

Gene expression data are accumulating exponentially in public repositories. Reanalysis and
integration of themed collections from these studies may provide new insights, but requires …

The Library of Integrated Network-based Cellular Signatures (LINCS) program is a national
consortium funded by the NIH to generate a diverse and extensive reference library of cell-…

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

Jupyter Notebooks have transformed the communication of data analysis pipelines by
facilitating a modular structure that brings together code, markdown text, and interactive …

The global relationship between drugs that are approved for therapeutic use and the human
genome is not known. We employed graph‐theory methods to analyze the Federal Food …

Connectivity mapping resources consist of signatures representing changes in cellular state
following systematic small-molecule, disease, gene, or other form of perturbations. Such …