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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: Standard biological parts

  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 genetic programming

  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
  2. Rebuilding microbial genomes

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

  1. The evolution of molecular biology into systems biology
  2. From systems biology to synthetic biology
  3. Bioinformatics analysis for genome design and synthetic biology
  4. Integrating 'omic information: A bridge between genomics and systems biology
  5. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
  6. Use of genome-scale microbial models for metabolic engineering
  7. Microbial regulatory and metabolic networks
  8. Global physiological understanding and metabolic engineering of microorganisms based on omics studies
  9. Biological networks
  10. Programming and engineering biological networks
  11. Modular approaches to expanding the functions of living matter

Assignment 16: Computational Biology

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

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