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Results: 1 to 20 of 39

1.

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.

PMID:
24273241
[PubMed - indexed for MEDLINE]
2.

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.

PMID:
23171629
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Spatial modeling of cell signaling networks.

Cowan AE, Moraru II, Schaff JC, Slepchenko BM, Loew LM.

Methods Cell Biol. 2012;110:195-221. doi: 10.1016/B978-0-12-388403-9.00008-4.

PMID:
22482950
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.

Waltemath D, Adams R, Bergmann FT, Hucka M, Kolpakov F, Miller AK, Moraru II, Nickerson D, Sahle S, Snoep JL, Le Novère N.

BMC Syst Biol. 2011 Dec 15;5:198. doi: 10.1186/1752-0509-5-198.

PMID:
22172142
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
22161349
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Virtual NEURON: a strategy for merged biochemical and electrophysiological modeling.

Brown SA, Moraru II, Schaff JC, Loew LM.

J Comput Neurosci. 2011 Oct;31(2):385-400. doi: 10.1007/s10827-011-0317-0. Epub 2011 Feb 22.

PMID:
21340454
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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
[PubMed - indexed for MEDLINE]
8.

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.

PMID:
19045831
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
19045830
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Cell shape and negative links in regulatory motifs together control spatial information flow in signaling networks.

Neves SR, Tsokas P, Sarkar A, Grace EA, Rangamani P, Taubenfeld SM, Alberini CM, Schaff JC, Blitzer RD, Moraru II, Iyengar R.

Cell. 2008 May 16;133(4):666-80. doi: 10.1016/j.cell.2008.04.025.

PMID:
18485874
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

XML Encoding of Features Describing Rule-Based Modeling of Reaction Networks with Multi-Component Molecular Complexes.

Blinov ML, Moraru II.

Proc IEEE Int Symp Bioinformatics Bioeng. 2007 Nov 5:987-994.

PMID:
21464833
[PubMed]
Free PMC Article
12.

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.

PMID:
20862270
[PubMed]
Free PMC Article
13.

Modeling and analysis of calcium signaling events leading to long-term depression in cerebellar Purkinje cells.

Hernjak N, Slepchenko BM, Fernald K, Fink CC, Fortin D, Moraru II, Watras J, Loew LM.

Biophys J. 2005 Dec;89(6):3790-806. Epub 2005 Sep 16.

PMID:
16169982
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Intracellular signaling: spatial and temporal control.

Moraru II, Loew LM.

Physiology (Bethesda). 2005 Jun;20:169-79. Review.

PMID:
15888574
[PubMed - indexed for MEDLINE]
Free Article
15.

A wave of IP3 production accompanies the fertilization Ca2+ wave in the egg of the frog, Xenopus laevis: theoretical and experimental support.

Wagner J, Fall CP, Hong F, Sims CE, Allbritton NL, Fontanilla RA, Moraru II, Loew LM, Nuccitelli R.

Cell Calcium. 2004 May;35(5):433-47.

PMID:
15003853
[PubMed - indexed for MEDLINE]
16.

The virtual cell: an integrated modeling environment for experimental and computational cell biology.

Moraru II, Schaff JC, Slepchenko BM, Loew LM.

Ann N Y Acad Sci. 2002 Oct;971:595-6. No abstract available.

PMID:
12438191
[PubMed - indexed for MEDLINE]
17.

Topology of the mitochondrial inner membrane: dynamics and bioenergetic implications.

Mannella CA, Pfeiffer DR, Bradshaw PC, Moraru II, Slepchenko B, Loew LM, Hsieh CE, Buttle K, Marko M.

IUBMB Life. 2001 Sep-Nov;52(3-5):93-100. Review.

PMID:
11798041
[PubMed - indexed for MEDLINE]
18.

An image-based model of calcium waves in differentiated neuroblastoma cells.

Fink CC, Slepchenko B, Moraru II, Watras J, Schaff JC, Loew LM.

Biophys J. 2000 Jul;79(1):163-83.

PMID:
10866945
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

An endogenous sulfated inhibitor of neuronal inositol trisphosphate receptors.

Watras J, Orlando R, Moraru II.

Biochemistry. 2000 Mar 28;39(12):3452-60.

PMID:
10727240
[PubMed - indexed for MEDLINE]
20.

An antibody to annexin V blocks Ca(2+)-dependent ATPase activity of sarcoplasmic reticulum in human failing hearts.

Moraru II, Syrbu S, Zecevic N, Hager WD, Watras J, Messineo F.

Ann N Y Acad Sci. 1998 Sep 16;853:333-7. No abstract available.

PMID:
10603973
[PubMed - indexed for MEDLINE]

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