CHE.496/2008/Assignments

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====Assignment 9: Biological machines====
====Assignment 9: Biological machines====
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# '''Designing biological systems [http://cs.calstatela.edu/wiki/images/7/75/Silver_overview.pdf link]
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# '''Designing biological systems [http://www.genesdev.org/cgi/content/abstract/21/3/242 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====
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====Assignment 10: Genetic circuit engineering (part 1)====
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# '''Essential genes of a minimal bacterium [http://lib.bioinfo.pl/pmid:16407165 link]
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# '''Leaner and meaner genomes in ''E. coli'' [http://genomebiology.com/2006/7/10/237 link]
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====Assignment 11: Minimal cells====
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# '''Toward synthesis of a minimal cell [http://www.nature.com/msb/journal/v2/n1/full/msb4100090.html link]
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# '''Rebuilding microbial genomes [http://www3.interscience.wiley.com/cgi-bin/abstract/114264051/ABSTRACT?CRETRY=1&SRETRY=0 link]
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====Assignment 12: Genetic circuit engineering====
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# '''A synthetic oscillatory network of transcriptional regulators [http://www.nature.com/nature/journal/v403/n6767/abs/403335a0.html link]
# '''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]
# '''Construction of a genetic toggle switch in ''Escherichia coli'' [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html link]
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====Assignment 13: Genetic circuit engineering====
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====Assignment 11: Genetic circuit engineering (part 2)====
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# '''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]
# '''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]
# '''Environmental signal integration by a modular AND gate [http://www.nature.com/msb/journal/v3/n1/synopsis/msb4100173.html link]
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====Assignment 14: Metabolic pathway engineering====
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====Assignment 12: Metabolic pathway engineering====
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# '''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]
# '''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]
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# '''Production of the antimalarial drug precursor artemisinic acid in engineered yeast [http://www.nature.com/nature/journal/v440/n7086/abs/nature04640.html link]
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# '''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 15: Systems biology====
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====Assignment 13: Systems biology and synthetic biology====
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# '''The evolution of molecular biology into systems biology [http://www.nature.com/nbt/journal/v22/n10/full/nbt1020.html link]
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# '''Integrating 'omic information: A bridge between genomics and systems biology [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCY-49FBB82-2&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=7907b41f57de8a1c4be05b8c0cd3d131 link]
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====Assignment 16: Systems biology and synthetic biology====
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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]
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# '''From systems biology to synthetic biology [http://www.nature.com/msb/journal/v1/n1/full/msb4100007.html link]
 
# '''Modular approaches to expanding the functions of living matter [http://www.nature.com/nchembio/journal/v2/n6/abs/nchembio789.html link]
# '''Modular approaches to expanding the functions of living matter [http://www.nature.com/nchembio/journal/v2/n6/abs/nchembio789.html link]
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====Assignment 17: Biological networks====
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====Assignment 14: Biological networks====
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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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====Assignment 18: Computational Biology====
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====Assignment 15: RNA synthetic biology====
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# '''Modelling cellular behaviour [http://www.nature.com/nature/journal/v409/n6818/abs/409391a0.html link]
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# '''Bioinformatics analysis for genome design and synthetic biology [http://ieeexplore.ieee.org/Xplore/login.jsp?url=/iel5/10363/32966/01544358.pdf link]
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====Assignment 19: Metabolic modeling====
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# '''Use of genome-scale microbial models for metabolic engineering [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4B7YPJB-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=5a4f561f1c766eca10ec53e1ab9223be link]
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# '''Microbial regulatory and metabolic networks [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRV-4PGXF5M-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=1df4f4d6151384eac22f5b5f37ad7d43 link]
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====Assignment 20: RNA synthetic biology====
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# '''RNA synthetic biology [http://www.bu.edu/abl/files/naturebiotech_isaacs.pdf link]
# '''RNA synthetic biology [http://www.bu.edu/abl/files/naturebiotech_isaacs.pdf link]
# '''RNA and RNP as new molecular parts in synthetic biology [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T3C-4PCGRPV-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=59ffbe8c79641a38cdf9d39750e8a7ae link]
# '''RNA and RNP as new molecular parts in synthetic biology [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T3C-4PCGRPV-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=59ffbe8c79641a38cdf9d39750e8a7ae link]
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====Assignment 21: The future of synthetic biology====
 
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# '''Synthetic biology: Navigating the challenges ahead [http://openwetware.org/images/0/02/Aj_bhutkar_synth_bio_jbb_2005.pdf link]
 
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# '''Economics of synthetic biology [http://www.nature.com/msb/journal/v3/n1/full/msb4100161.html link]
 
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Current revision

CHE.496: Biological Systems Design Seminar

Home        People        Schedule        Assignments        Responses        Projects        Links        Help       

Assigned Readings

Assignment 1: Synthetic biology overview

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

Assignment 2: Foundational technologies

  1. Foundations for engineering biology link
  2. Synthetic biology: promises and challenges link
  3. 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: 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: 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 11: 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 12: Metabolic pathway engineering

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

Assignment 13: Systems biology and synthetic biology

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

Assignment 14: Biological networks

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

Assignment 15: RNA synthetic biology

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