CyPathia

CyPathia implements genome-scale mechanistic modeling to link genotype measurements such as transcriptomics and genomics to cellular phenotypes and to analyze effects on cell signaling pathways using the Hipathia Bioconductor package.

Key Features:

• Genome-scale mechanistic models: Implements genome-scale mechanistic models that connect molecular measurements to cellular behavior.
• Interpretable predictors: Constructs interpretable predictors that explain how genetic-level changes translate into cellular functions.
• Perturbation analysis: Estimates the effects of perturbations, including drug interventions and environmental changes, on signaling pathways.
• Mutation impact assessment: Assesses the impact of mutations within complex biological scenarios to infer consequences for cellular processes.
• Hipathia integration: Leverages the Hipathia Bioconductor package to perform mechanistic pathway activity computations.

Scientific Applications:

• Cell signaling analysis: Interprets activity and modulation of cell signaling pathways from molecular data.
• Transcriptomic and genomic interpretation: Maps transcriptomics and genomics measurements to phenotypic behavior for dataset interpretation.
• Drug discovery and intervention prediction: Predicts the effects of interventions on pathway activity to inform drug discovery hypotheses.
• Personalized medicine and mutation analysis: Evaluates mutation impacts to support investigations in personalized medicine.

Methodology:

Implements genome-scale mechanistic models and interpretable predictor construction via the Hipathia Bioconductor package to link transcriptomics and genomics measurements to phenotypic behavior and to perform perturbation analysis and mutation impact assessment.