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1.

Comprehensive estimation of input signals and dynamics in biochemical reaction networks.

Schelker M, Raue A, Timmer J, Kreutz C.

Bioinformatics. 2012 Sep 15;28(18):i529-i534. doi: 10.1093/bioinformatics/bts393.

2.

Likelihood based observability analysis and confidence intervals for predictions of dynamic models.

Kreutz C, Raue A, Timmer J.

BMC Syst Biol. 2012 Sep 5;6:120. doi: 10.1186/1752-0509-6-120.

3.

Maximum profile likelihood estimation of differential equation parameters through model based smoothing state estimates.

Campbell DA, Chkrebtii O.

Math Biosci. 2013 Dec;246(2):283-92. doi: 10.1016/j.mbs.2013.03.011. Epub 2013 Apr 8.

PMID:
23579098
4.
5.

A simple work flow for biologically inspired model reduction--application to early JAK-STAT signaling.

Quaiser T, Dittrich A, Schaper F, Mönnigmann M.

BMC Syst Biol. 2011 Feb 21;5:30. doi: 10.1186/1752-0509-5-30.

6.

Extended kalman filter for estimation of parameters in nonlinear state-space models of biochemical networks.

Sun X, Jin L, Xiong M.

PLoS One. 2008;3(11):e3758. doi: 10.1371/journal.pone.0003758. Epub 2008 Nov 19.

7.

An integrated strategy for prediction uncertainty analysis.

Vanlier J, Tiemann CA, Hilbers PA, van Riel NA.

Bioinformatics. 2012 Apr 15;28(8):1130-5. doi: 10.1093/bioinformatics/bts088. Epub 2012 Feb 21.

8.

Optimal design of stimulus experiments for robust discrimination of biochemical reaction networks.

Flassig RJ, Sundmacher K.

Bioinformatics. 2012 Dec 1;28(23):3089-96. doi: 10.1093/bioinformatics/bts585. Epub 2012 Oct 9.

9.

Model-based selection of the robust JAK-STAT activation mechanism.

Rybiński M, Gambin A.

J Theor Biol. 2012 Sep 21;309:34-46. doi: 10.1016/j.jtbi.2012.04.031. Epub 2012 Jun 5.

PMID:
22677400
10.

Narrative-based computational modelling of the Gp130/JAK/STAT signalling pathway.

Guerriero ML, Dudka A, Underhill-Day N, Heath JK, Priami C.

BMC Syst Biol. 2009 Apr 15;3:40. doi: 10.1186/1752-0509-3-40.

11.

In silico labeling reveals the time-dependent label half-life and transit-time in dynamical systems.

Maiwald T, Blumberg J, Raue A, Hengl S, Schilling M, Sy SK, Becker V, Klingmüller U, Timmer J.

BMC Syst Biol. 2012 Feb 27;6:13. doi: 10.1186/1752-0509-6-13.

12.

Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems.

Raue A, Steiert B, Schelker M, Kreutz C, Maiwald T, Hass H, Vanlier J, Tönsing C, Adlung L, Engesser R, Mader W, Heinemann T, Hasenauer J, Schilling M, Höfer T, Klipp E, Theis F, Klingmüller U, Schöberl B, Timmer J.

Bioinformatics. 2015 Jul 3. pii: btv405. [Epub ahead of print]

PMID:
26142188
13.

Dynamics and non-canonical aspects of JAK/STAT signalling.

Mohr A, Chatain N, Domoszlai T, Rinis N, Sommerauer M, Vogt M, Müller-Newen G.

Eur J Cell Biol. 2012 Jun-Jul;91(6-7):524-32. doi: 10.1016/j.ejcb.2011.09.005. Epub 2011 Oct 21. Review.

PMID:
22018664
14.

Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood.

Raue A, Kreutz C, Maiwald T, Bachmann J, Schilling M, Klingmüller U, Timmer J.

Bioinformatics. 2009 Aug 1;25(15):1923-9. doi: 10.1093/bioinformatics/btp358. Epub 2009 Jun 8.

15.

Dynamical modeling and multi-experiment fitting with PottersWheel.

Maiwald T, Timmer J.

Bioinformatics. 2008 Sep 15;24(18):2037-43. doi: 10.1093/bioinformatics/btn350. Epub 2008 Jul 9.

16.

Reconstructing signaling pathways from RNAi data using probabilistic Boolean threshold networks.

Kaderali L, Dazert E, Zeuge U, Frese M, Bartenschlager R.

Bioinformatics. 2009 Sep 1;25(17):2229-35. doi: 10.1093/bioinformatics/btp375. Epub 2009 Jun 19.

17.

Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules.

Saez-Rodriguez J, Gayer S, Ginkel M, Gilles ED.

Bioinformatics. 2008 Aug 15;24(16):i213-9. doi: 10.1093/bioinformatics/btn289.

18.

A Bayesian approach to targeted experiment design.

Vanlier J, Tiemann CA, Hilbers PA, van Riel NA.

Bioinformatics. 2012 Apr 15;28(8):1136-42. doi: 10.1093/bioinformatics/bts092. Epub 2012 Feb 24.

19.

An error model for protein quantification.

Kreutz C, Bartolome Rodriguez MM, Maiwald T, Seidl M, Blum HE, Mohr L, Timmer J.

Bioinformatics. 2007 Oct 15;23(20):2747-53. Epub 2007 Sep 3.

20.

Systematic parameter estimation in data-rich environments for cell signalling dynamics.

Nim TH, Luo L, Clément MV, White JK, Tucker-Kellogg L.

Bioinformatics. 2013 Apr 15;29(8):1044-51. doi: 10.1093/bioinformatics/btt083. Epub 2013 Feb 19.

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