Research Papers in Synthetic Biology

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• Timothy S. Gardner, Charles R. Cantor, and James J. Collins. Nature 2000. Construction of a genetic toggle switch in Escherichia coli. (Bistable gene regu

• Knight, T., Idempotent Vector Design for Standard Assembly of Biobricks. Unpublished, MIT 2001.

• Weiss, R., Cellular Computation and Communications using Engineered Genetic regulatory Networks. MIT PhD Thesis, 2001.

http://www.ee.princeton.edu/~rweiss/bio-programming/rweiss-phd-thesis.pdf

• Müller-Hill, Benno, "The lac Operon: A Short History of a Genetic Paradigm," Walter de Gruyter, Berlin, 1996.

• Carlson R. 2003. The pace and proliferation of biological technologies. Biosecur Bioterror. 1:203.

• Kodumal SJ, Patel KG, Reid R, Menzella HG, Welch M, Santi DV. 2004. Total synthesis of long DNA sequences: Synthesis of a contiguous 32-kb polyketide synthase gene cluster. PNAS USA 101:15573.

• Smith HO, Hutchison CA 3rd, Pfannkoch C, Venter JC. Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15440-5.

• Stemmer WP, Crameri A, Ha KD, Brennan TM, Heyneker HL. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene. 1995 Oct 16;164(1):49-53.

• Tian J, Gong H, Sheng N, Zhou X, Gulari E, Gao X, Church G. Accurate multiplex gene synthesis from programmable DNA microchips. Nature. 2004 Dec 23; 432(7020): 1050-4.latory network, toggled by transient chemical or thermal induction, to serve as cellular memory) Pubmed Journal

• Elowitz MB, Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000 Jan 20;403(6767):335-8.

• Keiler, K. C., Waller, P. R. & Sauer, R. T. Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science 271, 990-993 (1996)

• Robert T. Batey, Sunny D. Gilbert, and Rebecca K. Montange. Nature 2004. Structure of a Natural Guanine-responsive Riboswitch Complexed with a Metabolite Hypoxanthine. (Distinguishes Riboswitches from Aptamers and Antiswitches; also shows 3D structure of aptamer and ligand) Pubmed Journal

• News Summary of Batey et al. 2004. (Batey et al., paper above)

• Laising Yen et al. Nature 2004. Exogenous Controlof Mammalian Gene Expression through Modulation of RNA Self-cleavage. (mRNA-mediated regulation of translation) Pubmed Journal

• Yina Kuang, Israel Biran, and David R. Walt. Analytical Chemistry 2004. Simultaneously Monitoring Gene Expression Kinetics and Genetic Noise in Single Cells by Optical Well Arrays. (Analysis of two promoters) Pubmed Journal

• Thomas Bulter, Sun-Gu Lee, Wilson WaiChun Wong, Eileen Fung, Michael R. Conner, and James C. Liao. PNAS 2004. Design of artificial cell-cell communication using gene and metabolic networks. (Quorum sensor using acetate signal) Pubmed Journal

• Hideki Kobayashi, Mads Kaern, Michihiro Araki, Kristy Chung, Timothy S. Gardner, Charles R. Cantor, and James J. Collins. Programmable cells: Interfacing natural and engineered gene networks. PNAS. 101(22): 8414-8419. (Toggle switch interfaced with 1) SOS signaling pathway for DNA damage response and 2) quorum sensing signalling pathway) Pubmed Journal

• Sara Hooshangi, Stephan Thiberge, and Ron Weiss. PNAS 2005. Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. (Basic Research Paper) Pubmed Journal

• Bayer, Travis S. and Christina D . Smolke. Nature Biotechnology 2005. Programmable ligand-controlled riboregulators of eukaryotic gene expression. (Antiswitches that turn off or on mRNA translation, regulated by amptamer binding ligands) Pubmed Journal

• Isaacs, Farren J. and James J. Collins. Nature Biotechnology 2005. Plug-and-play with RNA. (Commentary on Bayer & Smolke) Pubmed Journal

• Subhayu Basu, Yoram Gerchman, Cynthia H. Collins, Frances H. Arnold and Ron Weiss. 2005. A synthetic multicellular system for programmed pattern formation. Nature. Vol. 434:1130-1134 (Cool patterns, seeded with senders, with receivers responding to chemical gradients) Pubmed Journal