CHE.496/2009/Assignments: Difference between revisions

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==Assigned Readings==
==Assigned Readings==
<font color=blue>
===Assignment 1: Introduction===
===Assignment 1: Introduction===
* '''Synthetic biology: promises and challenges [http://www.nature.com/doifinder/10.1038/msb4100202 link]
* '''Synthetic biology: promises and challenges [http://www.nature.com/doifinder/10.1038/msb4100202 link]
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# '''Advances in synthetic biology: on the path from prototypes to applications [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4GM45W4-2&_user=10&_coverDate=08%2F31%2F2005&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_usrid=10&md5=a52006fd41df553f10c641cf1bd30272 link]
# '''Advances in synthetic biology: on the path from prototypes to applications [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4GM45W4-2&_user=10&_coverDate=08%2F31%2F2005&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_usrid=10&md5=a52006fd41df553f10c641cf1bd30272 link]
# '''Molecular switches for cellular sensors [http://eands.caltech.edu/articles/LXVII4/Smolke%20Feature.pdf link]
# '''Molecular switches for cellular sensors [http://eands.caltech.edu/articles/LXVII4/Smolke%20Feature.pdf link]
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===Assignment 7: Engineering biology===
# '''A partnership between biology and engineering [http://www.nature.com/nbt/journal/v22/n10/full/nbt1004-1211.html link]
# '''Fast, cheap and somewhat in control [http://genomics.lbl.gov/Stuff/Arkin_FastCheapGenomeBiology.pdf link]
===Assignment 8: Biological machines===
# '''Designing biological systems [http://openwetware.org/images/7/7d/Drubin_2007.pdf link]
# '''Biology by design: Reduction and synthesis of cellular components and behavior [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17251159  link]
===Assignment 9: Genetic circuit engineering (part 1)===
# '''A synthetic oscillatory network of transcriptional regulators [http://www.nature.com/nature/journal/v403/n6767/abs/403335a0.html link]
# '''Construction of a genetic toggle switch in ''Escherichia coli'' [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html link]
===Assignment 10: Genetic circuit engineering (part 2)===
# '''Environmentally controlled invasion of cancer cells by engineered bacteria [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4HJRXGD-4&_user=709071&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000039638&_version=1&_urlVersion=0&_userid=709071&md5=cac1dbad4022f85af3724a9ba787d3dd  link]
# '''Environmental signal integration by a modular AND gate [http://www.nature.com/msb/journal/v3/n1/synopsis/msb4100173.html link]
===Assignment 11: Metabolic pathway engineering===
# '''Bioengineering novel in vitro metabolic pathways using synthetic biology [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS2-4NWNF66-2&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=7914d28255c54bd144ea8516409bb86a  link]
# '''Synthetic biology for synthetic chemistry [http://pubs.acs.org/cgi-bin/sample.cgi/acbcct/2008/3/i01/pdf/cb7002434.pdf link]
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===Assignment 12: Systems biology and synthetic biology===
# '''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]
===Assignment 13: Biological networks===
<font color=red>
# '''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]
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Latest revision as of 15:58, 5 April 2009

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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