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Items: 11

1.

Using Mechanistic Models for Analysis of Proteomic Data.

Chylek LA.

Methods Mol Biol. 2019;1945:265-270. doi: 10.1007/978-1-4939-9102-0_12.

PMID:
30945251
2.

Using Equation-Free Computation to Accelerate Network-Free Stochastic Simulation of Chemical Kinetics.

Lin YT, Chylek LA, Lemons NW, Hlavacek WS.

J Phys Chem B. 2018 Jun 21;122(24):6351-6356. doi: 10.1021/acs.jpcb.8b02960. Epub 2018 Jun 8.

PMID:
29851484
3.

Timescale Separation of Positive and Negative Signaling Creates History-Dependent Responses to IgE Receptor Stimulation.

Harmon B, Chylek LA, Liu Y, Mitra ED, Mahajan A, Saada EA, Schudel BR, Holowka DA, Baird BA, Wilson BS, Hlavacek WS, Singh AK.

Sci Rep. 2017 Nov 14;7(1):15586. doi: 10.1038/s41598-017-15568-2.

4.

BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments.

Thomas BR, Chylek LA, Colvin J, Sirimulla S, Clayton AH, Hlavacek WS, Posner RG.

Bioinformatics. 2016 Mar 1;32(5):798-800. doi: 10.1093/bioinformatics/btv655. Epub 2015 Nov 9.

5.

Modeling for (physical) biologists: an introduction to the rule-based approach.

Chylek LA, Harris LA, Faeder JR, Hlavacek WS.

Phys Biol. 2015 Jul 16;12(4):045007. doi: 10.1088/1478-3975/12/4/045007. Review.

6.

Modeling biomolecular site dynamics in immunoreceptor signaling systems.

Chylek LA, Wilson BS, Hlavacek WS.

Adv Exp Med Biol. 2014;844:245-62. doi: 10.1007/978-1-4939-2095-2_12. Review.

PMID:
25480645
7.

Phosphorylation site dynamics of early T-cell receptor signaling.

Chylek LA, Akimov V, Dengjel J, Rigbolt KT, Hu B, Hlavacek WS, Blagoev B.

PLoS One. 2014 Aug 22;9(8):e104240. doi: 10.1371/journal.pone.0104240. eCollection 2014.

8.

An Interaction Library for the FcεRI Signaling Network.

Chylek LA, Holowka DA, Baird BA, Hlavacek WS.

Front Immunol. 2014 Apr 15;5:172. doi: 10.3389/fimmu.2014.00172. eCollection 2014. Review.

9.

Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems.

Chylek LA, Harris LA, Tung CS, Faeder JR, Lopez CF, Hlavacek WS.

Wiley Interdiscip Rev Syst Biol Med. 2014 Jan-Feb;6(1):13-36. doi: 10.1002/wsbm.1245. Epub 2013 Sep 30. Review.

10.

Decoding the language of phosphorylation site dynamics.

Chylek LA.

Sci Signal. 2013 May 7;6(274):jc2. doi: 10.1126/scisignal.2004061.

PMID:
23652201
11.

Guidelines for visualizing and annotating rule-based models.

Chylek LA, Hu B, Blinov ML, Emonet T, Faeder JR, Goldstein B, Gutenkunst RN, Haugh JM, Lipniacki T, Posner RG, Yang J, Hlavacek WS.

Mol Biosyst. 2011 Oct;7(10):2779-95. doi: 10.1039/c1mb05077j. Epub 2011 Jun 7.

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