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Items: 18

1.

Logical Modeling and Dynamical Analysis of Cellular Networks.

Abou-Jaoudé W, Traynard P, Monteiro PT, Saez-Rodriguez J, Helikar T, Thieffry D, Chaouiya C.

Front Genet. 2016 May 31;7:94. doi: 10.3389/fgene.2016.00094. eCollection 2016. Review.

2.

Systems Perturbation Analysis of a Large-Scale Signal Transduction Model Reveals Potentially Influential Candidates for Cancer Therapeutics.

Puniya BL, Allen L, Hochfelder C, Majumder M, Helikar T.

Front Bioeng Biotechnol. 2016 Feb 11;4:10. doi: 10.3389/fbioe.2016.00010. eCollection 2016.

3.

Programmatic access to logical models in the Cell Collective modeling environment via a REST API.

Kowal BM, Schreier TR, Dauer JT, Helikar T.

Biosystems. 2016 Jan;139:12-6. doi: 10.1016/j.biosystems.2015.11.005. Epub 2015 Nov 14.

PMID:
26589448
4.

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.

Chaouiya C, Keating SM, Berenguier D, Naldi A, Thieffry D, van Iersel MP, Le Novère N, Helikar T.

J Integr Bioinform. 2015 Sep 4;12(2):270. doi: 10.2390/biecoll-jib-2015-270.

PMID:
26528568
5.

Integrating interactive computational modeling in biology curricula.

Helikar T, Cutucache CE, Dahlquist LM, Herek TA, Larson JJ, Rogers JA.

PLoS Comput Biol. 2015 Mar 19;11(3):e1004131. doi: 10.1371/journal.pcbi.1004131. eCollection 2015 Mar.

6.

Cooperative development of logical modelling standards and tools with CoLoMoTo.

Naldi A, Monteiro PT, Müssel C; Consortium for Logical Models and Tools, Kestler HA, Thieffry D, Xenarios I, Saez-Rodriguez J, Helikar T, Chaouiya C.

Bioinformatics. 2015 Apr 1;31(7):1154-9. doi: 10.1093/bioinformatics/btv013. Epub 2015 Jan 25.

7.

Design, Assessment, and in vivo Evaluation of a Computational Model Illustrating the Role of CAV1 in CD4(+) T-lymphocytes.

Conroy BD, Herek TA, Shew TD, Latner M, Larson JJ, Allen L, Davis PH, Helikar T, Cutucache CE.

Front Immunol. 2014 Dec 5;5:599. doi: 10.3389/fimmu.2014.00599. eCollection 2014.

8.

Sensitivity analysis of biological Boolean networks using information fusion based on nonadditive set functions.

Kochi N, Helikar T, Allen L, Rogers JA, Wang Z, Matache MT.

BMC Syst Biol. 2014 Sep 5;8:92. doi: 10.1186/s12918-014-0092-4.

9.

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.

Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, Gonçalves E, Dorier J, Page M, Monteiro PT, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le Novère N, Saez-Rodriguez J, Helikar T.

BMC Syst Biol. 2013 Dec 10;7:135. doi: 10.1186/1752-0509-7-135.

10.

Molecular phylogeny and evolutionary dynamics of influenza A nonstructural (NS) gene.

Xu J, Zhong HA, Madrahimov A, Helikar T, Lu G.

Infect Genet Evol. 2014 Mar;22:192-200. doi: 10.1016/j.meegid.2013.10.011. Epub 2013 Oct 22.

PMID:
24161299
11.

A comprehensive, multi-scale dynamical model of ErbB receptor signal transduction in human mammary epithelial cells.

Helikar T, Kochi N, Kowal B, Dimri M, Naramura M, Raja SM, Band V, Band H, Rogers JA.

PLoS One. 2013 Apr 18;8(4):e61757. doi: 10.1371/journal.pone.0061757. Print 2013.

12.

A cell simulator platform: the cell collective.

Helikar T, Kowal B, Rogers JA.

Clin Pharmacol Ther. 2013 May;93(5):393-5. doi: 10.1038/clpt.2013.41. Epub 2013 Feb 20.

PMID:
23549147
13.

Bio-logic builder: a non-technical tool for building dynamical, qualitative models.

Helikar T, Kowal B, Madrahimov A, Shrestha M, Pedersen J, Limbu K, Thapa I, Rowley T, Satalkar R, Kochi N, Konvalina J, Rogers JA.

PLoS One. 2012;7(10):e46417. doi: 10.1371/journal.pone.0046417. Epub 2012 Oct 17.

14.

Dynamics of influenza virus and human host interactions during infection and replication cycle.

Madrahimov A, Helikar T, Kowal B, Lu G, Rogers J.

Bull Math Biol. 2013 Jun;75(6):988-1011. doi: 10.1007/s11538-012-9777-2. Epub 2012 Oct 19.

PMID:
23081726
15.

Ergodic sets as cell phenotype of budding yeast cell cycle.

Todd RG, Helikar T.

PLoS One. 2012;7(10):e45780. doi: 10.1371/journal.pone.0045780. Epub 2012 Oct 1.

16.

The Cell Collective: toward an open and collaborative approach to systems biology.

Helikar T, Kowal B, McClenathan S, Bruckner M, Rowley T, Madrahimov A, Wicks B, Shrestha M, Limbu K, Rogers JA.

BMC Syst Biol. 2012 Aug 7;6:96. doi: 10.1186/1752-0509-6-96.

17.

ChemChains: a platform for simulation and analysis of biochemical networks aimed to laboratory scientists.

Helikar T, Rogers JA.

BMC Syst Biol. 2009 Jun 6;3:58. doi: 10.1186/1752-0509-3-58.

18.

Emergent decision-making in biological signal transduction networks.

Helikar T, Konvalina J, Heidel J, Rogers JA.

Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):1913-8. doi: 10.1073/pnas.0705088105. Epub 2008 Feb 4.

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