Software and Datasets

INDIGO

INDIGO

 INDIGO (INferring Drug Interactions using chemoGenomics and Orthology) algorithm predicts how antibiotics prescribed in combinations will inhibit bacterial growth. INDIGO leverages genomics and drug-interaction data in the model organism – E. coli, to facilitate the discovery of effective combination therapies in less-studied pathogens, such as M. tuberculosis. [Download INDIGO algorithm]  (Ref: Chandrasekaran et al. Molecular Systems Biology 2016)

PROM

PROM (Probabilistic Regulation of Metabolism) enables the quantitative integration of regulatory and metabolic networks to build genome-scale integrated metabolic–regulatory models [Download PROM models for E. coli and Mycobacterium tuberculosis; latest version of the PROM algorithm]   (Ref: Chandrasekaran and Price, PNAS 2010)

GEMINI

GEMINI (Gene Expression and Metabolism Integrated for Network Inference) directly connects regulatory interactions to observable phenotypes and allows rapid assessment of inferred regulatory interactions using a metabolic network [GEMINI algorithm implementation and Data (Ref: Chandrasekaran and Price, Plos Computational Biology 2013) [GEMINI tutorial data]

ASTRIX

ASTRIX

ASTRIX (Analyzing Subsets of Transcriptional Regulators Influencing eXpression) uses gene expression data to identify regulatory interactions between transcription factors and their target genes. Ref: Chandrasekaran et al, PNAS, 2011. [Download ASTRIX algorithm and example data]