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Items: 22

1.

Specifying Combinatorial Designs with the Synthetic Biology Open Language (SBOL).

Roehner N, Bartley B, Beal J, McLaughlin J, Pocock M, Zhang M, Zundel Z, Myers CJ.

ACS Synth Biol. 2019 Jul 19;8(7):1519-1523. doi: 10.1021/acssynbio.9b00092. Epub 2019 Jul 1.

PMID:
31260271
2.

Synthetic Biology Open Language (SBOL) Version 2.3.

Madsen C, Goñi Moreno A, P U, Palchick Z, Roehner N, Atallah C, Bartley B, Choi K, Cox RS, Gorochowski T, Grünberg R, Macklin C, McLaughlin J, Meng X, Nguyen T, Pocock M, Samineni M, Scott-Brown J, Tarter Y, Zhang M, Zhang Z, Zundel Z, Beal J, Bissell M, Clancy K, Gennari JH, Misirli G, Myers C, Oberortner E, Sauro H, Wipat A.

J Integr Bioinform. 2019 Jun 13. pii: /j/jib.ahead-of-print/jib-2019-0025/jib-2019-0025.xml. doi: 10.1515/jib-2019-0025. [Epub ahead of print]

PMID:
31199770
3.

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1.

Madsen C, Goni Moreno A, Palchick Z, P U, Roehner N, Bartley B, Bhatia S, Bhakta S, Bissell M, Clancy K, Cox RS, Gorochowski T, Grunberg R, Luna A, McLaughlin J, Nguyen T, Le Novere N, Pocock M, Sauro H, Scott-Brown J, Sexton JT, Stan GB, Tabor JJ, Voigt CA, Zundel Z, Myers C, Beal J, Wipat A.

J Integr Bioinform. 2019 Jun 13. pii: /j/jib.ahead-of-print/jib-2018-0101/jib-2018-0101.xml. doi: 10.1515/jib-2018-0101. [Epub ahead of print]

4.

iBioSim 3: A Tool for Model-Based Genetic Circuit Design.

Watanabe L, Nguyen T, Zhang M, Zundel Z, Zhang Z, Madsen C, Roehner N, Myers C.

ACS Synth Biol. 2019 Jul 19;8(7):1560-1563. doi: 10.1021/acssynbio.8b00078. Epub 2018 Jul 11.

PMID:
29944839
5.

Synthetic Biology Open Language (SBOL) Version 2.2.0.

Cox RS, Madsen C, McLaughlin JA, Nguyen T, Roehner N, Bartley B, Beal J, Bissell M, Choi K, Clancy K, Grünberg R, Macklin C, Misirli G, Oberortner E, Pocock M, Samineni M, Zhang M, Zhang Z, Zundel Z, Gennari JH, Myers C, Sauro H, Wipat A.

J Integr Bioinform. 2018 Apr 2;15(1). pii: /j/jib.2018.15.issue-1/jib-2018-0001/jib-2018-0001.xml. doi: 10.1515/jib-2018-0001.

6.

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0.

Cox RS, Madsen C, McLaughlin J, Nguyen T, Roehner N, Bartley B, Bhatia S, Bissell M, Clancy K, Gorochowski T, Grünberg R, Luna A, Le Novère N, Pocock M, Sauro H, Sexton JT, Stan GB, Tabor JJ, Voigt CA, Zundel Z, Myers C, Beal J, Wipat A.

J Integr Bioinform. 2018 Mar 19;15(1). pii: /j/jib.2018.15.issue-1/jib-2017-0074/jib-2017-0074.xml. doi: 10.1515/jib-2017-0074.

7.

Needs and opportunities in bio-design automation: four areas for focus.

Appleton E, Densmore D, Madsen C, Roehner N.

Curr Opin Chem Biol. 2017 Oct;40:111-118. doi: 10.1016/j.cbpa.2017.08.005. Epub 2017 Sep 15. Review.

PMID:
28923279
8.

Design Automation in Synthetic Biology.

Appleton E, Madsen C, Roehner N, Densmore D.

Cold Spring Harb Perspect Biol. 2017 Apr 3;9(4). pii: a023978. doi: 10.1101/cshperspect.a023978. Review.

9.

Synthetic Biology Open Language (SBOL) Version 2.1.0.

Beal J, Cox RS, Grünberg R, McLaughlin J, Nguyen T, Bartley B, Bissell M, Choi K, Clancy K, Macklin C, Madsen C, Misirli G, Oberortner E, Pocock M, Roehner N, Samineni M, Zhang M, Zhang Z, Zundel Z, Gennari J, Myers C, Sauro H, Wipat A.

J Integr Bioinform. 2016 Dec 18;13(3):291. doi: 10.2390/biecoll-jib-2016-291.

PMID:
28187407
10.

Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration.

Woodruff LBA, Gorochowski TE, Roehner N, Mikkelsen TS, Densmore D, Gordon DB, Nicol R, Voigt CA.

Nucleic Acids Res. 2017 Feb 17;45(3):1567-1568. doi: 10.1093/nar/gkx032. No abstract available.

11.

Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration.

Woodruff LBA, Gorochowski TE, Roehner N, Mikkelsen TS, Densmore D, Gordon DB, Nicol R, Voigt CA.

Nucleic Acids Res. 2017 Feb 17;45(3):1553-1565. doi: 10.1093/nar/gkw1226. Erratum in: Nucleic Acids Res. 2017 Feb 17;45(3):1567-1568.

12.

Sharing Structure and Function in Biological Design with SBOL 2.0.

Roehner N, Beal J, Clancy K, Bartley B, Misirli G, Grünberg R, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang M, Zhang Z, Zundel Z, Densmore D, Gennari JH, Wipat A, Sauro HM, Myers CJ.

ACS Synth Biol. 2016 Jun 17;5(6):498-506. doi: 10.1021/acssynbio.5b00215. Epub 2016 May 4.

PMID:
27111421
13.

Double Dutch: A Tool for Designing Combinatorial Libraries of Biological Systems.

Roehner N, Young EM, Voigt CA, Gordon DB, Densmore D.

ACS Synth Biol. 2016 Jun 17;5(6):507-17. doi: 10.1021/acssynbio.5b00232. Epub 2016 May 3.

PMID:
27110633
14.

A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language.

Nguyen T, Roehner N, Zundel Z, Myers CJ.

ACS Synth Biol. 2016 Jun 17;5(6):479-86. doi: 10.1021/acssynbio.5b00212. Epub 2016 Jan 12.

PMID:
26696234
15.

Synthetic Biology Open Language (SBOL) Version 2.0.0.

Bartley B, Beal J, Clancy K, Misirli G, Roehner N, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang Z, Gennari JH, Myers C, Wipat A, Sauro H.

J Integr Bioinform. 2015 Sep 4;12(2):272. doi: 10.2390/biecoll-jib-2015-272.

PMID:
26528570
16.

Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language.

Roehner N, Zhang Z, Nguyen T, Myers CJ.

ACS Synth Biol. 2015 Aug 21;4(8):873-9. doi: 10.1021/sb5003289. Epub 2015 Apr 9.

PMID:
25822671
17.

The synthetic biology open language.

Myers C, Clancy K, Misirli G, Oberortner E, Pocock M, Quinn J, Roehner N, Sauro HM.

Methods Mol Biol. 2015;1244:323-36. doi: 10.1007/978-1-4939-1878-2_16.

PMID:
25487105
18.

Efficient analysis methods in synthetic biology.

Madsen C, Myers C, Roehner N, Winstead C, Zhang Z.

Methods Mol Biol. 2015;1244:217-57. doi: 10.1007/978-1-4939-1878-2_11.

PMID:
25487100
19.

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
20.

Proposed data model for the next version of the synthetic biology open language.

Roehner N, Oberortner E, Pocock M, Beal J, Clancy K, Madsen C, Misirli G, Wipat A, Sauro H, Myers CJ.

ACS Synth Biol. 2015 Jan 16;4(1):57-71. doi: 10.1021/sb500176h. Epub 2014 Jun 16.

PMID:
24896221
21.

Directed acyclic graph-based technology mapping of genetic circuit models.

Roehner N, Myers CJ.

ACS Synth Biol. 2014 Aug 15;3(8):543-55. doi: 10.1021/sb400135t. Epub 2014 Apr 1.

PMID:
24650240
22.

A methodology to annotate systems biology markup language models with the synthetic biology open language.

Roehner N, Myers CJ.

ACS Synth Biol. 2014 Feb 21;3(2):57-66. doi: 10.1021/sb400066m. Epub 2013 Sep 13.

PMID:
23977879

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