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Items: 47

1.

Fail-safe genetic codes designed to intrinsically contain engineered organisms.

Calles J, Justice I, Brinkley D, Garcia A, Endy D.

Nucleic Acids Res. 2019 Sep 12. pii: gkz745. doi: 10.1093/nar/gkz745. [Epub ahead of print]

PMID:
31511890
2.

Author Correction: Reconstruction of cysteine biosynthesis using engineered cysteine-free enzymes.

Fujishima K, Wang KM, Palmer JA, Abe N, Nakahigashi K, Endy D, Rothschild LJ.

Sci Rep. 2019 Apr 12;9(1):6242. doi: 10.1038/s41598-019-42196-9.

3.

Opening options for material transfer.

Kahl L, Molloy J, Patron N, Matthewman C, Haseloff J, Grewal D, Johnson R, Endy D.

Nat Biotechnol. 2018 Oct 11;36(10):923-927. doi: 10.1038/nbt.4263. No abstract available.

PMID:
30307930
4.

Reconstruction of cysteine biosynthesis using engineered cysteine-free enzymes.

Fujishima K, Wang KM, Palmer JA, Abe N, Nakahigashi K, Endy D, Rothschild LJ.

Sci Rep. 2018 Jan 29;8(1):1776. doi: 10.1038/s41598-018-19920-y. Erratum in: Sci Rep. 2019 Apr 12;9(1):6242.

5.

Measurements of translation initiation from all 64 codons in E. coli.

Hecht A, Glasgow J, Jaschke PR, Bawazer LA, Munson MS, Cochran JR, Endy D, Salit M.

Nucleic Acids Res. 2017 Apr 20;45(7):3615-3626. doi: 10.1093/nar/gkx070.

6.

Artificial Symmetry-Breaking for Morphogenetic Engineering Bacterial Colonies.

Nuñez IN, Matute TF, Del Valle ID, Kan A, Choksi A, Endy D, Haseloff J, Rudge TJ, Federici F.

ACS Synth Biol. 2017 Feb 17;6(2):256-265. doi: 10.1021/acssynbio.6b00149. Epub 2016 Nov 28.

PMID:
27794593
7.

When Wavelengths Collide: Bias in Cell Abundance Measurements Due to Expressed Fluorescent Proteins.

Hecht A, Endy D, Salit M, Munson MS.

ACS Synth Biol. 2016 Sep 16;5(9):1024-7. doi: 10.1021/acssynbio.6b00072. Epub 2016 Jun 6.

8.

Measurement and modeling of intrinsic transcription terminators.

Cambray G, Guimaraes JC, Mutalik VK, Lam C, Mai QA, Thimmaiah T, Carothers JM, Arkin AP, Endy D.

Nucleic Acids Res. 2016 Aug 19;44(14):7006. doi: 10.1093/nar/gkw379. Epub 2016 Apr 29. No abstract available.

9.

Voices of biotech.

Amit I, Baker D, Barker R, Berger B, Bertozzi C, Bhatia S, Biffi A, Demichelis F, Doudna J, Dowdy SF, Endy D, Helmstaedter M, Junca H, June C, Kamb S, Khvorova A, Kim DH, Kim JS, Krishnan Y, Lakadamyali M, Lappalainen T, Lewin S, Liao J, Loman N, Lundberg E, Lynd L, Martin C, Mellman I, Miyawaki A, Mummery C, Nelson K, Paz J, Peralta-Yahya P, Picotti P, Polyak K, Prather K, Qin J, Quake S, Regev A, Rogers JA, Shetty R, Sommer M, Stevens M, Stolovitzky G, Takahashi M, Tang F, Teichmann S, Torres-Padilla ME, Tripathi L, Vemula P, Verdine G, Vollmer F, Wang J, Ying JY, Zhang F, Zhang T.

Nat Biotechnol. 2016 Mar;34(3):270-5. doi: 10.1038/nbt.3502. No abstract available.

PMID:
26963549
10.

Detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates.

Courbet A, Endy D, Renard E, Molina F, Bonnet J.

Sci Transl Med. 2015 May 27;7(289):289ra83. doi: 10.1126/scitranslmed.aaa3601.

PMID:
26019219
11.

Reply to Intellectual property issues and synthetic biology standards.

Galdzicki M, Kahl LJ, Endy D, Sauro HM.

Nat Biotechnol. 2015 Jan;33(1):25. doi: 10.1038/nbt.3114. No abstract available.

PMID:
25574632
12.

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

Galdzicki M, Clancy KP, Oberortner E, Pocock M, Quinn JY, Rodriguez CA, Roehner N, Wilson ML, Adam L, Anderson JC, Bartley BA, Beal J, Chandran D, Chen J, Densmore D, Endy D, Grünberg R, Hallinan J, Hillson NJ, Johnson JD, Kuchinsky A, Lux M, Misirli G, Peccoud J, Plahar HA, Sirin E, Stan GB, Villalobos A, Wipat A, Gennari JH, Myers CJ, Sauro HM.

Nat Biotechnol. 2014 Jun;32(6):545-50. doi: 10.1038/nbt.2891. Epub 2014 Jun 6.

PMID:
24911500
13.

One-step cloning and chromosomal integration of DNA.

St-Pierre F, Cui L, Priest DG, Endy D, Dodd IB, Shearwin KE.

ACS Synth Biol. 2013 Sep 20;2(9):537-41. doi: 10.1021/sb400021j. Epub 2013 May 20.

PMID:
24050148
14.

Composability of regulatory sequences controlling transcription and translation in Escherichia coli.

Kosuri S, Goodman DB, Cambray G, Mutalik VK, Gao Y, Arkin AP, Endy D, Church GM.

Proc Natl Acad Sci U S A. 2013 Aug 20;110(34):14024-9. doi: 10.1073/pnas.1301301110. Epub 2013 Aug 7.

15.

A survey of enabling technologies in synthetic biology.

Kahl LJ, Endy D.

J Biol Eng. 2013 May 10;7(1):13. doi: 10.1186/1754-1611-7-13.

16.

Refactored M13 bacteriophage as a platform for tumor cell imaging and drug delivery.

Ghosh D, Kohli AG, Moser F, Endy D, Belcher AM.

ACS Synth Biol. 2012 Dec 21;1(12):576-582. doi: 10.1021/sb300052u. Epub 2012 Sep 24.

17.

Amplifying genetic logic gates.

Bonnet J, Yin P, Ortiz ME, Subsoontorn P, Endy D.

Science. 2013 May 3;340(6132):599-603. doi: 10.1126/science.1232758. Epub 2013 Mar 28.

18.

Measurement and modeling of intrinsic transcription terminators.

Cambray G, Guimaraes JC, Mutalik VK, Lam C, Mai QA, Thimmaiah T, Carothers JM, Arkin AP, Endy D.

Nucleic Acids Res. 2013 May;41(9):5139-48. doi: 10.1093/nar/gkt163. Epub 2013 Mar 19. Erratum in: Nucleic Acids Res. 2016 Aug 19;44(14):7006.

19.

Quantitative estimation of activity and quality for collections of functional genetic elements.

Mutalik VK, Guimaraes JC, Cambray G, Mai QA, Christoffersen MJ, Martin L, Yu A, Lam C, Rodriguez C, Bennett G, Keasling JD, Endy D, Arkin AP.

Nat Methods. 2013 Apr;10(4):347-53. doi: 10.1038/nmeth.2403. Epub 2013 Mar 10.

PMID:
23474467
20.

Precise and reliable gene expression via standard transcription and translation initiation elements.

Mutalik VK, Guimaraes JC, Cambray G, Lam C, Christoffersen MJ, Mai QA, Tran AB, Paull M, Keasling JD, Arkin AP, Endy D.

Nat Methods. 2013 Apr;10(4):354-60. doi: 10.1038/nmeth.2404. Epub 2013 Mar 10.

PMID:
23474465
21.

Switches, switches, every where, in any drop we drink.

Bonnet J, Endy D.

Mol Cell. 2013 Jan 24;49(2):232-3. doi: 10.1016/j.molcel.2013.01.005.

22.

A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast.

Jaschke PR, Lieberman EK, Rodriguez J, Sierra A, Endy D.

Virology. 2012 Dec 20;434(2):278-84. doi: 10.1016/j.virol.2012.09.020. Epub 2012 Oct 15.

23.

Engineered cell-cell communication via DNA messaging.

Ortiz ME, Endy D.

J Biol Eng. 2012 Sep 7;6(1):16. doi: 10.1186/1754-1611-6-16.

24.

Rewritable digital data storage in live cells via engineered control of recombination directionality.

Bonnet J, Subsoontorn P, Endy D.

Proc Natl Acad Sci U S A. 2012 Jun 5;109(23):8884-9. doi: 10.1073/pnas.1202344109. Epub 2012 May 21.

25.

Scaffold number in yeast signaling system sets tradeoff between system output and dynamic range.

Thomson TM, Benjamin KR, Bush A, Love T, Pincus D, Resnekov O, Yu RC, Gordon A, Colman-Lerner A, Endy D, Brent R.

Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):20265-70. doi: 10.1073/pnas.1004042108. Epub 2011 Nov 23.

26.

Editorial-synthetic biology.

Collins JJ, Endy D, Hutchison CA 3rd, Roberts RJ.

Nucleic Acids Res. 2010 May;38(8):2513. doi: 10.1093/nar/gkq221. No abstract available.

27.

Gemini, a bifunctional enzymatic and fluorescent reporter of gene expression.

Martin L, Che A, Endy D.

PLoS One. 2009 Nov 4;4(11):e7569. doi: 10.1371/journal.pone.0007569.

28.

Measuring the activity of BioBrick promoters using an in vivo reference standard.

Kelly JR, Rubin AJ, Davis JH, Ajo-Franklin CM, Cumbers J, Czar MJ, de Mora K, Glieberman AL, Monie DD, Endy D.

J Biol Eng. 2009 Mar 20;3:4. doi: 10.1186/1754-1611-3-4.

29.

Determination of cell fate selection during phage lambda infection.

St-Pierre F, Endy D.

Proc Natl Acad Sci U S A. 2008 Dec 30;105(52):20705-10. doi: 10.1073/pnas.0808831105. Epub 2008 Dec 19.

30.

The Alpha Project: a model system for systems biology research.

Yu RC, Resnekov O, Abola AP, Andrews SS, Benjamin KR, Bruck J, Burbulis IE, Colman-Lerner A, Endy D, Gordon A, Holl M, Lok L, Pesce CG, Serra E, Smith RD, Thomson TM, Tsong AE, Brent R.

IET Syst Biol. 2008 Sep;2(5):222-33. doi: 10.1049/iet-syb:20080127. Review.

31.

Refinement and standardization of synthetic biological parts and devices.

Canton B, Labno A, Endy D.

Nat Biotechnol. 2008 Jul;26(7):787-93. doi: 10.1038/nbt1413.

PMID:
18612302
32.

Engineering BioBrick vectors from BioBrick parts.

Shetty RP, Endy D, Knight TF Jr.

J Biol Eng. 2008 Apr 14;2:5. doi: 10.1186/1754-1611-2-5.

33.

Genomics. Reconstruction of the genomes.

Endy D.

Science. 2008 Feb 29;319(5867):1196-7. doi: 10.1126/science.1155749. No abstract available.

PMID:
18309068
34.

Stimulus design for model selection and validation in cell signaling.

Apgar JF, Toettcher JE, Endy D, White FM, Tidor B.

PLoS Comput Biol. 2008 Feb;4(2):e30. doi: 10.1371/journal.pcbi.0040030.

35.

TABASCO: A single molecule, base-pair resolved gene expression simulator.

Kosuri S, Kelly JR, Endy D.

BMC Bioinformatics. 2007 Dec 19;8:480.

36.

Synthetic genomics | options for governance.

Garfinkel MS, Endy D, Epstein GL, Friedman RM.

Biosecur Bioterror. 2007 Dec;5(4):359-62. No abstract available.

PMID:
18081496
37.

DNA synthesis and biological security.

Bügl H, Danner JP, Molinari RJ, Mulligan JT, Park HO, Reichert B, Roth DA, Wagner R, Budowle B, Scripp RM, Smith JA, Steele SJ, Church G, Endy D.

Nat Biotechnol. 2007 Jun;25(6):627-9. Review. No abstract available.

PMID:
17557094
38.

Refactoring bacteriophage T7.

Chan LY, Kosuri S, Endy D.

Mol Syst Biol. 2005;1:2005.0018. Epub 2005 Sep 13.

39.

Engineering life: building a fab for biology.

Bio FAB Group, Baker D, Church G, Collins J, Endy D, Jacobson J, Keasling J, Modrich P, Smolke C, Weiss R.

Sci Am. 2006 Jun;294(6):44-51. No abstract available.

PMID:
16711359
40.

Foundations for engineering biology.

Endy D.

Nature. 2005 Nov 24;438(7067):449-53. Review.

PMID:
16306983
41.

Regulated cell-to-cell variation in a cell-fate decision system.

Colman-Lerner A, Gordon A, Serra E, Chin T, Resnekov O, Endy D, Pesce CG, Brent R.

Nature. 2005 Sep 29;437(7059):699-706. Epub 2005 Sep 18. Erratum in: Nature. 2006 Jan 26;439(7075):502.

42.

Signal transduction: molecular monogamy.

Endy D, Yaffe MB.

Nature. 2003 Dec 11;426(6967):614-5. No abstract available.

PMID:
14668845
43.

Signal transduction. Decoding NF-kappaB signaling.

Ting AY, Endy D.

Science. 2002 Nov 8;298(5596):1189-90. No abstract available.

PMID:
12424362
44.

Modelling cellular behaviour.

Endy D, Brent R.

Nature. 2001 Jan 18;409(6818):391-5. No abstract available.

PMID:
11201753
45.

Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes.

Endy D, You L, Yin J, Molineux IJ.

Proc Natl Acad Sci U S A. 2000 May 9;97(10):5375-80.

46.

Toward antiviral strategies that resist viral escape.

Endy D, Yin J.

Antimicrob Agents Chemother. 2000 Apr;44(4):1097-9.

47.

Intracellular kinetics of a growing virus: a genetically structured simulation for bacteriophage T7.

Endy D, Kong D, Yin J.

Biotechnol Bioeng. 1997 Jul 20;55(2):375-89.

PMID:
18636496

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