cMonkey detects putative co-regulated gene groupings by integrating the biclustering of gene expression data and various functional associations with the de novo detection of sequence motifs.
This is the Python implementation of the cMonkey algorithm based on the original R implementation by David J. Reiss, Institute for Systems Biology.
EGRIN 2.0 is a systems-level model that delineates the complex relationship between environment, gene regulation, and phenotype in prokaryotes
We developed the SYstems Genetic Network AnaLysis (SYGNAL) pipeline to integrate correlative, causal and mechanistic inference approaches into a unified framework that systematically infers the causal flow of information from mutations to TFs and miRNAs to perturbed gene expression patterns across patients.
MTB Portal serves as a portal for computational modeling program to generate an integrated, predictive gene regulatory network model of host/pathogen interactions.