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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

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

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

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

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

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

TABASCO: A single molecule, base-pair resolved gene expression simulator
BMC Bioinformatics 2007, 8:480
Sriram Kosuri, Jason R Kelly, Drew Endy

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

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

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


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, Portuguese Edition
Comic Book Format!
Drew Endy, Isadora Deese and Chuck Wadey

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