Endy:Reprints: Difference between revisions
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''Tools and reference standards supporting the engineering and evolution of synthetic biological systems''<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> | 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> | '''Sriram Kosuri'''<br> | ||
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''Analysis of Targeted and Combinatorial Approaches to Phage T7 Genome Generation''<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> | 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> | '''Reshma Shetty''' (co-advisee with Tom Knight<br> | ||
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''Determination of cell fate selection during phage lambda infection''<br> | ''Determination of cell fate selection during phage lambda infection''<br> | ||
MIT PhD, 2009 [[Media:StPierre thesis rev2.PDF | dissertation]] (PDF), doi: pending<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> | '''Samantha Sutton'''<br> | ||
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===Peer Reviewed Research Articles=== | ===Peer Reviewed Research Articles=== | ||
''' | '''Detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates'''<br> | ||
''Nature Methods,'' | ''Science Translational Medicine''<br> | ||
Vivek Mutalik | Alexis Courbet, [[Drew Endy]], Eric Renard, Franck Molina1, and Jérôme Bonnet<br> | ||
[http://www. | [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> | '''A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast'''<br> | ||
''Virology,'' | ''Virology,'' published online 15 October 2012, doi: 10.1016/j.virol.2012.09.020<br> | ||
Paul Jaschke | Paul Jaschke, Erica Lieberman, Jon Rodriguez, Adrian Sierra, [[Drew Endy]]<br> | ||
[http://www. | [http://www.sciencedirect.com/science/article/pii/S0042682212004618# URL] [[Media:PhageInYeast.pdf | PDF reprint]] | ||
'''Engineered cell-cell communication via DNA messaging'''<br> | '''Engineered cell-cell communication via DNA messaging'''<br> | ||
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''ACS Synthetic Biology,'' doi:10.1021/sb300052u, August 17, 2012<br> | ''ACS Synthetic Biology,'' doi:10.1021/sb300052u, August 17, 2012<br> | ||
Debadyuti Ghosh, Aditya Kohli, Felix Moser, Drew Endy, and Angela Belcher<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 | [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> | '''Rewritable digital data storage in live cells via engineered control of recombination directionality'''<br> | ||
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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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'''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> | ||
===Edited Book Chapters=== | ===Edited Book Chapters=== |
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 |