CHE.496/2008/Assignments

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CHE.496: Biological Systems Design Seminar

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Assigned Readings

Assignment 1: Synthetic biology overview

  1. Intelligent Design link
  2. Extreme genetic engineering: an introduction to synthetic biology link

Assignment 2: Foundational technologies

  1. Foundations for engineering biology link
  2. Synthetic biology: promises and challenges link
  3. The iGEM competition: building with biology link

Assignment 3: Engineering principles

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

Assignment 4: Genetic programming

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

Assignment 5: Natural biological parts

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

Assignment 6: Practical applications

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

Assignment 7: Social implications

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

Assignment 8: Engineering biology

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

Assignment 9: Biological machines

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

Assignment 10: Minimal genomes

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

Assignment 11: Minimal cells

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

Assignment 12: Genetic circuit engineering

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

Assignment 13: Genetic circuit engineering

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

Assignment 14: Metabolic pathway engineering

  1. Bioengineering novel in vitro metabolic pathways using synthetic biology link
  2. Production of the antimalarial drug precursor artemisinic acid in engineered yeast link

Assignment 15: Systems biology

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

Assignment 16: Systems biology and synthetic biology

  1. Systems biology as a foundation for genome-scale synthetic biology link
  2. From systems biology to synthetic biology link
  3. Modular approaches to expanding the functions of living matter link

Assignment 17: Computational Biology

  1. Modelling cellular behaviour link
  2. Bioinformatics analysis for genome design and synthetic biology link

Assignment 18: Biological networks

  1. Biological networks link
  2. Programming and engineering biological networks link

Assignment 19: Metabolic modeling

  1. Use of genome-scale microbial models for metabolic engineering link
  2. Microbial regulatory and metabolic networks link

Assignment 20: RNA synthetic biology

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

Assignment 21: The future of synthetic biology

  1. Synthetic biology: Navigating the challenges ahead link
  2. Economics of synthetic biology link
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