Course

ChE-411: Principles and applications of systems biology

Lectures in this course (18)

Covers genome-scale model reconstruction, data integration, and metabolic simulation.

Covers the basics of MATLAB and includes an exercise session on metabolic modeling.

Systems Biology: Metabolism Modeling and Analysis

Covers systems biology fundamentals, metabolism modeling, and analysis techniques, emphasizing metabolic flux distributions and omics integration.

Metabolic Flux Balance Analysis

Covers modeling and analyzing complex biological networks, focusing on metabolism and signaling, using techniques like flux balance analysis and kinetic modeling.

Introduction to MATLAB Tools and Installation

Covers the introduction to MATLAB tools and provides installation instructions for Thermodynamics-based Flux Analysis, including pre-requirements like GIT and CPLEX.

MATLAB Tools: Installation and Requirements

Covers the installation of pre-requirements for MATLAB tools and introduces Thermodynamics-based Flux Analysis packages.

Metabolic Fluxes Analysis

Explores metabolic pathways, flux balance analysis, genome-scale models, and underdetermined systems in understanding complex microbiomes.

Metabolic Modeling: FBA and TFA

Introduces Flux Balance Analysis (FBA) and Total Flux Analysis (TFA) in metabolic modeling using MATLAB.

Metabolic Modeling: TFA and Kinetic Models

Explores metabolic modeling using TFA and kinetic models, covering growth simulation, nutrient trade-offs, phenotypic analysis, and metabolomics integration.

Cellular Composition

Explores the composition of a cell, costs of biosynthesis, biosynthetic pathways, flux balance analysis, and gene essentiality.

Bioenergetics: Cellular Energy Generation

Explores cellular energy generation through bioenergetics and metabolic pathways.

Flux Balance Analysis: Optimization and Phenotypic Phase Planes

Explores Flux Balance Analysis principles, optimization, Phenotypic Phase Planes, and bioenergetics in metabolic networks.

Systems Biology: Warburg Effect

Explores the Warburg Effect in cancer cells, discussing metabolic shifts and kinetic model construction.

Metabolic Modeling Exercises

Covers exercises on genome-scale metabolic models, including FBA and TFA analysis, as well as modeling kinetics.

Thermodynamics in Metabolic Pathways

Delves into applying thermodynamics in metabolic pathways, discussing constraints, bi-directional reactions, and estimation methods.

Stochastic Chemical Reactions

Examines stochastic chemical reactions, from spatial models to enzyme kinetics, including the impact of crowding on reactions.

Kinetic models: Enzyme Catalysis and Mass Action Laws

Explores enzyme catalysis, mass action laws, Michaelis-Menten kinetics, and the Warburg Effect in cancer cells.

Kinetic model of Warburg effect

Explores the kinetic model of the Warburg Effect in cancer cells, covering model construction, parameter estimation, and metabolic control analysis.