CHE.496/2008/Assignments: Difference between revisions
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# '''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] | ||
</font> | </font> | ||
====Assignment 10 | ====Assignment 10: Genetic circuit engineering (part 1)==== | ||
<font color=green> | <font color=green> | ||
# '''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 | ====Assignment 11: Genetic circuit engineering (part 2)==== | ||
<font color=green> | <font color=green> | ||
# '''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 | ====Assignment 12: Metabolic pathway engineering==== | ||
<font color=green> | <font color=green> | ||
# '''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] | ||
# '''Production of the antimalarial drug precursor artemisinic acid in engineered yeast [http://www.nature.com/nature/journal/v440/n7086/abs/nature04640.html link] | # '''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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====Assignment | ====Assignment 13: Systems biology and synthetic biology==== | ||
<font color=red> | <font color=red> | ||
# '''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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# '''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 | ====Assignment 14: Biological networks==== | ||
<font color=red> | <font color=red> | ||
# '''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 | ====Assignment 15: RNA synthetic biology==== | ||
<font color=red> | <font color=red> | ||
# '''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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Revision as of 11:52, 1 February 2008
Assigned Readings
Assignment 1: Synthetic biology overview
Assignment 2: Foundational technologies
- Foundations for engineering biology link
- Synthetic biology: promises and challenges link
- The iGEM competition: building with biology link
Assignment 3: Engineering principles
- Synthetic biology - putting engineering into biology link
- Synthetic biology: new engineering rules for an emerging discipline link
Assignment 4: Genetic programming
- Idempotent vector design for standard assembly of biobricks link
- Genetic parts to program bacteria link
Assignment 5: Natural biological parts
- Another side of genomics: Synthetic biology as a means for the exploitation of whole-genome sequence information link
- Codon bias and heterologous protein expression link
Assignment 6: Practical applications
- Advances in synthetic biology: on the path from prototypes to applications link
- Molecular switches for cellular sensors link
Assignment 7: Social implications
Assignment 8: Engineering biology
Assignment 9: Biological machines
- Designing biological systems link
- Biology by design: Reduction and synthesis of cellular components and behavior link
Assignment 10: Genetic circuit engineering (part 1)
- A synthetic oscillatory network of transcriptional regulators link
- Construction of a genetic toggle switch in Escherichia coli link
Assignment 11: Genetic circuit engineering (part 2)
- Environmentally controlled invasion of cancer cells by engineered bacteria link
- Environmental signal integration by a modular AND gate link
Assignment 12: Metabolic pathway engineering
- Bioengineering novel in vitro metabolic pathways using synthetic biology link
- Production of the antimalarial drug precursor artemisinic acid in engineered yeast link
Assignment 13: Systems biology and synthetic biology
- Systems biology as a foundation for genome-scale synthetic biology link
- From systems biology to synthetic biology link
- Modular approaches to expanding the functions of living matter link
Assignment 14: Biological networks
Assignment 15: RNA synthetic biology