sriram-lab / egem

epigenome scale metabolic modeling for cancer metabolism

MIT License

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cancer-metabolism drug-sensitivity epigenomics genome-scale-modeling histone-acetylation histone-ptms metabolic-models metabolic-reconstruction

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epiGenome-Scale Metabolic Modeling and Reconstruction Analysis

Summary

This repository contains data and analyses from contraint-based modeling of the metabolic effects on histone post-translational modifications

Installation

The code for this is stored under lib/matlab.

Description:

constrain_flux_regulation.m: A function that uses transcriptomics data to generate context-specific metabolic fluxes and models.
MATLAB_CODE.m: The MATLAB code used to generate all the analysis in Shen et al., 2019
supplementary_software_code.mat: The data used to generate all of the analysis.

References

Please cite

Shen, F., Boccuto, L., Pauly, R., Srikanth, S., & Chandrasekaran, S. (2019). Genome-scale network model of metabolism and histone acetylation reveals metabolic dependencies of histone deacetylase inhibitors. Genome biology, 20(1), 1-15.
Chandrasekaran, Sriram. "Tying Metabolic Branches With Histone Tails Using Systems Biology." Epigenetics insights 12 (2019)