Endy:Reprints

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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

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

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 [[Media:StPierre thesis rev2.PDF | dissertation]] (PDF), doi: pending

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
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 [[Media:Journal.pone.0007569.pdf | 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 [[Media:PNAS_Lambda2008.pdf | 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 [[Media:Nbt1413.pdf | 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

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 10.1038/nature04342 Drew Endy URL PDF reprint

Refactoring bacteriophage T7 Nature/EMBO Molecular Systems Biology 13 September 2005 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 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 [[Media:Ind.2008.4.340.pdf | PDF reprint]]

Other Articles, Not Peer Reviewed
Cribsheet #16: Synthetic Biology SEED July 2008 Lee Billings, Drew Endy Illustrator: Thomas Porostocky URL [[Media:16cribsheet.pdf | PDF reprint]]

Reconstruction of the genomes Science 2008 Feb 29;319(5867):1196-7 Drew Endy URL

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 US Government October 2003 Drew Endy, Patrick Lincoln, Richard Murray 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 1721.1/29794

Books
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 email isadora AT mit DOT edu

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


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