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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. A partnership between biology and engineering

Assignment 3: Engineering principles

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

Assignment 4: Biobricks and genetic programming

  1. Idempotent vector design for standard assembly of biobricks
  2. Designing biological systems
  3. Biology by design: Reduction and synthesis of cellular components and behavior

Assignment 5: Bioinformatics and systems biology

  1. Systems biology as a foundation for genome-scale synthetic biology
  2. Another side of genomics: Synthetic biology as a means for the exploitation of whole-genome sequence information

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. Synthetic biology: Navigating the challenges ahead
  3. Synthetic biology: Caught between property rights, the public domain, & the commons
  4. Economics of synthetic biology
  5. DNA synthesis and biological security
  6. Characterization of the reconstructed 1918 Spanish influenza pandemic virus

Assignment 8: Synthetic genes, biological machines, and minimal genomes

  1. Genetic parts to program bacteria
  2. Codon bias and heterologous protein expression
  3. Fast, cheap and somewhat in control

Assignment 9: Dr. Craig Venter's minimal genome work

  1. Global transposon mutagenesis and a minimal mycoplasma genome

Assignment 10: Dr. George Church's minimal cell work

  1. Toward synthesis of a minimal cell

Assignment 11: Dr. Michael Elowitz's genetic circuit engineering work

  1. A synthetic oscillatory network of transcriptional regulators

Assignment 12: Dr. Jim Collins' genetic circuit engineering work

  1. Construction of a genetic toggle switch in Escherichia coli
  2. Engineered gene circuits

Assignment 13: Dr. Chris Voigt's genetic circuit engineering work

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

Assignment 14: Dr. Jay Keasling's metabolic pathway engineering work

  1. Production of isoprenoid pharmaceuticals by engineered microbes

Assignment 15: Systems biology and the omic sciences

Assignment 16: Mathematical biology

Assignment 17: Computational biology

Assignment 18: Metabolic flux analysis

Assignment 19: Genome-scale metabolic models

Assignment 20: Modeling genetic regulatory networks

Assignment 21: Systems biotechnology