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Items: 29

1.

Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0.

Rougny A, Touré V, Moodie S, Balaur I, Czauderna T, Borlinghaus H, Dogrusoz U, Mazein A, Dräger A, Blinov ML, Villéger A, Haw R, Demir E, Mi H, Sorokin A, Schreiber F, Luna A.

J Integr Bioinform. 2019 Jun 13;16(2). pii: /j/jib.2019.16.issue-2/jib-2019-0022/jib-2019-0022.xml. doi: 10.1515/jib-2019-0022.

PMID:
31199769
2.

Corrigendum to: Report: NIA Workshop on Measures of Physiologic Resiliencies in Human Aging.

Hadley EC, Kuchel GA, Newman AB, Allore HG, Bartley JM, Bergeman CS, Blinov ML, Colon-Emeric CS, Dabhar FS, Dugan LL, Dutta C, Eldadah BA, Ferrucci L, Kirkland JL, Kritchevsky SB, Lipsitz LA, Nadkarni NK, Reed MJ, Schmader KE, Sierra F, Studenski SA, Varadhan R, Walston JD, Whitson HE, Yung R.

J Gerontol A Biol Sci Med Sci. 2018 Jun 14;73(7):995. doi: 10.1093/gerona/glx172. No abstract available.

3.

Compartmental and Spatial Rule-Based Modeling with Virtual Cell.

Blinov ML, Schaff JC, Vasilescu D, Moraru II, Bloom JE, Loew LM.

Biophys J. 2017 Oct 3;113(7):1365-1372. doi: 10.1016/j.bpj.2017.08.022.

4.

Multivalent Molecules as Modulators of RNA Granule Size and Composition.

Falkenberg CV, Carson JH, Blinov ML.

Biophys J. 2017 Jul 25;113(2):235-245. doi: 10.1016/j.bpj.2017.01.031. Epub 2017 Feb 24.

5.

Rule-based modeling with Virtual Cell.

Schaff JC, Vasilescu D, Moraru II, Loew LM, Blinov ML.

Bioinformatics. 2016 Sep 15;32(18):2880-2. doi: 10.1093/bioinformatics/btw353. Epub 2016 Jun 9.

6.

Pleomorphic ensembles: formation of large clusters composed of weakly interacting multivalent molecules.

Falkenberg CV, Blinov ML, Loew LM.

Biophys J. 2013 Dec 3;105(11):2451-60. doi: 10.1016/j.bpj.2013.10.016.

7.

Pathway Commons at virtual cell: use of pathway data for mathematical modeling.

Blinov ML, Schaff JC, Ruebenacker O, Wei X, Vasilescu D, Gao F, Morgan F, Ye L, Lakshminarayana A, Moraru II, Loew LM.

Bioinformatics. 2014 Jan 15;30(2):292-4. doi: 10.1093/bioinformatics/btt660. Epub 2013 Nov 22.

8.

A predictive mathematical model of the DNA damage G2 checkpoint.

Kesseler KJ, Blinov ML, Elston TC, Kaufmann WK, Simpson DA.

J Theor Biol. 2013 Mar 7;320:159-69. doi: 10.1016/j.jtbi.2012.12.011. Epub 2012 Dec 22.

9.

Logic modeling and the ridiculome under the rug.

Blinov ML, Moraru II.

BMC Biol. 2012 Nov 21;10:92. doi: 10.1186/1741-7007-10-92.

10.

Leveraging modeling approaches: reaction networks and rules.

Blinov ML, Moraru II.

Adv Exp Med Biol. 2012;736:517-30. doi: 10.1007/978-1-4419-7210-1_30.

11.

Proliferating dynamic modeling in systems biology studies.

Blinov ML.

Mol Biosyst. 2011 Oct;7(10):2735-6. doi: 10.1039/c1mb90033a. Epub 2011 Aug 26. No abstract available.

PMID:
21874191
12.

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.

13.

Integrating BioPAX pathway knowledge with SBML models.

Ruebenacker O, Moraru II, Schaff JC, Blinov ML.

IET Syst Biol. 2009 Sep;3(5):317-28. doi: 10.1049/iet-syb.2009.0007.

PMID:
21028923
14.

A detailed mathematical model predicts that serial engagement of IgE-Fc epsilon RI complexes can enhance Syk activation in mast cells.

Nag A, Monine MI, Blinov ML, Goldstein B.

J Immunol. 2010 Sep 15;185(6):3268-76. doi: 10.4049/jimmunol.1000326. Epub 2010 Aug 23.

15.

Molecular machines or pleiomorphic ensembles: signaling complexes revisited.

Mayer BJ, Blinov ML, Loew LM.

J Biol. 2009 Oct 16;8(9):81. doi: 10.1186/jbiol185.

16.

Rule-based modeling of biochemical systems with BioNetGen.

Faeder JR, Blinov ML, Hlavacek WS.

Methods Mol Biol. 2009;500:113-67. doi: 10.1007/978-1-59745-525-1_5.

PMID:
19399430
17.

Complexity and modularity of intracellular networks: a systematic approach for modelling and simulation.

Blinov ML, Ruebenacker O, Moraru II.

IET Syst Biol. 2008 Sep;2(5):363-8. doi: 10.1049/iet-syb:20080092.

18.

Virtual Cell modelling and simulation software environment.

Moraru II, Schaff JC, Slepchenko BM, Blinov ML, Morgan F, Lakshminarayana A, Gao F, Li Y, Loew LM.

IET Syst Biol. 2008 Sep;2(5):352-62. doi: 10.1049/iet-syb:20080102.

19.
20.

Kinetic Modeling using BioPAX ontology.

Ruebenacker O, Moraru II, Schaff JC, Blinov ML.

Proceedings (IEEE Int Conf Bioinformatics Biomed). 2007 Nov 2;2007:339-348.

21.

Combinatorial complexity and dynamical restriction of network flows in signal transduction.

Faeder JR, Blinov ML, Goldstein B, Hlavacek WS.

Syst Biol (Stevenage). 2005 Mar;2(1):5-15.

PMID:
17091578
22.

Rules for modeling signal-transduction systems.

Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W.

Sci STKE. 2006 Jul 18;2006(344):re6. Review.

PMID:
16849649
23.

Depicting signaling cascades.

Blinov ML, Yang J, Faeder JR, Hlavacek WS.

Nat Biotechnol. 2006 Feb;24(2):137-8; author reply 138. No abstract available.

PMID:
16465147
24.

'On-the-fly' or 'generate-first' modeling?

Blinov ML, Faeder JR, Yang J, Goldstein B, Hlavacek WS.

Nat Biotechnol. 2005 Nov;23(11):1344-5; author reply 1345. No abstract available.

PMID:
16273053
25.

A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity.

Blinov ML, Faeder JR, Goldstein B, Hlavacek WS.

Biosystems. 2006 Feb-Mar;83(2-3):136-51. Epub 2005 Oct 17.

PMID:
16233948
26.

BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains.

Blinov ML, Faeder JR, Goldstein B, Hlavacek WS.

Bioinformatics. 2004 Nov 22;20(17):3289-91. Epub 2004 Jun 24.

PMID:
15217809
27.

The complexity of complexes in signal transduction.

Hlavacek WS, Faeder JR, Blinov ML, Perelson AS, Goldstein B.

Biotechnol Bioeng. 2003 Dec 30;84(7):783-94. Review.

PMID:
14708119
28.

Investigation of early events in Fc epsilon RI-mediated signaling using a detailed mathematical model.

Faeder JR, Hlavacek WS, Reischl I, Blinov ML, Metzger H, Redondo A, Wofsy C, Goldstein B.

J Immunol. 2003 Apr 1;170(7):3769-81.

29.

Modeling the early signaling events mediated by FcepsilonRI.

Goldstein B, Faeder JR, Hlavacek WS, Blinov ML, Redondo A, Wofsy C.

Mol Immunol. 2002 Sep;38(16-18):1213-9. Review.

PMID:
12217386

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