CHE.496/2008/Assignments

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====Assignment 5: Natural biological parts====
====Assignment 5: Natural biological parts====
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# '''Another side of genomics: Synthetic biology as a means for the exploitation of whole-genome sequence information
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# '''Another side of genomics: Synthetic biology as a means for the exploitation of whole-genome sequence information [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T3C-4J3WG6G-2&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=991e2e60d1fea5abc67784f073c716dd link]
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# '''Codon bias and heterologous protein expression
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# '''Codon bias and heterologous protein expression [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCW-4C8NKCY-3&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=45ad088ad31ff6fef31fa219d8f4099d link]
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====Assignment 6: Practical applications====
====Assignment 6: Practical applications====
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====Assignment 7: Social implications====
====Assignment 7: Social implications====
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# '''The promises and perils of synthetic biology
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# '''The promises and perils of synthetic biology [http://www.thenewatlantis.com/archive/12/tuckerzilinskas.htm link]
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# '''DNA synthesis and biological security
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# '''DNA synthesis and biological security [http://cstsp.aaas.org/files/DNA_synthesis_NGP2007.pdf link]
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====Assignment 8: Engineering biology====
====Assignment 8: Engineering biology====
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# '''A partnership between biology and engineering [http://www.nature.com/nbt/journal/v22/n10/full/nbt1004-1211.html link]
# '''A partnership between biology and engineering [http://www.nature.com/nbt/journal/v22/n10/full/nbt1004-1211.html link]
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# '''Fast, cheap and somewhat in control
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# '''Fast, cheap and somewhat in control [http://genomics.lbl.gov/Stuff/Arkin_FastCheapGenomeBiology.pdf link]
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====Assignment 9: Biological machines====
====Assignment 9: Biological machines====
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# '''Designing biological systems
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# '''Designing biological systems [http://cs.calstatela.edu/wiki/images/7/75/Silver_overview.pdf link]
# '''Biology by design: Reduction and synthesis of cellular components and behavior [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17251159&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum  link]
# '''Biology by design: Reduction and synthesis of cellular components and behavior [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17251159&ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum  link]
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====Assignment 10: Minimal genomes====
====Assignment 10: Minimal genomes====
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# '''Essential genes of a minimal bacterium
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# '''Essential genes of a minimal bacterium  
# '''Leaner and meaner genomes in ''E. coli''
# '''Leaner and meaner genomes in ''E. coli''
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Revision as of 14:58, 3 January 2008

CHE.496: Biological Systems Design Seminar

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Assigned Readings

Assignment 1: Synthetic biology overview

  1. Intelligent Life link
  2. Extreme genetic engineering: an introduction to synthetic biology link

Assignment 2: Foundational technologies

  1. Foundations for engineering biology link
  2. Economics of synthetic 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: Social implications

  1. The promises and perils of synthetic biology link
  2. DNA synthesis and biological security link

Assignment 8: Engineering biology

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

Assignment 9: Biological machines

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

Assignment 10: Minimal genomes

  1. Essential genes of a minimal bacterium
  2. Leaner and meaner genomes in E. coli

Assignment 11: Minimal cells

  1. Toward synthesis of a minimal cell
  2. Rebuilding microbial genomes

Assignment 12: Genetic circuit engineering

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

Assignment 13: Genetic circuit engineering

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

Assignment 14: Metabolic pathway engineering

  1. Production of isoprenoid pharmaceuticals by engineered microbes link
  2. Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli link

Assignment 15: Systems biology

  1. The evolution of molecular biology into systems biology
  2. Integrating 'omic information: A bridge between genomics and systems biology
  3. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

Assignment 16: Systems biology and synthetic biology

  1. Systems biology as a foundation for genome-scale synthetic biology link
  2. From systems biology to synthetic biology
  3. Modular approaches to expanding the functions of living matter

Assignment 17: Computational Biology

  1. Modelling cellular behaviour
  2. Bioinformatics analysis for genome design and synthetic biology

Assignment 18: Biological networks

  1. Biological networks
  2. Programming and engineering biological networks

Assignment 19: Metabolic modeling

  1. Use of genome-scale microbial models for metabolic engineering
  2. Global physiological understanding and metabolic engineering of microorganisms based on omics studies
  3. Microbial regulatory and metabolic networks

Assignment 20: RNA synthetic biology

  1. RNA synthetic biology
  2. RNA and RNP as new molecular parts in synthetic biology

Assignment 21: The future of synthetic biology

  1. Synthetic biology: Navigating the challenges ahead
  2. Synthetic biology through the prism of scenarios
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