IGEM:IMPERIAL/2006/Bibliography & Papers

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This site contains all of the papers and books which may be of interest and may be used in the final report.
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==
==Synthetic Biology/General Papers==
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[http://155.198.83.35/igemwiki2006/mediawiki-1.6.6/images/4/4a/Nature01257.pdf Engineered Gene Circuits] (Hasty, McMillin, and Collins) ''Nature'' (14 November 2002)
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[ Engineered Gene Circuits] (Hasty, McMillin, and Collins) ''Nature'' (14 November 2002)
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[http://155.198.83.35/igemwiki2006/mediawiki-1.6.6/images/d/df/0103034.pdf Designer Gene Networks: Towards Fundamental Cellular Control] (Hasty et al.) ''Chaos'' (13 March 2001)
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[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
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[http://155.198.83.35/igemwiki2006/mediawiki-1.6.6/images/1/10/Modeling-ssbc04.pdf Modelling the Lux/AiiA Relaxion Oscillator] (Christopher Batten) - MIT Computer Science and Artifical Intelligence Laboratory
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[ 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
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[http://155.198.83.35/igemwiki2006/mediawiki-1.6.6/images/1/10/System-spec-ssbc04.pdf Specification paper from MIT's Synthetic Biology Competition of 2004] - Details for their design and methology
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[ 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==
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[http://155.198.83.35/igemwiki2006/mediawiki-1.6.6/images/3/3b/LuxRevolution.pdf 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
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[ 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
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[http://155.198.83.35/igemwiki2006/mediawiki-1.6.6/index.php/Image:J.1365-2958.2003.03351.pdf 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
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[ 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
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[http://155.198.83.35/igemwiki2006/mediawiki-1.6.6/images/a/a3/AhlDpaper.pdf AhlD, an N-acylhomoserine lactonase in Arthrobacter sp., and predicted homologues in other bacteria] (Park, et. al) ''Microbiology'' 2003
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[ 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 10:31, 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.

Contents

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

AiiA, an enzyme that inactivates the acylhomoserine lactone quorum-sensing signal and attenuates the virulence of Erwinia carotovora PNAS 2000

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