CHE.496/2008/Assignments: Difference between revisions
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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 | # '''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] | ||
# '''Codon bias and heterologous protein expression | # '''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 | # '''The promises and perils of synthetic biology [http://www.thenewatlantis.com/archive/12/tuckerzilinskas.htm link] | ||
# '''DNA synthesis and biological security | # '''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] | ||
# '''Fast, cheap and somewhat in control | # '''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 | # '''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 | # '''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 11:58, 3 January 2008
Assigned Readings
Assignment 1: Synthetic biology overview
Assignment 2: Foundational technologies
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: Minimal genomes
- Essential genes of a minimal bacterium
- Leaner and meaner genomes in E. coli
Assignment 11: Minimal cells
- Toward synthesis of a minimal cell
- Rebuilding microbial genomes
Assignment 12: Genetic circuit engineering
- A synthetic oscillatory network of transcriptional regulators link
- Construction of a genetic toggle switch in Escherichia coli link
Assignment 13: Genetic circuit engineering
- Environmentally controlled invasion of cancer cells by engineered bacteria link
- Environmental signal integration by a modular AND gate
Assignment 14: Metabolic pathway engineering
- Production of isoprenoid pharmaceuticals by engineered microbes link
- Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli link
Assignment 15: Systems biology
- The evolution of molecular biology into systems biology
- Integrating 'omic information: A bridge between genomics and systems biology
- Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles
Assignment 16: Systems biology and synthetic biology
- Systems biology as a foundation for genome-scale synthetic biology link
- From systems biology to synthetic biology
- Modular approaches to expanding the functions of living matter
Assignment 17: Computational Biology
- Modelling cellular behaviour
- Bioinformatics analysis for genome design and synthetic biology
Assignment 18: Biological networks
- Biological networks
- Programming and engineering biological networks
Assignment 19: Metabolic modeling
- Use of genome-scale microbial models for metabolic engineering
- Global physiological understanding and metabolic engineering of microorganisms based on omics studies
- Microbial regulatory and metabolic networks
Assignment 20: RNA synthetic biology
- RNA synthetic biology
- RNA and RNP as new molecular parts in synthetic biology
Assignment 21: The future of synthetic biology
- Synthetic biology: Navigating the challenges ahead
- Synthetic biology through the prism of scenarios