IGEM:IMPERIAL/2006/Bibliography & Papers

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==Synthetic Biology/General Papers==
==Synthetic Biology/General Papers==
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[ Engineered Gene Circuits] (Hasty, McMillin, and Collins) ''Nature'' (14 November 2002)
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[http://www.nature.com/nature/journal/v420/n6912/abs/nature01257.html Engineered Gene Circuits] (Hasty, McMillin, and Collins) ''Nature'' (14 November 2002)
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[Designer Gene Networks: Towards Fundamental Cellular Control] (Hasty et al.) ''Chaos'' (13 March 2001)
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[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
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[ Modelling the Lux/AiiA Relaxion Oscillator] (Christopher Batten) - MIT Computer Science and Artifical Intelligence Laboratory
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[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
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[ Specification paper from MIT's Synthetic Biology Competition of 2004] - Details for their design and methology
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[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==
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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://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
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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
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[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
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[ AhlD, an N-acylhomoserine lactonase in Arthrobacter sp., and predicted homologues in other bacteria] (Park, et. al) ''Microbiology'' 2003
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[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 11:45, 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.

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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