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Items: 1 to 20 of 78


Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems.

Bilitchenko L, Liu A, Cheung S, Weeding E, Xia B, Leguia M, Anderson JC, Densmore D.

PLoS One. 2011 Apr 29;6(4):e18882. doi: 10.1371/journal.pone.0018882.



Casanova H, Berman F, Bartol T, Gokcay E, Sejnowski T, Birnbaum A, Dongarra J, Miller M, Ellisman M, Faerman M, Obertelli G, Wolski R, Pomerantz S, Stiles J.

Int J High Perform Comput Appl. 2004 Feb 1;18(1):3-17.


OntoFox: web-based support for ontology reuse.

Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y.

BMC Res Notes. 2010 Jun 22;3:175. doi: 10.1186/1756-0500-3-175.


Creation of a bacterial cell controlled by a chemically synthesized genome.

Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA 3rd, Smith HO, Venter JC.

Science. 2010 Jul 2;329(5987):52-6. doi: 10.1126/science.1190719. Epub 2010 May 20.


Algorithms for automated DNA assembly.

Densmore D, Hsiau TH, Kittleson JT, DeLoache W, Batten C, Anderson JC.

Nucleic Acids Res. 2010 May;38(8):2607-16. doi: 10.1093/nar/gkq165. Epub 2010 Mar 23.


Detailed simulations of cell biology with Smoldyn 2.1.

Andrews SS, Addy NJ, Brent R, Arkin AP.

PLoS Comput Biol. 2010 Mar 12;6(3):e1000705. doi: 10.1371/journal.pcbi.1000705.


Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch.

Lou C, Liu X, Ni M, Huang Y, Huang Q, Huang L, Jiang L, Lu D, Wang M, Liu C, Chen D, Chen C, Chen X, Yang L, Ma H, Chen J, Ouyang Q.

Mol Syst Biol. 2010;6:350. doi: 10.1038/msb.2010.2. Epub 2010 Mar 9.


GeneDesign 3.0 is an updated synthetic biology toolkit.

Richardson SM, Nunley PW, Yarrington RM, Boeke JD, Bader JS.

Nucleic Acids Res. 2010 May;38(8):2603-6. doi: 10.1093/nar/gkq143. Epub 2010 Mar 8.


GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs.

Cai Y, Wilson ML, Peccoud J.

Nucleic Acids Res. 2010 May;38(8):2637-44. doi: 10.1093/nar/gkq086. Epub 2010 Feb 18.


Standard virtual biological parts: a repository of modular modeling components for synthetic biology.

Cooling MT, Rouilly V, Misirli G, Lawson J, Yu T, Hallinan J, Wipat A.

Bioinformatics. 2010 Apr 1;26(7):925-31. doi: 10.1093/bioinformatics/btq063. Epub 2010 Feb 16.


Predicting strength and function for promoters of the Escherichia coli alternative sigma factor, sigmaE.

Rhodius VA, Mutalik VK.

Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):2854-9. doi: 10.1073/pnas.0915066107. Epub 2010 Feb 1.


A synchronized quorum of genetic clocks.

Danino T, Mondragón-Palomino O, Tsimring L, Hasty J.

Nature. 2010 Jan 21;463(7279):326-30. doi: 10.1038/nature08753.


Listening to the noise: random fluctuations reveal gene network parameters.

Munsky B, Trinh B, Khammash M.

Mol Syst Biol. 2009;5:318. doi: 10.1038/msb.2009.75. Epub 2009 Oct 13.


TinkerCell: modular CAD tool for synthetic biology.

Chandran D, Bergmann FT, Sauro HM.

J Biol Eng. 2009 Oct 29;3:19. doi: 10.1186/1754-1611-3-19.


Modeling structure-function relationships in synthetic DNA sequences using attribute grammars.

Cai Y, Lux MW, Adam L, Peccoud J.

PLoS Comput Biol. 2009 Oct;5(10):e1000529. doi: 10.1371/journal.pcbi.1000529. Epub 2009 Oct 9.


Emergent bistability by a growth-modulating positive feedback circuit.

Tan C, Marguet P, You L.

Nat Chem Biol. 2009 Nov;5(11):842-8. doi: 10.1038/nchembio.218. Epub 2009 Oct 4.


Automated design of synthetic ribosome binding sites to control protein expression.

Salis HM, Mirsky EA, Voigt CA.

Nat Biotechnol. 2009 Oct;27(10):946-50. doi: 10.1038/nbt.1568. Epub 2009 Oct 4.


RNA-based computation in live cells.

Benenson Y.

Curr Opin Biotechnol. 2009 Aug;20(4):471-8. doi: 10.1016/j.copbio.2009.08.002. Epub 2009 Aug 31. Review.


A genetically encoded photoactivatable Rac controls the motility of living cells.

Wu YI, Frey D, Lungu OI, Jaehrig A, Schlichting I, Kuhlman B, Hahn KM.

Nature. 2009 Sep 3;461(7260):104-8. doi: 10.1038/nature08241. Epub 2009 Aug 19.

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