Endy:Reprints

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(Student Dissertations)
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'''Barry Canton'''<br>
'''Barry Canton'''<br>
''Engineering the interface between cellular chassis and synthetic biological systems''<br>
''Engineering the interface between cellular chassis and synthetic biological systems''<br>
-
MIT 2008 [http://dspace.mit.edu/bitstream/handle/1721.1/44918/301953836.pdf?sequence=1 dissertation] (PDF)<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>
'''Jeff Gritton'''<br>
''Architecture and evolutionary stability of yeast signaling pathways''<br>
''Architecture and evolutionary stability of yeast signaling pathways''<br>
-
MIT 2006 [http://dspace.mit.edu/bitstream/handle/1721.1/37258/85844464.pdf?sequence=1 thesis] (PDF)<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>
'''Jason Kelly'''<br>
''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 2008 [http://dspace.mit.edu/bitstream/handle/1721.1/44917/301953777.pdf?sequence=1 dissertation] (PDF)<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 Bachelor's [[Media:Koutsoubelis BS Thesis Stanford Freiburg.pdf | thesis]] (PDF)<br>  
'''Sriram Kosuri'''<br>
'''Sriram Kosuri'''<br>
''Simulation, models, and refactoring of bacteriophage T7 gene expression''<br>
''Simulation, models, and refactoring of bacteriophage T7 gene expression''<br>
-
MIT 2007 [http://dspace.mit.edu/bitstream/handle/1721.1/39912/182579919.pdf?sequence=1 dissertation] (PDF)<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>
'''Alex Mallet'''<br>
''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 2007 [http://dspace.mit.edu/bitstream/handle/1721.1/35880/MastersThesis.pdf?sequence=1 thesis] (PDF)<br>
+
MIT MS, 2007 [http://dspace.mit.edu/bitstream/handle/1721.1/35880/MastersThesis.pdf?sequence=1 thesis] (PDF), doi: 1721.1/35880<br>
'''Reshma Shetty''' (co-advisee with Tom Knight<br>
'''Reshma Shetty''' (co-advisee with Tom Knight<br>
''Applying engineering principles to the design and construction of transcriptional devices''<br>
''Applying engineering principles to the design and construction of transcriptional devices''<br>
-
MIT 2008 [http://dspace.mit.edu/bitstream/handle/1721.1/44921/302346650.pdf?sequence=1 dissertation] (PDF)<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>
'''Francois St-Pierre'''<br>
''Determination of cell fate selection during phage lambda infection''<br>
''Determination of cell fate selection during phage lambda infection''<br>
-
MIT 2009 [[Media:StPierre thesis rev2.PDF | dissertation]] (PDF)<br>
+
MIT PhD, 2009 [[Media:StPierre thesis rev2.PDF | dissertation]] (PDF), doi: pending<br>
'''Samantha Sutton'''<br>
'''Samantha Sutton'''<br>
''Engineering phosphorylation-dependent post-translational protein devices''<br>
''Engineering phosphorylation-dependent post-translational protein devices''<br>
-
MIT 2008 [http://dspace.mit.edu/bitstream/handle/1721.1/45205/301815200.pdf?sequence=1 dissertation] (PDF)<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>
'''Ty Thompson'''<br>
''Models and analysis of yeast mating response: tools for model building, from documentation to time-dependent stimulation''<br>
''Models and analysis of yeast mating response: tools for model building, from documentation to time-dependent stimulation''<br>
-
MIT 2008 [http://dspace.mit.edu/bitstream/handle/1721.1/45206/301815747.pdf?sequence=1 dissertation] (PDF)<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===
 +
'''Living digital logic via engineered genetic transistors'''<br>
 +
In review<br>
 +
''Jerome Bonnet et al.''<br>
 +
 
 +
'''Precise and reliable gene expression engineering via active coupling and genetic nesting'''<br>
 +
''Nature Methods,'' in revision<br>
 +
Vivek Mutalik et al.<br>
 +
[http://www.nature.com URL pending] [http://www.nature.com/| PDF reprint pending]
 +
 
 +
'''Composition and quality of irregular genetic elements controlling transcription and translation'''<br>
 +
''Nature Methods,'' in revision<br>
 +
Vivek Mutalik et al.<br>
 +
[http://www.pnas.org URL pending] [http://www.pnas.org/| PDF reprint pending]
 +
 
 +
'''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]]
-
===Peer Reviewed Articles===
 
'''Measuring the activity of BioBrick promoters using an in vivo reference standard'''<br>
'''Measuring the activity of BioBrick promoters using an in vivo reference standard'''<br>
''Journal of Biological Engineering,'' 2009 March 20;3:4<br>
''Journal of Biological Engineering,'' 2009 March 20;3:4<br>
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<font color="green">For a reprint, please email isadora AT mit DOT edu</font>
<font color="green">For a reprint, please email isadora AT mit DOT edu</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>  
Line 202: Line 250:
===Selected Online Lectures or Debates===
===Selected Online Lectures or Debates===
-
'''Synthetic Biology Debate: Drew Endy & Jim Thomas'''<br>
+
'''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>

Revision as of 12:57, 26 November 2012

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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.

Contents

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 Bachelor's 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

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

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

Living digital logic via engineered genetic transistors
In review
Jerome Bonnet et al.

Precise and reliable gene expression engineering via active coupling and genetic nesting
Nature Methods, in revision
Vivek Mutalik et al.
URL pending PDF reprint pending

Composition and quality of irregular genetic elements controlling transcription and translation
Nature Methods, in revision
Vivek Mutalik et al.
URL pending PDF reprint pending

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, Not Peer Reviewed

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
US Government October 2003
Drew Endy, Patrick 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

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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