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1.

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.

2.

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.

3.

Addressing parameter identifiability by model-based experimentation.

Raue A, Kreutz C, Maiwald T, Klingmuller U, Timmer J.

IET Syst Biol. 2011 Mar;5(2):120-30. doi: 10.1049/iet-syb.2010.0061.

PMID:
21405200
4.

SensSB: a software toolbox for the development and sensitivity analysis of systems biology models.

Rodriguez-Fernandez M, Banga JR.

Bioinformatics. 2010 Jul 1;26(13):1675-6. doi: 10.1093/bioinformatics/btq242. Epub 2010 May 5.

5.

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.

6.

Software for dynamic analysis of tracer-based metabolomic data: estimation of metabolic fluxes and their statistical analysis.

Selivanov VA, Marin S, Lee PW, Cascante M.

Bioinformatics. 2006 Nov 15;22(22):2806-12. Epub 2006 Sep 25.

7.

Bayesian learning of biological pathways on genomic data assimilation.

Yoshida R, Nagasaki M, Yamaguchi R, Imoto S, Miyano S, Higuchi T.

Bioinformatics. 2008 Nov 15;24(22):2592-601. doi: 10.1093/bioinformatics/btn483. Epub 2008 Sep 25.

8.

Stochastic simulation GUI for biochemical networks.

Vallabhajosyula RR, Sauro HM.

Bioinformatics. 2007 Jul 15;23(14):1859-61. Epub 2007 Jun 22.

9.

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.

10.

Structural systems identification of genetic regulatory networks.

Xiong H, Choe Y.

Bioinformatics. 2008 Feb 15;24(4):553-60. doi: 10.1093/bioinformatics/btm623. Epub 2008 Jan 5.

11.

MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data.

Ulitsky I, Gat-Viks I, Shamir R.

Genome Biol. 2008 Jan 2;9(1):R1. doi: 10.1186/gb-2008-9-1-r1.

12.

Calibrating E-values for hidden Markov models using reverse-sequence null models.

Karplus K, Karchin R, Shackelford G, Hughey R.

Bioinformatics. 2005 Nov 15;21(22):4107-15. Epub 2005 Aug 25.

13.

Module networks revisited: computational assessment and prioritization of model predictions.

Joshi A, De Smet R, Marchal K, Van de Peer Y, Michoel T.

Bioinformatics. 2009 Feb 15;25(4):490-6. doi: 10.1093/bioinformatics/btn658. Epub 2009 Jan 9.

14.

Complexity reduction of biochemical rate expressions.

Schmidt H, Madsen MF, Danø S, Cedersund G.

Bioinformatics. 2008 Mar 15;24(6):848-54. doi: 10.1093/bioinformatics/btn035. Epub 2008 Feb 10.

15.

Easy parameter identifiability analysis with COPASI.

Schaber J.

Biosystems. 2012 Dec;110(3):183-5. doi: 10.1016/j.biosystems.2012.09.003. Epub 2012 Oct 4.

PMID:
23041463
16.

Efficient estimation of graphlet frequency distributions in protein-protein interaction networks.

Przulj N, Corneil DG, Jurisica I.

Bioinformatics. 2006 Apr 15;22(8):974-80. Epub 2006 Feb 1.

17.

A stochastic model for the evolution of metabolic networks with neighbor dependence.

Mithani A, Preston GM, Hein J.

Bioinformatics. 2009 Jun 15;25(12):1528-35. doi: 10.1093/bioinformatics/btp262. Epub 2009 Apr 17.

18.

Accessible methods for the dynamic time-scale decomposition of biochemical systems.

Surovtsova I, Simus N, Lorenz T, König A, Sahle S, Kummer U.

Bioinformatics. 2009 Nov 1;25(21):2816-23. doi: 10.1093/bioinformatics/btp451. Epub 2009 Jul 24.

19.

Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application.

Xirasagar S, Gustafson SF, Huang CC, Pan Q, Fostel J, Boyer P, Merrick BA, Tomer KB, Chan DD, Yost KJ 3rd, Choi D, Xiao N, Stasiewicz S, Bushel P, Waters MD.

Bioinformatics. 2006 Apr 1;22(7):874-82. Epub 2006 Jan 12.

20.
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