CHE.496/2009/Assignments

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(Assigned Readings)
Current revision (18:58, 5 April 2009) (view source)
m (Assignment 14: Biological networks)
 
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# '''Systems biology as a foundation for genome-scale synthetic biology [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KPX8RY-1&_user=709071&_coverDate=10%2F31%2F2006&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000039638&_version=1&_urlVersion=0&_userid=709071&md5=7a316893fbee50cab2742cc3b6de73b4  link]
# '''Systems biology as a foundation for genome-scale synthetic biology [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4KPX8RY-1&_user=709071&_coverDate=10%2F31%2F2006&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000039638&_version=1&_urlVersion=0&_userid=709071&md5=7a316893fbee50cab2742cc3b6de73b4  link]
# '''Network Benchmarking: A Happy Marriage between Systems and Synthetic Biology [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRP-4VXKM2P-3&_user=709071&_coverDate=03/27/2009&_alid=894022930&_rdoc=2&_fmt=full&_orig=mlkt&_cdi=6240&_st=17&_docanchor=&_ct=18&_acct=C000039638&_version=1&_urlVersion=0&_userid=709071&md5=0901b0cd65d61d89e5486a080ad4e23f#sec1 link]
# '''Network Benchmarking: A Happy Marriage between Systems and Synthetic Biology [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRP-4VXKM2P-3&_user=709071&_coverDate=03/27/2009&_alid=894022930&_rdoc=2&_fmt=full&_orig=mlkt&_cdi=6240&_st=17&_docanchor=&_ct=18&_acct=C000039638&_version=1&_urlVersion=0&_userid=709071&md5=0901b0cd65d61d89e5486a080ad4e23f#sec1 link]
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===Assignment 14: Biological networks===
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===Assignment 13: Biological networks===
<font color=red>
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# '''Biological networks [http://www.ecs.umass.edu/~mettu/ece697s/papers/systems%20biology/biological%20networks.pdf link]
# '''Biological networks [http://www.ecs.umass.edu/~mettu/ece697s/papers/systems%20biology/biological%20networks.pdf link]
# '''Programming and engineering biological networks [http://lib.bioinfo.pl/pmid:16842994 link]
# '''Programming and engineering biological networks [http://lib.bioinfo.pl/pmid:16842994 link]
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Current revision

CHE.496: Biological Systems Design Seminar

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Assigned Readings

Assignment 1: Introduction

  • Synthetic biology: promises and challenges link

Assignment 2: Foundational technologies

  1. Foundations for engineering biology link
  2. The iGEM competition: building with biology link

Assignment 3: Engineering principles

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

Assignment 4: Genetic programming

  1. Idempotent vector design for standard assembly of biobricks link
  2. Genetic parts to program bacteria link

Assignment 5: Natural biological parts

  1. Another side of genomics: Synthetic biology as a means for the exploitation of whole-genome sequence information link
  2. Codon bias and heterologous protein expression link

Assignment 6: Practical applications

  1. Advances in synthetic biology: on the path from prototypes to applications link
  2. Molecular switches for cellular sensors link

Assignment 7: Engineering biology

  1. A partnership between biology and engineering link
  2. Fast, cheap and somewhat in control link

Assignment 8: Biological machines

  1. Designing biological systems link
  2. Biology by design: Reduction and synthesis of cellular components and behavior link

Assignment 9: Genetic circuit engineering (part 1)

  1. A synthetic oscillatory network of transcriptional regulators link
  2. Construction of a genetic toggle switch in Escherichia coli link

Assignment 10: Genetic circuit engineering (part 2)

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

Assignment 11: Metabolic pathway engineering

  1. Bioengineering novel in vitro metabolic pathways using synthetic biology link
  2. Synthetic biology for synthetic chemistry link

Assignment 12: Systems biology and synthetic biology

  1. Systems biology as a foundation for genome-scale synthetic biology link
  2. Network Benchmarking: A Happy Marriage between Systems and Synthetic Biology link

Assignment 13: Biological networks

  1. Biological networks link
  2. Programming and engineering biological networks link

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