IGEM:IMPERIAL/2006/Bibliography & Papers: Difference between revisions
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==Synthetic Biology/General Papers== | ==Synthetic Biology/General Papers== | ||
[ Engineered Gene Circuits] (Hasty, McMillin, and Collins) ''Nature'' (14 November 2002) | [http://www.nature.com/nature/journal/v420/n6912/abs/nature01257.html Engineered Gene Circuits] (Hasty, McMillin, and Collins) ''Nature'' (14 November 2002) | ||
[Designer Gene Networks: Towards Fundamental Cellular Control] (Hasty et al.) ''Chaos'' (13 March 2001) | [http://arxiv.org/abs/physics/0103034 Designer Gene Networks: Towards Fundamental Cellular Control] (Hasty et al.) ''Chaos'' (13 March 2001) | ||
==Biological Modelling== | ==Biological Modelling== | ||
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[http://genetics.med.harvard.edu/~perrimon/Vidal%20Class%20Papers/Ferrell.pdf Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability] (James E Ferrell Jr) ''Current Opinion in Chemical Biology'' 12 February 2002 | [http://genetics.med.harvard.edu/~perrimon/Vidal%20Class%20Papers/Ferrell.pdf Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability] (James E Ferrell Jr) ''Current Opinion in Chemical Biology'' 12 February 2002 | ||
[ Modelling the Lux/AiiA Relaxion Oscillator] (Christopher Batten) - MIT Computer Science and Artifical Intelligence Laboratory | [http://www.mit.edu/~cbatten/work/ssbc04/modeling-ssbc04.pdf Modelling the Lux/AiiA Relaxion Oscillator] (Christopher Batten) - MIT Computer Science and Artifical Intelligence Laboratory | ||
[http://web.mit.edu/~cbatten/www/work/ssbc04/final-presentation-ssbc04.pdf Presentation from MIT's Synthetic Biology Competition of 2004] - Previous version of iGEM competition, describes oscillator | [http://web.mit.edu/~cbatten/www/work/ssbc04/final-presentation-ssbc04.pdf Presentation from MIT's Synthetic Biology Competition of 2004] - Previous version of iGEM competition, describes oscillator | ||
[ Specification paper from MIT's Synthetic Biology Competition of 2004] - Details for their design and methology | [http://web.mit.edu/~cbatten/www/work/ssbc04/system-spec-ssbc04.pdf Specification paper from MIT's Synthetic Biology Competition of 2004] - Details for their design and methology | ||
[http://www.pojman.com/nlcd/intro.html Lotka-Volterra Model] - Implementation in Chemcial Systems | [http://www.pojman.com/nlcd/intro.html Lotka-Volterra Model] - Implementation in Chemcial Systems | ||
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==Quorum Sensing/Quenching== | ==Quorum Sensing/Quenching== | ||
[ Directed evolution of Vibrio fischeri LuxR for increased sensitivity to a broad spectrum of acyl-homoserine lactones] (Cynthia H. Collins, Frances H. Arnold and Jared R. Leadbetter) ''Molecular Microbiology'' 2005 | [http://www.blackwell-synergy.com/links/doi/10.1111/j.1365-2958.2004.04437.x/enhancedabs/?cookieSet=1 Directed evolution of Vibrio fischeri LuxR for increased sensitivity to a broad spectrum of acyl-homoserine lactones] (Cynthia H. Collins, Frances H. Arnold and Jared R. Leadbetter) ''Molecular Microbiology'' 2005 | ||
[ Acyl-homoserine lactone acylase from Ralstonia strain XJ12B represents a novel and potent class of quorum-quenching enzymes] (Yi-Han Lin, Jin-Ling Xu, Jiangyong Hu, Lian-Hui Wang, Say Leong, Jared Renton Leadbetter and Lian-Hui Zhang) ''Molecular Microbiology'' 2003 | [http://www.blackwell-synergy.com/links/doi/10.1046/j.1365-2958.2003.03351.x/abs/ Acyl-homoserine lactone acylase from Ralstonia strain XJ12B represents a novel and potent class of quorum-quenching enzymes] (Yi-Han Lin, Jin-Ling Xu, Jiangyong Hu, Lian-Hui Wang, Say Leong, Jared Renton Leadbetter and Lian-Hui Zhang) ''Molecular Microbiology'' 2003 | ||
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15765063&dopt=Abstract Quorum Sensing and Quorum-quenching enzymes] (Yi-Hu Dong and Lian-Hui Zhang) ''Journal of Microbiology'' 2005 | [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15765063&dopt=Abstract Quorum Sensing and Quorum-quenching enzymes] (Yi-Hu Dong and Lian-Hui Zhang) ''Journal of Microbiology'' 2005 | ||
[ AhlD, an N-acylhomoserine lactonase in Arthrobacter sp., and predicted homologues in other bacteria] (Park, et. al) ''Microbiology'' 2003 | [http://mic.sgmjournals.org/cgi/content/abstract/149/6/1541 AhlD, an N-acylhomoserine lactonase in Arthrobacter sp., and predicted homologues in other bacteria] (Park, et. al) ''Microbiology'' 2003 | ||
[http://www.pnas.org/cgi/content/full/97/7/3526 AiiA, an enzyme that inactivates the acylhomoserine lactone quorum-sensing signal and attenuates the virulence of Erwinia carotovora] ''PNAS'' 2000 | [http://www.pnas.org/cgi/content/full/97/7/3526 AiiA, an enzyme that inactivates the acylhomoserine lactone quorum-sensing signal and attenuates the virulence of Erwinia carotovora] ''PNAS'' 2000 | ||
Revision as of 08:45, 17 July 2006
This site contains all of the papers and books which may be of interest and may be used in the final report.
Synthetic Biology/General Papers
Engineered Gene Circuits (Hasty, McMillin, and Collins) Nature (14 November 2002)
Designer Gene Networks: Towards Fundamental Cellular Control (Hasty et al.) Chaos (13 March 2001)
Biological Modelling
Modelling Gene Expression with Differential Equations (Ching, He, and Church), Pacific Symposium on Biocomputing, 1999, p. 29-40.
Michaelis-Menten Kinetics on Wikipedia
Biology
Molecular Biology of the Cell, 4th ed. (Alberts, et al.) - Online Textbook
Oscillators
Synchronizing Genetic Relaxation Oscillators by Intercell Signalling (David McMillen, Nancy Kopell, Jeff Hasty and J.J. Collins)
A Synthetic Oscillatory Network of Transcriptional Regulators (Michael B. Elowitz & Stanislas Leibler) NATURE, 20 January 2000, vol 403
A Synthetic Gene–Metabolic Oscillator (Eileen Fung, Wilson W. Wong, Jason K. Suen, Thomas Bulter, Sun-gu Lee & James C. Liao) NATURE, 5 May 2005, vol 435
Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability (James E Ferrell Jr) Current Opinion in Chemical Biology 12 February 2002
Modelling the Lux/AiiA Relaxion Oscillator (Christopher Batten) - MIT Computer Science and Artifical Intelligence Laboratory
Presentation from MIT's Synthetic Biology Competition of 2004 - Previous version of iGEM competition, describes oscillator
Specification paper from MIT's Synthetic Biology Competition of 2004 - Details for their design and methology
Lotka-Volterra Model - Implementation in Chemcial Systems
Lotka-Volterra Equations on Wikipedia
Quorum Sensing/Quenching
Directed evolution of Vibrio fischeri LuxR for increased sensitivity to a broad spectrum of acyl-homoserine lactones (Cynthia H. Collins, Frances H. Arnold and Jared R. Leadbetter) Molecular Microbiology 2005
Acyl-homoserine lactone acylase from Ralstonia strain XJ12B represents a novel and potent class of quorum-quenching enzymes (Yi-Han Lin, Jin-Ling Xu, Jiangyong Hu, Lian-Hui Wang, Say Leong, Jared Renton Leadbetter and Lian-Hui Zhang) Molecular Microbiology 2003
Quorum Sensing and Quorum-quenching enzymes (Yi-Hu Dong and Lian-Hui Zhang) Journal of Microbiology 2005
AhlD, an N-acylhomoserine lactonase in Arthrobacter sp., and predicted homologues in other bacteria (Park, et. al) Microbiology 2003
