Computational Methods for Synthetic and Systems Biology

last updated 2021/02/15

Flux Balance Analysis

Flux balance analysis is a mathematical approach for analyzing the flow of metabolites through a metabolic network. It is based on the assumption that the metabolic network is in a steady state, meaning that the concentration of metabolites does not change over time. The goal of flux balance analysis is to find the optimal flux distribution that maximizes or minimizes a specific objective function, such as biomass production or energy generation.

The COBRA Toolbox: Computational framework for exploring genome-scale metabolic networks (Schellenberger et al. 2011, Nature Protocols) [paper] [github].

Genome-scale Metabolic Models (GEMs)

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models”

Publications

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models (Zachary et al. 2016, Nucleic Acids Research) [paper] [homepage]

Gene Expression

Matrix factorization recovers consistent regulatory signals from disparate datasets (BioArxiv, 2020) [paper]

• Task:
• Data: integrated from five transcriptomics datasets:
  • modulonsRNAseq-1 (PRECISE) [paper] [github]
• Method: Independent Component Analysis (ICA)

Boolean modelling reveals new regulatory connections between transcription factors orchestrating the development of the ventral spinal cord [paper]

• Method: boolean network model
• Evaluation: tested by comparing simulation results with time series observations