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Items: 12

1.

JigCell Model Connector: building large molecular network models from components.

Jones TC Jr, Hoops S, Watson LT, Palmisano A, Tyson JJ, Shaffer CA.

Simulation. 2018 Nov;94(11):993-1008. doi: 10.1177/0037549717754121. Epub 2018 Feb 14.

2.

Efficiently Encoding Complex Biochemical Models with the Multistate Model Builder (MSMB).

Palmisano A, Hoops S, Watson LT, Jones TC Jr, Tyson JJ, Shaffer CA.

Methods Mol Biol. 2019;1945:119-139. doi: 10.1007/978-1-4939-9102-0_5.

PMID:
30945244
3.

Quasi-Newton Stochastic Optimization Algorithm for Parameter Estimation of a Stochastic Model of the Budding Yeast Cell Cycle.

Chen M, Amos BD, Watson LT, Tyson JJ, Cao Y, Shaffer CA, Trosset MW, Oguz C, Kakoti G.

IEEE/ACM Trans Comput Biol Bioinform. 2019 Jan-Feb;16(1):301-311. doi: 10.1109/TCBB.2017.2773083. Epub 2017 Nov 14.

PMID:
29990127
4.

JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations.

Palmisano A, Hoops S, Watson LT, Jones TC Jr, Tyson JJ, Shaffer CA.

BMC Syst Biol. 2015 Dec 24;9:95. doi: 10.1186/s12918-015-0237-0.

5.

Multistate Model Builder (MSMB): a flexible editor for compact biochemical models.

Palmisano A, Hoops S, Watson LT, Jones TC Jr, Tyson JJ, Shaffer CA.

BMC Syst Biol. 2014 Apr 4;8:42. doi: 10.1186/1752-0509-8-42.

6.

Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle.

Liu Z, Pu Y, Li F, Shaffer CA, Hoops S, Tyson JJ, Cao Y.

J Chem Phys. 2012 Jan 21;136(3):034105. doi: 10.1063/1.3677190.

7.

Model composition for macromolecular regulatory networks.

Randhawa R, Shaffer CA, Tyson JJ.

IEEE/ACM Trans Comput Biol Bioinform. 2010 Apr-Jun;7(2):278-87. doi: 10.1109/TCBB.2008.64.

8.

Model aggregation: a building-block approach to creating large macromolecular regulatory networks.

Randhawa R, Shaffer CA, Tyson JJ.

Bioinformatics. 2009 Dec 15;25(24):3289-95. doi: 10.1093/bioinformatics/btp581. Epub 2009 Oct 29.

9.

Modeling molecular regulatory networks with JigCell and PET.

Shaffer CA, Zwolak JW, Randhawa R, Tyson JJ.

Methods Mol Biol. 2009;500:81-111. doi: 10.1007/978-1-59745-525-1_4.

10.

The JigCell model builder: a spreadsheet interface for creating biochemical reaction network models.

Vass MT, Shaffer CA, Ramakrishnan N, Watson LT, Tyson JJ.

IEEE/ACM Trans Comput Biol Bioinform. 2006 Apr-Jun;3(2):155-64.

PMID:
17048401
11.

the JigCell model builder and run manager.

Vass M, Allen N, Shaffer CA, Ramakrishnan N, Watson LT, Tyson JJ.

Bioinformatics. 2004 Dec 12;20(18):3680-1. Epub 2004 Jul 23.

PMID:
15273159
12.

Modeling regulatory networks at Virginia Tech.

Allen NA, Calzone L, Chen KC, Ciliberto A, Ramakrishnan N, Shaffer CA, Sible JC, Tyson JJ, Vass MT, Watson LT, Zwolak JW.

OMICS. 2003 Fall;7(3):285-99.

PMID:
14583117

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