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Items: 1 to 20 of 54

1.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.

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. 2018 Mar 9;15(1). pii: /j/jib.2018.15.issue-1/jib-2017-0081/jib-2017-0081.xml. doi: 10.1515/jib-2017-0081.

PMID:
29522418
2.

Agents and networks to model the dynamic interactions of intracellular transport.

Mayorga LS, Verma M, Hontecillas R, Hoops S, Bassaganya-Riera J.

Cell Logist. 2017 Nov 29;7(4):e1392401. doi: 10.1080/21592799.2017.1392401. eCollection 2017.

PMID:
29296512
3.

COPASI and its applications in biotechnology.

Bergmann FT, Hoops S, Klahn B, Kummer U, Mendes P, Pahle J, Sahle S.

J Biotechnol. 2017 Nov 10;261:215-220. doi: 10.1016/j.jbiotec.2017.06.1200. Epub 2017 Jun 24. Review.

4.

Modeling the Mechanisms by Which HIV-Associated Immunosuppression Influences HPV Persistence at the Oral Mucosa.

Verma M, Erwin S, Abedi V, Hontecillas R, Hoops S, Leber A, Bassaganya-Riera J, Ciupe SM.

PLoS One. 2017 Jan 6;12(1):e0168133. doi: 10.1371/journal.pone.0168133. eCollection 2017.

5.

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.

PMID:
26947272
6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

PMID:
26357217
12.

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.

13.

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.

14.

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.

15.

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.

16.

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 Jun 1;12(2):731-901. doi: 10.1515/jib-2015-271.

PMID:
29220970
17.

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 Jun 1;12(2):382-549. doi: 10.1515/jib-2015-266.

PMID:
29220965
18.

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 Jun 1;12(2):603-659. doi: 10.1515/jib-2015-268.

PMID:
29220960
19.

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.

20.

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.

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