Systems Biology at University of Michigan

egem

epigenome scale metabolic modeling for cancer metabolism

emt-cobra

Modeling the metabolic changes during the epithelial-to-mesenchymal transition.

metabolicmodeling

Constraint-based metabolic modeling software from the Chandrasekaran Lab

bme499

BME499 course materials

CARAMeL

Condition-specific Antibiotic Regimen Assessment using Mechanistic Learning

dfa

Fitting time-course metabolomics onto genome-scale metabolic models for inferring metabolic activity.

INDIGOpy

Implementation of INDIGO (INferring Drug Interactions using chemoGenomics and Orthology) as a Python package.

MAGENTA

Metabolism And GENomics-based Tailoring of Antibiotic regimens: predicts the impact of pathogen environment on antibiotic potency based on chemogenomic data.

MetOncoFit

Common biochemical and topological attributes of metabolic genes recurrently dysregulated in tumors.

astrix

Using gene expression data to identify regulatory interactions between transcription factors and target genes.

gemini

Integrating the transcriptional regulatory network with genome-scale metabolic models.

github-tutorials

Another version control resource and tutorial repo

met-ptm-drug-cancer

Machine learning to learn metabolite-histone-drug interactions in cancer.

metoncofit-website

A dashboard for the MetOncoFit tumor models.

single-cell-neutrophil-flux-analysis

Analysis of neutrophil metabolic activity during metastasis using single-cell RNASeq and COnstraint-Based Reconstruction and Analysis.

docker-tutorials

Another tutorial and resource for using docker to launch web applications

quiescence-depth-modulation

Leveraging Metabolic Modeling and Machine Learning to Uncover Modulators of Quiescence Depth

SCOOTI

TACTIC