CHE.496/2008/Assignments: Difference between revisions
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====Assignment 1: Synthetic biology overview==== | ====Assignment 1: Synthetic biology overview==== | ||
<font color=blue> | <font color=blue> | ||
# Extreme genetic engineering: An introduction to synthetic biology | # '''Extreme genetic engineering: An introduction to synthetic biology | ||
# Intelligent Life | # '''Intelligent Life | ||
</font> | </font> | ||
====Assignment 2: Foundational technologies==== | ====Assignment 2: Foundational technologies==== | ||
<font color=blue> | <font color=blue> | ||
# Foundations for engineering biology | # '''Foundations for engineering biology | ||
# A partnership between biology and engineering | # '''A partnership between biology and engineering | ||
</font> | </font> | ||
====Assignment 3: Engineering principles==== | ====Assignment 3: Engineering principles==== | ||
<font color=blue> | <font color=blue> | ||
# Synthetic biology - putting engineering into biology | # '''Synthetic biology - putting engineering into biology | ||
# Synthetic biology: New engineering rules for an emerging discipline | # '''Synthetic biology: New engineering rules for an emerging discipline | ||
</font> | </font> | ||
====Assignment 4: Biobricks and genetic programming==== | ====Assignment 4: Biobricks and genetic programming==== | ||
<font color=blue> | <font color=blue> | ||
# Idempotent vector design for standard assembly of biobricks | # '''Idempotent vector design for standard assembly of biobricks | ||
# Designing biological systems | # '''Designing biological systems | ||
# Biology by design: Reduction and synthesis of cellular components and behavior | # '''Biology by design: Reduction and synthesis of cellular components and behavior | ||
</font> | </font> | ||
====Assignment 5: Bioinformatics and systems biology==== | ====Assignment 5: Bioinformatics and systems biology==== | ||
<font color=blue> | <font color=blue> | ||
# Systems biology as a foundation for genome-scale synthetic 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 | # '''Another side of genomics: Synthetic biology as a means for the exploitation of whole-genome sequence information | ||
</font> | </font> | ||
====Assignment 6: Practical applications==== | ====Assignment 6: Practical applications==== | ||
<font color=blue> | <font color=blue> | ||
# Advances in synthetic biology: on the path from prototypes to applications | # '''Advances in synthetic biology: on the path from prototypes to applications | ||
# Molecular switches for cellular sensors | # '''Molecular switches for cellular sensors | ||
</font> | </font> | ||
====Assignment 7: Social implications==== | ====Assignment 7: Social implications==== | ||
<font color=blue> | <font color=blue> | ||
# The promises and perils of synthetic biology | # '''The promises and perils of synthetic biology | ||
# Synthetic biology: Navigating the challenges ahead | # '''Synthetic biology: Navigating the challenges ahead | ||
# Synthetic biology: Caught between property rights, the public domain, & the commons | # '''Synthetic biology: Caught between property rights, the public domain, & the commons | ||
# Economics of synthetic biology | # '''Economics of synthetic biology | ||
# DNA synthesis and biological security | # '''DNA synthesis and biological security | ||
# Characterization of the reconstructed 1918 Spanish influenza pandemic virus | # '''Characterization of the reconstructed 1918 Spanish influenza pandemic virus | ||
</font> | </font> | ||
====Assignment 8: Synthetic genes, biological machines, and minimal genomes==== | ====Assignment 8: Synthetic genes, biological machines, and minimal genomes==== | ||
<font color=green> | <font color=green> | ||
# Genetic parts to program bacteria | # '''Genetic parts to program bacteria | ||
# Codon bias and heterologous protein expression | # '''Codon bias and heterologous protein expression | ||
# Fast, cheap and somewhat in control | # '''Fast, cheap and somewhat in control | ||
</font> | </font> | ||
====Assignment 9: Dr. Craig Venter's minimal genome work==== | ====Assignment 9: Dr. Craig Venter's minimal genome work==== | ||
<font color=green> | <font color=green> | ||
# Global transposon mutagenesis and a minimal mycoplasma genome | # '''Global transposon mutagenesis and a minimal mycoplasma genome | ||
</font> | </font> | ||
====Assignment 10: Dr. George Church's minimal cell work==== | ====Assignment 10: Dr. George Church's minimal cell work==== | ||
<font color=green> | <font color=green> | ||
# Toward synthesis of a minimal cell | # '''Toward synthesis of a minimal cell | ||
</font> | </font> | ||
====Assignment 11: Dr. Michael Elowitz's genetic circuit engineering work==== | ====Assignment 11: Dr. Michael Elowitz's genetic circuit engineering work==== | ||
<font color=green> | <font color=green> | ||
# A synthetic oscillatory network of transcriptional regulators | # '''A synthetic oscillatory network of transcriptional regulators | ||
</font> | </font> | ||
====Assignment 12: Dr. Jim Collins' genetic circuit engineering work==== | ====Assignment 12: Dr. Jim Collins' genetic circuit engineering work==== | ||
<font color=green> | <font color=green> | ||
# Construction of a genetic toggle switch in ''Escherichia coli'' | # '''Construction of a genetic toggle switch in ''Escherichia coli'' | ||
# Engineered gene circuits | # '''Engineered gene circuits | ||
</font> | </font> | ||
====Assignment 13: Dr. Chris Voigt's genetic circuit engineering work==== | ====Assignment 13: Dr. Chris Voigt's genetic circuit engineering work==== | ||
<font color=green> | <font color=green> | ||
# Environmentally controlled invasion of cancer cells by engineered bacteria | # '''Environmentally controlled invasion of cancer cells by engineered bacteria | ||
# Environmental signal integration by a modular AND gate | # '''Environmental signal integration by a modular AND gate | ||
</font> | </font> | ||
====Assignment 14: Dr. Jay Keasling's metabolic pathway engineering work==== | ====Assignment 14: Dr. Jay Keasling's metabolic pathway engineering work==== | ||
<font color=green> | <font color=green> | ||
# Production of isoprenoid pharmaceuticals by engineered microbes | # '''Production of isoprenoid pharmaceuticals by engineered microbes | ||
</font> | </font> | ||
====Assignment 15: Systems biology and the omic sciences==== | ====Assignment 15: Systems biology and the omic sciences==== |
Revision as of 14:57, 8 November 2007
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
Assignment 9: Dr. Craig Venter's minimal genome work
- Global transposon mutagenesis and a minimal mycoplasma genome
Assignment 10: Dr. George Church's minimal cell work
- Toward synthesis of a minimal cell
Assignment 11: Dr. Michael Elowitz's genetic circuit engineering work
- A synthetic oscillatory network of transcriptional regulators
Assignment 12: Dr. Jim Collins' genetic circuit engineering work
- Construction of a genetic toggle switch in Escherichia coli
- Engineered gene circuits
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 metabolic pathway engineering work
- 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