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Items: 1 to 20 of 64

1.

Recent advances in biomedical simulations: a manifesto for model engineering.

Hellerstein JL, Gu S, Choi K, Sauro HM.

F1000Res. 2019 Mar 5;8. pii: F1000 Faculty Rev-261. doi: 10.12688/f1000research.15997.1. eCollection 2019. Review.

2.

Harmonizing semantic annotations for computational models in biology.

Neal ML, König M, Nickerson D, Mısırlı 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. 2019 Mar 22;20(2):540-550. doi: 10.1093/bib/bby087.

3.

pySBOL: A Python Package for Genetic Design Automation and Standardization.

Bartley BA, Choi K, Samineni M, Zundel Z, Nguyen T, Myers CJ, Sauro HM.

ACS Synth Biol. 2018 Dec 6. doi: 10.1021/acssynbio.8b00336. [Epub ahead of print]

PMID:
30424601
4.

Tellurium: An extensible python-based modeling environment for systems and synthetic biology.

Choi K, Medley JK, König M, Stocking K, Smith L, Gu S, Sauro HM.

Biosystems. 2018 Sep;171:74-79. doi: 10.1016/j.biosystems.2018.07.006. Epub 2018 Jul 25.

PMID:
30053414
5.

Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology.

Medley JK, Choi K, König M, Smith L, Gu S, Hellerstein J, Sealfon SC, Sauro HM.

PLoS Comput Biol. 2018 Jun 15;14(6):e1006220. doi: 10.1371/journal.pcbi.1006220. eCollection 2018 Jun.

6.

A portable structural analysis library for reaction networks.

Bedaso Y, Bergmann FT, Choi K, Medley K, Sauro HM.

Biosystems. 2018 Jul;169-170:20-25. doi: 10.1016/j.biosystems.2018.05.008. Epub 2018 May 30.

PMID:
29857031
7.

Synthetic Biology: Engineering Living Systems from Biophysical Principles.

Bartley BA, Kim K, Medley JK, Sauro HM.

Biophys J. 2017 Mar 28;112(6):1050-1058. doi: 10.1016/j.bpj.2017.02.013. Review.

8.

Control and regulation of pathways via negative feedback.

Sauro HM.

J R Soc Interface. 2017 Feb;14(127). pii: 20160848. doi: 10.1098/rsif.2016.0848. Review. Erratum in: J R Soc Interface. 2017 Apr;14 (129):.

9.

A Visual Language for Protein Design.

Cox RS 3rd, McLaughlin JA, Grünberg R, Beal J, Wipat A, Sauro HM.

ACS Synth Biol. 2017 Jul 21;6(7):1120-1123. doi: 10.1021/acssynbio.6b00286. Epub 2017 Mar 7.

10.

phraSED-ML: A paraphrased, human-readable adaptation of SED-ML.

Choi K, Smith LP, Medley JK, Sauro HM.

J Bioinform Comput Biol. 2016 Dec;14(6):1650035. doi: 10.1142/S0219720016500359. Epub 2016 Sep 30.

11.

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
12.

SBOL Visual: A Graphical Language for Genetic Designs.

Quinn JY, Cox RS 3rd, Adler A, Beal J, Bhatia S, Cai Y, Chen J, Clancy K, Galdzicki M, Hillson NJ, Le Novère N, Maheshwari AJ, McLaughlin JA, Myers CJ, P U, Pocock M, Rodriguez C, Soldatova L, Stan GB, Swainston N, Wipat A, Sauro HM.

PLoS Biol. 2015 Dec 3;13(12):e1002310. doi: 10.1371/journal.pbio.1002310. eCollection 2015 Dec.

13.

Controlling E. coli Gene Expression Noise.

Kim KH, Choi K, Bartley B, Sauro HM.

IEEE Trans Biomed Circuits Syst. 2015 Aug;9(4):497-504. doi: 10.1109/TBCAS.2015.2461135. Epub 2015 Sep 10.

PMID:
26372647
14.

libRoadRunner: a high performance SBML simulation and analysis library.

Somogyi ET, Bouteiller JM, Glazier JA, König M, Medley JK, Swat MH, Sauro HM.

Bioinformatics. 2015 Oct 15;31(20):3315-21. doi: 10.1093/bioinformatics/btv363. Epub 2015 Jun 17.

15.

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
16.

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.

Bergmann FT, Adams R, Moodie S, Cooper J, Glont M, Golebiewski M, Hucka M, Laibe C, Miller AK, Nickerson DP, Olivier BG, Rodriguez N, Sauro HM, Scharm M, Soiland-Reyes S, Waltemath D, Yvon F, Le Novère N.

BMC Bioinformatics. 2014 Dec 14;15:369. doi: 10.1186/s12859-014-0369-z.

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.

Stochastic modular analysis for gene circuits: interplay among retroactivity, nonlinearity, and stochasticity.

Kim KH, Sauro HM.

Methods Mol Biol. 2015;1244:287-97. doi: 10.1007/978-1-4939-1878-2_14.

PMID:
25487103
19.

A reappraisal of how to build modular, reusable models of biological systems.

Neal ML, Cooling MT, Smith LP, Thompson CT, Sauro HM, Carlson BE, Cook DL, Gennari JH.

PLoS Comput Biol. 2014 Oct 2;10(10):e1003849. doi: 10.1371/journal.pcbi.1003849. eCollection 2014 Oct. No abstract available.

20.

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

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