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CHE.496: Biological Systems Design Seminar

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Assigned Readings

Assignment 1: Synthetic biology overview

  1. Extreme genetic engineering: An introduction to synthetic biology
  2. Intelligent Life

Assignment 2: Foundational technologies

  1. Foundations for engineering biology
  2. Economics of synthetic biology

Assignment 3: Engineering principles

  1. Synthetic biology - putting engineering into biology
  2. Synthetic biology: New engineering rules for an emerging discipline

Assignment 4: Genetic programming

  1. Idempotent vector design for standard assembly of biobricks
  2. Genetic parts to program bacteria

Assignment 5: Natural biological parts

  1. Another side of genomics: Synthetic biology as a means for the exploitation of whole-genome sequence information
  2. Codon bias and heterologous protein expression

Assignment 6: Practical applications

  1. Advances in synthetic biology: on the path from prototypes to applications
  2. Molecular switches for cellular sensors

Assignment 7: Social implications

  1. The promises and perils of synthetic biology
  2. DNA synthesis and biological security

Assignment 8: Biological machines

  1. Designing biological systems
  2. Biology by design: Reduction and synthesis of cellular components and behavior

Assignment 9: RNA synthetic biology

  1. RNA synthetic biology
  2. RNA and RNP as new molecular parts in synthetic biology

Assignment 10: Minimal genomes

  1. Essential genes of a minimal bacterium
  2. Leaner and meaner genomes in E. coli

Assignment 11: Minimal cells

  1. Toward synthesis of a minimal cell
  2. Rebuilding microbial genomes

Assignment 12: Genetic circuit engineering

  1. A synthetic oscillatory network of transcriptional regulators
  2. Construction of a genetic toggle switch in Escherichia coli

Assignment 13: Genetic circuit engineering

  1. Environmentally controlled invasion of cancer cells by engineered bacteria
  2. Environmental signal integration by a modular AND gate

Assignment 14: Metabolic pathway engineering

  1. Production of isoprenoid pharmaceuticals by engineered microbes
  2. Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli

Assignment 15: Systems biology

  1. A partnership between biology and engineering
  2. Fast, cheap and somewhat in control

Assignment 16: Systems biology and synthetic biology

  1. The evolution of molecular biology into systems biology
  2. Integrating 'omic information: A bridge between genomics and systems biology

Assignment 16: Systems biology and synthetic biology

  1. Systems biology as a foundation for genome-scale synthetic biology
  2. From systems biology to synthetic biology

Assignment 17: Systems biology and synthetic biology

  1. Biological networks
  2. Programming and engineering biological networks

Assignment 16: Computational Biology

  1. From molecular to modular cell biology
  2. Modelling cellular behaviour

Assignment 17: Computational biology

  1. Bioinformatics analysis for genome design and synthetic biology
  2. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

Assignment 18: Metabolic flux analysis

  1. Use of genome-scale microbial models for metabolic engineering
  2. Global physiological understanding and metabolic engineering of microorganisms based on omics studies

Assignment 19: Genome-scale metabolic models

  1. Microbial regulatory and metabolic networks

Assignment 20: Modeling genetic regulatory networks

  1. Modular approaches to expanding the functions of living matter

Assignment 21: Systems biotechnology

  1. Synthetic biology: Navigating the challenges ahead
  2. Synthetic biology through the prism of scenarios