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Items: 1 to 20 of 40

1.

Harmonizing semantic annotations for computational models in biology.

Neal ML, König M, Nickerson D, Misirli G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling MT, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, Gleeson P, Golebiewski M, Hucka M, Juty N, Myers C, Olivier BG, Sauro HM, Scharm M, Snoep JL, Touré V, Wipat A, Wolkenhauer O, Waltemath D.

Brief Bioinform. 2018 Nov 21. doi: 10.1093/bib/bby087. [Epub ahead of print]

PMID:
30462164
2.

A Genetic Circuit Compiler: Generating Combinatorial Genetic Circuits with Web Semantics and Inference.

Waites W, Mısırlı G, Cavaliere M, Danos V, Wipat A.

ACS Synth Biol. 2018 Nov 20. doi: 10.1021/acssynbio.8b00201. [Epub ahead of print]

PMID:
30408409
3.

A Computational Workflow for the Automated Generation of Models of Genetic Designs.

Misirli G, Nguyen T, McLaughlin JA, Vaidyanathan P, Jones TS, Densmore D, Myers C, Wipat A.

ACS Synth Biol. 2018 Jun 5. doi: 10.1021/acssynbio.7b00459. [Epub ahead of print]

PMID:
29782151
4.

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.

PMID:
29605823
5.

SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology.

McLaughlin JA, Myers CJ, Zundel Z, Mısırlı G, Zhang M, Ofiteru ID, Goñi-Moreno A, Wipat A.

ACS Synth Biol. 2018 Feb 16;7(2):682-688. doi: 10.1021/acssynbio.7b00403. Epub 2018 Jan 30.

PMID:
29316788
6.

A standard-enabled workflow for synthetic biology.

Myers CJ, Beal J, Gorochowski TE, Kuwahara H, Madsen C, McLaughlin JA, Mısırlı G, Nguyen T, Oberortner E, Samineni M, Wipat A, Zhang M, Zundel Z.

Biochem Soc Trans. 2017 Jun 15;45(3):793-803. doi: 10.1042/BST20160347. Review.

PMID:
28620041
7.

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
8.

Data Integration and Mining for Synthetic Biology Design.

Mısırlı G, Hallinan J, Pocock M, Lord P, McLaughlin JA, Sauro H, Wipat A.

ACS Synth Biol. 2016 Oct 21;5(10):1086-1097. Epub 2016 Jun 20.

9.

The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs.

Madsen C, McLaughlin JA, Mısırlı G, Pocock M, Flanagan K, Hallinan J, Wipat A.

ACS Synth Biol. 2016 Jun 17;5(6):487-97. doi: 10.1021/acssynbio.5b00210. Epub 2016 Jun 8.

10.

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
11.

VisBOL: Web-Based Tools for Synthetic Biology Design Visualization.

McLaughlin JA, Pocock M, Mısırlı G, Madsen C, Wipat A.

ACS Synth Biol. 2016 Aug 19;5(8):874-6. doi: 10.1021/acssynbio.5b00244. Epub 2016 Feb 9.

PMID:
26808703
12.

Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization.

Misirli G, Cavaliere M, Waites W, Pocock M, Madsen C, Gilfellon O, Honorato-Zimmer R, Zuliani P, Danos V, Wipat A.

Bioinformatics. 2016 Mar 15;32(6):908-17. doi: 10.1093/bioinformatics/btv660. Epub 2015 Nov 11.

13.

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
14.

Estimating the chance of success in IVF treatment using a ranking algorithm.

Güvenir HA, Misirli G, Dilbaz S, Ozdegirmenci O, Demir B, Dilbaz B.

Med Biol Eng Comput. 2015 Sep;53(9):911-20. doi: 10.1007/s11517-015-1299-2. Epub 2015 Apr 17.

15.

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
16.

BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species.

Misirli G, Hallinan J, Röttger R, Baumbach J, Wipat A.

J Integr Bioinform. 2014 Jul 8;11(2):244. doi: 10.2390/biecoll-jib-2014-244.

PMID:
25001169
17.

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
18.

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
19.

Proteomic analysis of Bacillus subtilis strains engineered for improved production of heterologous proteins.

Pohl S, Bhavsar G, Hulme J, Bloor AE, Misirli G, Leckenby MW, Radford DS, Smith W, Wipat A, Williamson ED, Harwood CR, Cranenburgh RM.

Proteomics. 2013 Nov;13(22):3298-308. doi: 10.1002/pmic.201300183. Epub 2013 Oct 27.

PMID:
24115457
20.

The authors reply.

Misirli G, Benetou V, Lagiou P, Bamia C, Trichopoulos D, Trichopoulou A.

Am J Epidemiol. 2013 Aug 15;178(4):661-2. No abstract available.

PMID:
24073441

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