CHE.496/2008/Assignments: Difference between revisions
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<div style="padding: 10px; width: 720px; border: 5px solid #B3CD4E;"> | <div style="padding: 10px; width: 720px; border: 5px solid #B3CD4E;"> | ||
==Assigned Readings== | |||
==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 | ||
| Line 26: | Line 26: | ||
# 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: Societal implications== | ====Assignment 7: Societal implications==== | ||
<font color=blue> | <font color=blue> | ||
# The promises and perils of synthetic biology | # The promises and perils of synthetic biology | ||
| Line 45: | Line 45: | ||
# 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 | ||
| Line 52: | Line 52: | ||
# Global transposon mutagenesis and a minimal mycoplasma genome | # Global transposon mutagenesis and a minimal mycoplasma genome | ||
</font> | </font> | ||
==Assignment 9: Cases studies in synthetic biology== | ====Assignment 9: Cases studies in synthetic biology==== | ||
<font color=green> | <font color=green> | ||
# Environmentally controlled invasion of cancer cells by engineered bacteria | # Environmentally controlled invasion of cancer cells by engineered bacteria | ||
# Production of isoprenoid pharmaceuticals by engineered microbes | # Production of isoprenoid pharmaceuticals by engineered microbes | ||
</font> | </font> | ||
==Assignment 10: Genetic circuit engineering== | ====Assignment 10: Genetic circuit engineering==== | ||
<font color=green> | <font color=green> | ||
# A synthetic oscillatory network of transcriptional regulators | # A synthetic oscillatory network of transcriptional regulators | ||
| Line 63: | Line 63: | ||
# Engineered gene circuits | # Engineered gene circuits | ||
</font> | </font> | ||
==Assignment 11: Metabolic pathway engineering== | ====Assignment 11: Metabolic pathway engineering==== | ||
<font color=green> | <font color=green> | ||
# Bioengineering novel in vitro metabolic pathways using synthetic biology | # Bioengineering novel in vitro metabolic pathways using synthetic biology | ||
</font> | </font> | ||
==Assignment 12: Biological network engineering== | ====Assignment 12: Biological network engineering==== | ||
<font color=green> | <font color=green> | ||
# Programming and engineering biological networks | # Programming and engineering biological networks | ||
# Modular approaches to expanding the functions of living matter | # Modular approaches to expanding the functions of living matter | ||
</font> | </font> | ||
==Assignment 13: Systems biology and the omic sciences== | ====Assignment 13: Systems biology and the omic sciences==== | ||
<font color=red> | <font color=red> | ||
</font> | </font> | ||
==Assignment 14: Mathematical biology== | ====Assignment 14: Mathematical biology==== | ||
<font color=red> | <font color=red> | ||
</font> | </font> | ||
==Assignment 15: Computational biology== | ====Assignment 15: Computational biology==== | ||
<font color=red> | <font color=red> | ||
</font> | </font> | ||
==Assignment 16: Metabolic flux analysis== | ====Assignment 16: Metabolic flux analysis==== | ||
<font color=red> | <font color=red> | ||
</font> | </font> | ||
==Assignment 17: Genome-scale metabolic models== | ====Assignment 17: Genome-scale metabolic models==== | ||
<font color=red> | <font color=red> | ||
</font> | </font> | ||
==Assignment 18: Modeling genetic regulatory networks== | ====Assignment 18: Modeling genetic regulatory networks==== | ||
<font color=red> | <font color=red> | ||
</font> | </font> | ||
==Assignment 19: Systems biotechnology== | ====Assignment 19: Systems biotechnology==== | ||
<font color=red> | <font color=red> | ||
Revision as of 11:36, 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: Societal 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: Cases studies in synthetic biology
- Environmentally controlled invasion of cancer cells by engineered bacteria
- Production of isoprenoid pharmaceuticals by engineered microbes
Assignment 10: Genetic circuit engineering
- A synthetic oscillatory network of transcriptional regulators
- Construction of a genetic toggle switch in Escherichia coli
- Engineered gene circuits
Assignment 11: Metabolic pathway engineering
- Bioengineering novel in vitro metabolic pathways using synthetic biology
Assignment 12: Biological network engineering
- Programming and engineering biological networks
- Modular approaches to expanding the functions of living matter
Assignment 13: Systems biology and the omic sciences
Assignment 14: Mathematical biology
Assignment 15: Computational biology
Assignment 16: Metabolic flux analysis
Assignment 17: Genome-scale metabolic models
Assignment 18: Modeling genetic regulatory networks
Assignment 19: Systems biotechnology
