IGEM:IMPERIAL/2006/Bibliography & Papers
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
The molecular structure and catalytic mechanism of a quorum-quenching N-acyl-L-homoserine lactone hydrolase (Kim et al.) PNAS 2005
