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bibtexCitation	bibtexEntryType	author	title	journal	year	month	day	volume	issue	pages	keywords	note	issn	url	abstract
Benner2005a	article	Benner, Steven A. ; Sismour, A. Michael	Synthetic biology	Nature reviews. Genetics.	2005	Jul	xx	6	7	533--543	synthetic biology	10.1038/nrg1637	1471-0056	http://www.nature.com/nrg/journal/v6/n7/abs/nrg1637.html
Brenner2008	article	Brenner, Katie ; You, Lingchong ; Arnold, Frances H.	Engineering microbial consortia: a new frontier in synthetic biology.	Trends in biotechnology	2008	Jul	31				biotechnology	10.1016/j.tibtech.2008.05.004	0167-7799	http://www.ncbi.nlm.nih.gov/pubmed/18675483
Kodumal2004	article	Kodumal, Sarah ; Patel, Kedar ; Reid, Ralph ; Menzella, Hugo ; Welch, Mark ; Santi, Daniel	Total synthesis of long DNA sequences: Synthesis of a contiguous 32-kb polyketide synthase gene cluster	Proceedings of the National Academy of Sciences of the United States of America	2004	Nov	02	101	44	15573--15578	synthetic biology	10.1073/pnas.0406911101		http://www.pnas.org/content/101/44/15573.abstract
Hammann2007	article	Hammann, Christian ; Westhof, Eric	Searching genomes for ribozymes and riboswitches	Genome Biology	2007	Apr	30	8	4	210	synthetic biology	10.1186/gb-2007-8-4-210		http://genomebiology.com/2007/8/4/210
Arkin2008	article	Arkin, Adam	Setting the standard in synthetic biology	Nat Biotech	2008	Jul	xx	26	7	771--774	OPINION	10.1038/nbt0708-771		http://www.nature.com/nbt/journal/v26/n7/full/nbt0708-771.html
Church2005a	article	Church, George	Let us go forth and safely multiply	Nature	2005	Nov	24	438	7067	423	synthetic biology	10.1038/438423a	0028-0836	http://dx.doi.org/10.1038/438423a
Check2005a	article	Check, Erika	Synthetic biology: Designs on life	Nature	2005	Nov	24	438	7067	417--418	synthetic biology	10.1038/438417a		http://dx.doi.org/10.1038/438417a
Pryciak2008	article	Pryciak, Peter	SYSTEMS BIOLOGY: Customized Signaling Circuits	Science	2008	Mar	14	319	5869	1489--1490	signalling	10.1126/science.1156414		http://www.sciencemag.org/cgi/content/full/319/5869/1489?ck=nck
ref9	article		Rewiring Bacteria, Two Components at a Time	Cell	2008	xx	xx	133	6	947	synthetic biology	10.1016/j.cell.2008.05.035	00928674	http://dx.doi.org/10.1016/j.cell.2008.05.035
Greber2007	article	Greber, David ; Fussenegger, Martin	Mammalian synthetic biology: Engineering of sophisticated gene networks	Journal of Biotechnology	2007	Jul	xx	130		329--345	Biopharmaceutical manufacturing	10.1016/j.jbiotec.2007.05.014		http://www.sciencedirect.com/science/article/B6T3C-4NT9G60-6/1/be91f43dd87b2e4e80afa221d5ffbc18	With the recent development of a wide range of inducible mammalian transgene control systems it has now become possible to create functional synthetic gene networks by linking and connecting systems into various configurations. The past 5 years has thus seen the design and construction of the first synthetic mammalian gene regulatory networks. These networks have built upon pioneering advances in prokaryotic synthetic networks and possess an impressive range of functionalities that will some day enable the engineering of sophisticated inter- and intra-cellular functions to become a reality. At a relatively simple level, the modular linking of transcriptional components has enabled the creation of genetic networks that are strongly analogous to the architectural design and functionality of electronic circuits. Thus, by combining components in different serial or parallel configurations it is possible to produce networks that follow strict logic in integrating multiple independent signals (logic gates and transcriptional cascades) or which temporally modify input signals (time-delay circuits). Progressing in terms of sophistication, synthetic transcriptional networks have also been constructed which emulate naturally occurring genetic properties, such as bistability or dynamic instability. Toggle switches which possess ``memory'' so as to remember transient administered inputs, hysteric switches which are resistant to stochastic fluctuations in inputs, and oscillatory networks which produce regularly timed expression outputs, are all examples of networks that have been constructed using such properties. Initial steps have also been made in designing the above networks to respond not only to exogenous signals, but also endogenous signals that may be associated with aberrant cellular function or physiology thereby providing a means for tightly controlled gene therapy applications. Moving beyond pure transcriptional control, synthetic networks have also been created which utilize phenomena, such as post-transcriptional silencing, translational control, or inter-cellular signaling to produce novel network-based control both within and between cells. It is envisaged in the not-too-distant future that these networks will provide the basis for highly sophisticated genetic manipulations in biopharmaceutical manufacturing, gene therapy and tissue engineering applications.
ref11	electronic		Bacteria can be turned into living computers - Telegraph - on article in J Biol Eng								synthetic biology			http://www.telegraph.co.uk/earth/main.jhtml?view=DETAILS&grid=&xml=/earth/2008/05/20/scibacteria120.xml	Bacteria have been turned into ``living computers'' and used to solve a mathematical problem. The feat by an American team shows that computing using living cells is feasible, opening the door to a number of applications including data storage. The research is part of a general effort in ``synthetic biology'' to improve on four billion years of evolution and turn bacteria into living machines to do our bidding. The results, published in the Journal of Biological Engineering, are reported by Karmella Haynes and colleagues from the biology and the mathematics departments of Davidson College, North Carolina and Missouri Western State University, Missouri. They added genes to an innocuous form of the gut bacterium Escherichia coli, a workhorse of genetics research, creating bacterial computers able to solve a classic mathematical puzzle, known as the Burnt Pancake Problem.
ref12	electronic		The crucial role of CS in systems and synthetic biology								computer science			http://portal.acm.org/citation.cfm?id=1342332
Bashor2008a	article	Bashor, Caleb ; Helman, Noah ; Yan, Shude ; Lim, Wendell	Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics	Science	2008	Mar	14	319	5869	1539--1543	Biotech	10.1126/science.1151153		http://www.sciencemag.org/cgi/content/abstract/319/5869/1539
Linshiz2008	article	Linshiz, Gregory ; ben Yehezkel, Tuval ; Kaplan, Shai ; Gronau, Ilan ; Ravid, Sivan ; Adar, Rivka ; Shapiro, Ehud	Recursive construction of perfect DNA molecules from imperfect oligonucleotides	Mol Syst Biol	2008	May	06	4			DNA synthesis	10.1038/msb.2008.26		http://www.nature.com/msb/journal/v4/n1/full/msb200826.html
ref15	electronic		Main Page - 2008.igem.org								genome			http://2008.igem.org/Main_Page	iGEM is the premiere undergraduate Synthetic Biology competition. Student teams are given a kit of biological parts at the beginning of the summer. Working at their own schools over the summer, they use these parts and new parts of their own design to build biological systems and operate them in living cells. During the weekend of November 8-9, they present their work at the iGEM Competition Jamboree at MIT and have a chance to win awards. They add their new parts to the Registry of Standard Biological Parts for the students in the next year's competition.
ref16	electronic		PLoS Computational Biology: Biosynthetic Potentials of Metabolites and Their Hierarchical Organization								to read			http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000049
ref17	electronic		PLoS Computational Biology: The Evolution of Robust Development and Homeostasis in Artificial Organisms								synthetic biology			http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000030
Serrano2007	article	Serrano, Luis	Synthetic biology: promises and challenges	Mol Syst Biol	2007	Dec	18	3			synthetic biology	10.1038/msb4100202		http://www.nature.com/msb/journal/v3/n1/full/msb4100202.html
Doktycz2007	article	Doktycz, Mitchel ; Simpson, Michael	Nano-enabled synthetic biology	Mol Syst Biol	2007	Jul	10	3			synthetic biology	10.1038/msb4100165		http://www.nature.com/msb/journal/v3/n1/full/msb4100165.html
Bashor2008b	article	Bashor, Caleb ; Helman, Noah ; Yan, Shude ; Lim, Wendell	Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics	Science	2008	Mar	14	319	5869	1539--1543	synthetic biology	10.1126/science.1151153		http://www.sciencemag.org/cgi/content/full/319/5869/1539
Gibson2008	article	Gibson, Daniel G. ; Benders, Gwynedd A. ; Andrews-Pfannkoch, Cynthia ; Denisova, Evgeniya A. ; Baden-Tillson, Holly ; Zaveri, Jayshree ; Stockwell, Timothy B. ; Brownley, Anushka ; Thomas, David W. ; Algire, Mikkel A. ; Merryman, Chuck ; Young, Lei ; Noskov, Vladimir N. ; Glass, John I. ; Venter, J. Craig ; Hutchison, Clyde A. III ; Smith, Hamilton O.	Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome	Science (New York, N.Y.)	2008	Jan	24	319	5867	1151721--1220	Venter	10.1126/science.1151721	1095-9203	http://dx.doi.org/10.1126/science.1151721
ref22	electronic		Synthetic Gene Circuits: Design with Directed Evolution - Annual Review of Biophysics and Biomolecular Structure, 36(1):1 - Abstract								review			http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.biophys.36.040306.132600
ref23	article		Synthetic Gene Circuits: Design with Directed Evolution	Annual Review of Biophysics and Biomolecular Structure	2007	xx	xx	36	1	1	BioBrick Characterisation	10.1146/annurev.biophys.36.040306.132600	10568700	http://dx.doi.org/10.1146/annurev.biophys.36.040306.132600
Sauro2008	article	Sauro, Herbert	Modularity defined	Mol Syst Biol	2008	Feb	12	4			systems biology	10.1038/msb.2008.3		http://www.nature.com/msb/journal/v4/n1/full/msb20083.html	commentary on Del Vecchio et al (2008).
ref25	electronic		From the cells up | Science | The Guardian								synthetic biology			http://www.guardian.co.uk/science/2005/mar/10/science.research
ref26	electronic		Laying the foundations for a bio-economy 2008								carlson			http://www.springerlink.com/content/n211746672413507/fulltext.pdf
ref27	electronic		hackwriters.com - 21st Century Identity - Memory and Personality - Kim Pfiefer								emergent evolution			http://www.hackwriters.com/identity21.htm	The coming horrors of body-parts manufacture and cloning.
Benders2008	article	Benders, Gwynedd ; Hamilton, And	Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome	Science	2008	Jan	24			1151721	synthetic biology	10.1126/science.1151721		http://www.sciencemag.org/cgi/content/abstract/319/5867/1215?sa_campaign=Email/toc/29-February-2008/10.1126/science.1151721	We have synthesized a 582,970 bp Mycoplasma genitalium genome. This synthetic genome, named M. genitalium JCVI-1.0, contains all the genes of wild-type M. genitalium G37 except MG408, which was disrupted by an antibiotic marker to block pathogenicity and to allow for selection. To identify the genome as synthetic, we inserted ``watermarks'' at intergenic sites known to tolerate transposon insertions. Overlapping ``cassettes'' of 5 to 7 kb, assembled from chemically synthesized oligonucleotides, were joined by in vitro recombination to produce intermediate assemblies of approximately 24 kb, 72 kb (``1/8 genome''), and 144 kb (``1/4 genome''), which were all cloned as bacterial artificial chromosomes (BACs) in Escherichia coli. Most of these intermediate clones were sequenced, and clones of all four 1/4 genomes with the correct sequence were identified. The complete synthetic genome was assembled by transformation-associated recombination (TAR) cloning in the yeast Saccharomyces cerevisiae, then isolated and sequenced. A clone with the correct sequence was identified. The methods described here will be generally useful for constructing large DNA molecules from chemically synthesized pieces and also from combinations of natural and synthetic DNA segments.
ref29	electronic		Genome stitched together by hand : Nature News - on article in Science								synthetic biology			http://www.nature.com/news/2008/080124/full/news.2008.522.html	Scientists have succeeded in stitching together an entire bacterial genome, creating in the lab the full set of instructions needed to make a living thing. The stage is now set for the creation of the first artificial organism — and it could be achieved within the year. The genome for the pathogenic bacterium Mycoplasma genitalium was made in the laboratory by Hamilton Smith and his colleagues at the J. Craig Venter Institute in Rockville, Maryland. The genome has 582,970 of the fundamental building blocks of DNA, called nucleotide bases, making it more than a factor of ten longer than the previous-longest stretch of genetic material created by chemical means.
ref30	electronic		ETC Group -								synthetic biology			http://www.etcgroup.org/en/	Synthetic Biology Cartoons
Pennisi2008	article	Pennisi, Elizabeth	Scientists Synthesize a Genome From Scratch - on article in Science	ScienceNOW	2008	Jan	24	2008	124	3	synthetic biology			http://sciencenow.sciencemag.org/cgi/content/full/2008/124/3	Researchers have rebuilt an entire genome from scratch, they report online today in Science. Although the team has yet to demonstrate that this DNA can substitute for the real thing, the work paves the way for customized bacteria that could efficiently produce drugs, biofuels, and other molecules useful to humankind. Ever since his group decoded the genome of Mycoplasma genitalium, a parasitic bacterium that lives in the human urogenital tract, sequencing maverick J. Craig Venter has wanted to remake the bug's genome in the lab. At just under 600,000 bases, M. genitalium sports the smallest known genome for a free-living organism, and Venter hoped that an artificial genome could be modified to turn the bacterium into a living chemical-manufacturing plant.
ref32	electronic		Scientists Take New Step Toward Man-Made Life - on article in Science								synthetic biology			http://www.nytimes.com/2008/01/24/science/24cnd-genome.html	Taking a significant step toward the creation of man-made forms of life, researchers reported Thursday that they had manufactured the entire genome of a bacterium by painstakingly stitching together its chemical components. While scientists had previously synthesized the complete DNA of viruses, this is the first time it has been done for bacteria, which are much more complex. The genome is more than 10 times as long as the longest piece of DNA ever previously synthesized.
Sidney2007a	article	Sidney, Robert ; Cox, ; Surette, Michael ; Elowitz, Michael	Programming gene expression with combinatorial promoters	Mol Syst Biol	2007	Nov	13	3			Promoter	10.1038/msb4100187		http://www.nature.com/msb/journal/v3/n1/full/msb4100187.html
ref34	article		Systems interface biology	Journal of The Royal Society Interface	2006	xx	xx	3	10	603	stochastic	10.1098/rsif.2006.0143		http://dx.doi.org/10.1098/rsif.2006.0143
Cox2007	article	Cox, Robert Sidney ; Surette, Michael ; Elowitz, Michael	Programming gene expression with combinatorial promoters	Mol Syst Biol	2007	Nov	13	3			synthetic biology	10.1038/msb4100187		http://www.nature.com/msb/journal/v3/n1/full/msb4100187.html
ref36	article		Programming and engineering biological networks	Current Opinion in Structural Biology	2006	xx	xx	16	4	551	synthetic biology	10.1016/j.sbi.2006.06.011		http://dx.doi.org/10.1016/j.sbi.2006.06.011
ref37	electronic		Registry of Standard Biological Parts								registry			http://parts.mit.edu/registry/index.php/Main_Page
ref38	electronic		BioMed Central | Abstract | 1752-0509-1-50 | Noise-induced switches in network systems of the genetic toggle switch								noise			http://www.biomedcentral.com/1752-0509/1/50
Sidney2007b	article	Sidney, Robert ; Cox, ; Surette, Michael ; Elowitz, Michael	Programming gene expression with combinatorial promoters	Mol Syst Biol	2007	Nov	13	3			synthetic biology	10.1038/msb4100187		http://www.nature.com/msb/journal/v3/n1/full/msb4100187.html
ref40	article		Noise and kinetics of LuxR positive feedback loops	Biochemical and Biophysical Research Communications	2007	xx	xx	363	3	667	synthetic biology	10.1016/j.bbrc.2007.09.057		http://dx.doi.org/10.1016/j.bbrc.2007.09.057
ref41	article		Design and implementation of three incoherent feed-forward motif based biological concentration sensors	Systems and Synthetic Biology	2007	xx	xx				synthetic biology	10.1007/s11693-007-9008-6	18725325	http://dx.doi.org/10.1007/s11693-007-9008-6
ref42	electronic		BBC NEWS | Science/Nature | Creating life in the laboratory								synthetic biology			http://news.bbc.co.uk/2/hi/science/nature/7041353.stm	The race to create life version 2.0 is under way. The J Craig Venter Institute scientists are aiming to craft a ``minimal genome''- the smallest group of genes an organism needs to survive and function - and insert it into an empty cell. This stripped-down genome has been established with the help of a simple bacterium, Mycoplasma genitalium, by knocking out its genes, one by one, until only the genetic material vital for survival was found.
ref43	article		Expanding the metabolic engineering toolbox: more options to engineer cells	Trends in Biotechnology	2007	xx	xx	25	3	132	BioBrick Characterisation	10.1016/j.tibtech.2007.01.003		http://dx.doi.org/10.1016/j.tibtech.2007.01.003
Wu2007	article	Wu, Gang ; Dress, Laura ; Freeland, Stephen	Optimal encoding rules for synthetic genes: the need for a community effort	Mol Syst Biol	2007	Sep	18	3			synthetic biology	10.1038/msb4100176		http://www.nature.com/msb/journal/v3/n1/full/msb4100176.html
Murphy2007a	article	Murphy, Kevin ; Bal{\'a}zsi, G{\'a}bor ; Collins, James	Combinatorial promoter design for engineering noisy gene expression.	Proceedings of the National Academy of Sciences of the United States of America	2007	Jul	31	104	31	12726--12731	synthetic biology	10.1073/pnas.0608451104		http://www.pnas.org/cgi/content/abstract/0608451104v1?maxtoshow=&HITS=1&hits=1&RESULTFORMAT=&andorexacttitle=and&titleabstract=synthetic+biology&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&usestrictdates=yes&resourcetype=HWCIT&ct
Luisi2007	article	Luisi, Pier	Chemical Aspects of Synthetic Biology	Chemistry \& Biodiversity	2007	xx	xx	4	4	603--621	synthetic biology	10.1002/cbdv.200790053		http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17443874&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus
ref47	article		Synthetic biology: lessons from the history of synthetic organic chemistry	Nature Chemical Biology	2007	xx	xx	3	9	521--521	synthetic biology	10.1038/nchembio0907-521		http://dx.doi.org/10.1038/nchembio0907-521
ref48	electronic		Prather Group - Home Page								Lab			http://web.mit.edu/prathergroup/index.html	Our research is centered on the design and assembly of recombinant microorganisms for the production of small molecules. More simply, we are harnessing the synthetic power of biology to build microbial chemical factories. Current efforts include the development of tools and methodologies for novel biosynthetic pathway design and the investigation of gene dosage effects on the physiology and productivity of engineered microbes. Our research combines the traditions of metabolic engineering with the practices of biocatalysis to expand and optimize the biosynthetic capacity of microbial systems. A particular focus is the elucidation of design principles for the production of unnatural organic compounds within the framework of the nascent field of synthetic biology. Major Research Areas
Pedraza2005a	article	Pedraza, Juan ; van Oudenaarden, Alexander	Noise propagation in gene networks.	Science (New York, N.Y.)	2005	Mar	25	307	5717	1965--1969	synthetic biology	10.1126/science.1109090		http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15790857&query_hl=12
Hooshangi2005a	article	Hooshangi, Sara ; Thiberge, Stephan ; Weiss, Ron	Ultrasensitivity and noise propagation in a synthetic transcriptional cascade	Proceedings of the National Academy of Sciences	2005	Mar	08	102	10	3581--3586	inverter composition	10.1073/pnas.0408507102		http://dx.doi.org/10.1073/pnas.0408507102
ref51	electronic		Cell -- Deans et al.								synthetic biology			http://www.cell.com/content/article/abstract?uid=PIIS0092867407006848
Murphy2007b	article	Murphy, Kevin ; Balazsi, Gabor ; Collins, James	Combinatorial promoter design for engineering noisy gene expression	Proceedings of the National Academy of Sciences	2007	Jul	31	104	31	12726--12731	synthetic biology	10.1073/pnas.0608451104		http://www.pnas.org/cgi/content/abstract/0608451104v1?maxtoshow=&HITS=1&hits=1&RESULTFORMAT=&andorexacttitle=and&titleabstract=synthetic+biology&andorexacttitleabs=and&andorexactfulltext=and&searchid=1&usestrictdates=yes&resourcetype=HWCIT&ct
Grilly2007	article	Grilly, Chris ; Stricker, Jesse ; Pang, Wyming ; Bennett, Matthew ; Hasty, Jeff	A synthetic gene network for tuning protein degradation in Saccharomyces cerevisiae	Mol Syst Biol	2007	Jul	31	3			synthetic biology	10.1038/msb4100168		http://www.nature.com/msb/journal/v3/n1/full/msb4100168.html
Waldminghaus2007	article	Waldminghaus, Torsten ; Gaubig, Lena ; Narberhaus, Franz	Genome-wide bioinformatic prediction and experimental evaluation of potential RNA thermometers.	Mol Genet Genomics	2007	Jul	24				synthetic biology	10.1007/s00438-007-0272-7		http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17647020&itool=pubmed_DocSum
ref55	article		Toward an artificial cell based on gene expression in vesicles.	Physical Biology	2005	xx	xx	2	3	1--1	synthetic biology	10.1088/1478-3975/2/3/p01		http://www.ncbi.nlm.nih.gov/pubmed/16224117?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus
Rinaudo2007a	article	Rinaudo, Keller ; Bleris, Leonidas ; Maddamsetti, Rohan ; Subramanian, Sairam ; Weiss, Ron ; Benenson, Yaakov	A universal RNAi-based logic evaluator that operates in mammalian cells	Nat Biotech	2007	Jul	xx	25	7	795--801	synthetic biology	10.1038/nbt1307		http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt1307.html
Szczepek2007	article	Szczepek, Michal ; Brondani, Vincent ; B{\"u}chel, Janine ; Serrano, Luis ; Segal, David ; Cathomen, Toni	Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases.	Nature biotechnology	2007	Jul	xx	25	7	786--793	zinc-finger nuclease	10.1038/nbt1317		http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt1317.html
Miller2007	article	Miller, Jeffrey ; Holmes, Michael ; Wang, Jianbin ; Guschin, Dmitry ; Lee, Ya-Li ; Rupniewski, Igor ; Beausejour, Christian ; Waite, Adam ; Wang, Nathaniel ; Kim, Kenneth ; Gregory, Philip ; Pabo, Carl ; Rebar, Edward	An improved zinc-finger nuclease architecture for highly specific genome editing.	Nature biotechnology	2007	Jul	xx	25	7	778--785	Protein engineering	10.1038/nbt1319		http://dx.doi.org/10.1038/nbt1319
Wang2007	article	Wang, Kaihang ; Neumann, Heinz ; Peak-Chew, Sew ; Chin, Jason	Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion.	Nature biotechnology	2007	Jul	xx	25	7	770--777	orthogonal	10.1038/nbt1314		http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt1314.html
Walter2007	article	Walter, Jessica ; Greenfield, Derek ; Bustamante, Carlos ; Liphardt, Jan	Light-powering Escherichia coli with proteorhodopsin	Proceedings of the National Academy of Sciences	2007	Feb	13	104	7	2408--2412	proteorhodopsin	10.1073/pnas.0611035104		http://dx.doi.org/10.1073/pnas.0611035104
Drubin2007a	article	Drubin, David ; Way, Jeffrey ; Silver, Pamela	Designing biological systems.	Genes \& development	2007	Feb	01	21	3	242--254	be theory	10.1101/gad.1507207		http://www.genesdev.org/cgi/content/full/21/3/242
Andrianantoandro2006a	article	Andrianantoandro, Ernesto ; Basu, Subhayu ; Karig, David ; Weiss, Ron	Synthetic biology: new engineering rules for an emerging discipline.	Molecular systems biology	2006	xx	xx	2		2006--0028	synthetic biology	10.1038/msb4100073		http://www.nature.com/msb/journal/v2/n1/full/msb4100073.html
Ball2007a	article	Ball, Philip	Synthetic biology: Designs for life	Nature	2007	Jul	05	448	7149	32--33	synthetic biology	10.1038/448032a		http://www.nature.com/nature/journal/v448/n7149/full/448032a.html
Ball2007b	article	Ball, Philip	Synthetic biology: Designs for life - on article in Science	Nature	2007	Jul	05	448	7149	32--33	synthetic biology	10.1038/448032a		http://www.nature.com/nature/journal/v448/n7149/full/448032a.html	The genome of one bacterium has been successfully replaced with that of a different bacterium, transforming one species into another. This development is a harbinger of whole-genome engineering for practical ends.
Yeh2007a	article	Yeh, Brian ; Rutigliano, Robert ; Deb, Anrica ; Bar-Sagi, Dafna ; Lim, Wendell	Rewiring cellular morphology pathways with synthetic guanine nucleotide exchange factors	Nature	2007	May	31	447	7144	596--600	gtpase	10.1038/nature05851		http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature05851.html
Lartigue2007a	article	Lartigue, Carole ; Glass, John ; Alperovich, Nina ; Pieper, Rembert ; Parmar, Prashanth ; Hutchison, III Clyde ; Smith, Hamilton ; Venter, J.	Genome Transplantation in Bacteria: Changing One Species to Another	Science	2007	Jun	28			1144622--1144622	synthetic biology	10.1126/science.1144622		http://www.sciencemag.org/cgi/content/abstract/1144622	My comments: Venter and colleagues describe a method for replacing a chromosome in one bacteria by another from another bacteria (the two bacteria being distinct species, although {\textasciitilde}95\% identical at the genome level in this case). One of the challenges was in the extraction of intact, protein-free chromosomes from cells. The actual transfer then relies on polyethylene glycol (PEG), known to promote fusion of eukaryotic cells, but the actual transplantation mechanism is not understood. The authors hypothesize that two chromosome-free cells might fuse around a naked chromosome, with low frequency (but the resulting cells are selected using an antibiotics resistance gene). Nonetheless, this is clearly an important step forward for synthetic biology (you can imagine that entirely synthesized chromosomes will be inserted into empty host cells using this type of approaches).
ref67	electronic		Scientists Report DNA Transplant - washingtonpost.com - on article in Science								synthetic biology			http://www.washingtonpost.com/wp-dyn/content/article/2007/06/28/AR2007062802046.html	Scientists said yesterday that they had transplanted a microbe's entire, tangled mass of DNA into a closely related organism, a delicate operation that cleanly transformed the recipient from one species into the other. After the operations, the ``patients'' -- single-celled organisms resembling bacteria -- dutifully obeyed their new genomes and by every measure exhibited the biological personas of the donors.
Pennisi2007	article	Pennisi, Elizabeth	GENETICS: Replacement Genome Gives Microbe New Identity	Science	2007	Jun	29	316	5833	1827--1827	synthetic biology	10.1126/science.316.5833.1827a		http://www.sciencemag.org/cgi/content/full/316/5833/1827a	For decades, molecular biologists have genetically modified microbes and other kinds of cells by adding short DNA sequences, whole genes, and even large pieces of chromosomes. Now, in a feat reported in a paper published online by Science this week (www.sciencemag.org/cgi/content/abstract/1144622), one group has induced a bacterium to take up an entire 1.08-million-base genome in one gulp. In doing so, microbiologist John Glass and his colleagues at the J. Craig Venter Institute in Rockville, Maryland, have transformed one bacterial species into another.
Lartigue2007b	article	Lartigue, Carole ; Glass, John ; Alperovich, Nina ; Pieper, Rembert ; Parmar, Prashanth ; Hutchison, III Clyde ; Smith, Hamilton ; Venter, J.	Genome Transplantation in Bacteria: Changing One Species to Another	Science	2007	Jun	28			1144622--1144622	synthetic biology	10.1126/science.1144622		http://www.sciencemag.org/cgi/content/abstract/1144622	As a step toward propagation of synthetic genomes, we completely replaced the genome of a bacterial cell with one from another species by transplanting a whole genome as naked DNA. Intact genomic DNA from Mycoplasma mycoides large colony (LC), virtually free of protein, was transplanted into Mycoplasma capricolum cells by polyethylene glycol-mediated transformation. Cells selected for tetracycline resistance, carried by the M. mycoides LC chromosome, contain the complete donor genome and are free of detectable recipient genomic sequences. These cells that result from genome transplantation are phenotypically identical to the M. mycoides LC donor strain as judged by several criteria.
ref70	electronic		Genome transplant makes species switch - on article in Science								synthetic biology			http://www.nature.com/news/2007/070625/full/070625-9.html	By transplanting their genomes, US scientists have converted one species into another. John Glass and his co-workers at the J. Craig Venter Institute in Rockville, Maryland, have taken DNA from a bacterium called Mycoplasma mycoides and inserted it into cells of the closely related species Mycoplasma capricolum. They find that the recipient cells with the new genome behave like those of the donor species, making protein molecules characteristic of the donor. It's like re-booting a cell with a new operating system, says Glass.
ref71	article		Meanings of 'life'	Nature	2007	Jun	28	447	7148	1031--1032	synthetic biology	10.1038/4471031b		http://www.nature.com/nature/journal/v447/n7148/full/4471031b.html
Kaiser2007	article	Kaiser, Jocelyn	SYNTHETIC BIOLOGY: Attempt to Patent Artificial Organism Draws a Protest	Science	2007	Jun	15	316	5831	1557--1557	synthetic biology	10.1126/science.316.5831.1557		http://www.sciencemag.org/cgi/content/full/316/5831/1557	An activist group's concern about maverick genome sequencer J. Craig Venter's intention to patent an entirely synthetic free-living organism has thrown a spotlight on the emerging intellectual-property landscape in this hot new field. The protesters claim that Venter wants his company to become the Microsoft of synthetic biology, dominating the industry.
ref73	electronic		Man-made microbe 'to create endless biofuel' | Uk News | News | Telegraph								synthetic biology			http://www.telegraph.co.uk/news/main.jhtml?xml=/news/2007/06/08/nbiofuel108.xml	A scientist is poised to create the world's first man-made species, a synthetic microbe that could lead to an endless supply of biofuel. Craig Venter, an American who cracked the human genome in 2000, has applied for a patent at more than 100 national offices to make a bacterium from laboratory-made DNA. It is part of an effort to create designer bugs to manufacture hydrogen and biofuels, as well as absorb carbon dioxide and other harmful greenhouse gases.
Rinaudo2007b	article	Rinaudo, Keller ; Bleris, Leonidas ; Maddamsetti, Rohan ; Subramanian, Sairam ; Weiss, Ron ; Benenson, Yaakov	A universal RNAi-based logic evaluator that operates in mammalian cells	Nat Biotech	2007	May	21	advanced online publication			synthetic biology	10.1038/nbt1307		http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt1307.html
Dueber2007	article	Dueber, John ; Mirsky, Ethan ; Lim, Wendell	Engineering synthetic signaling proteins with ultrasensitive input/output control	Nat Biotech	2007	Jun	xx	25	6	660--662	synthetic biology	10.1038/nbt1308		http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt1308.html
ref76	electronic		ETC Group - Publications - Patenting Pandora’s Bug: Goodbye, Dolly...Hello, Synthia! J. Craig Venter Institute Seeks Monopoly Patents on the World’s First-Ever Human-Made Life Form								synthetic biology			http://www.etcgroup.org/en/materials/publications.html?pub_id=631	The Venter Institute - named for its founder and CEO, J. Craig Venter, the scientist who led the private sector race to map the Human Genome - is applying for worldwide patents on what they refer to as ``Mycoplasma laboratorium.''
ref77	electronic		Second Life, or Not? -- Kaiser 2007 (607): 3 -- ScienceNOW								synthetic biology			http://sciencenow.sciencemag.org/cgi/content/full/2007/607/3	An activist group is raising a ruckus about what it says may be the first effort to patent an entirely synthetic free-living organism. It says the patent application, filed by maverick genome sequencer Craig Venter's institute on an idea that has likely not yet been achieved, would tie up a new technology and could aid bioterrorists. But others say there's nothing new or surprising about the patenting effort. The work involves a simple bacterium called Mycoplasma genitalium that Venter's eponymous institute in Rockville, Maryland, has been tinkering with for years. An early goal was to determine the minimum number of genes for life, and in 1999, scientists there published a rough tally. Now, they want to synthesize this ``minimal genome'' from scratch, get it working inside a cell, then add genes that would enable the bug to crank out hydrogen or ethanol to produce cheap energy.
Andrianantoandro2006b	article	Andrianantoandro, Ernesto ; Basu, Subhayu ; Karig, David ; Weiss, Ron	Synthetic biology: new engineering rules for an emerging discipline.	Molecular systems biology	2006	xx	xx	2		2006--0028	synthetic biology	10.1038/msb4100073		http://www.nature.com/msb/journal/v2/n1/full/msb4100073.html
Yeh2007b	article	Yeh, Brian ; Rutigliano, Robert ; Deb, Anrica ; Bar-Sagi, Dafna ; Lim, Wendell	Rewiring cellular morphology pathways with synthetic guanine nucleotide exchange factors	Nature	2007	May	31	447	7144	596--600	synthetic biology	10.1038/nature05851		http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature05851.html
ref80	electronic		Scientists Push the Boundaries of Human Life - Newsweek: International Editions - MSNBC.com								synthetic biology			http://www.msnbc.msn.com/id/18882828/site/newsweek/page/0/
ref81	electronic		Synthetic biology--putting engineering into biology -- Heinemann and Panke 22 (22): 2790 -- Bioinformatics								synthetic biology			http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/22/2790
ref82	electronic		Main Page - IGEM								synthetic biology			http://parts2.mit.edu/wiki/index.php/Main_Page	The international Genetically Engineered Machine competition iGEM is an international arena where student teams compete to design and assemble engineered machines using advanced genetic components and technologies. Learn more.
ref83	electronic		SynBERC - Synthetic Biology Engineering Research Center								synthetic biology			http://www.synberc.org/index.html	Consortium of organizations to develop synthetic biology applocations, tools and ethics. Promoted by Drew Endy and George Church. also linked to the IGEM program.
ref84	article		The Generation of New Protein Functions by the Combination of Domains	Structure	2007	xx	xx	15	1	85--85	synthetic biology	10.1016/j.str.2006.11.009		http://dx.doi.org/10.1016/j.str.2006.11.009
Chen2007	article	Chen, Chun-Hong ; Huang, Haixia ; Ward, Catherine ; Su, Jessica ; Schaeffer, Lorian ; Guo, Ming ; Hay, Bruce	A synthetic maternal-effect selfish genetic element drives population replacement in Drosophila.	Science (New York, N.Y.)	2007	Apr	27	316	5824	597--600	synthetic biology	10.1126/science. 1138595		http://www.sciencemag.org/cgi/content/abstract/1138595
ref86	article		A synthetic biology challenge: making cells compute	Molecular BioSystems	2007	xx	xx				synthetic biology	10.1039/b618473c		http://dx.doi.org/10.1039/b618473c
ref87	article		Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations	Science	2007	xx	xx	316	5824	593--593	Lab techniques	10.1126/science.1132067		http://www.sciencemag.org/cgi/content/abstract/1132067v1?etoc
ref88	electronic		In situ DNA synthesis on glass substrate for microarray fabrication using self-focusing acoustic transducer								synthetic biology			http://ieeexplore.ieee.org/search/srchabstract.jsp?arnumber=1613915&isnumber=33881&punumber=8856&k2dockey=1613915@ieeejrns&query=(+eun+sok+kim%3Cin%3Eau)&pos=3	A proof of concept of using SFATs (self-focusing acoustic transducers) to print DNA oligos.
Chan2005	article	Chan, Leon ; Kosuri, Sriram ; Endy, Drew	Refactoring bacteriophage T7.	Molecular systems biology	2005	xx	xx	1		2005--0018	refactoring	10.1038/msb4100025		http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16729053&query_hl=5&itool=pubmed_docsum
Zhang2007	article	Zhang, Feng ; Wang, Li-Ping ; Brauner, Martin ; Liewald, Jana ; Kay, Kenneth ; Watzke, Natalie ; Wood, Phillip ; Bamberg, Ernst ; Nagel, Georg ; Gottschalk, Alexander ; Deisseroth, Karl	Multimodal fast optical interrogation of neural circuitry	Nature	2007	Apr	05	446	7136	633--639	Neurobiology	10.1038/nature05744		http://www.nature.com/nature/journal/v446/n7136/abs/nature05744.html
ref91	electronic		Applied Biodynamics Laboratory, Boston U.								Lab			http://www.bu.edu/abl/	Our lab is focused on developing and using nonlinear dynamics approaches to study, mimic and improve the function of biological systems. We are currently working in three areas:SB andsynrhetic biology
Andrianantoandro2006c	article	Andrianantoandro, Ernesto ; Basu, Subhayu ; Karig, David ; Weiss, Ron	Synthetic biology: new engineering rules for an emerging discipline.	Molecular systems biology [electronic resource].	2006	xx	xx	2		2006--0028	systems biology	10.1038/msb4100073		http://www.nature.com/msb/journal/v2/n1/full/msb4100073.html
Heinemann2006	article	Heinemann, Matthias ; Panke, Sven	Synthetic biology--putting engineering into biology.	Bioinformatics (Oxford, England)	2006	Nov	15	22	22	2790--2799	systems biology	10.1093/bioinformatics/btl469		http://dx.doi.org/10.1093/bioinformatics/btl469
Drubin2007b	article	Drubin, David ; Way, Jeffrey ; Silver, Pamela	Designing biological systems.	Genes \& development	2007	Feb	01	21	3	242--254	systems biology	10.1101/gad.1507207		http://www.genesdev.org/cgi/content/full/21/3/242
Sismour2005	article	Sismour, A. ; Benner, Steven	Synthetic biology.	Expert opinion on biological therapy	2005	Nov	xx	5	11	1409--1414	systems biology	10.1517/14712598.5.11.1409		http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16255644&query_hl=1&itool=pubmed_DocSum
ref96	electronic		SpringerLink - Journal Article								synthetic biology			http://www.springerlink.com/content/k7377586j4305247/
Yokobayashi2002a	article	Yokobayashi, Yohei ; Weiss, Ron ; Arnold, Frances	From the Cover: Directed evolution of a genetic circuit	Proceedings of the National Academy of Sciences	2002	Dec	24	99	26	16587--16591	synthetic biology	10.1073/pnas.252535999		http://www.pnas.org/cgi/content/abstract/99/26/16587?etoc
ref98	article		Genetic parts to program bacteria	Current Opinion in Biotechnology	2006	xx	xx	17	5	548--548	synthetic biology	10.1016/j.copbio.2006.09.001		http://dx.doi.org/10.1016/j.copbio.2006.09.001
ref99	article		The Generation of New Protein Functions by the Combination of Domains	Structure	2007	xx	xx	15	1	85--85	structures	10.1016/j.str.2006.11.009		http://dx.doi.org/10.1016/j.str.2006.11.009
Sprinzak2005a	article	Sprinzak, David ; Elowitz, Michael	Reconstruction of genetic circuits	Nature	2005	Nov	24	438	7067	443--448	synthetic biology	10.1038/nature04335		http://www.nature.com/nature/journal/v438/n7067/full/nature04335.html
Hasty2001	book	Hasty, Jeff ; Isaacs, Farren ; Dolnik, Milos ; McMillen, David ; Collins, J. J.	Designer Gene Networks: Towards Fundamental Cellular Control		2001	Mar	13				genetic network			http://arxiv.org/abs/physics/0103034
Fox2007	article	Fox, Richard ; Davis, S. ; Mundorff, Emily ; Newman, Lisa ; Gavrilovic, Vesna ; Ma, Steven ; Chung, Loleta ; Ching, Charlene ; Tam, Sarena ; Muley, Sheela ; Grate, John ; Gruber, John ; Whitman, John ; Sheldon, Roger ; Huisman, Gjalt	Improving catalytic function by ProSAR-driven enzyme evolution	Nat Biotech	2007	Feb	18	advanced online publication			directed evolution	10.1038/nbt1286		http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt1286.html
ref103	article		Synthetic biology projects in vitro	Genome Research	2006	xx	xx	17	1	1--1	Cell-Free System	10.1101/gr.5776007		http://www.genome.org/cgi/content/abstract/gr.5776007v1?papetoc
ref104	article		Genome Biology | Full text | Fast, cheap and somewhat in control	Genome Biology	2006	xx	xx	7	8	114--114	synthetic biology	10.1186/gb-2006-7-8-114		http://dx.doi.org/10.1186/gb-2006-7-8-114
Thattai2004	article	Thattai, Mukund ; Van Oudenaarden, Alexander	Stochastic Gene Expression in Fluctuating Environments	Genetics	2004	May	01	167	1	523--530	gene expression	10.1534/genetics.167.1.523		http://www.genetics.org/cgi/content/abstract/167/1/523
Li2007	article	Li, Mamie ; Elledge, Stephen	Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC	Nat Meth	2007	Feb	11	advanced online publication			method	10.1038/nmeth1010		http://www.nature.com/nmeth/journal/vaop/ncurrent/abs/nmeth1010.html
ref107	electronic		ETC Group - Publications - Extreme Genetic Engineering: An Introduction to Synthetic Biology								tech talk 2-12-07	a contrary position on some synthetic bio issues. well worth checking out to be aware of the government and world-wide issues that may shape this field's future. (smolkelab 2007-02-12 16:56:43)		http://www.etcgroup.org/en/materials/publications.html?id=602	* If a small circle of synthetic biologists get their way, governance of extreme genetic engineering will be left entirely in their hands. * There must be a broad societal debate on synthetic biology’s wider socio-economic and ethical implications, including potential impacts on health, environment, human rights and security. * It is not for scientists to either control public discourse or determine regulatory frameworks.
Shou2007a	article	Shou, Wenying ; Ram, Sri ; Vilar, Jose	From the Cover: Synthetic cooperation in engineered yeast populations	Proceedings of the National Academy of Sciences	2007	Feb	06	104	6	1877--1882	tech talk 2-12-07	10.1073/pnas.0610575104		http://www.pnas.org/cgi/content/abstract/0610575104v1	Cooperative interactions are key to diverse biological phenomena ranging from multicellularity to mutualism. Such diversity makes the ability to create and control cooperation desirable for potential applications in areas as varied as agriculture, pollutant treatment, and medicine. Here we show that persistent cooperation can be engineered by introducing a small set of genetic modifications into previously noninteracting cell populations. Specifically, we report the construction of a synthetic obligatory cooperative system, termed CoSMO (cooperation that is synthetic and mutually obligatory), which consists of a pair of nonmating yeast strains, each supplying an essential metabolite to the other strain. The behavior of the two strains in isolation, however, revealed unintended constraints that restrict cooperation, such as asymmetry in starvation tolerance and delays in nutrient release until near cell death. However, the joint system is shown mathematically and experimentally to be viable over a wide range of initial conditions, with oscillating population ratio settling to a value predicted by nutrient supply and consumption. Unexpectedly, even in the absence of explicitly engineered mechanisms to stabilize cooperation, the cooperative system can consistently develop increased ability to survive reductions in population density. Extending synthetic biology from the design of genetic circuits to the engineering of ecological interactions, CoSMO provides a quantitative system for linking processes at the cellular level to the collective behavior at the system level, as well as a genetically tractable system for studying the evolution of cooperation.
Drubin2007c	article	Drubin, David ; Way, Jeffrey ; Silver, Pamela	Designing biological systems	Genes and Development	2007	Feb	01	21	3	242--254	review	10.1101/gad.1507207		http://www.genesdev.org/cgi/content/full/21/3/242
ref110	article		Light-powering Escherichia coli with proteorhodopsin	Proceedings of the National Academy of Sciences	2007	xx	xx				energy	10.1073/pnas.0611035104		http://dx.doi.org/10.1073/pnas.0611035104
Shou2007b	article	Shou, Wenying ; Ram, Sri ; Vilar, J. M. G.	Synthetic cooperation in engineered yeast populations	Proceedings of the National Academy of Sciences	2007	Jan	31			0610575104--0610575104	yeast	10.1073/pnas.0610575104		http://www.pnas.org/cgi/content/abstract/0610575104v1
Lim2007	article	Lim, Han ; Van Oudenaarden, Alexander	A multistep epigenetic switch enables the stable inheritance of DNA methylation states	Nat Genet	2007	Feb	xx	39	2	269--275	synthetic biology	10.1038/ng1956		http://www.nature.com/ng/journal/vaop/ncurrent/abs/ng1956.html
ref113	article		Synthetic biology projects in vitro	Genome Research	2006	xx	xx	17	1	1--1	synthetic biology	10.1101/gr.5776007		http://www.genome.org/cgi/content/abstract/gr.5776007v1?papetoc
ref114	article		Genetic parts to program bacteria	Current Opinion in Biotechnology	2006	xx	xx	17	5	548--548	synthetic biology	10.1016/j.copbio.2006.09.001		http://dx.doi.org/10.1016/j.copbio.2006.09.001
Simpson2006	article	Simpson, Michael	Cell-free synthetic biology: a bottom-up approach to discovery by design	Mol Syst Biol	2006	Dec	12	2			Cell-Free System	10.1038/msb4100104		http://www.nature.com/msb/journal/v2/n1/full/msb4100104.html
Kim2006	article	Kim, Jongmin ; White, Kristin ; Winfree, Erik	Construction of an in vitro bistable circuit from synthetic transcriptional switches	Mol Syst Biol	2006	Dec	12	2			synthetic biology	10.1038/msb4100099		http://www.nature.com/msb/journal/v2/n1/full/msb4100099.html
ref117	article		A synthetic multicellular system for programmed pattern formation	Nature	2005	xx	xx	434	7037	1130--1130	synthetic biology	10.1038/nature03461		http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15858574
ref118	article		Cellular Logic with Orthogonal Ribosomes	Journal of the American Chemical Society	2005	xx	xx	127	50	17584--17584	synthetic biology	10.1021/ja055338d		http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16351070&query_hl=8&itool=pubmed_docsum
Hasty2002	article	Hasty, Jeff ; McMillen, David ; Collins, J.	Engineered gene circuits	Nature	2002	Nov	14	420	6912	224--230	genetic network	10.1038/nature01257		http://www.nature.com/nature/journal/v420/n6912/full/nature01257.html
ref120	electronic		Zinc Fingers Consortium								genetic network			http://www.zincfingers.org/scientific-background.htm
ref121	article		Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly	Nature Protocols	2006	xx	xx	1	4	1637--1637	genetic network	10.1038/nprot.2006.259		http://www.nature.com/nprot/journal/v1/n3/full/nprot.2006.259.html
ref122	article		Synthetic biology--putting engineering into biology	Bioinformatics	2006	xx	xx	22	22	2790--2790	synthetic biology	10.1093/bioinformatics/btl469		http://dx.doi.org/10.1093/bioinformatics/btl469
Seelig2006	article	Seelig, Georg ; Soloveichik, David ; Zhang, David ; Winfree, Erik	Enzyme-Free Nucleic Acid Logic Circuits	Science	2006	Dec	08	314	5805	1585--1588	genetic network	10.1126/science.1132493		http://www.sciencemag.org/cgi/content/full/314/5805/1585
Forster2006a	article	Forster, Anthony ; Church, George	Synthetic biology projects in vitro	Genome Research	2006	Dec	06			5776007--5776007	synthetic biology	10.1101/gr.5776007		http://www.genome.org/cgi/content/abstract/gr.5776007v1?papetoc
Atsumi2006	article	Atsumi, Shota ; Little, John	A synthetic phage \{lambda\} regulatory circuit	Proceedings of the National Academy of Sciences	2006	Nov	29			0603052103--0603052103	synthetic biology	10.1073/pnas.0603052103		http://www.pnas.org/cgi/content/abstract/0603052103v1?etoc
ref126	electronic		The New Atlantis - The Promise and Perils of Synthetic Biology - Jonathan B. Tucker and Raymond A. Zilinskas								synthetic biology			http://www.thenewatlantis.com/archive/12/tuckerzilinskas.htm
ref127	electronic		Optimizing Biological Circuits: Integrating Rational Design with Directed Evolution								synthetic biology			http://aiche.confex.com/aiche/2006/preliminaryprogram/abstract_52714.htm
Collins2005	article	Collins, Cynthia ; Arnold, Frances ; Leadbetter, Jared	Directed evolution of Vibrio fischeri LuxR for increased sensitivity to a broad spectrum of acyl-homoserine lactones	Molecular Microbiology	2005	xx	xx	55	3	712--723	synthetic biology	10.1111/j.1365-2958.2004.04437.x		http://www.blackwell-synergy.com/links/doi/10.1111/j.1365-2958.2004.04437.x/enhancedabs/
Vilar2006	article	Vilar, Jose	Modularizing gene regulation	Mol Syst Biol	2006	Mar	21	2			gene expression	10.1038/msb4100058		http://www.nature.com/msb/journal/v2/n1/full/msb4100058.html
Wolf2003	article	Wolf, Denise ; Arkin, Adam	Motifs, modules and games in bacteria.	Current opinion in microbiology.	2003	Apr	xx	6	2	125--134	synthetic biology			http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12732301&dopt=Abstract
Michnick2006	article	Michnick, Stephen	A luxRury of synthetic signals	Nat Biotech	2006	Jun	xx	24	6	658--660	pLuxR	10.1038/nbt0606-658		http://www.nature.com/nbt/journal/v24/n6/full/nbt0606-658.html
Cookson2005	article	Cookson, Scott ; Ostroff, Natalie ; Pang, Wyming ; Volfson, Dmitri ; Hasty, And	Monitoring dynamics of single-cell gene expression over multiple cell cycles	Mol Syst Biol	2005	Nov	22	1	1	4100032--4100031	thesis\_chapter\_2	10.1038/msb4100032		http://www.nature.com/msb/journal/v1/n1/full/msb4100032.html
Anderson2006	article	Anderson, J. ; Clarke, Elizabeth ; Arkin, Adam ; Voigt, Christopher	Environmentally controlled invasion of cancer cells by engineered bacteria.	Journal of molecular biology.	2006	Jan	27	355	4	619--627	synthetic biology	10.1016/j.jmb.2005.10.076		http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=16330045&dopt=Citation
ref134	electronic		Tuning genetic control through promoter engineering -- Alper et al. 102 (36): 12678 -- Proceedings of the National Academy of Sciences								synthetic biology			http://www.pnas.org/cgi/content/abstract/102/36/12678
Schibler2005	article	Schibler, Ueli ; Naef, Felix	Cellular oscillators: rhythmic gene expression and metabolism.	Current opinion in cell biology.	2005	Apr	xx	17	2	223--229	synthetic biology	10.1016/j.ceb.2005.01.007		http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15780601&dopt=Citation
Atsumi2004	article	Atsumi, Shota ; Little, John	Regulatory circuit design and evolution using phage \{lambda\}	Genes and Development	2004	Sep	01	18	17	2086--2094	synthetic biology	10.1101/gad.1226004		http://www.genesdev.org/cgi/content/abstract/18/17/2086
Balagadde2005	article	Balagadde, Frederick ; You, Lingchong ; Hansen, Carl ; Arnold, Frances ; Quake, Stephen	Long-Term Monitoring of Bacteria Undergoing Programmed Population Control in a Microchemostat	Science	2005	Jul	01	309	5731	137--140	synthetic biology	10.1126/science.1109173		http://www.sciencemag.org/cgi/content/abstract/309/5731/137
ref138	electronic		The Device Physics of Cellular Logic Gates - Weiss, Basu (ResearchIndex)								synthetic biology			http://citeseer.ist.psu.edu/weiss02device.html
Ehrenberg2003	article	Ehrenberg, Mans ; Elf, Johan ; Aurell, Erik ; Sandberg, Rickard ; Tegner, And	Systems Biology Is Taking Off	Genome Research	2003	Nov	01	13	11	2377--2380	thesis\_chapter\_1			http://www.genome.org/cgi/content/full/13/11/2377
Hooshangi2005b	article	Hooshangi, Sara ; Thiberge, Stephan ; Weiss, And	Ultrasensitivity and noise propagation in a synthetic transcriptional cascade	Proceedings of the National Academy of Sciences	2005	Mar	08	102	10	3581--3586	thesis\_chapter\_2	10.1073/pnas.0408507102		http://dx.doi.org/10.1073/pnas.0408507102
Bulter2004	article	Bulter, Thomas ; Lee, Sun-Gu ; Wong, Wilson ; Fung, Eileen ; Connor, Michael ; Liao, James	From the Cover: Design of artificial cell-cell communication using gene and metabolic networks	Proceedings of the National Academy of Sciences	2004	Feb	24	101	8	2299--2304	synthetic biology	10.1073/pnas.0306484101		http://www.pnas.org/cgi/content/abstract/pnas;101/8/2299
You2004	article	You, Lingchong ; Sidney-Cox, Robert ; Weiss, Ron ; Arnold, And	Programmed population control by cell-cell communication and regulated killing	Nature	2004	Apr	22	428	6985	868--871	thesis\_chapter\_1	10.1038/nature02491		http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15064770
Weiss2003	article	Weiss, Ron ; Basu, Subhayu ; Hooshangi, Sara ; Kalmbach, Abigail ; Karig, David ; Mehreja, Rishabh ; Netravali, Ilka	Genetic circuit building blocks for cellular computation, communications, and signal processing	Natural Computing	2003	xx	xx	2	1	47--47	thesis\_chapter\_1	10.1023/a:1023307812034		http://dx.doi.org/10.1023/a:1023307812034
McAdams2000	article	McAdams, H. H. ; Arkin, A.	Towards a circuit engineering discipline.	Current biology : CB.	2000	Apr	20	10	8	318--320	synthetic biology			http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10801411&dopt=Abstract
McMillen2002	article	McMillen, David ; Kopell, Nancy ; Hasty, Jeff ; Collins, J. J.	Synchronizing genetic relaxation oscillators by intercell signaling	Proceedings of the National Academy of Sciences	2002	Jan	22	99	2	679--684	application	10.1073/pnas.022642299		http://www.pnas.org/cgi/content/abstract/99/2/679
Kobayashi2004	article	Kobayashi, Hideki ; Kaern, Mads ; Araki, Michihiro ; Chung, Kristy ; Gardner, Timothy ; Cantor, Charles ; Collins, James	Programmable cells: Interfacing natural and engineered gene networks	Proceedings of the National Academy of Sciences	2004	Jun	01	101	22	8414--8419	cell-cell signaling	10.1073/pnas.0402940101		http://www.pnas.org/cgi/content/abstract/101/22/8414?etoc
Tegner2003	article	Tegner, Jesper ; Yeung, M. K. ; Hasty, Jeff ; Collins, James	Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling	Proceedings of the National Academy of Sciences	2003	May	13	100	10	5944--5949	synthetic biology	10.1073/pnas.0933416100		http://www.pnas.org/cgi/content/full/100/10/5944?ijkey=8ceb79f77cfcaade8d7b71bbdafdd0e60853460e&keytype2=tf_ipsecsha
Alm2003	article	Alm, Eric ; Arkin, Adam	Biological networks.	Current opinion in structural biology.	2003	Apr	xx	13	2	193--202	synthetic biology			http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=12727512&dopt=Citation
Isaacs2003	article	Isaacs, Farren ; Hasty, Jeff ; Cantor, Charles ; Collins, J. J.	Prediction and measurement of an autoregulatory genetic module	Proceedings of the National Academy of Sciences	2003	Jun	24	100	13	7714--7719	thesis\_chapter\_2	10.1073/pnas.1332628100		http://www.pnas.org/cgi/content/abstract/100/13/7714
Yokobayashi2002b	article	Yokobayashi, Yohei ; Weiss, Ron ; Arnold, Frances	Directed evolution of a genetic circuit	Proceedings of the National Academy of Sciences	2002	Dec	24	99	26	16587--16591	synthetic biology	10.1073/pnas.252535999		http://www.pnas.org/cgi/content/abstract/99/26/16587?etoc
ref151	book	Dunlop, Mary ; Murray, Richard	Towards Biological System Identification: Fast and Accurate Estimates								synthetic biology			http://www.its.caltech.edu/~mjdunlop/papers/CDC06-draft.pdf
Pottage2006	article	Pottage, Alain	Too Much Ownership: Bio-prospecting in the Age of Synthetic Biology	BioSocieties. Cambridge University Press	2006	Jun	xx			137--158	synthetic biology	10.1017/S1745855206050241		http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=446754
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ref155	article	Keasling, Jay	Engineering Bacteria for Drug Production	Engineering Bacteria for Drug Production							synthetic biology			http://www.nae.edu/nae/naefoe.nsf/0754c87f163f599e85256cca00588f49/85256dad0044ef2a852570bd00521b49/$FILE/Keasling.pdf
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Pfleger2006a	article	Pfleger, Brian ; Pitera, Douglas ; Smolke, Christina ; Keasling, And	Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes	Nat Biotech	2006	Aug	xx	24	8	1027--1032	synthetic biology	10.1038/nbt1226		http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt1226.html
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Andrianantoandro2006d	article	Andrianantoandro, Ernesto ; Basu, Subhayu ; Karig, David ; Weiss, And	Synthetic biology: new engineering rules for an emerging discipline	Mol Syst Biol	2006	xx	xx	2		4100073--4100071	synthetic biology	10.1038/msb4100073		http://www.nature.com/msb/journal/v2/n1/full/msb4100073.html
Endy2005a	article	Endy, Drew	Foundations for engineering biology	Nature	2005	Nov	24	438	7067	449--453	synthetic biology	10.1038/nature04342		http://www.nature.com/nature/journal/v438/n7067/full/nature04342.html
Ball2004	article	Ball, Philip	Synthetic biology: Starting from scratch	Nature	2004	Oct	07	431	7009	624--626	synthetic biology	10.1038/431624a		http://www.nature.com/nature/journal/v431/n7009/full/431624a.html
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Brent2004	article	Brent, Roger	A partnership between biology and engineering	Nat Biotech	2004	Oct	xx	22	10	1211--1214	thesis\_chapter\_1	10.1038/nbt1004-1211		http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15470452
Isaacs2006	article	Isaacs, Farren ; Dwyer, Daniel ; Collins, And	RNA synthetic biology	Nat Biotech	2006	May	xx	24	5	545--554	riboswitch	10.1038/nbt1208		http://dx.doi.org/10.1038/nbt1208
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ref168	article		Synthetic biology--putting engineering into biology	Bioinformatics	2006	xx	xx	22	22	2790--2790	review	10.1093/bioinformatics/btl469		http://dx.doi.org/10.1093/bioinformatics/btl469
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ref174	electronic		Library of Synthetic 5' Secondary Structures To Manipulate mRNA Stability in Escherichia coli								synthetic biology			http://pubs.acs.org/cgi-bin/abstract.cgi/bipret/1999/15/i01/abs/bp9801143.html
Arraiano2003	article	Arraiano, Cecilia Maria ; Maquat, Lynne Elizabeth	Post-transcriptional control of gene expression: effectors of mRNA decay	Molecular Microbiology	2003	xx	xx	49	1	267--276	synthetic biology	10.1046/j.1365-2958.2003.03545.x		http://www.blackwell-synergy.com/links/doi/10.1046/j.1365-2958.2003.03545.x	Description of various mechanisms of mRNA degredation
ref176	electronic		A comprehensive library of fluorescent transcriptional reporters for Escherichia coli								synthetic biology			http://www.weizmann.ac.il/mcb/UriAlon/Papers/Zaslaver_Ecoli_library.pdf
ref177	electronic		Synthetic biology | Life 2.0 | Economist.com								synthetic biology			http://www.economist.com/business/displaystory.cfm?story_id=7854314
ref178	electronic		Synthetic Biology								synthetic biology			http://syntheticbiology.org/
Maeda2006a	article	Maeda, Yusuke T. ; Sano, Masaki	Regulatory dynamics of synthetic gene networks with positive feedback.	Journal of molecular biology.	2006	Jun	16	359	4	1107--1124	synthetic biology	10.1016/j.jmb.2006.03.064	0022-2836	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16701695&query_hl=12&itool=pubmed_docsum
ref180	electronic		Cell -- Banaszynski et al.								synthetic biology			http://www.cell.com/content/article/fulltext?uid=PIIS0092867406010130
ref181	electronic		Synthetic biology | Playing demigods | Economist.com								synthetic biology			http://www.economist.com/opinion/displaystory.cfm?story_id=E1_SRVQSST
ref182	electronic		Synthetic biology | Life 2.0 | Economist.com								synthetic biology			http://www.economist.com/business/displaystory.cfm?story_id=7854314
Church2005b	article	Church, George	From systems biology to synthetic biology	Mol Syst Biol	2005	Mar	29	1		1--1	synthetic biology	10.1038/msb4100007		http://www.nature.com/msb/journal/v1/n1/full/msb4100007.html#b5
Forster2006b	article	Forster, Anthony ; Church, George	Towards synthesis of a minimal cell	Mol Syst Biol	2006	Aug	22	2			synthetic biology	10.1038/msb4100090		http://www.nature.com/msb/journal/v2/n1/full/msb4100090.html
Forster2006c	article	Forster, Anthony ; Church, George	Towards synthesis of a minimal cell	Mol Syst Biol	2006	Aug	22	2			synthetic biology	10.1038/msb4100090		http://www.nature.com/msb/journal/v2/n1/full/msb4100090.html
Lim2006	article	Lim, Kwang-il ; Lang, Tobias ; Lam, Vy ; Yin, John	Model-Based Design of Growth-Attenuated Viruses	PLoS Computational Biology	2006	Sep	01	2	9	e116	systems biology	10.1371/journal.pcbi.0020116		http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0020116
ref187	electronic		Synthetic biology | Bedroom biotech | Economist.com								synthetic biology			http://www.economist.com/displayStory.cfm?Story_id=7854327	Like information technology before it, biotech is starting to spawn hackers
ref188	electronic		Synthetic biology | Life 2.0 | Economist.com								synthetic biology			http://www.economist.com/displayStory.cfm?Story_id=7854314	The new science of synthetic biology is poised between hype and hope. But its time will soon come. Describes this vein of science being on an innovation curve quite similar to Moore's law. Discusses BioBricks and work by Rob Carlson.
ref189	electronic		Synthetic biology | Playing demigods | Economist.com								ethics			http://www.economist.com/research/articlesBySubject/displayStory.cfm?story_id=7854771&subjectid=526354	Discusses innovation, possibilities and fears of synthetic biology. Recommends caution and monitoring, but not shut down.
Fu2006b	article	Fu, Pengcheng	A perspective of synthetic biology: Assembling building blocks for novel functions.	Biotechnology journal.	2006	Jun	xx	1	6	690--699	synthetic biology	10.1002/biot.200600019	1860-6768	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16892318&itool=pubmed_DocSum
Maeda2006b	article	Maeda, Yusuke T. ; Sano, Masaki	Regulatory dynamics of synthetic gene networks with positive feedback.	Journal of molecular biology.	2006	Jun	16	359	4	1107--1124	synthetic biology	10.1016/j.jmb.2006.03.064	0022-2836	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16701695&query_hl=12&itool=pubmed_docsum
Chin2006b	article	Chin, Jason W.	Programming and engineering biological networks.	Current opinion in structural biology.	2006	Aug	xx	16	4	551--556	gene	10.1016/j.sbi.2006.06.011	0959-440X	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16842994&itool=pubmed_DocSum
Pfleger2006b	article	Pfleger, Brian ; Pitera, Douglas ; Smolke, Christina ; Keasling, Jay	Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes	Nature Biotechnology	2006	Jul	16	advanced online publication	8	1027--1032	synthetic biology	10.1038/nbt1226	10870156	http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt1226.html
Pfleger2006c	article	Pfleger, Brian ; Pitera, Douglas ; Smolke, Christina ; Keasling, Jay	Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes	Nature Biotechnology	2006	Jul	16	advanced online publication	8	1027--1032	synthetic biology	10.1038/nbt1226	10870156	http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt1226.html
Posfai2006	article	Posfai, Gyorgy ; Plunkett, Guy III ; Feher, Tamas ; Frisch, David ; Keil, Gunther M. ; Umenhoffer, Kinga ; Kolisnychenko, Vitaliy ; Stahl, Buffy ; Sharma, Shamik S. ; de Arruda, Monika ; Burland, Valerie ; Harcum, Sarah W. ; Blattner, Frederick R.	Emergent Properties of Reduced-Genome Escherichia coli	Science	2006	May	19	312	5776	1044--1046	emergence			http://www.sciencemag.org/cgi/content/abstract/312/5776/1044?etoc
Villalobos2006	article	Villalobos, Alan ; Ness, Jon ; Gustafsson, Claes ; Minshull, Jeremy ; Govindarajan, Sridhar	Gene Designer: A Synthetic Biology Tool for Constructing Artificial DNA Segments.	BMC Bioinformatics	2006	Jun	06	7	1	285	synthetic biology	10.1186/1471-2105-7-285	1471-2105	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16756672&itool=pubmed_DocSum
Andrianantoandro2006e	article	Andrianantoandro, Ernesto ; Basu, Subhayu ; Karig, David ; Weiss, Ron	Synthetic biology: new engineering rules for an emerging discipline.	Molecular systems biology [electronic resource].	2006	xx	xx	2		msb4100073--0028	synthetic biology	10.1038/msb4100073	1744-4292	http://www.nature.com/msb/journal/v2/n1/full/msb4100073.html
Xiang2006	article	Xiang, Shuanglin ; Fruehauf, Johannes ; Li, Chiang	Short hairpin RNA-expressing bacteria elicit RNA interference in mammals	Nature Biotechnology	2006	May	14	advanced online publication	6	697--702	synthetic biology	10.1038/nbt1211	10870156	http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt1211.html	Nonpathogenic Escherichia coli were engineered to transcribe shRNAs from a plasmid containing the invasin gene Inv and the listeriolysin O gene HlyA, which encode two bacterial factors needed for successful transfer of the shRNAs into mammalian cells.
ref199	article		Computational redesign of endonuclease DNA binding and cleavage specificity	Nature	2006	xx	xx	441	7093	656--656	Protein	10.1038/nature04818		http://www.nature.com/nature/journal/v441/n7093/full/nature04818.html
Church2005c	article	Church, George	From systems biology to synthetic biology	Molecular systems biology [electronic resource].	2005	Mar	29	1	1	msb4100007--0032	synthetic biology	10.1038/msb4100007	1744-4292	http://www.nature.com/msb/journal/v1/n1/full/msb4100007.html#b5	editorial
ref201	electronic		Synthetic Biology								synthetic biology			http://syntheticbiology.org/
Endy2005b	article	Endy, Drew	Foundations for engineering biology	Nature	2005	Nov	24	438	7067	449--453	synthetic biology	10.1038/nature04342	0028-0836	http://www.nature.com/nature/journal/v438/n7067/full/nature04342.html
ref203	electronic		OpenWetWare								synthetic biology			http://openwetware.org/wiki/Main_Page	see the comic Adventures in synthetic biology
ref204	electronic		Comic 1 : Adventures in Synthetic Biology : Nature								synthetic biology			http://www.nature.com/nature/comics/syntheticbiologycomic/index.html
Benner2003	article	Benner, Steven	Synthetic biology: Act natural	Nature	2003	Jan	09	421	6919	118	nature concepts	10.1038/421118a	0028-0836	http://www.nature.com/nature/journal/v421/n6919/full/421118a.html
ref206	electronic		Engineering Life: Building a Fab for Biology -- [ BIOTECHNOLOGY ] -- Principles and practices learned from engineering successes can help transform biotechnology from a specialized craft into a mature industry								synthetic biology	By the Bio FAB group (ht265 2006-06-06 13:24:51)		http://www.sciam.com/article.cfm?chanID=sa006&colID=1&articleID=000E491E-B2F9-146C-B2F983414B7F0000	Synthetic Biology by Baker
ref207	electronic		Synthetic biologists try to calm fears								synthetic biology			http://www.nature.com/news/2006/060522/full/441388a.html
Morton2006a	article	Morton, Oliver	Synthetic Biology 2.0: More bloggers	MainlyMartian	2006	May	23				synthetic biology			http://mainlymartian.blogs.com/semijournal/2006/05/synthetic_biolo_6.html
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Chin2006c	article	Chin, Jason	Modular approaches to expanding the functions of living matter	Nature chemical biology.	2006	Jun	xx	2	6	304--311	synthetic biology	10.1038/nchembio789	1552-4450	http://www.nature.com/nchembio/journal/v2/n6/abs/nchembio789.html
Morton2006b	article	Morton, Oliver	Synthetic Biology 2.0: Medicine (and its malcontents?)	MainlyMartian	2006	May	22				synthetic biology			http://mainlymartian.blogs.com/semijournal/2006/05/synthetic_biolo_5.html
Morton2006c	article	Morton, Oliver	Synthetic Biology 2.0: Also blogging the meeting...	MainlyMartian	2006	May	21				synthetic biology			http://mainlymartian.blogs.com/semijournal/2006/05/syhtetic_biolog.html
Morton2006d	article	Morton, Oliver	Synthetic Biology 2.0: Opposing views	MainlyMartian	2006	May	20				synthetic biology			http://mainlymartian.blogs.com/semijournal/2006/05/synthetic_biolo_3.html
Morton2006e	article	Morton, Oliver	Synthetic Biology 2.0: Fun to come	MainlyMartian	2006	May	20				synthetic biology			http://mainlymartian.blogs.com/semijournal/2006/05/synthetic_biolo_2.html
Morton2006f	article	Morton, Oliver	Synthetic Biology 2.0: BTUs per bushel	MainlyMartian	2006	May	20				synthetic biology			http://mainlymartian.blogs.com/semijournal/2006/05/synthetic_biolo_1.html
Morton2006g	article	Morton, Oliver	Synthetic Biology 2.0: What's afoot?	MainlyMartian	2006	May	20				synthetic biology			http://mainlymartian.blogs.com/semijournal/2006/05/synthetic_biolo.html
Andrianantoandro2006f	article	Andrianantoandro, Ernesto ; Basu, Subhayu ; Karig, David ; Weiss, Ron	Synthetic biology: new engineering rules for an emerging discipline	Molecular systems biology [electronic resource].	2006	xx	xx	2		msb4100073--0028	synthetic biology	10.1038/msb4100073	1744-4292	http://www.nature.com/msb/journal/v2/n1/full/msb4100073.html
Endy2005c	article	Endy, Drew	Foundations for engineering biology	Nature	2005	Nov	24	438	7067	449--453	fun	10.1038/nature04342	0028-0836	http://www.nature.com/nature/journal/v438/n7067/full/nature04342.html
Elowitz2000b	article	Elowitz, M. B. ; Leibler, S.	A synthetic oscillatory network of transcriptional regulators.	Nature.	2000	Jan	20	403	6767	335--338	synthetic biology	10.1038/35002125	0028-0836	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10659856&query_hl=7
Guet2002a	article	Guet, Călin C. ; Elowitz, Michael B. ; Hsing, Weihong ; Leibler, Stanislas	Combinatorial synthesis of genetic networks.	Science.	2002	May	24	296	5572	1466--1470	synthetic biology	10.1126/science.1067407	1095-9203	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12029133&query_hl=7
Levskaya2005a	article	Levskaya, Anselm ; Chevalier, Aaron ; Tabor, Jeffrey ; Simpson, Zachary Booth ; Lavery, Laura ; Levy, Matthew ; Davidson, Eric ; Scouras, Alexander ; Ellington, Andrew ; Marcotte, Edward ; Voigt, Christopher	Synthetic biology: Engineering Escherichia coli to see light	Nature.	2005	Nov	24	438	7067	441--442	synthetic biology	10.1038/nature04405	1476-4687	http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html
Bray1995	article	Bray, Dennis	Protein molecules as computational elements in living cells	Nature.	1995	Jul	27	376	6538	307--312	synthetic biology	10.1038/376307a0	0028-0836	http://www.nature.com/nature/journal/v376/n6538/abs/376307a0.html
Pawson1995	article	Pawson, Tony	Protein modules and signalling networks	Nature	1995	Feb	16	373	6515	573--580	synthetic biology	10.1038/373573a0		http://www.nature.com/nature/journal/v373/n6515/abs/373573a0.html
ref224	article		BioMed Central | Abstract | 1471-2105-7-55 | PathSys: integrating molecular interaction graphs for systems biology	BMC Bioinformatics	2006	Feb	07	7	1	55	synthetic biology	10.1186/1471-2105-7-55	14712105	http://dx.doi.org/10.1186/1471-2105-7-55
ref225	electronic		Synthetic Biology in Practice								synthetic biology			http://blog.lib.umn.edu/sali0090/synbio/
ref226	electronic		General Review Papers - IGEM								synthetic biology			http://parts.mit.edu/wiki/index.php/General_Review_Papers
ref227	electronic		Synthetic systems biology								synthetic biology			http://www.ncbs.res.in/~faculty/ssb/apply1.html
Boonyarattanakalin2006	article	Boonyarattanakalin, Siwarutt ; Athavankar, Sonalee ; Sun, Qi ; Peterson, Blake R.	Synthesis of an Artificial Cell Surface Receptor that Enables Oligohistidine Affinity Tags to Function as Metal-Dependent Cell-Penetrating Peptides.	Journal of the American Chemical Society.	2006	Jan	18	128	2	386--387	synthetic biology	10.1021/ja056126j	0002-7863	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16402806&query_hl=1&itool=pubmed_docsum
Rackham2005	article	Rackham, Oliver ; Chin, Jason W.	A network of orthogonal ribosome x mRNA pairs.	Nature chemical biology.	2005	Aug	xx	1	3	159--166	synthetic biology	10.1038/nchembio719	1552-4450	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16408021&query_hl=1&itool=pubmed_docsum
Volgraf2006	article	Volgraf, Matthew ; Gorostiza, Pau ; Numano, Rika ; Kramer, Richard H. ; Isacoff, Ehud Y. ; Trauner, Dirk	Allosteric control of an ionotropic glutamate receptor with an optical switch.	Nature chemical biology.	2006	Jan	xx	2	1	47--52	synthetic biology	10.1038/nchembio756	1552-4450	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16408092&query_hl=1&itool=pubmed_docsum
Simpson2004a	article	Simpson, Michael L.	Rewiring the cell: synthetic biology moves towards higher functional complexity.	Trends Biotechnol	2004	Nov	xx	22	11	555--557	synthetic biology	10.1016/j.tibtech.2004.09.003	0167-7799	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15491797&query_hl=4
ref232	electronic		Research Papers in Synthetic Biology - IGEM								synthetic biology			http://parts.mit.edu/wiki/index.php/Research_Papers_in_Synthetic_Biology
ref233	electronic		Registry of Standard Biological Parts								synthetic biology			http://parts.mit.edu/
ref234	electronic		Main Page - IGEM								synthetic biology			http://parts.mit.edu/wiki/index.php/Main_Page
ref235	electronic		SignOnSanDiego.com > News > Science -- Command performances								synthetic biology			http://www.signonsandiego.com/news/science/20051214-9999-lz1c14circuit.html#	``Controlling organisms with biological circuits, opens up a world of possibilities and dangers''
Chen2005a	article	Chen, Ming-Tang ; Weiss, Ron	Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana	Nature biotechnology.	2005	Nov	20	advanced online publication	12	1551--1555	synthetic biology	10.1038/nbt1162	1087-0156	http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt1162.html
Fung2005	article	Fung, Eileen ; Wong, Wilson ; Suen, Jason ; Bulter, Thomas ; Lee, Sun-gu ; Liao, James	A synthetic gene-metabolic oscillator	Nature	2005	May	05	435	7038	118--122	synthetic biology	10.1038/nature03508	0028-0836	http://www.nature.com/nature/journal/v435/n7038/abs/nature03508.html
Endy2005d	article	Endy, Drew	Foundations for engineering biology	Nature	2005	Nov	24	438	7067	449--453	synthetic biology	10.1038/nature04342	0028-0836	http://www.nature.com/nature/journal/v438/n7067/full/nature04342.html	Engineered biological systems have been used to manipulate information, construct materials, process chemicals, produce energy, provide food, and help maintain or enhance human health and our environment. Unfortunately, our ability to quickly and reliably engineer biological systems that behave as expected remains quite limited. Foundational technologies that make routine the engineering of biology are needed. Vibrant, open research communities and strategic leadership are necessary to ensure that the development and application of biological technologies remains overwhelmingly constructive.
Levskaya2005b	article	Levskaya, Anselm ; Chevalier, Aaron ; Tabor, Jeffrey ; Simpson, Zachary Booth ; Lavery, Laura ; Levy, Matthew ; Davidson, Eric ; Scouras, Alexander ; Ellington, Andrew ; Marcotte, Edward ; Voigt, Christopher	Synthetic biology: Engineering Escherichia coli to see light	Nature.	2005	Nov	24	438	7067	441--442	synthetic biology	10.1038/nature04405	1476-4687	http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html
Endy2005e	article	Endy, Drew	Foundations for engineering biology	Nature	2005	Nov	24	438	7067	449--453	synthetic biology	10.1038/nature04342	0028-0836	http://www.nature.com/nature/journal/v438/n7067/full/nature04342.html
Sprinzak2005b	article	Sprinzak, David ; Elowitz, Michael	Reconstruction of genetic circuits	Nature	2005	Nov	24	438	7067	443--448	synthetic biology	10.1038/nature04335	0028-0836	http://www.nature.com/nature/journal/v438/n7067/full/nature04335.html
Levskaya2005c	article	Levskaya, Anselm ; Chevalier, Aaron ; Tabor, Jeffrey ; Simpson, Zachary Booth ; Lavery, Laura ; Levy, Matthew ; Davidson, Eric ; Scouras, Alexander ; Ellington, Andrew ; Marcotte, Edward ; Voigt, Christopher	Synthetic biology: Engineering Escherichia coli to see light - article in Nature	Nature.	2005	Nov	24	438	7067	441--442	Photography	10.1038/nature04405	1476-4687	http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html	We have designed a bacterial system that is switched between different states by red light. The system consists of a synthetic sensor kinase that allows a lawn of bacteria to function as a biological film, such that the projection of a pattern of light on to the bacteria produces a high-definition (about 100 megapixels per square inch), two-dimensional chemical image. This spatial control of bacterial gene expression could be used to 'print' complex biological materials, for example, and to investigate signalling pathways through precise spatial and temporal control of their phosphorylation steps.
ref243	electronic		Bacterial film : Nature								Photography			http://www.nature.com/nature/journal/v438/n7067/edsumm/e051124-07.html	Phytochromes are membrane-bound photoreceptors found in plants and some bacteria. There are none in Escherichia coli, but with the introduction of a genetic circuit that fuses a cyanobacterial photoreceptor to an intracellular kinase, E. coli sees the light. The bacteria then act as a photographic film, producing a chemical image when light is projected onto it.
ref244	electronic		Guardian Unlimited || Super-sensitive film made from living bacteria - on article in Nature								Photography			http://www.guardian.co.uk/science/story/0,3605,1649439,00.html	Scientists have created a new kind of photographic film, made from living bacteria, which is able to detect nano-scale features and print ultra-detailed images. By genetically engineering a common form of bacterium they were able to make it switch its pigment production on and off in response to a light.
Endy2005f	article	Endy, Drew	Foundations for engineering biology	Nature	2005	Nov	24	438	7067	449--453	synthetic biology	10.1038/nature04342	0028-0836	http://www.nature.com/nature/journal/v438/n7067/pdf/nature04342.pdf
ref246	electronic		Bacteria can take pictures of themselves - Boston.com - on article in Nature								synthetic biology			http://www.boston.com/news/science/articles/2005/11/23/bacteria_can_take_pictures_of_themselves/	The notorious E. coli bug made its film debut Wednesday. That's when researchers at the University of California, San Francisco and the University of Texas announced in the journal Nature that they had created photographs of themselves by programming the bacteria -- best known for outbreaks of food poisoning -- to make pictures in much the same way Kodak film produces images.
Chen2005b	article	Chen, Ming-Tang ; Weiss, Ron	Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana	Nature biotechnology.	2005	Nov	20	advanced online publication	12	1551--1555	synthetic biology	10.1038/nbt1162	1087-0156	http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt1162.html
Pennisi2005	article	Pennisi, Elizabeth	SYNTHETIC BIOLOGY: Synthetic Biology Remakes Small Genomes	Science	2005	Nov	04	310	5749	769--770	synthetic biology			http://www.sciencemag.org/cgi/content/full/310/5749/769
ref249	electronic		Qualitative Reasoning in biology - symposium collection								synthetic biology			http://monet.aber.ac.uk:8080/monet/docs/pdf_files/aime_03/mbqr-aime03.pdf
ref250	electronic		Welcome to Synthetic and Systems Biology								synthetic biology			http://www.ssbjournal.com/	Journal Homepage
ref251	article		Combining two genomes in one cell: Stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome	Proceedings of the National Academy of Sciences of the United States of America	2005	Nov	01	102	44	15971--15976	synthetic biology	10.1073/pnas.0503868102	0027-8424	http://dx.doi.org/10.1073/pnas.0503868102
ref252	electronic		VIROLOGY: Resurrected Influenza Virus Yields Secrets of Deadly 1918 Pandemic -- Kaiser 310 (5745): 28 -- Science								AvianFlu			http://www.sciencemag.org/cgi/content/summary/310/5745/28
Simpson2004b	article	Simpson, Michael L.	Rewiring the cell: synthetic biology moves towards higher functional complexity.	Trends Biotechnol	2004	Nov	xx	22	11	555--557	synthetic biology	10.1016/j.tibtech.2004.09.003	0167-7799	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15491797&query_hl=4	Nice overview of the present state of the field and some of its future research goals
Pedraza2005b	article	Pedraza, Juan M. ; van Oudenaarden, Alexander	Noise propagation in gene networks.	Science (New York, N.Y.)	2005	Mar	25	307	5717	1965--1969	Synthetic	10.1126/science.1109090	1095-9203	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15790857&query_hl=12
Elowitz2002	article	Elowitz, Michael B. ; Levine, Arnold J. ; Siggia, Eric D. ; Swain, Peter S.	Stochastic gene expression in a single cell.	Science	2002	Aug	16	297	5584	1183--1186	synthetic biology	10.1126/science.1070919	1095-9203	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12183631&query_hl=7
Guet2002b	article