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IIIUC

Computational Biology @ UC

Topics Discussed in the Courses



Cell Signaling and Metabolism

Wednesday, 2nd September & Thursday, 3rd September

  • Cell signaling I

    • From extracellular signal to cellular response.
    • Studying cell surface receptors and signal transduction pathways.
    • G protein-coupled receptors.
  • From genes to protein

    • Transcriptional control of gene expression.
    • Post-transcriptional gene control.
  • Cell signaling II

    • Cell-cell and cell-matrix adhesion: an overview.
    • Cell-cell and cell-ECM junctions and their adhesion molecules.
    • Adhesive interactions in cancer cells.
  • Metabolism



Tools for Modeling Biological Systems: a “hands-on” course

Wednesday, 2nd September & Thursday, 3rd September

  • Mathematical models of intra-cellular processes

    • Quantitative mathematical descriptions of coupled reactions by ordinary differential equations (ODEs)
    • Michaelis Menten kinetics, Hill kinetics, stochastic terms and other common variations of ODEs used in the literature
  • Computational modeling of Biological systems 

    • Introduction to computational modeling and coding in MatLab.
    • Practical examples of modeling intra-cellular processes
  • Mathematical models of extra-cellular processes

    • Quantitative mathematical descriptions of diffusion and chemotaxis through partial differential equations (PDEs)
    • Computational implementation


Modeling Proteins and Membranes: folding and aggregation

Thursday, 3rd September & Friday, 4th September

  • Foundations of molecular dynamics
  • Molecular dynamics for lipid bilayers
  • Molecular dynamics for proteins
  • Studying protein folding and aggregation
  • Protein-Ligand interactions and  Drug Discovery


Transcriptomics to Characterize Cellular Mechanisms

To be announced.



Modeling Metabolic and Signaling Pathways

Monday, 7th September

  • Graphical representation of regulatory networks
  • From diagrams to equations
  • Relating concentrations to process rates 
  • Handling compartments
  • Studying steady state behavior
  • Simulating dynamics
  • Taming complexity
  • The dynamic bestiary


Mathematical Models of Age-Related Diseases

Tuesday, 8th September

  • Modeling physiological systems using continuous and discrete methods.

  • Exemplification of the methods by analysing tumor growth, blood vessel formation and vessel irrigation in pathological settings.

    • Angiogenesis and tumor growth using cell based models.
    • Coupling cell signalling to matrix elasticity to regulate vessel morphology.
    • Quantifying blood flow and hypoxia in pathological vascular network.
    • Models of drug release in the context of glaucoma.