Chapter 10

Lecture Videos #

A Massive Open Online Course on Computational Systems Biology, which is in part, a basis for this book, is also available, through the Indian educational platforms, NPTEL (National Programme on Technology Enhanced Learning) and SWAYAM.

The lectures (including hands-on lab sessions), totalling over 30 hours of content, are also available on YouTube.

Chapter 10: Perturbations to metabolic networks #

Perturbations to Metabolic Networks: Deletions (12:50)

  • Gene Deletions
  • Reaction Deletions
  • Gene-Protein-Reaction Associations

Perturbations to Metabolic Networks: Over-expression (15:36)

  • FSEOF

Perturbations to Metabolic Networks: Synthetic Lethals (13:07)

  • Synthetic Lethals

Perturbations to Metabolic Networks: Synthetic Lethals (16:16)

  • Fast-SL Algorithm

Constraint-based Modelling of Metabolic Networks (10:54)

  • Limitations of Constraint-Based Approaches

Lab: Gene Deletions (30:39)

  • Gene Deletions using COBRA Toolbox
  • Escher
  • Single and Double Deletions

Integrating Regulatory Information into Constraint-Based Models (17:53)

  • rFBA
  • E-Flux

Constraint-based Modelling of Metabolic Networks: Applications (15:04)

  • Introduction
  • Drug Target Identification: Mycolic Acid Pathway in TB

Constraint-based Modelling of Metabolic Networks: Applications (8:30)

  • Metabolic Engineering: Lycopene Biosynthesis

Constraint-based Modelling of Metabolic Networks: Applications (17:12)

  • targetTB

Lab: Gene Deletions (25:25)

  • Single Reaction Deletion
  • Minimal Reactome

Constraint-based Modelling of Metabolic Networks: Recap (16:03)

  • Stoichiometric Matrix
  • Constraints
  • Choice of Objective Function

Constraint-based Modelling of Metabolic Networks: Recap (17:57)

  • Perturbations

Constraint-based Modelling of Metabolic Networks: Recap (15:34)

  • FSEOF
  • Synthetic Lethals