CHE.496/2008/Assignments
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Assigned Readings
Assignment 1: Synthetic biology overview
- Extreme genetic engineering: An introduction to synthetic biology
- Intelligent Life
Assignment 2: Foundational technologies
- Foundations for engineering biology
- A partnership between biology and engineering
Assignment 3: Engineering principles
- Synthetic biology - putting engineering into biology
- Synthetic biology: New engineering rules for an emerging discipline
Assignment 4: Biobricks and genetic programming
- Idempotent vector design for standard assembly of biobricks
- Designing biological systems
- Biology by design: Reduction and synthesis of cellular components and behavior
Assignment 5: Bioinformatics and systems biology
- Systems biology as a foundation for genome-scale synthetic biology
- Another side of genomics: Synthetic biology as a means for the exploitation of whole-genome sequence information
Assignment 6: Practical applications
- Advances in synthetic biology: on the path from prototypes to applications
- Molecular switches for cellular sensors
Assignment 7: Social implications
- The promises and perils of synthetic biology
- Synthetic biology: Navigating the challenges ahead
- Synthetic biology: Caught between property rights, the public domain, & the commons
- Economics of synthetic biology
- DNA synthesis and biological security
- Characterization of the reconstructed 1918 Spanish influenza pandemic virus
Assignment 8: Synthetic genes, biological machines, and minimal genomes
- Genetic parts to program bacteria
- Codon bias and heterologous protein expression
- Fast, cheap and somewhat in control
- Global transposon mutagenesis and a minimal mycoplasma genome
Assignment 9: Dr. Craig Venter's minimal genome work
- Environmentally controlled invasion of cancer cells by engineered bacteria
- Production of isoprenoid pharmaceuticals by engineered microbes
Assignment 10: Dr. George Church's minimal cell work
- A synthetic oscillatory network of transcriptional regulators
- Construction of a genetic toggle switch in Escherichia coli
- Engineered gene circuits
Assignment 11: Dr. Michael Elowitz's genetic circuit engineering work
- Bioengineering novel in vitro metabolic pathways using synthetic biology
Assignment 12: Dr. Jim Collins' genetic circuit engineering work
- Programming and engineering biological networks
- Modular approaches to expanding the functions of living matter
Assignment 13: Dr. Chris Voigt's genetic circuit engineering work
- Environmentally controlled invasion of cancer cells by engineered bacteria
- Environmental signal integration by a modular AND gate
Assignment 14: Dr. Jay Keasling's pathway engineering work
- Programming and engineering biological networks
- Modular approaches to expanding the functions of living matter
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