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bibtexCitation	bibtexEntryType	title	keywords	url	author	journal	year	month	day	volume	issue	pages	note	abstract	issn
ref1	electronic	The crucial role of CS in systems and synthetic biology	computer science	http://portal.acm.org/citation.cfm?id=1342332
Bashor2008a	article	Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics	Biotech	http://www.sciencemag.org/cgi/content/abstract/319/5869/1539	Bashor, Caleb ; Helman, Noah ; Yan, Shude ; Lim, Wendell	Science	2008	Mar	14	319	5869	1539--1543	10.1126/science.1151153
Linshiz2008	article	Recursive construction of perfect DNA molecules from imperfect oligonucleotides	DNA synthesis	http://www.nature.com/msb/journal/v4/n1/full/msb200826.html	Linshiz, Gregory ; ben Yehezkel, Tuval ; Kaplan, Shai ; Gronau, Ilan ; Ravid, Sivan ; Adar, Rivka ; Shapiro, Ehud	Mol Syst Biol	2008	May	06	4			10.1038/msb.2008.26
ref4	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.
ref5	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
ref6	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	Synthetic biology: promises and challenges	synthetic biology	http://www.nature.com/msb/journal/v3/n1/full/msb4100202.html	Serrano, Luis	Mol Syst Biol	2007	Dec	18	3			10.1038/msb4100202
Doktycz2007	article	Nano-enabled synthetic biology	synthetic biology	http://www.nature.com/msb/journal/v3/n1/full/msb4100165.html	Doktycz, Mitchel ; Simpson, Michael	Mol Syst Biol	2007	Jul	10	3			10.1038/msb4100165
Bashor2008b	article	Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics	synthetic biology	http://www.sciencemag.org/cgi/content/full/319/5869/1539	Bashor, Caleb ; Helman, Noah ; Yan, Shude ; Lim, Wendell	Science	2008	Mar	14	319	5869	1539--1543	10.1126/science.1151153
Gibson2008	article	Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome	Venter	http://dx.doi.org/10.1126/science.1151721	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.	Science (New York, N.Y.)	2008	Jan	24	319	5867	1151721--1220	10.1126/science.1151721		1095-9203
ref11	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
ref12	article	Synthetic Gene Circuits: Design with Directed Evolution	BioBrick Characterisation	http://dx.doi.org/10.1146/annurev.biophys.36.040306.132600		Annual Review of Biophysics and Biomolecular Structure	2007	xx	xx	36	1	1	10.1146/annurev.biophys.36.040306.132600		10568700
Sauro2008	article	Modularity defined	systems biology	http://www.nature.com/msb/journal/v4/n1/full/msb20083.html	Sauro, Herbert	Mol Syst Biol	2008	Feb	12	4			10.1038/msb.2008.3	commentary on Del Vecchio et al (2008).
ref14	electronic	From the cells up | Science | The Guardian	synthetic biology	http://www.guardian.co.uk/science/2005/mar/10/science.research
ref15	electronic	Laying the foundations for a bio-economy 2008	carlson	http://www.springerlink.com/content/n211746672413507/fulltext.pdf
ref16	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	Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome	synthetic biology	http://www.sciencemag.org/cgi/content/abstract/319/5867/1215?sa_campaign=Email/toc/29-February-2008/10.1126/science.1151721	Benders, Gwynedd ; Hamilton, And	Science	2008	Jan	24			1151721	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.
ref18	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.
ref19	electronic	ETC Group -	synthetic biology	http://www.etcgroup.org/en/										Synthetic Biology Cartoons
Pennisi2008	article	Scientists Synthesize a Genome From Scratch - on article in Science	synthetic biology	http://sciencenow.sciencemag.org/cgi/content/full/2008/124/3	Pennisi, Elizabeth	ScienceNOW	2008	Jan	24	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.
ref21	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	Programming gene expression with combinatorial promoters	Promoter	http://www.nature.com/msb/journal/v3/n1/full/msb4100187.html	Sidney, Robert ; Cox, ; Surette, Michael ; Elowitz, Michael	Mol Syst Biol	2007	Nov	13	3			10.1038/msb4100187
ref23	article	Systems interface biology	stochastic	http://dx.doi.org/10.1098/rsif.2006.0143		Journal of The Royal Society Interface	2006	xx	xx	3	10	603	10.1098/rsif.2006.0143
Cox2007	article	Programming gene expression with combinatorial promoters	synthetic biology	http://www.nature.com/msb/journal/v3/n1/full/msb4100187.html	Cox, Robert Sidney ; Surette, Michael ; Elowitz, Michael	Mol Syst Biol	2007	Nov	13	3			10.1038/msb4100187
ref25	article	Programming and engineering biological networks	synthetic biology	http://dx.doi.org/10.1016/j.sbi.2006.06.011		Current Opinion in Structural Biology	2006	xx	xx	16	4	551	10.1016/j.sbi.2006.06.011
ref26	electronic	Registry of Standard Biological Parts	registry	http://parts.mit.edu/registry/index.php/Main_Page
ref27	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	Programming gene expression with combinatorial promoters	synthetic biology	http://www.nature.com/msb/journal/v3/n1/full/msb4100187.html	Sidney, Robert ; Cox, ; Surette, Michael ; Elowitz, Michael	Mol Syst Biol	2007	Nov	13	3			10.1038/msb4100187
ref29	article	Noise and kinetics of LuxR positive feedback loops	synthetic biology	http://dx.doi.org/10.1016/j.bbrc.2007.09.057		Biochemical and Biophysical Research Communications	2007	xx	xx	363	3	667	10.1016/j.bbrc.2007.09.057
ref30	article	Design and implementation of three incoherent feed-forward motif based biological concentration sensors	synthetic biology	http://dx.doi.org/10.1007/s11693-007-9008-6		Systems and Synthetic Biology	2007	xx	xx				10.1007/s11693-007-9008-6		18725325
ref31	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.
ref32	article	Expanding the metabolic engineering toolbox: more options to engineer cells	BioBrick Characterisation	http://dx.doi.org/10.1016/j.tibtech.2007.01.003		Trends in Biotechnology	2007	xx	xx	25	3	132	10.1016/j.tibtech.2007.01.003
Wu2007	article	Optimal encoding rules for synthetic genes: the need for a community effort	synthetic biology	http://www.nature.com/msb/journal/v3/n1/full/msb4100176.html	Wu, Gang ; Dress, Laura ; Freeland, Stephen	Mol Syst Biol	2007	Sep	18	3			10.1038/msb4100176
Murphy2007a	article	Combinatorial promoter design for engineering noisy gene expression.	synthetic biology	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	Murphy, Kevin ; Bal{\'a}zsi, G{\'a}bor ; Collins, James	Proceedings of the National Academy of Sciences of the United States of America	2007	Jul	31	104	31	12726--12731	10.1073/pnas.0608451104
Luisi2007	article	Chemical Aspects of Synthetic Biology	synthetic biology	http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17443874&ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus	Luisi, Pier	Chemistry \& Biodiversity	2007	xx	xx	4	4	603--621	10.1002/cbdv.200790053
ref36	article	Synthetic biology: lessons from the history of synthetic organic chemistry	synthetic biology	http://dx.doi.org/10.1038/nchembio0907-521		Nature Chemical Biology	2007	xx	xx	3	9	521--521	10.1038/nchembio0907-521
ref37	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	Noise propagation in gene networks.	synthetic biology	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15790857&query_hl=12	Pedraza, Juan ; van Oudenaarden, Alexander	Science (New York, N.Y.)	2005	Mar	25	307	5717	1965--1969	10.1126/science.1109090
Hooshangi2005a	article	Ultrasensitivity and noise propagation in a synthetic transcriptional cascade	inverter composition	http://dx.doi.org/10.1073/pnas.0408507102	Hooshangi, Sara ; Thiberge, Stephan ; Weiss, Ron	Proceedings of the National Academy of Sciences	2005	Mar	08	102	10	3581--3586	10.1073/pnas.0408507102
ref40	electronic	Cell -- Deans et al.	synthetic biology	http://www.cell.com/content/article/abstract?uid=PIIS0092867407006848
Murphy2007b	article	Combinatorial promoter design for engineering noisy gene expression	synthetic biology	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	Murphy, Kevin ; Balazsi, Gabor ; Collins, James	Proceedings of the National Academy of Sciences	2007	Jul	31	104	31	12726--12731	10.1073/pnas.0608451104
Grilly2007	article	A synthetic gene network for tuning protein degradation in Saccharomyces cerevisiae	synthetic biology	http://www.nature.com/msb/journal/v3/n1/full/msb4100168.html	Grilly, Chris ; Stricker, Jesse ; Pang, Wyming ; Bennett, Matthew ; Hasty, Jeff	Mol Syst Biol	2007	Jul	31	3			10.1038/msb4100168
Waldminghaus2007	article	Genome-wide bioinformatic prediction and experimental evaluation of potential RNA thermometers.	synthetic biology	http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17647020&itool=pubmed_DocSum	Waldminghaus, Torsten ; Gaubig, Lena ; Narberhaus, Franz	Mol Genet Genomics	2007	Jul	24				10.1007/s00438-007-0272-7
ref44	article	Toward an artificial cell based on gene expression in vesicles.	synthetic biology	http://www.ncbi.nlm.nih.gov/pubmed/16224117?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVAbstractPlus		Physical Biology	2005	xx	xx	2	3	1--1	10.1088/1478-3975/2/3/p01
Rinaudo2007a	article	A universal RNAi-based logic evaluator that operates in mammalian cells	synthetic biology	http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt1307.html	Rinaudo, Keller ; Bleris, Leonidas ; Maddamsetti, Rohan ; Subramanian, Sairam ; Weiss, Ron ; Benenson, Yaakov	Nat Biotech	2007	Jul	xx	25	7	795--801	10.1038/nbt1307
Szczepek2007	article	Structure-based redesign of the dimerization interface reduces the toxicity of zinc-finger nucleases.	zinc-finger nuclease	http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt1317.html	Szczepek, Michal ; Brondani, Vincent ; B{\"u}chel, Janine ; Serrano, Luis ; Segal, David ; Cathomen, Toni	Nature biotechnology	2007	Jul	xx	25	7	786--793	10.1038/nbt1317
Miller2007	article	An improved zinc-finger nuclease architecture for highly specific genome editing.	Protein engineering	http://dx.doi.org/10.1038/nbt1319	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	Nature biotechnology	2007	Jul	xx	25	7	778--785	10.1038/nbt1319
Wang2007	article	Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion.	orthogonal	http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt1314.html	Wang, Kaihang ; Neumann, Heinz ; Peak-Chew, Sew ; Chin, Jason	Nature biotechnology	2007	Jul	xx	25	7	770--777	10.1038/nbt1314
Walter2007	article	Light-powering Escherichia coli with proteorhodopsin	proteorhodopsin	http://dx.doi.org/10.1073/pnas.0611035104	Walter, Jessica ; Greenfield, Derek ; Bustamante, Carlos ; Liphardt, Jan	Proceedings of the National Academy of Sciences	2007	Feb	13	104	7	2408--2412	10.1073/pnas.0611035104
Drubin2007a	article	Designing biological systems.	be theory	http://www.genesdev.org/cgi/content/full/21/3/242	Drubin, David ; Way, Jeffrey ; Silver, Pamela	Genes \& development	2007	Feb	01	21	3	242--254	10.1101/gad.1507207
Andrianantoandro2006a	article	Synthetic biology: new engineering rules for an emerging discipline.	synthetic biology	http://www.nature.com/msb/journal/v2/n1/full/msb4100073.html	Andrianantoandro, Ernesto ; Basu, Subhayu ; Karig, David ; Weiss, Ron	Molecular systems biology	2006	xx	xx	2		2006--0028	10.1038/msb4100073
Ball2007a	article	Synthetic biology: Designs for life	synthetic biology	http://www.nature.com/nature/journal/v448/n7149/full/448032a.html	Ball, Philip	Nature	2007	Jul	05	448	7149	32--33	10.1038/448032a
Ball2007b	article	Synthetic biology: Designs for life - on article in Science	synthetic biology	http://www.nature.com/nature/journal/v448/n7149/full/448032a.html	Ball, Philip	Nature	2007	Jul	05	448	7149	32--33	10.1038/448032a	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	Rewiring cellular morphology pathways with synthetic guanine nucleotide exchange factors	gtpase	http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature05851.html	Yeh, Brian ; Rutigliano, Robert ; Deb, Anrica ; Bar-Sagi, Dafna ; Lim, Wendell	Nature	2007	May	31	447	7144	596--600	10.1038/nature05851
Lartigue2007a	article	Genome Transplantation in Bacteria: Changing One Species to Another	synthetic biology	http://www.sciencemag.org/cgi/content/abstract/1144622	Lartigue, Carole ; Glass, John ; Alperovich, Nina ; Pieper, Rembert ; Parmar, Prashanth ; Hutchison, III Clyde ; Smith, Hamilton ; Venter, J.	Science	2007	Jun	28			1144622--1144622	10.1126/science.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).
ref56	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	GENETICS: Replacement Genome Gives Microbe New Identity	synthetic biology	http://www.sciencemag.org/cgi/content/full/316/5833/1827a	Pennisi, Elizabeth	Science	2007	Jun	29	316	5833	1827--1827	10.1126/science.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	Genome Transplantation in Bacteria: Changing One Species to Another	synthetic biology	http://www.sciencemag.org/cgi/content/abstract/1144622	Lartigue, Carole ; Glass, John ; Alperovich, Nina ; Pieper, Rembert ; Parmar, Prashanth ; Hutchison, III Clyde ; Smith, Hamilton ; Venter, J.	Science	2007	Jun	28			1144622--1144622	10.1126/science.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.
ref59	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.
ref60	article	Meanings of 'life'	synthetic biology	http://www.nature.com/nature/journal/v447/n7148/full/4471031b.html		Nature	2007	Jun	28	447	7148	1031--1032	10.1038/4471031b
Kaiser2007	article	SYNTHETIC BIOLOGY: Attempt to Patent Artificial Organism Draws a Protest	synthetic biology	http://www.sciencemag.org/cgi/content/full/316/5831/1557	Kaiser, Jocelyn	Science	2007	Jun	15	316	5831	1557--1557	10.1126/science.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.
ref62	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	A universal RNAi-based logic evaluator that operates in mammalian cells	synthetic biology	http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt1307.html	Rinaudo, Keller ; Bleris, Leonidas ; Maddamsetti, Rohan ; Subramanian, Sairam ; Weiss, Ron ; Benenson, Yaakov	Nat Biotech	2007	May	21	advanced online publication			10.1038/nbt1307
Dueber2007	article	Engineering synthetic signaling proteins with ultrasensitive input/output control	synthetic biology	http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt1308.html	Dueber, John ; Mirsky, Ethan ; Lim, Wendell	Nat Biotech	2007	Jun	xx	25	6	660--662	10.1038/nbt1308
ref65	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.''
ref66	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	Synthetic biology: new engineering rules for an emerging discipline.	synthetic biology	http://www.nature.com/msb/journal/v2/n1/full/msb4100073.html	Andrianantoandro, Ernesto ; Basu, Subhayu ; Karig, David ; Weiss, Ron	Molecular systems biology	2006	xx	xx	2		2006--0028	10.1038/msb4100073
Yeh2007b	article	Rewiring cellular morphology pathways with synthetic guanine nucleotide exchange factors	synthetic biology	http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature05851.html	Yeh, Brian ; Rutigliano, Robert ; Deb, Anrica ; Bar-Sagi, Dafna ; Lim, Wendell	Nature	2007	May	31	447	7144	596--600	10.1038/nature05851
ref69	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/
ref70	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
ref71	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.
ref72	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.
ref73	article	The Generation of New Protein Functions by the Combination of Domains	synthetic biology	http://dx.doi.org/10.1016/j.str.2006.11.009		Structure	2007	xx	xx	15	1	85--85	10.1016/j.str.2006.11.009
Chen2007	article	A synthetic maternal-effect selfish genetic element drives population replacement in Drosophila.	synthetic biology	http://www.sciencemag.org/cgi/content/abstract/1138595	Chen, Chun-Hong ; Huang, Haixia ; Ward, Catherine ; Su, Jessica ; Schaeffer, Lorian ; Guo, Ming ; Hay, Bruce	Science (New York, N.Y.)	2007	Apr	27	316	5824	597--600	10.1126/science. 1138595
ref75	article	A synthetic biology challenge: making cells compute	synthetic biology	http://dx.doi.org/10.1039/b618473c		Molecular BioSystems	2007	xx	xx				10.1039/b618473c
ref76	article	Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations	Lab techniques	http://www.sciencemag.org/cgi/content/abstract/1132067v1?etoc		Science	2007	xx	xx	316	5824	593--593	10.1126/science.1132067
ref77	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	Refactoring bacteriophage T7.	refactoring	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16729053&query_hl=5&itool=pubmed_docsum	Chan, Leon ; Kosuri, Sriram ; Endy, Drew	Molecular systems biology	2005	xx	xx	1		2005--0018	10.1038/msb4100025
Zhang2007	article	Multimodal fast optical interrogation of neural circuitry	Neurobiology	http://www.nature.com/nature/journal/v446/n7136/abs/nature05744.html	Zhang, Feng ; Wang, Li-Ping ; Brauner, Martin ; Liewald, Jana ; Kay, Kenneth ; Watzke, Natalie ; Wood, Phillip ; Bamberg, Ernst ; Nagel, Georg ; Gottschalk, Alexander ; Deisseroth, Karl	Nature	2007	Apr	05	446	7136	633--639	10.1038/nature05744
ref80	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	Synthetic biology: new engineering rules for an emerging discipline.	systems biology	http://www.nature.com/msb/journal/v2/n1/full/msb4100073.html	Andrianantoandro, Ernesto ; Basu, Subhayu ; Karig, David ; Weiss, Ron	Molecular systems biology [electronic resource].	2006	xx	xx	2		2006--0028	10.1038/msb4100073
Heinemann2006	article	Synthetic biology--putting engineering into biology.	systems biology	http://dx.doi.org/10.1093/bioinformatics/btl469	Heinemann, Matthias ; Panke, Sven	Bioinformatics (Oxford, England)	2006	Nov	15	22	22	2790--2799	10.1093/bioinformatics/btl469
Drubin2007b	article	Designing biological systems.	systems biology	http://www.genesdev.org/cgi/content/full/21/3/242	Drubin, David ; Way, Jeffrey ; Silver, Pamela	Genes \& development	2007	Feb	01	21	3	242--254	10.1101/gad.1507207
Sismour2005	article	Synthetic biology.	systems biology	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16255644&query_hl=1&itool=pubmed_DocSum	Sismour, A. ; Benner, Steven	Expert opinion on biological therapy	2005	Nov	xx	5	11	1409--1414	10.1517/14712598.5.11.1409
ref85	electronic	SpringerLink - Journal Article	synthetic biology	http://www.springerlink.com/content/k7377586j4305247/
Yokobayashi2002a	article	From the Cover: Directed evolution of a genetic circuit	synthetic biology	http://www.pnas.org/cgi/content/abstract/99/26/16587?etoc	Yokobayashi, Yohei ; Weiss, Ron ; Arnold, Frances	Proceedings of the National Academy of Sciences	2002	Dec	24	99	26	16587--16591	10.1073/pnas.252535999
ref87	article	Genetic parts to program bacteria	synthetic biology	http://dx.doi.org/10.1016/j.copbio.2006.09.001		Current Opinion in Biotechnology	2006	xx	xx	17	5	548--548	10.1016/j.copbio.2006.09.001
ref88	article	The Generation of New Protein Functions by the Combination of Domains	structures	http://dx.doi.org/10.1016/j.str.2006.11.009		Structure	2007	xx	xx	15	1	85--85	10.1016/j.str.2006.11.009
Sprinzak2005a	article	Reconstruction of genetic circuits	synthetic biology	http://www.nature.com/nature/journal/v438/n7067/full/nature04335.html	Sprinzak, David ; Elowitz, Michael	Nature	2005	Nov	24	438	7067	443--448	10.1038/nature04335
Hasty2001	book	Designer Gene Networks: Towards Fundamental Cellular Control	genetic network	http://arxiv.org/abs/physics/0103034	Hasty, Jeff ; Isaacs, Farren ; Dolnik, Milos ; McMillen, David ; Collins, J. J.		2001	Mar	13
Fox2007	article	Improving catalytic function by ProSAR-driven enzyme evolution	directed evolution	http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt1286.html	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	Nat Biotech	2007	Feb	18	advanced online publication			10.1038/nbt1286
ref92	article	Synthetic biology projects in vitro	Cell-Free System	http://www.genome.org/cgi/content/abstract/gr.5776007v1?papetoc		Genome Research	2006	xx	xx	17	1	1--1	10.1101/gr.5776007
ref93	article	Genome Biology | Full text | Fast, cheap and somewhat in control	synthetic biology	http://dx.doi.org/10.1186/gb-2006-7-8-114		Genome Biology	2006	xx	xx	7	8	114--114	10.1186/gb-2006-7-8-114
Thattai2004	article	Stochastic Gene Expression in Fluctuating Environments	gene expression	http://www.genetics.org/cgi/content/abstract/167/1/523	Thattai, Mukund ; Van Oudenaarden, Alexander	Genetics	2004	May	01	167	1	523--530	10.1534/genetics.167.1.523
Li2007	article	Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC	method	http://www.nature.com/nmeth/journal/vaop/ncurrent/abs/nmeth1010.html	Li, Mamie ; Elledge, Stephen	Nat Meth	2007	Feb	11	advanced online publication			10.1038/nmeth1010
ref96	electronic	ETC Group - Publications - Extreme Genetic Engineering: An Introduction to Synthetic Biology	tech talk 2-12-07	http://www.etcgroup.org/en/materials/publications.html?id=602									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)	* 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	From the Cover: Synthetic cooperation in engineered yeast populations	tech talk 2-12-07	http://www.pnas.org/cgi/content/abstract/0610575104v1	Shou, Wenying ; Ram, Sri ; Vilar, Jose	Proceedings of the National Academy of Sciences	2007	Feb	06	104	6	1877--1882	10.1073/pnas.0610575104	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	Designing biological systems	review	http://www.genesdev.org/cgi/content/full/21/3/242	Drubin, David ; Way, Jeffrey ; Silver, Pamela	Genes and Development	2007	Feb	01	21	3	242--254	10.1101/gad.1507207
ref99	article	Light-powering Escherichia coli with proteorhodopsin	energy	http://dx.doi.org/10.1073/pnas.0611035104		Proceedings of the National Academy of Sciences	2007	xx	xx				10.1073/pnas.0611035104
Shou2007b	article	Synthetic cooperation in engineered yeast populations	yeast	http://www.pnas.org/cgi/content/abstract/0610575104v1	Shou, Wenying ; Ram, Sri ; Vilar, J. M. G.	Proceedings of the National Academy of Sciences	2007	Jan	31			0610575104--0610575104	10.1073/pnas.0610575104
Lim2007	article	A multistep epigenetic switch enables the stable inheritance of DNA methylation states	synthetic biology	http://www.nature.com/ng/journal/vaop/ncurrent/abs/ng1956.html	Lim, Han ; Van Oudenaarden, Alexander	Nat Genet	2007	Feb	xx	39	2	269--275	10.1038/ng1956
ref102	article	Synthetic biology projects in vitro	synthetic biology	http://www.genome.org/cgi/content/abstract/gr.5776007v1?papetoc		Genome Research	2006	xx	xx	17	1	1--1	10.1101/gr.5776007
ref103	article	Genetic parts to program bacteria	synthetic biology	http://dx.doi.org/10.1016/j.copbio.2006.09.001		Current Opinion in Biotechnology	2006	xx	xx	17	5	548--548	10.1016/j.copbio.2006.09.001
Simpson2006	article	Cell-free synthetic biology: a bottom-up approach to discovery by design	Cell-Free System	http://www.nature.com/msb/journal/v2/n1/full/msb4100104.html	Simpson, Michael	Mol Syst Biol	2006	Dec	12	2			10.1038/msb4100104
Kim2006	article	Construction of an in vitro bistable circuit from synthetic transcriptional switches	synthetic biology	http://www.nature.com/msb/journal/v2/n1/full/msb4100099.html	Kim, Jongmin ; White, Kristin ; Winfree, Erik	Mol Syst Biol	2006	Dec	12	2			10.1038/msb4100099
ref106	article	A synthetic multicellular system for programmed pattern formation	synthetic biology	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15858574		Nature	2005	xx	xx	434	7037	1130--1130	10.1038/nature03461
ref107	article	Cellular Logic with Orthogonal Ribosomes	synthetic biology	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16351070&query_hl=8&itool=pubmed_docsum		Journal of the American Chemical Society	2005	xx	xx	127	50	17584--17584	10.1021/ja055338d
Hasty2002	article	Engineered gene circuits	genetic network	http://www.nature.com/nature/journal/v420/n6912/full/nature01257.html	Hasty, Jeff ; McMillen, David ; Collins, J.	Nature	2002	Nov	14	420	6912	224--230	10.1038/nature01257
ref109	electronic	Zinc Fingers Consortium	genetic network	http://www.zincfingers.org/scientific-background.htm
ref110	article	Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly	genetic network	http://www.nature.com/nprot/journal/v1/n3/full/nprot.2006.259.html		Nature Protocols	2006	xx	xx	1	4	1637--1637	10.1038/nprot.2006.259
ref111	article	Synthetic biology--putting engineering into biology	synthetic biology	http://dx.doi.org/10.1093/bioinformatics/btl469		Bioinformatics	2006	xx	xx	22	22	2790--2790	10.1093/bioinformatics/btl469
Seelig2006	article	Enzyme-Free Nucleic Acid Logic Circuits	genetic network	http://www.sciencemag.org/cgi/content/full/314/5805/1585	Seelig, Georg ; Soloveichik, David ; Zhang, David ; Winfree, Erik	Science	2006	Dec	08	314	5805	1585--1588	10.1126/science.1132493
Forster2006a	article	Synthetic biology projects in vitro	synthetic biology	http://www.genome.org/cgi/content/abstract/gr.5776007v1?papetoc	Forster, Anthony ; Church, George	Genome Research	2006	Dec	06			5776007--5776007	10.1101/gr.5776007
Atsumi2006	article	A synthetic phage \{lambda\} regulatory circuit	synthetic biology	http://www.pnas.org/cgi/content/abstract/0603052103v1?etoc	Atsumi, Shota ; Little, John	Proceedings of the National Academy of Sciences	2006	Nov	29			0603052103--0603052103	10.1073/pnas.0603052103
ref115	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
ref116	electronic	Optimizing Biological Circuits: Integrating Rational Design with Directed Evolution	synthetic biology	http://aiche.confex.com/aiche/2006/preliminaryprogram/abstract_52714.htm
Collins2005	article	Directed evolution of Vibrio fischeri LuxR for increased sensitivity to a broad spectrum of acyl-homoserine lactones	synthetic biology	http://www.blackwell-synergy.com/links/doi/10.1111/j.1365-2958.2004.04437.x/enhancedabs/	Collins, Cynthia ; Arnold, Frances ; Leadbetter, Jared	Molecular Microbiology	2005	xx	xx	55	3	712--723	10.1111/j.1365-2958.2004.04437.x
Vilar2006	article	Modularizing gene regulation	gene expression	http://www.nature.com/msb/journal/v2/n1/full/msb4100058.html	Vilar, Jose	Mol Syst Biol	2006	Mar	21	2			10.1038/msb4100058
Wolf2003	article	Motifs, modules and games in bacteria.	synthetic biology	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12732301&dopt=Abstract	Wolf, Denise ; Arkin, Adam	Current opinion in microbiology.	2003	Apr	xx	6	2	125--134
Michnick2006	article	A luxRury of synthetic signals	pLuxR	http://www.nature.com/nbt/journal/v24/n6/full/nbt0606-658.html	Michnick, Stephen	Nat Biotech	2006	Jun	xx	24	6	658--660	10.1038/nbt0606-658
Cookson2005	article	Monitoring dynamics of single-cell gene expression over multiple cell cycles	thesis\_chapter\_2	http://www.nature.com/msb/journal/v1/n1/full/msb4100032.html	Cookson, Scott ; Ostroff, Natalie ; Pang, Wyming ; Volfson, Dmitri ; Hasty, And	Mol Syst Biol	2005	Nov	22	1	1	4100032--4100031	10.1038/msb4100032
Anderson2006	article	Environmentally controlled invasion of cancer cells by engineered bacteria.	synthetic biology	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=16330045&dopt=Citation	Anderson, J. ; Clarke, Elizabeth ; Arkin, Adam ; Voigt, Christopher	Journal of molecular biology.	2006	Jan	27	355	4	619--627	10.1016/j.jmb.2005.10.076
ref123	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	Cellular oscillators: rhythmic gene expression and metabolism.	synthetic biology	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15780601&dopt=Citation	Schibler, Ueli ; Naef, Felix	Current opinion in cell biology.	2005	Apr	xx	17	2	223--229	10.1016/j.ceb.2005.01.007
Atsumi2004	article	Regulatory circuit design and evolution using phage \{lambda\}	synthetic biology	http://www.genesdev.org/cgi/content/abstract/18/17/2086	Atsumi, Shota ; Little, John	Genes and Development	2004	Sep	01	18	17	2086--2094	10.1101/gad.1226004
Balagadde2005	article	Long-Term Monitoring of Bacteria Undergoing Programmed Population Control in a Microchemostat	synthetic biology	http://www.sciencemag.org/cgi/content/abstract/309/5731/137	Balagadde, Frederick ; You, Lingchong ; Hansen, Carl ; Arnold, Frances ; Quake, Stephen	Science	2005	Jul	01	309	5731	137--140	10.1126/science.1109173
ref127	electronic	The Device Physics of Cellular Logic Gates - Weiss, Basu (ResearchIndex)	synthetic biology	http://citeseer.ist.psu.edu/weiss02device.html
Ehrenberg2003	article	Systems Biology Is Taking Off	thesis\_chapter\_1	http://www.genome.org/cgi/content/full/13/11/2377	Ehrenberg, Mans ; Elf, Johan ; Aurell, Erik ; Sandberg, Rickard ; Tegner, And	Genome Research	2003	Nov	01	13	11	2377--2380
Hooshangi2005b	article	Ultrasensitivity and noise propagation in a synthetic transcriptional cascade	thesis\_chapter\_2	http://dx.doi.org/10.1073/pnas.0408507102	Hooshangi, Sara ; Thiberge, Stephan ; Weiss, And	Proceedings of the National Academy of Sciences	2005	Mar	08	102	10	3581--3586	10.1073/pnas.0408507102
Bulter2004	article	From the Cover: Design of artificial cell-cell communication using gene and metabolic networks	synthetic biology	http://www.pnas.org/cgi/content/abstract/pnas;101/8/2299	Bulter, Thomas ; Lee, Sun-Gu ; Wong, Wilson ; Fung, Eileen ; Connor, Michael ; Liao, James	Proceedings of the National Academy of Sciences	2004	Feb	24	101	8	2299--2304	10.1073/pnas.0306484101
You2004	article	Programmed population control by cell-cell communication and regulated killing	thesis\_chapter\_1	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15064770	You, Lingchong ; Sidney-Cox, Robert ; Weiss, Ron ; Arnold, And	Nature	2004	Apr	22	428	6985	868--871	10.1038/nature02491
Weiss2003	article	Genetic circuit building blocks for cellular computation, communications, and signal processing	thesis\_chapter\_1	http://dx.doi.org/10.1023/a:1023307812034	Weiss, Ron ; Basu, Subhayu ; Hooshangi, Sara ; Kalmbach, Abigail ; Karig, David ; Mehreja, Rishabh ; Netravali, Ilka	Natural Computing	2003	xx	xx	2	1	47--47	10.1023/a:1023307812034
McAdams2000	article	Towards a circuit engineering discipline.	synthetic biology	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10801411&dopt=Abstract	McAdams, H. H. ; Arkin, A.	Current biology : CB.	2000	Apr	20	10	8	318--320
McMillen2002	article	Synchronizing genetic relaxation oscillators by intercell signaling	application	http://www.pnas.org/cgi/content/abstract/99/2/679	McMillen, David ; Kopell, Nancy ; Hasty, Jeff ; Collins, J. J.	Proceedings of the National Academy of Sciences	2002	Jan	22	99	2	679--684	10.1073/pnas.022642299
Kobayashi2004	article	Programmable cells: Interfacing natural and engineered gene networks	cell-cell signaling	http://www.pnas.org/cgi/content/abstract/101/22/8414?etoc	Kobayashi, Hideki ; Kaern, Mads ; Araki, Michihiro ; Chung, Kristy ; Gardner, Timothy ; Cantor, Charles ; Collins, James	Proceedings of the National Academy of Sciences	2004	Jun	01	101	22	8414--8419	10.1073/pnas.0402940101
Tegner2003	article	Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling	synthetic biology	http://www.pnas.org/cgi/content/full/100/10/5944?ijkey=8ceb79f77cfcaade8d7b71bbdafdd0e60853460e&keytype2=tf_ipsecsha	Tegner, Jesper ; Yeung, M. K. ; Hasty, Jeff ; Collins, James	Proceedings of the National Academy of Sciences	2003	May	13	100	10	5944--5949	10.1073/pnas.0933416100
Alm2003	article	Biological networks.	synthetic biology	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=12727512&dopt=Citation	Alm, Eric ; Arkin, Adam	Current opinion in structural biology.	2003	Apr	xx	13	2	193--202
Isaacs2003	article	Prediction and measurement of an autoregulatory genetic module	thesis\_chapter\_2	http://www.pnas.org/cgi/content/abstract/100/13/7714	Isaacs, Farren ; Hasty, Jeff ; Cantor, Charles ; Collins, J. J.	Proceedings of the National Academy of Sciences	2003	Jun	24	100	13	7714--7719	10.1073/pnas.1332628100
Yokobayashi2002b	article	Directed evolution of a genetic circuit	synthetic biology	http://www.pnas.org/cgi/content/abstract/99/26/16587?etoc	Yokobayashi, Yohei ; Weiss, Ron ; Arnold, Frances	Proceedings of the National Academy of Sciences	2002	Dec	24	99	26	16587--16591	10.1073/pnas.252535999
ref140	book	Towards Biological System Identification: Fast and Accurate Estimates	synthetic biology	http://www.its.caltech.edu/~mjdunlop/papers/CDC06-draft.pdf	Dunlop, Mary ; Murray, Richard
Pottage2006	article	Too Much Ownership: Bio-prospecting in the Age of Synthetic Biology	synthetic biology	http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=446754	Pottage, Alain	BioSocieties. Cambridge University Press	2006	Jun	xx			137--158	10.1017/S1745855206050241
Swain2006	article	Noise in genetic and neural networks	synthetic biology	http://link.aip.org/link/?CHA/16/026101/1	Swain, Peter ; Longtin, Andre	Chaos: An Interdisciplinary Journal of Nonlinear Science	2006	xx	xx	16	2	026101--026101
McDaniel2005	article	Advances in synthetic biology: on the path from prototypes to applications.	thesis\_chapter\_1	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16019200	McDaniel, Ryan ; Weiss, Ron	Current opinion in biotechnology.	2005	Aug	xx	16	4	476--483	10.1016/j.copbio.2005.07.002
ref144	article	Engineering Bacteria for Drug Production	synthetic biology	http://www.nae.edu/nae/naefoe.nsf/0754c87f163f599e85256cca00588f49/85256dad0044ef2a852570bd00521b49/$FILE/Keasling.pdf	Keasling, Jay	Engineering Bacteria for Drug Production
Blake2004	article	Synthetic biology evolves.	synthetic biology	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15245901&dopt=Citation	Blake, William ; Isaacs, Farren	Trends in biotechnology.	2004	Jul	xx	22	7	321--324	10.1016/j.tibtech.2004.04.008
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Pfleger2006a	article	Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes	synthetic biology	http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt1226.html	Pfleger, Brian ; Pitera, Douglas ; Smolke, Christina ; Keasling, And	Nat Biotech	2006	Aug	xx	24	8	1027--1032	10.1038/nbt1226
Check2005	article	Synthetic biology: Designs on life	synthetic biology	http://www.nature.com/nature/journal/v438/n7067/full/438417a.html	Check, Erika	Nature	2005	Nov	24	438	7067	417--418	10.1038/438417a
Andrianantoandro2006d	article	Synthetic biology: new engineering rules for an emerging discipline	synthetic biology	http://www.nature.com/msb/journal/v2/n1/full/msb4100073.html	Andrianantoandro, Ernesto ; Basu, Subhayu ; Karig, David ; Weiss, And	Mol Syst Biol	2006	xx	xx	2		4100073--4100071	10.1038/msb4100073
Endy2005a	article	Foundations for engineering biology	synthetic biology	http://www.nature.com/nature/journal/v438/n7067/full/nature04342.html	Endy, Drew	Nature	2005	Nov	24	438	7067	449--453	10.1038/nature04342
Ball2004	article	Synthetic biology: Starting from scratch	synthetic biology	http://www.nature.com/nature/journal/v431/n7009/full/431624a.html	Ball, Philip	Nature	2004	Oct	07	431	7009	624--626	10.1038/431624a
Elowitz2000a	article	A synthetic oscillatory network of transcriptional regulators	synthetic biology	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10659856&query_hl=7	Elowitz, Michael ; Leibler, Stanislas	Nature	2000	Jan	20	403	6767	335--338	10.1038/35002125
Brent2004	article	A partnership between biology and engineering	thesis\_chapter\_1	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15470452	Brent, Roger	Nat Biotech	2004	Oct	xx	22	10	1211--1214	10.1038/nbt1004-1211
Isaacs2006	article	RNA synthetic biology	riboswitch	http://dx.doi.org/10.1038/nbt1208	Isaacs, Farren ; Dwyer, Daniel ; Collins, And	Nat Biotech	2006	May	xx	24	5	545--554	10.1038/nbt1208
Fu2006a	article	A perspective of synthetic biology: assembling building blocks for novel functions.	review	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16892318&itool=pubmed_DocSum	Fu, Pengcheng	Biotechnology journal.	2006	Jun	xx	1	6	690--699	10.1002/biot.200600019
Benner2005	article	Synthetic biology.	review	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15995697	Benner, Steven ; Sismour, A.	Nature reviews. Genetics.	2005	Jul	xx	6	7	533--543	10.1038/nrg1637
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Smolke2002	article	Effect of gene location, mRNA secondary structures, and RNase sites on expression of two genes in an engineered operon	synthetic biology	http://www3.interscience.wiley.com/cgi-bin/abstract/99019005/ABSTRACT?CRETRY=1&SRETRY=0	Smolke, Christina D. ; Keasling, Jay D.	Biotechnology and Bioengineering	2002	xx	xx	80	7	762--776	10.1002/bit.10434
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ref163	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	Post-transcriptional control of gene expression: effectors of mRNA decay	synthetic biology	http://www.blackwell-synergy.com/links/doi/10.1046/j.1365-2958.2003.03545.x	Arraiano, Cecilia Maria ; Maquat, Lynne Elizabeth	Molecular Microbiology	2003	xx	xx	49	1	267--276	10.1046/j.1365-2958.2003.03545.x	Description of various mechanisms of mRNA degredation
ref165	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
ref166	electronic	Synthetic biology | Life 2.0 | Economist.com	synthetic biology	http://www.economist.com/business/displaystory.cfm?story_id=7854314
ref167	electronic	Synthetic Biology	synthetic biology	http://syntheticbiology.org/
Maeda2006a	article	Regulatory dynamics of synthetic gene networks with positive feedback.	synthetic biology	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16701695&query_hl=12&itool=pubmed_docsum	Maeda, Yusuke T. ; Sano, Masaki	Journal of molecular biology.	2006	Jun	16	359	4	1107--1124	10.1016/j.jmb.2006.03.064		0022-2836
ref169	electronic	Cell -- Banaszynski et al.	synthetic biology	http://www.cell.com/content/article/fulltext?uid=PIIS0092867406010130
ref170	electronic	Synthetic biology | Playing demigods | Economist.com	synthetic biology	http://www.economist.com/opinion/displaystory.cfm?story_id=E1_SRVQSST
ref171	electronic	Synthetic biology | Life 2.0 | Economist.com	synthetic biology	http://www.economist.com/business/displaystory.cfm?story_id=7854314
Church2005a	article	From systems biology to synthetic biology	synthetic biology	http://www.nature.com/msb/journal/v1/n1/full/msb4100007.html#b5	Church, George	Mol Syst Biol	2005	Mar	29	1		1--1	10.1038/msb4100007
Forster2006b	article	Towards synthesis of a minimal cell	synthetic biology	http://www.nature.com/msb/journal/v2/n1/full/msb4100090.html	Forster, Anthony ; Church, George	Mol Syst Biol	2006	Aug	22	2			10.1038/msb4100090
Forster2006c	article	Towards synthesis of a minimal cell	synthetic biology	http://www.nature.com/msb/journal/v2/n1/full/msb4100090.html	Forster, Anthony ; Church, George	Mol Syst Biol	2006	Aug	22	2			10.1038/msb4100090
Lim2006	article	Model-Based Design of Growth-Attenuated Viruses	systems biology	http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pcbi.0020116	Lim, Kwang-il ; Lang, Tobias ; Lam, Vy ; Yin, John	PLoS Computational Biology	2006	Sep	01	2	9	e116	10.1371/journal.pcbi.0020116
ref176	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
ref177	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.
ref178	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	A perspective of synthetic biology: Assembling building blocks for novel functions.	synthetic biology	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16892318&itool=pubmed_DocSum	Fu, Pengcheng	Biotechnology journal.	2006	Jun	xx	1	6	690--699	10.1002/biot.200600019		1860-6768
Maeda2006b	article	Regulatory dynamics of synthetic gene networks with positive feedback.	synthetic biology	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16701695&query_hl=12&itool=pubmed_docsum	Maeda, Yusuke T. ; Sano, Masaki	Journal of molecular biology.	2006	Jun	16	359	4	1107--1124	10.1016/j.jmb.2006.03.064		0022-2836
Chin2006b	article	Programming and engineering biological networks.	gene	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16842994&itool=pubmed_DocSum	Chin, Jason W.	Current opinion in structural biology.	2006	Aug	xx	16	4	551--556	10.1016/j.sbi.2006.06.011		0959-440X
Pfleger2006b	article	Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes	synthetic biology	http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt1226.html	Pfleger, Brian ; Pitera, Douglas ; Smolke, Christina ; Keasling, Jay	Nature Biotechnology	2006	Jul	16	advanced online publication	8	1027--1032	10.1038/nbt1226		10870156
Pfleger2006c	article	Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes	synthetic biology	http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt1226.html	Pfleger, Brian ; Pitera, Douglas ; Smolke, Christina ; Keasling, Jay	Nature Biotechnology	2006	Jul	16	advanced online publication	8	1027--1032	10.1038/nbt1226		10870156
Posfai2006	article	Emergent Properties of Reduced-Genome Escherichia coli	emergence	http://www.sciencemag.org/cgi/content/abstract/312/5776/1044?etoc	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.	Science	2006	May	19	312	5776	1044--1046
Villalobos2006	article	Gene Designer: A Synthetic Biology Tool for Constructing Artificial DNA Segments.	synthetic biology	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16756672&itool=pubmed_DocSum	Villalobos, Alan ; Ness, Jon ; Gustafsson, Claes ; Minshull, Jeremy ; Govindarajan, Sridhar	BMC Bioinformatics	2006	Jun	06	7	1	285	10.1186/1471-2105-7-285		1471-2105
Andrianantoandro2006e	article	Synthetic biology: new engineering rules for an emerging discipline.	synthetic biology	http://www.nature.com/msb/journal/v2/n1/full/msb4100073.html	Andrianantoandro, Ernesto ; Basu, Subhayu ; Karig, David ; Weiss, Ron	Molecular systems biology [electronic resource].	2006	xx	xx	2		msb4100073--0028	10.1038/msb4100073		1744-4292
Xiang2006	article	Short hairpin RNA-expressing bacteria elicit RNA interference in mammals	synthetic biology	http://www.nature.com/nbt/journal/vaop/ncurrent/abs/nbt1211.html	Xiang, Shuanglin ; Fruehauf, Johannes ; Li, Chiang	Nature Biotechnology	2006	May	14	advanced online publication	6	697--702	10.1038/nbt1211	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.	10870156
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Church2005b	article	From systems biology to synthetic biology	synthetic biology	http://www.nature.com/msb/journal/v1/n1/full/msb4100007.html#b5	Church, George	Molecular systems biology [electronic resource].	2005	Mar	29	1	1	msb4100007--0032	10.1038/msb4100007	editorial	1744-4292
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Endy2005b	article	Foundations for engineering biology	synthetic biology	http://www.nature.com/nature/journal/v438/n7067/full/nature04342.html	Endy, Drew	Nature	2005	Nov	24	438	7067	449--453	10.1038/nature04342		0028-0836
ref192	electronic	OpenWetWare	synthetic biology	http://openwetware.org/wiki/Main_Page										see the comic Adventures in synthetic biology
ref193	electronic	Comic 1 : Adventures in Synthetic Biology : Nature	synthetic biology	http://www.nature.com/nature/comics/syntheticbiologycomic/index.html
Benner2003	article	Synthetic biology: Act natural	nature concepts	http://www.nature.com/nature/journal/v421/n6919/full/421118a.html	Benner, Steven	Nature	2003	Jan	09	421	6919	118	10.1038/421118a		0028-0836
ref195	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	http://www.sciam.com/article.cfm?chanID=sa006&colID=1&articleID=000E491E-B2F9-146C-B2F983414B7F0000									By the Bio FAB group (ht265 2006-06-06 13:24:51)	Synthetic Biology by Baker
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Morton2006a	article	Synthetic Biology 2.0: More bloggers	synthetic biology	http://mainlymartian.blogs.com/semijournal/2006/05/synthetic_biolo_6.html	Morton, Oliver	MainlyMartian	2006	May	23
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Chin2006c	article	Modular approaches to expanding the functions of living matter	synthetic biology	http://www.nature.com/nchembio/journal/v2/n6/abs/nchembio789.html	Chin, Jason	Nature chemical biology.	2006	Jun	xx	2	6	304--311	10.1038/nchembio789		1552-4450
Morton2006b	article	Synthetic Biology 2.0: Medicine (and its malcontents?)	synthetic biology	http://mainlymartian.blogs.com/semijournal/2006/05/synthetic_biolo_5.html	Morton, Oliver	MainlyMartian	2006	May	22
Morton2006c	article	Synthetic Biology 2.0: Also blogging the meeting...	synthetic biology	http://mainlymartian.blogs.com/semijournal/2006/05/syhtetic_biolog.html	Morton, Oliver	MainlyMartian	2006	May	21
Morton2006d	article	Synthetic Biology 2.0: Opposing views	synthetic biology	http://mainlymartian.blogs.com/semijournal/2006/05/synthetic_biolo_3.html	Morton, Oliver	MainlyMartian	2006	May	20
Morton2006e	article	Synthetic Biology 2.0: Fun to come	synthetic biology	http://mainlymartian.blogs.com/semijournal/2006/05/synthetic_biolo_2.html	Morton, Oliver	MainlyMartian	2006	May	20
Morton2006f	article	Synthetic Biology 2.0: BTUs per bushel	synthetic biology	http://mainlymartian.blogs.com/semijournal/2006/05/synthetic_biolo_1.html	Morton, Oliver	MainlyMartian	2006	May	20
Morton2006g	article	Synthetic Biology 2.0: What's afoot?	synthetic biology	http://mainlymartian.blogs.com/semijournal/2006/05/synthetic_biolo.html	Morton, Oliver	MainlyMartian	2006	May	20
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Endy2005c	article	Foundations for engineering biology	fun	http://www.nature.com/nature/journal/v438/n7067/full/nature04342.html	Endy, Drew	Nature	2005	Nov	24	438	7067	449--453	10.1038/nature04342		0028-0836
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Bray1995	article	Protein molecules as computational elements in living cells	synthetic biology	http://www.nature.com/nature/journal/v376/n6538/abs/376307a0.html	Bray, Dennis	Nature.	1995	Jul	27	376	6538	307--312	10.1038/376307a0		0028-0836
Pawson1995	article	Protein modules and signalling networks	synthetic biology	http://www.nature.com/nature/journal/v373/n6515/abs/373573a0.html	Pawson, Tony	Nature	1995	Feb	16	373	6515	573--580	10.1038/373573a0
ref213	article	BioMed Central | Abstract | 1471-2105-7-55 | PathSys: integrating molecular interaction graphs for systems biology	synthetic biology	http://dx.doi.org/10.1186/1471-2105-7-55		BMC Bioinformatics	2006	Feb	07	7	1	55	10.1186/1471-2105-7-55		14712105
ref214	electronic	Synthetic Biology in Practice	synthetic biology	http://blog.lib.umn.edu/sali0090/synbio/
ref215	electronic	General Review Papers - IGEM	synthetic biology	http://parts.mit.edu/wiki/index.php/General_Review_Papers
ref216	electronic	Synthetic systems biology	synthetic biology	http://www.ncbs.res.in/~faculty/ssb/apply1.html
Boonyarattanakalin2006	article	Synthesis of an Artificial Cell Surface Receptor that Enables Oligohistidine Affinity Tags to Function as Metal-Dependent Cell-Penetrating Peptides.	synthetic biology	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16402806&query_hl=1&itool=pubmed_docsum	Boonyarattanakalin, Siwarutt ; Athavankar, Sonalee ; Sun, Qi ; Peterson, Blake R.	Journal of the American Chemical Society.	2006	Jan	18	128	2	386--387	10.1021/ja056126j		0002-7863
Rackham2005	article	A network of orthogonal ribosome x mRNA pairs.	synthetic biology	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16408021&query_hl=1&itool=pubmed_docsum	Rackham, Oliver ; Chin, Jason W.	Nature chemical biology.	2005	Aug	xx	1	3	159--166	10.1038/nchembio719		1552-4450
Volgraf2006	article	Allosteric control of an ionotropic glutamate receptor with an optical switch.	synthetic biology	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16408092&query_hl=1&itool=pubmed_docsum	Volgraf, Matthew ; Gorostiza, Pau ; Numano, Rika ; Kramer, Richard H. ; Isacoff, Ehud Y. ; Trauner, Dirk	Nature chemical biology.	2006	Jan	xx	2	1	47--52	10.1038/nchembio756		1552-4450
Simpson2004a	article	Rewiring the cell: synthetic biology moves towards higher functional complexity.	synthetic biology	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15491797&query_hl=4	Simpson, Michael L.	Trends Biotechnol	2004	Nov	xx	22	11	555--557	10.1016/j.tibtech.2004.09.003		0167-7799
ref221	electronic	Research Papers in Synthetic Biology - IGEM	synthetic biology	http://parts.mit.edu/wiki/index.php/Research_Papers_in_Synthetic_Biology
ref222	electronic	Registry of Standard Biological Parts	synthetic biology	http://parts.mit.edu/
ref223	electronic	Main Page - IGEM	synthetic biology	http://parts.mit.edu/wiki/index.php/Main_Page
ref224	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	Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana	synthetic biology	http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt1162.html	Chen, Ming-Tang ; Weiss, Ron	Nature biotechnology.	2005	Nov	20	advanced online publication	12	1551--1555	10.1038/nbt1162		1087-0156
Fung2005	article	A synthetic gene-metabolic oscillator	synthetic biology	http://www.nature.com/nature/journal/v435/n7038/abs/nature03508.html	Fung, Eileen ; Wong, Wilson ; Suen, Jason ; Bulter, Thomas ; Lee, Sun-gu ; Liao, James	Nature	2005	May	05	435	7038	118--122	10.1038/nature03508		0028-0836
Endy2005d	article	Foundations for engineering biology	synthetic biology	http://www.nature.com/nature/journal/v438/n7067/full/nature04342.html	Endy, Drew	Nature	2005	Nov	24	438	7067	449--453	10.1038/nature04342	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.	0028-0836
Levskaya2005b	article	Synthetic biology: Engineering Escherichia coli to see light	synthetic biology	http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html	Levskaya, Anselm ; Chevalier, Aaron ; Tabor, Jeffrey ; Simpson, Zachary Booth ; Lavery, Laura ; Levy, Matthew ; Davidson, Eric ; Scouras, Alexander ; Ellington, Andrew ; Marcotte, Edward ; Voigt, Christopher	Nature.	2005	Nov	24	438	7067	441--442	10.1038/nature04405		1476-4687
Endy2005e	article	Foundations for engineering biology	synthetic biology	http://www.nature.com/nature/journal/v438/n7067/full/nature04342.html	Endy, Drew	Nature	2005	Nov	24	438	7067	449--453	10.1038/nature04342		0028-0836
Sprinzak2005b	article	Reconstruction of genetic circuits	synthetic biology	http://www.nature.com/nature/journal/v438/n7067/full/nature04335.html	Sprinzak, David ; Elowitz, Michael	Nature	2005	Nov	24	438	7067	443--448	10.1038/nature04335		0028-0836
Levskaya2005c	article	Synthetic biology: Engineering Escherichia coli to see light - article in Nature	Photography	http://www.nature.com/nature/journal/v438/n7067/abs/nature04405.html	Levskaya, Anselm ; Chevalier, Aaron ; Tabor, Jeffrey ; Simpson, Zachary Booth ; Lavery, Laura ; Levy, Matthew ; Davidson, Eric ; Scouras, Alexander ; Ellington, Andrew ; Marcotte, Edward ; Voigt, Christopher	Nature.	2005	Nov	24	438	7067	441--442	10.1038/nature04405	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.	1476-4687
ref232	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.
ref233	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.
ref234	electronic	Foundations for engineering biology	synthetic biology	http://www.nature.com/nature/journal/v438/n7067/pdf/nature04342.pdf
ref235	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	Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana	synthetic biology	http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt1162.html	Chen, Ming-Tang ; Weiss, Ron	Nature biotechnology.	2005	Nov	20	advanced online publication	12	1551--1555	10.1038/nbt1162		1087-0156
Pennisi2005	article	SYNTHETIC BIOLOGY: Synthetic Biology Remakes Small Genomes	synthetic biology	http://www.sciencemag.org/cgi/content/full/310/5749/769	Pennisi, Elizabeth	Science	2005	Nov	04	310	5749	769--770
ref238	electronic	Qualitative Reasoning in biology - symposium collection	synthetic biology	http://monet.aber.ac.uk:8080/monet/docs/pdf_files/aime_03/mbqr-aime03.pdf
ref239	electronic	Welcome to Synthetic and Systems Biology	synthetic biology	http://www.ssbjournal.com/										Journal Homepage
ref240	article	Combining two genomes in one cell: Stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome	synthetic biology	http://dx.doi.org/10.1073/pnas.0503868102		Proceedings of the National Academy of Sciences of the United States of America	2005	Nov	01	102	44	15971--15976	10.1073/pnas.0503868102		0027-8424
ref241	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	Rewiring the cell: synthetic biology moves towards higher functional complexity.	synthetic biology	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15491797&query_hl=4	Simpson, Michael L.	Trends Biotechnol	2004	Nov	xx	22	11	555--557	10.1016/j.tibtech.2004.09.003	Nice overview of the present state of the field and some of its future research goals	0167-7799
Pedraza2005b	article	Noise propagation in gene networks.	Synthetic	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15790857&query_hl=12	Pedraza, Juan M. ; van Oudenaarden, Alexander	Science (New York, N.Y.)	2005	Mar	25	307	5717	1965--1969	10.1126/science.1109090		1095-9203
Elowitz2002	article	Stochastic gene expression in a single cell.	synthetic biology	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12183631&query_hl=7	Elowitz, Michael B. ; Levine, Arnold J. ; Siggia, Eric D. ; Swain, Peter S.	Science	2002	Aug	16	297	5584	1183--1186	10.1126/science.1070919		1095-9203
Guet2002b	article	Combinatorial synthesis of genetic networks.	network	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12029133&query_hl=7	Guet, Călin C. ; Elowitz, Michael B. ; Hsing, Weihong ; Leibler, Stanislas	Science.	2002	May	24	296	5572	1466--1470	10.1126/science.1067407		1095-9203
Elowitz2000c	article	A synthetic oscillatory network of transcriptional regulators.	synthetic biology	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=10659856&query_hl=7	Elowitz, M. B. ; Leibler, S.	Nature.	2000	Jan	20	403	6767	335--338	10.1038/35002125	Fundamental paper in Synthetic Biology	0028-0836
ref247	electronic	picrender.fcgi (application/pdf Object)	synthetic biology	http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=550990&action=stream&blobtype=pdf