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Items: 1 to 20 of 47


Bistability analyses of CD4+ T follicular helper and regulatory cells during Helicobacter pylori infection.

Leber A, Abedi V, Hontecillas R, Viladomiu M, Hoops S, Ciupe S, Caughman J, Andrew T, Bassaganya-Riera J.

J Theor Biol. 2016 Jun 7;398:74-84. doi: 10.1016/j.jtbi.2016.02.036. Epub 2016 Mar 3.


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.


Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.

Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ.

J Integr Bioinform. 2015 Sep 4;12(2):271. doi: 10.2390/biecoll-jib-2015-271.


SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3.

Smith LP, Hucka M, Hoops S, Finney A, Ginkel M, Myers CJ, Moraru I, Liebermeister W.

J Integr Bioinform. 2015 Sep 4;12(2):268. doi: 10.2390/biecoll-jib-2015-268.


The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.

Hucka M, Bergmann FT, Hoops S, Keating SM, Sahle S, Schaff JC, Smith LP, Wilkinson DJ.

J Integr Bioinform. 2015 Sep 4;12(2):266. doi: 10.2390/biecoll-jib-2015-266.


Modeling the Regulatory Mechanisms by Which NLRX1 Modulates Innate Immune Responses to Helicobacter pylori Infection.

Philipson CW, Bassaganya-Riera J, Viladomiu M, Kronsteiner B, Abedi V, Hoops S, Michalak P, Kang L, Girardin SE, Hontecillas R.

PLoS One. 2015 Sep 14;10(9):e0137839. doi: 10.1371/journal.pone.0137839. eCollection 2015.


ENISI SDE: A New Web-Based Tool for Modeling Stochastic Processes.

Mei Y, Carbo A, Hoops S, Hontecillas R, Bassaganya-Riera J.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Mar-Apr;12(2):289-97. doi: 10.1109/TCBB.2014.2351823.


Supervised learning methods in modeling of CD4+ T cell heterogeneity.

Lu P, Abedi V, Mei Y, Hontecillas R, Hoops S, Carbo A, Bassaganya-Riera J.

BioData Min. 2015 Sep 4;8:27. doi: 10.1186/s13040-015-0060-6. eCollection 2015.


Multiscale modeling of mucosal immune responses.

Mei Y, Abedi V, Carbo A, Zhang X, Lu P, Philipson C, Hontecillas R, Hoops S, Liles N, Bassaganya-Riera J.

BMC Bioinformatics. 2015;16 Suppl 12:S2. doi: 10.1186/1471-2105-16-S12-S2. Epub 2015 Aug 25.


Sensitivity Analysis of an ENteric Immunity SImulator (ENISI)-Based Model of Immune Responses to Helicobacter pylori Infection.

Alam M, Deng X, Philipson C, Bassaganya-Riera J, Bisset K, Carbo A, Eubank S, Hontecillas R, Hoops S, Mei Y, Abedi V, Marathe M.

PLoS One. 2015 Sep 1;10(9):e0136139. doi: 10.1371/journal.pone.0136139. eCollection 2015.


Systems Modeling of Interactions between Mucosal Immunity and the Gut Microbiome during Clostridium difficile Infection.

Leber A, Viladomiu M, Hontecillas R, Abedi V, Philipson C, Hoops S, Howard B, Bassaganya-Riera J.

PLoS One. 2015 Jul 31;10(7):e0134849. doi: 10.1371/journal.pone.0134849. eCollection 2015.


A novel approach to adolescents with type 1 diabetes: the team clinic model.

Raymond JK, Shea JJ, Berget C, Cain C, Fay-Itzkowitz E, Gilmer L, Hoops S, Owen D, Shepard D, Spiegel G, Klingensmith G.

Diabetes Spectr. 2015 Jan;28(1):68-71. doi: 10.2337/diaspect.28.1.68. No abstract available.


Computational modeling of heterogeneity and function of CD4+ T cells.

Carbo A, Hontecillas R, Andrew T, Eden K, Mei Y, Hoops S, Bassaganya-Riera J.

Front Cell Dev Biol. 2014 Jul 29;2:31. doi: 10.3389/fcell.2014.00031. eCollection 2014. Review.


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.


Predictive computational modeling of the mucosal immune responses during Helicobacter pylori infection.

Carbo A, Bassaganya-Riera J, Pedragosa M, Viladomiu M, Marathe M, Eubank S, Wendelsdorf K, Bisset K, Hoops S, Deng X, Alam M, Kronsteiner B, Mei Y, Hontecillas R.

PLoS One. 2013 Sep 5;8(9):e73365. doi: 10.1371/journal.pone.0073365. eCollection 2013.


Systems modeling of molecular mechanisms controlling cytokine-driven CD4+ T cell differentiation and phenotype plasticity.

Carbo A, Hontecillas R, Kronsteiner B, Viladomiu M, Pedragosa M, Lu P, Philipson CW, Hoops S, Marathe M, Eubank S, Bisset K, Wendelsdorf K, Jarrah A, Mei Y, Bassaganya-Riera J.

PLoS Comput Biol. 2013 Apr;9(4):e1003027. doi: 10.1371/journal.pcbi.1003027. Epub 2013 Apr 4.


Modeling the role of peroxisome proliferator-activated receptor γ and microRNA-146 in mucosal immune responses to Clostridium difficile.

Viladomiu M, Hontecillas R, Pedragosa M, Carbo A, Hoops S, Michalak P, Michalak K, Guerrant RL, Roche JK, Warren CA, Bassaganya-Riera J.

PLoS One. 2012;7(10):e47525. doi: 10.1371/journal.pone.0047525. Epub 2012 Oct 11.


ENteric Immunity SImulator: a tool for in silico study of gastroenteric infections.

Wendelsdorf KV, Alam M, Bassaganya-Riera J, Bisset K, Eubank S, Hontecillas R, Hoops S, Marathe M.

IEEE Trans Nanobioscience. 2012 Sep;11(3):273-88. doi: 10.1109/TNB.2012.2211891.


Condor-COPASI: high-throughput computing for biochemical networks.

Kent E, Hoops S, Mendes P.

BMC Syst Biol. 2012 Jul 26;6:91. doi: 10.1186/1752-0509-6-91.


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.

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