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

• Hasty J, McMillen D, Isaacs F, Collins JJ. 2001. Computational studies of gene regulatory networks: in numero molecular biology. Nat Rev Genet. 2001 Apr;2(4):268-79.
• Guet, Călin C., Elowitz, Michael B., Hsing, Weihong, Leibler, Stanislas Combinatorial Synthesis of Genetic Networks Science 2002 296: 1466-1470

• McAdams HH, Arkin A. Simulation of prokaryotic genetic circuits. Annu Rev Biophys Biomol Struct. 1998; 27:199-224. [http://dx.doi.org/10.1146/annurev.biophys.27.1.199 Link]

• 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 Unpublished, MIT 2001.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) [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10659857&query_hl=2&itool=pubmed_docsum Pubmed] [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html;jsessionid=CFE6987D6A70E6800842DA88D0C63536 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) [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15549109&query_hl=4&itool=pubmed_docsum Pubmed] [http://www.nature.com/nature/journal/v432/n7015/abs/nature03037.html 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) [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15386015&query_hl=7&itool=pubmed_docsum Pubmed] [http://www.nature.com/nature/journal/v431/n7007/abs/nature02844.html 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) [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15516119&query_hl=9&itool=pubmed_docsum Pubmed] [http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ac049053f 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) [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14983004&query_hl=11&itool=pubmed_docsum Pubmed] [http://www.pnas.org/cgi/content/full/101/8/2299 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) [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15159530&query_hl=15&itool=pubmed_docsum Pubmed] [http://www.pnas.org/cgi/content/full/101/22/8414 Journal]

• Sara Hooshangi, Stephan Thiberge, and Ron Weiss. PNAS 2005. Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. (Basic Research Paper) [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15738412&query_hl=17&itool=pubmed_docsum Pubmed] [http://www.pnas.org/cgi/content/full/102/10/3581 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) [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15723047&query_hl=19&itool=pubmed_docsum Pubmed] [http://www.nature.com/nbt/journal/v23/n3/abs/nbt1069.html Journal]

• Isaacs, Farren J. and James J. Collins. Nature Biotechnology 2005. Plug-and-play with RNA. (Commentary on Bayer & Smolke) [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15765083&query_hl=23&itool=pubmed_docsum Pubmed] [http://www.nature.com/nbt/journal/v23/n3/abs/nbt0305-306.html 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) [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15858574&query_hl=21&itool=pubmed_docsum Pubmed] [http://www.nature.com/nature/journal/v434/n7037/abs/nature03461.html Journal]