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Note: We also publish thesis proposals, dissertations, and technical reports via DSpace, an online digital repository operated by the MIT Library. Note: PDF reprints are provided below within the context of fair use. Please obtain copies from the publisher if appropriate. Note: Search "endy d" via PubGet for a third-party automatically generated set of PubMed-listed publications from the lab. Student Dissertations Barry Canton Engineering the interface between cellular chassis and synthetic biological systems MIT PhD, 2008 dissertation (PDF), doi: 1721.1/44918 Jeff Gritton Architecture and evolutionary stability of yeast signaling pathways MIT MS, 2006 thesis (PDF), doi: 1721.1/37258 Jason Kelly Tools and reference standards supporting the engineering and evolution of synthetic biological systems MIT PhD, 2008 dissertation (PDF), doi: 1721.1/44917 Nicolas Koutsoubelis Quantitative in silico and in vivo characterization of the recombinase addressable data storage University of Freiburg BS @ Stanford, 2012 thesis (PDF) Sriram Kosuri Simulation, models, and refactoring of bacteriophage T7 gene expression MIT PhD, 2007 dissertation (PDF), doi: 1721.1/39912 Alex Mallet Analysis of Targeted and Combinatorial Approaches to Phage T7 Genome Generation MIT MS, 2007 thesis (PDF), doi: 1721.1/35880 Monica Ortiz Engineering bacterial populations via DNA messaging Stanford PhD, 2013 dissertation (PDF) Beatrice Ramm Observations, quantitation and application of contact-dependent growth inhibition for controlling cell growth and patterning Technische Universität München MS @ Stanford, 2015 thesis (PDF) Reshma Shetty (co-advisee with Tom Knight Applying engineering principles to the design and construction of transcriptional devices MIT PhD, 2008 dissertation (PDF), doi: 1721.1/44921 Francois St-Pierre Determination of cell fate selection during phage lambda infection MIT PhD, 2009 dissertation (PDF), doi: pending Pakpoom Subsoontorn Reliable functional composition of a recombinase device family Stanford PhD, 2014 dissertation (PDF) Samantha Sutton Engineering phosphorylation-dependent post-translational protein devices MIT PhD, 2008 dissertation (PDF), doi: 1721.1/45205 Ty Thompson Models and analysis of yeast mating response: tools for model building, from documentation to time-dependent stimulation MIT PhD, 2008 dissertation (PDF), doi: 1721.1/45206 Peer Reviewed Research Articles Detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates Science Translational Medicine Alexis Courbet, Drew Endy, Eric Renard, Franck Molina1, and Jérôme Bonnet URL PDF reprint The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nature Biotechnology 32, 545–550 (2014) doi:10.1038/nbt.2891 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 URL PDF reprint pending 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. One-step cloning and chromosomal integration of DNA ACS Synthetic Biology, 2013 Sep 20;2(9):537-41. doi: 10.1021/sb400021j. Epub 2013 May 20. Francois St.Pierre, Lun Cui, David Priest, Drew Endy, Ian Dodd, Keith Shearwin URL A survey of enabling technologies in synthetic biology Journal of Biological Engineering, 7:13, 10 May 2013, doi:10.1186/1754-1611-7-13 Linda J. Kahl & Drew Endy URL PDF reprint pending Amplifying genetic logic gates Science, 28 March 2013, doi: 10.1126/science.1232758 Jerome Bonnet, Peter Yin, Monica E. Ortiz, Pakpoom Subsoontorn, Drew Endy URL NPR YouTube primer Measurement and modeling of intrinsic transcription terminators Nucleic Acids Research, March 19, 2013, doi: 10.1093/nar/gkt163 Guillaume Cambray, Joao C. Guimaraes, Vivek K. Mutalik, Colin Lam1, Quynh-Anh Mai, Tim Thimmaiah, James M. Carothers, Adam P. Arkin, Drew Endy URL Precise and reliable gene expression via standard transcription and translation initiation elements Nature Methods, 10,354–360 (2013), doi:10.1038/nmeth.2404 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 URL Quantitative estimation of activity and quality for collections of functional genetic elements. Nature Methods, 10,347–353 (2013), doi:10.1038/nmeth.2403 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 URL Design and analysis of genetically encoded counters Procedia Computer Science, v11 (2012) pp.43-54 Pakpoom Subsoontorn and Drew Endy URL PDF reprint A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast Virology, published online 15 October 2012, doi: 10.1016/j.virol.2012.09.020 Paul Jaschke, Erica Lieberman, Jon Rodriguez, Adrian Sierra, Drew Endy URL PDF reprint Engineered cell-cell communication via DNA messaging Journal of Biological Engineering Sept 2012, 6:16 doi:10.1186/1754-1611-6-16 Monica Ortiz and Drew Endy URL Final PDF pending Refactored M13 bacteriophage as a platform for tumor cell imaging and drug delivery ACS Synthetic Biology, doi:10.1021/sb300052u, August 17, 2012 Debadyuti Ghosh, Aditya Kohli, Felix Moser, Drew Endy, and Angela Belcher URL PDF reprint Rewritable digital data storage in live cells via engineered control of recombination directionality PNAS USA, 21 May 2012, doi: 10.1073/pnas.1202344109 Jerome Bonnet, Pakpoom Subsoontorn and Drew Endy URL PDF reprint Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range PNAS USA, 2011 November; doi: 10.1073/pnas.1004042108 Ty Thomson, Kirsten Benjamin, Alan Bush, Tonya Love, David Pincus, Orna Resnekov, Richard Yu, Andrew Gordon, Alejandro Colman-Lerner, Drew Endy, Roger Brent URL | PDF reprint Gemini, a bifunctional enzymatic and fluorescent reporter of gene expression PLoS ONE 4(11): e7569. doi:10.1371/journal.pone.0007569 Lance Martin, Austin Che, Drew Endy URL PDF reprint Measuring the activity of BioBrick promoters using an in vivo reference standard Journal of Biological Engineering, 2009 March 20;3:4 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 URL PDF reprint Determination of cell fate selection during phage lambda infection PNAS USA, 2008 December; 105(52), 20705-20710 Francois St-Pierre, Drew Endy URL PDF reprint Refinement and standardization of synthetic biological parts and devices Nature Biotechnology, 2008 July; 26(6), 787-93 Barry Canton, Anna Labno, Drew Endy URL PDF reprint News & Views Engineering BioBrick vectors from BioBrick parts Journal of Biological Engineering, 2008 Apr 14;2:5 Reshma Shetty, Drew Endy, Tom Knight URL Stimulus design for model selection and validation in cell signaling PLoS Comput Biol. 2008 Feb 15;4(2):e30 Josh Apgar, Jared Toettcher, Drew Endy, Forest White, Bruce Tidor URL TABASCO: A single molecule, base-pair resolved gene expression simulator BMC Bioinformatics 2007, 8:480 Sriram Kosuri, Jason R Kelly, Drew Endy URL DNA synthesis and biological security Nature Biotechnology June 2007 Hans Bugl, John P Danner, Robert J Molinari, John T Mulligan, Han-Oh Park, Bas Reichert, David A Roth, Ralf Wagner, Bruce Budowle, Robert M Scripp, Jenifer A L Smith, Scott J Steele, George Church & Drew Endy URL PDF reprint Synthetic genomics: Options for governance Biosecur Bioterror 2007 Dec;5(4):359-62 Michele Garfinkel, Drew Endy, Gerald Epstein, Robert Friedman URL (Full Report) Foundations for engineering biology Nature 24 November 2005 doi:10.1038/nature04342 Drew Endy URL PDF reprint Refactoring bacteriophage T7 Nature/EMBO Molecular Systems Biology 13 September 2005 doi:10.1038/msb4100025 Leon Y. Chan, Sriram Kosuri and Drew Endy URL PDF reprint News & Views October 2004 version Regulated cell to cell variation in a cell fate decision system Nature 18 September 2005 doi:10.1038/nature03998 Alejandro Colman-Lerner, Andrew Gordon, Eduard Serra, Tina Chin, Orna Resnekov, Drew Endy, C. Gustavo Pesce and Roger Brent URL PDF reprint News & Views Modelling cellular behaviour (insight feature) Nature 409, 391-395 Drew Endy and Roger Brent PDF reprint Computation, prediction, and experimental test of fitness for bacteriophage T7 mutants with permuted genomes Proceedings of the National Academy of Sciences USA 97, 5375-5380 Drew Endy, Lingchong You, John Yin and Ian Molineux PDF reprint Toward antiviral strategies that resist viral escape Antimicrobial Agents & Chemotherapy 44, 1097-1099 Drew Endy and John Yin PDF reprint Intracellular kinetics of a growing virus: A genetically-structured simulation for bacteriophage T7 Biotechnology & Bioengineering 55, 375-389 Drew Endy, Deyu Kong, and John Yin PDF reprint Transcribed Lectures Synthetic biology: Can we make biology easy to engineer? <--note: transcription was not proofed Industrial Biotechnology' 1 December 2008, 4(4): 340-351 Drew Endy URL PDF reprint Other Articles, edited but not peer reviewed Switches, switches, every where, in any drop we drink Molecular Cell, 25 January 2013 Jerome Bonnet, Drew Endy URL pending, PDF reprint pending Cribsheet #16: Synthetic Biology SEED July 2008 Lee Billings, Drew Endy Illustrator: Thomas Porostocky URL PDF reprint Reconstruction of the genomes Science 2008 Feb 29;319(5867):1196-7 Drew Endy URL PDF reprint Building a fab for biology Scientific American June 2006 David Baker, George Church, Jim Collins, Drew Endy, Joe Jacobson, Jay Keasling, Paul Modrich, Christina Smolke, Ron Weiss PMID: 16711359 A biological engineer searches for simplicity Nature 449, 5 Drew Endy URL Useful construction The Scientist January 2006 Drew Endy URL (login likely req'd.) URL (login not req'd., as of 24 March 2009) 2003 Synthetic Biology study DARPA ISAT Study & briefing to Director, October 2003 Drew Endy, Pat Lincoln, Richard Murray doi:1721.1/38455 Molecular monogamy Nature 426, 614-615 Drew Endy and Michael B. Yaffe PDF reprint Decoding NF-kB signaling Science 298, 1189-1190 Alice Y. Ting and Drew Endy PDF reprint A standard parts list for biological circuitry DARPA white paper October 1999 Drew Endy, Adam Arkin doi:1721.1/29794 Books Synthetic Aesthetics: Investigating Synthetic Biology's Designs on Nature MIT Press, in press, 2013/2014 Alexandra Daisy Ginsberg, Jane Calvert, Pablo Schyfter, Alistair Elfick, Drew Endy Adventures in synthetic biology Nature 24 November 2005 Cover & Online Drew Endy, Isadora Deese and Chuck Wadey PDF, links, and background information For a reprint, please download a free .PDF from the link above Edited Book Chapters Synthetic Biology Bioethics Briefing Book, The Hastings Center, 2008, Chapter 35 Michele Garfinkel, Drew Endy, Gerald Epstein, Robert Friedman Free Online Towards a predictive biology: The example of bacteriophage T7 Evolution as Computation, Landweber & Winfree (eds.), DIMACS Workshop, Princeton, 1999, 201-209 (book chapter). Drew Endy no e-print currently available (sorry!) Selected Online Lectures or Debates Synthetic Biology Debate with Jim Thomas, moderated by Stewart Brand The Long Now Foundation, 17 November 2008 Cowell Theater, Fort Mason Center, San Francisco Online w/ transcription via FORA.tv, DVD for purchase via Whole Earth Films Programming DNA: A 2-bit language for engineering biology 24C3, The 24th Chaos Communication Congress, 27 December 2007 Berliner Congress Center, Berlin Online via Google video