Endy:Reprints: Difference between revisions
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*'''Note:''' We also publish thesis proposals, dissertations, and technical reports via [https://dspace.mit.edu/handle/1721.1/18186/browse-date DSpace], an online digital repository operated by the MIT Library. | *'''Note:''' We also publish thesis proposals, dissertations, and technical reports via [https://dspace.mit.edu/handle/1721.1/18186/browse-date DSpace], an online digital repository operated by the MIT Library. | ||
*'''Note:''' PDF reprints are provided below within the context of [http://www.copyright.gov/fls/fl102.html fair use]. Please obtain copies from the publisher if appropriate. | *'''Note:''' PDF reprints are provided below within the context of [http://www.copyright.gov/fls/fl102.html fair use]. Please obtain copies from the publisher if appropriate. | ||
*'''Note:''' Search [http://pubget.com/search?q=%22endy%20d%22 "endy d"] via PubGet for a third-party automatically generated set of PubMed-listed publications from the lab. | |||
===Student Dissertations=== | |||
'''Barry Canton'''<br> | |||
''Engineering the interface between cellular chassis and synthetic biological systems''<br> | |||
MIT PhD, 2008 [http://dspace.mit.edu/bitstream/handle/1721.1/44918/301953836.pdf?sequence=1 dissertation] (PDF), doi: 1721.1/44918<br> | |||
'''Jeff Gritton'''<br> | |||
''Architecture and evolutionary stability of yeast signaling pathways''<br> | |||
MIT MS, 2006 [http://dspace.mit.edu/bitstream/handle/1721.1/37258/85844464.pdf?sequence=1 thesis] (PDF), doi: 1721.1/37258<br> | |||
'''Jason Kelly'''<br> | |||
''Tools and reference standards supporting the engineering and evolution of synthetic biological systems''<br> | |||
MIT PhD, 2008 [http://dspace.mit.edu/bitstream/handle/1721.1/44917/301953777.pdf?sequence=1 dissertation] (PDF), doi: 1721.1/44917<br> | |||
'''Nicolas Koutsoubelis'''<br> | |||
''Quantitative in silico and in vivo characterization of the recombinase addressable data storage''<br> | |||
University of Freiburg BS @ Stanford, 2012 [[Media:Koutsoubelis BS Thesis Stanford Freiburg.pdf | thesis]] (PDF)<br> | |||
'''Sriram Kosuri'''<br> | |||
''Simulation, models, and refactoring of bacteriophage T7 gene expression''<br> | |||
MIT PhD, 2007 [http://dspace.mit.edu/bitstream/handle/1721.1/39912/182579919.pdf?sequence=1 dissertation] (PDF), doi: 1721.1/39912<br> | |||
'''Alex Mallet'''<br> | |||
''Analysis of Targeted and Combinatorial Approaches to Phage T7 Genome Generation''<br> | |||
MIT MS, 2007 [http://dspace.mit.edu/bitstream/handle/1721.1/35880/MastersThesis.pdf?sequence=1 thesis] (PDF), doi: 1721.1/35880<br> | |||
'''Monica Ortiz'''<br> | |||
''Engineering bacterial populations via DNA messaging''<br> | |||
Stanford PhD, 2013 [http://purl.stanford.edu/ht577gs4955 dissertation] (PDF)<br> | |||
'''Beatrice Ramm'''<br> | |||
''Observations, quantitation and application of contact-dependent growth inhibition for controlling cell growth and patterning''<br> | |||
Technische Universität München MS @ Stanford, 2015 [[Media:MasterThesis Beatrice Ramm.pdf | thesis]] (PDF)<br> | |||
'''Reshma Shetty''' (co-advisee with Tom Knight<br> | |||
''Applying engineering principles to the design and construction of transcriptional devices''<br> | |||
MIT PhD, 2008 [http://dspace.mit.edu/bitstream/handle/1721.1/44921/302346650.pdf?sequence=1 dissertation] (PDF), doi: 1721.1/44921<br> | |||
'''Francois St-Pierre'''<br> | |||
''Determination of cell fate selection during phage lambda infection''<br> | |||
MIT PhD, 2009 [[Media:StPierre thesis rev2.PDF | dissertation]] (PDF), doi: pending<br> | |||
'''Pakpoom Subsoontorn'''<br> | |||
''Reliable functional composition of a recombinase device family''<br> | |||
Stanford PhD, 2014 [http://purl.stanford.edu/sm186rb9123 dissertation] (PDF)<br> | |||
'''Samantha Sutton'''<br> | |||
''Engineering phosphorylation-dependent post-translational protein devices''<br> | |||
MIT PhD, 2008 [http://dspace.mit.edu/bitstream/handle/1721.1/45205/301815200.pdf?sequence=1 dissertation] (PDF), doi: 1721.1/45205<br> | |||
'''Ty Thompson'''<br> | |||
''Models and analysis of yeast mating response: tools for model building, from documentation to time-dependent stimulation''<br> | |||
MIT PhD, 2008 [http://dspace.mit.edu/bitstream/handle/1721.1/45206/301815747.pdf?sequence=1 dissertation] (PDF), doi: 1721.1/45206<br> | |||
===Peer Reviewed Research Articles=== | |||
'''Detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates'''<br> | |||
''Science Translational Medicine''<br> | |||
Alexis Courbet, [[Drew Endy]], Eric Renard, Franck Molina1, and Jérôme Bonnet<br> | |||
[http://stm.sciencemag.org/content/7/289/289ra83 URL] [[Media:Aaa3601_ArticleContent_v13.pdf | PDF reprint]]<br> | |||
'''The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.'''<br> | |||
''Nature Biotechnology'' 32, 545–550 (2014) doi:10.1038/nbt.2891<br> | |||
Michal Galdzicki, Kevin P Clancy, Ernst Oberortner, Matthew Pocock, Jacqueline Y Quinn, Cesar A Rodriguez, Nicholas Roehner, Mandy L Wilson, Laura Adam, J Christopher Anderson, Bryan A Bartley, Jacob Beal, Deepak Chandran, Joanna Chen, Douglas Densmore, [[Drew Endy]], Raik Grünberg, Jennifer Hallinan, Nathan J Hillson, Jeffrey D Johnson, Allan Kuchinsky, Matthew Lux, Goksel Misirli, Jean Peccoud, Hector A Plahar, Evren Sirin, Guy-Bart Stan, Alan Villalobos, Anil Wipat, John H Gennari, Chris J Myers, & Herbert M Sauro<br> | |||
[http://www.nature.com/nbt/journal/v32/n6/full/nbt.2891.html URL] [http://www.jbioleng.org/| PDF reprint pending]<br> | |||
and '''Reply to Intellectual property issues and synthetic biology standards.''' ''Nat Biotechnol.'' 2015 Jan;33(1):25. doi: 10.1038/nbt.3114. by Galdzicki M, Kahl LJ, [[Drew Endy]], Sauro HM.<br> | |||
'''One-step cloning and chromosomal integration of DNA'''<br> | |||
''ACS Synthetic Biology,'' 2013 Sep 20;2(9):537-41. doi: 10.1021/sb400021j. Epub 2013 May 20.<br> | |||
Francois St.Pierre, Lun Cui, David Priest, [[Drew Endy]], Ian Dodd, Keith Shearwin<br> | |||
[http://pubs.acs.org/doi/abs/10.1021/sb400021j URL]<br> | |||
'''A survey of enabling technologies in synthetic biology'''<br> | |||
''Journal of Biological Engineering,'' 7:13, 10 May 2013, doi:10.1186/1754-1611-7-13<br> | |||
Linda J. Kahl & [[Drew Endy]]<br> | |||
[http://www.jbioleng.org/content/7/1/13/abstract URL] [http://www.jbioleng.org/| PDF reprint pending]<br> | |||
'''Amplifying genetic logic gates'''<br> | |||
''Science,'' 28 March 2013, doi: 10.1126/science.1232758 <br> | |||
Jerome Bonnet, Peter Yin, Monica E. Ortiz, Pakpoom Subsoontorn, [[Drew Endy]]<br> | |||
[http://www.sciencemag.org/content/340/6132/599 URL] [http://www.npr.org/2013/03/29/175604770/tiny-dna-switches-aim-to-revolutionize-cellular-computing NPR] [http://youtu.be/ahYZBeP_r5U YouTube primer] | |||
'''Measurement and modeling of intrinsic transcription terminators'''<br> | |||
''Nucleic Acids Research,'' March 19, 2013, doi: 10.1093/nar/gkt163<br> | |||
Guillaume Cambray, Joao C. Guimaraes, Vivek K. Mutalik, Colin Lam1, Quynh-Anh Mai, Tim Thimmaiah, James M. Carothers, Adam P. Arkin, [[Drew Endy]]<br> | |||
[http://nar.oxfordjournals.org/content/41/9/5139.long URL] | |||
'''Precise and reliable gene expression via standard transcription and translation initiation elements'''<br> | |||
''Nature Methods,'' 10,354–360 (2013), doi:10.1038/nmeth.2404<br> | |||
Vivek K Mutalik, Joao C Guimaraes, Guillaume Cambray, Colin Lam, Marc Juul Christoffersen, Quynh-Anh Mai, Andrew B Tran, Morgan Paull, Jay D Keasling, Adam P Arkin, [[Drew Endy]]<br> | |||
[http://www.nature.com/nmeth/journal/v10/n4/full/nmeth.2404.html URL]<br> | |||
'''Quantitative estimation of activity and quality for collections of functional genetic elements.'''<br> | |||
''Nature Methods,'' 10,347–353 (2013), doi:10.1038/nmeth.2403<br> | |||
Vivek K Mutalik, Joao C Guimaraes, Guillaume Cambray, Quynh-Anh Mai, Marc Juul Christoffersen, Lance Martin, Ayumi Yu, Colin Lam, Cesar Rodriguez, Gaymon Bennett, Jay D Keasling, [[Drew Endy]],Adam P Arkin<br> | |||
[http://www.nature.com/nmeth/journal/v10/n4/full/nmeth.2403.html URL]<br> | |||
'''Design and analysis of genetically encoded counters'''<br> | |||
''Procedia Computer Science,'' v11 (2012) pp.43-54<br> | |||
Pakpoom Subsoontorn and [[Drew Endy]]<br> | |||
[http://www.sciencedirect.com/science/article/pii/S1877050912005893 URL] [[Media:TonGoesRogue 2012.pdf | PDF reprint]] | |||
'''A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast'''<br> | |||
''Virology,'' published online 15 October 2012, doi: 10.1016/j.virol.2012.09.020<br> | |||
Paul Jaschke, Erica Lieberman, Jon Rodriguez, Adrian Sierra, [[Drew Endy]]<br> | |||
[http://www.sciencedirect.com/science/article/pii/S0042682212004618# URL] [[Media:PhageInYeast.pdf | PDF reprint]] | |||
'''Engineered cell-cell communication via DNA messaging'''<br> | |||
''Journal of Biological Engineering'' Sept 2012, 6:16 doi:10.1186/1754-1611-6-16<br> | |||
Monica Ortiz and [[Drew Endy]]<br> | |||
[http://www.jbioleng.org/content/6/1/16/ URL] [http://www.jbioleng.org/| Final PDF pending] | |||
'''Refactored M13 bacteriophage as a platform for tumor cell imaging and drug delivery'''<br> | |||
''ACS Synthetic Biology,'' doi:10.1021/sb300052u, August 17, 2012<br> | |||
Debadyuti Ghosh, Aditya Kohli, Felix Moser, Drew Endy, and Angela Belcher<br> | |||
[http://pubs.acs.org/doi/full/10.1021/sb300052u URL] [http://pubs.acs.org/doi/pdf/10.1021/sb300052u PDF reprint] | |||
'''Rewritable digital data storage in live cells via engineered control of recombination directionality'''<br> | |||
''PNAS USA,'' 21 May 2012, doi: 10.1073/pnas.1202344109<br> | |||
Jerome Bonnet, Pakpoom Subsoontorn and [[Drew Endy]]<br> | |||
[http://www.pnas.org/content/early/2012/05/14/1202344109.abstract URL] [http://www.pnas.org/content/early/2012/05/14/1202344109.full.pdf PDF reprint] | |||
'''Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range'''<br> | |||
''PNAS USA,'' 2011 November; doi: 10.1073/pnas.1004042108<br> | |||
Ty Thomson, Kirsten Benjamin, Alan Bush, Tonya Love, David Pincus, Orna Resnekov, Richard Yu, Andrew Gordon, Alejandro Colman-Lerner, [[Drew Endy]], Roger Brent<br> | |||
[http://www.pnas.org/content/early/2011/11/22/1004042108.abstract URL] [http://www.pnas.org/content/early/2011/11/22/1004042108.full.pdf+html | PDF reprint] | |||
'''Gemini, a bifunctional enzymatic and fluorescent reporter of gene expression'''<br> | |||
''PLoS ONE'' 4(11): e7569. doi:10.1371/journal.pone.0007569<br> | |||
Lance Martin, Austin Che, [[Drew Endy]]<br> | |||
[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0007569 URL] [[Media:Journal.pone.0007569.pdf | PDF reprint]] | |||
'''Measuring the activity of BioBrick promoters using an in vivo reference standard'''<br> | |||
''Journal of Biological Engineering,'' 2009 March 20;3:4<br> | |||
[[Jason_Kelly | Jason R Kelly]], Adam J Rubin, Caroline M Ajo-Franklin, John Cumbers, Michael J. Czar, Kim de Mora, Aaron L Glieberman, Dileep D Monie, [[Drew Endy]]<br> | |||
[http://www.jbioleng.org/content/3/1/4 URL] [http://www.jbioleng.org/content/pdf/1754-1611-3-4.pdf PDF reprint] | |||
'''Determination of cell fate selection during phage lambda infection'''<br> | '''Determination of cell fate selection during phage lambda infection'''<br> | ||
''PNAS USA,'' 2008 December; 105(52), 20705-20710<br> | ''PNAS USA,'' 2008 December; 105(52), 20705-20710<br> | ||
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[[Leon Chan|Leon Y. Chan]], [[Sriram Kosuri]] and [[Drew Endy]]<br> | [[Leon Chan|Leon Y. Chan]], [[Sriram Kosuri]] and [[Drew Endy]]<br> | ||
[http://www.nature.com/msb/journal/v1/n1/full/msb4100025.html URL] | [http://www.nature.com/msb/journal/v1/n1/full/msb4100025.html URL] | ||
[http://openwetware. | [http://openwetware.org/images/e/ef/Msb4100025.pdf PDF reprint] | ||
[http://www.nature.com/msb/journal/v1/n1/full/msb4100028.html News & Views] | [http://www.nature.com/msb/journal/v1/n1/full/msb4100028.html News & Views] | ||
[https://dspace.mit.edu/handle/1721.1/27501 October 2004 version] | [https://dspace.mit.edu/handle/1721.1/27501 October 2004 version] | ||
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''Nature'' '''409''', 391-395<br> | ''Nature'' '''409''', 391-395<br> | ||
[[Drew Endy]] and Roger Brent<br> | [[Drew Endy]] and Roger Brent<br> | ||
[http://openwetware. | [http://openwetware.org/images/a/ae/409391a0.pdf PDF reprint] | ||
'''Computation, prediction, and experimental test of fitness for bacteriophage T7 mutants with permuted genomes'''<br> | '''Computation, prediction, and experimental test of fitness for bacteriophage T7 mutants with permuted genomes'''<br> | ||
''Proceedings of the National Academy of Sciences USA'' '''97''', 5375-5380<br> | ''Proceedings of the National Academy of Sciences USA'' '''97''', 5375-5380<br> | ||
[[Drew Endy]], Lingchong You, John Yin and Ian Molineux<br> | [[Drew Endy]], Lingchong You, John Yin and Ian Molineux<br> | ||
[http://openwetware. | [http://openwetware.org/images/e/ea/PNAS%2897%295375.pdf PDF reprint] | ||
'''Toward antiviral strategies that resist viral escape'''<br> | '''Toward antiviral strategies that resist viral escape'''<br> | ||
''Antimicrobial Agents & Chemotherapy'' '''44''', 1097-1099<br> | ''Antimicrobial Agents & Chemotherapy'' '''44''', 1097-1099<br> | ||
[[Drew Endy]] and John Yin<br> | [[Drew Endy]] and John Yin<br> | ||
[http://openwetware. | [http://openwetware.org/images/0/04/1097.pdf PDF reprint] | ||
'''Intracellular kinetics of a growing virus: A genetically-structured simulation for bacteriophage T7'''<br> | '''Intracellular kinetics of a growing virus: A genetically-structured simulation for bacteriophage T7'''<br> | ||
''Biotechnology & Bioengineering'' '''55''', 375-389<br> | ''Biotechnology & Bioengineering'' '''55''', 375-389<br> | ||
[[Drew Endy]], Deyu Kong, and John Yin<br> | [[Drew Endy]], Deyu Kong, and John Yin<br> | ||
[http://openwetware. | [http://openwetware.org/images/7/73/BB%2855%29375.pdf PDF reprint] | ||
===Transcribed Lectures=== | ===Transcribed Lectures=== | ||
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[[Media:Ind.2008.4.340.pdf | PDF reprint]] | [[Media:Ind.2008.4.340.pdf | PDF reprint]] | ||
===Other Articles, | ===Other Articles, edited but not peer reviewed=== | ||
'''Switches, switches, every where, in any drop we drink'''<br> | |||
''Molecular Cell,'' 25 January 2013<br> | |||
Jerome Bonnet, [[Drew Endy]]<br> | |||
URL pending, PDF reprint pending<br> | |||
'''Cribsheet #16: Synthetic Biology'''<br> | '''Cribsheet #16: Synthetic Biology'''<br> | ||
''SEED'' July 2008<br> | ''SEED'' July 2008<br> | ||
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''The Scientist'' January 2006<br> | ''The Scientist'' January 2006<br> | ||
[[Drew Endy]]<br> | [[Drew Endy]]<br> | ||
[http://www.the-scientist.com/article/display/18856/ URL] | [http://www.the-scientist.com/article/display/18856/ URL] (login likely req'd.)<br> | ||
[http://www.exacteditions.com/exact/browse/328/344/1189/3/39/0/endy URL] (login not req'd., as of 24 March 2009) | |||
'''2003 Synthetic Biology study'''<br> | '''2003 Synthetic Biology study'''<br> | ||
'' | ''DARPA ISAT Study'' & briefing to Director, October 2003<br> | ||
[[Drew Endy]], | [[Drew Endy]], Pat Lincoln, Richard Murray<br> | ||
[[doi:1721.1/38455]] | [[doi:1721.1/38455]] | ||
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===Books=== | ===Books=== | ||
'''Synthetic Aesthetics: Investigating Synthetic Biology's Designs on Nature'''<br> | |||
''MIT Press'', in press, 2013/2014<br> | |||
Alexandra Daisy Ginsberg, Jane Calvert, Pablo Schyfter, Alistair Elfick, [[Drew Endy]]<br> | |||
'''Adventures in synthetic biology'''<br> | '''Adventures in synthetic biology'''<br> | ||
''Nature'' 24 November 2005 Cover & Online<br> | ''Nature'' 24 November 2005 Cover & Online<br> | ||
[[Drew Endy]], Isadora Deese and [http://www.chuckwadey.com Chuck Wadey]<br> | [[Drew Endy]], Isadora Deese and [http://www.chuckwadey.com Chuck Wadey]<br> | ||
[[Adventures | PDF, links, and background information]]<br> | [[Adventures | PDF, links, and background information]]<br> | ||
<font color="green">For a reprint, please | <font color="green">For a reprint, please download a free .PDF from the link above</font> | ||
===Book Chapters=== | ===Edited Book Chapters=== | ||
'''Synthetic Biology'''<br> | '''Synthetic Biology'''<br> | ||
''Bioethics Briefing Book'', The Hastings Center, 2008, Chapter 35<br> | ''Bioethics Briefing Book'', The Hastings Center, 2008, Chapter 35<br> | ||
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''no e-print currently available (sorry!)'' | ''no e-print currently available (sorry!)'' | ||
===Online Lectures or Debates=== | ===Selected Online Lectures or Debates=== | ||
'''Synthetic Biology Debate | '''Synthetic Biology Debate with Jim Thomas, moderated by Stewart Brand'''<br> | ||
The Long Now Foundation, 17 November 2008<br> | The Long Now Foundation, 17 November 2008<br> | ||
Cowell Theater, Fort Mason Center, San Francisco<br> | Cowell Theater, Fort Mason Center, San Francisco<br> | ||
[http://fora.tv/2008/11/17/Drew_Endy_and_Jim_Thomas_Debate_Synthetic_Biology Online w/ transcription via FORA.tv], [http://www.wholeearthfilms.com/endy_drew.html DVD for purchase via Whole Earth Films]<br> | [http://fora.tv/2008/11/17/Drew_Endy_and_Jim_Thomas_Debate_Synthetic_Biology Online w/ transcription via FORA.tv], [http://www.wholeearthfilms.com/endy_drew.html DVD for purchase via Whole Earth Films]<br> | ||
'''Programming DNA: A 2-bit language for engineering biology'''<br> | |||
24C3, The 24th Chaos Communication Congress, 27 December 2007<br> | |||
Berliner Congress Center, Berlin<br> | |||
[http://video.google.com/videoplay?docid=-6950604815683841321 Online via Google video] | |||
|}<br style="clear:both" /> | |}<br style="clear:both" /> |
Revision as of 16:49, 27 May 2015
Student DissertationsBarry Canton Jeff Gritton Jason Kelly Nicolas Koutsoubelis Sriram Kosuri Alex Mallet Monica Ortiz Beatrice Ramm Reshma Shetty (co-advisee with Tom Knight Francois St-Pierre Pakpoom Subsoontorn Samantha Sutton Ty Thompson Peer Reviewed Research ArticlesDetection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. One-step cloning and chromosomal integration of DNA A survey of enabling technologies in synthetic biology Amplifying genetic logic gates Measurement and modeling of intrinsic transcription terminators Precise and reliable gene expression via standard transcription and translation initiation elements Quantitative estimation of activity and quality for collections of functional genetic elements. Design and analysis of genetically encoded counters A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast Engineered cell-cell communication via DNA messaging Refactored M13 bacteriophage as a platform for tumor cell imaging and drug delivery Rewritable digital data storage in live cells via engineered control of recombination directionality Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range Gemini, a bifunctional enzymatic and fluorescent reporter of gene expression Measuring the activity of BioBrick promoters using an in vivo reference standard Determination of cell fate selection during phage lambda infection Refinement and standardization of synthetic biological parts and devices Engineering BioBrick vectors from BioBrick parts Stimulus design for model selection and validation in cell signaling TABASCO: A single molecule, base-pair resolved gene expression simulator DNA synthesis and biological security Synthetic genomics: Options for governance Foundations for engineering biology Refactoring bacteriophage T7 Regulated cell to cell variation in a cell fate decision system Modelling cellular behaviour (insight feature) Computation, prediction, and experimental test of fitness for bacteriophage T7 mutants with permuted genomes Toward antiviral strategies that resist viral escape Intracellular kinetics of a growing virus: A genetically-structured simulation for bacteriophage T7 Transcribed LecturesSynthetic biology: Can we make biology easy to engineer? <--note: transcription was not proofed Other Articles, edited but not peer reviewedSwitches, switches, every where, in any drop we drink Cribsheet #16: Synthetic Biology Reconstruction of the genomes Building a fab for biology A biological engineer searches for simplicity Useful construction 2003 Synthetic Biology study Molecular monogamy Decoding NF-kB signaling A standard parts list for biological circuitry BooksSynthetic Aesthetics: Investigating Synthetic Biology's Designs on Nature Adventures in synthetic biology Edited Book ChaptersSynthetic Biology Towards a predictive biology: The example of bacteriophage T7 Selected Online Lectures or DebatesSynthetic Biology Debate with Jim Thomas, moderated by Stewart Brand Programming DNA: A 2-bit language for engineering biology |