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Items: 1 to 20 of 113

1.

A framework for scalable parameter estimation of gene circuit models using structural information.

Kuwahara H, Fan M, Wang S, Gao X.

Bioinformatics. 2013 Jul 1;29(13):i98-107. doi: 10.1093/bioinformatics/btt232.

2.

Parameter estimation methods for gene circuit modeling from time-series mRNA data: a comparative study.

Fan M, Kuwahara H, Wang X, Wang S, Gao X.

Brief Bioinform. 2015 Nov;16(6):987-99. doi: 10.1093/bib/bbv015. Epub 2015 Mar 26.

PMID:
25818863
3.

Hybrid regulatory models: a statistically tractable approach to model regulatory network dynamics.

Ocone A, Millar AJ, Sanguinetti G.

Bioinformatics. 2013 Apr 1;29(7):910-6. doi: 10.1093/bioinformatics/btt069. Epub 2013 Feb 13.

PMID:
23407360
4.

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 Nov 1;31(21):3558-60. doi: 10.1093/bioinformatics/btv405. Epub 2015 Jul 3.

PMID:
26142188
5.

Recent developments in parameter estimation and structure identification of biochemical and genomic systems.

Chou IC, Voit EO.

Math Biosci. 2009 Jun;219(2):57-83. doi: 10.1016/j.mbs.2009.03.002. Epub 2009 Mar 25. Review.

6.

Piecewise parameter estimation for stochastic models in COPASI.

Bergmann FT, Sahle S, Zimmer C.

Bioinformatics. 2016 May 15;32(10):1586-8. doi: 10.1093/bioinformatics/btv759. Epub 2016 Jan 18.

PMID:
26787664
7.

KDDN: an open-source Cytoscape app for constructing differential dependency networks with significant rewiring.

Tian Y, Zhang B, Hoffman EP, Clarke R, Zhang Z, Shih IeM, Xuan J, Herrington DM, Wang Y.

Bioinformatics. 2015 Jan 15;31(2):287-9. doi: 10.1093/bioinformatics/btu632. Epub 2014 Sep 30.

8.

OKVAR-Boost: a novel boosting algorithm to infer nonlinear dynamics and interactions in gene regulatory networks.

Lim N, Senbabaoglu Y, Michailidis G, d'Alché-Buc F.

Bioinformatics. 2013 Jun 1;29(11):1416-23. doi: 10.1093/bioinformatics/btt167. Epub 2013 Apr 10.

9.

Efficient parameter search for qualitative models of regulatory networks using symbolic model checking.

Batt G, Page M, Cantone I, Goessler G, Monteiro P, de Jong H.

Bioinformatics. 2010 Sep 15;26(18):i603-10. doi: 10.1093/bioinformatics/btq387.

10.

Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy.

Penas DR, González P, Egea JA, Doallo R, Banga JR.

BMC Bioinformatics. 2017 Jan 21;18(1):52. doi: 10.1186/s12859-016-1452-4.

11.

List-decoding methods for inferring polynomials in finite dynamical gene network models.

Dingel J, Milenkovic O.

Bioinformatics. 2009 Jul 1;25(13):1686-93. doi: 10.1093/bioinformatics/btp281. Epub 2009 Apr 28.

PMID:
19401400
12.

Evaluating a common semi-mechanistic mathematical model of gene-regulatory networks.

Mizeranschi A, Zheng H, Thompson P, Dubitzky W.

BMC Syst Biol. 2015;9 Suppl 5:S2. doi: 10.1186/1752-0509-9-S5-S2. Epub 2015 Sep 1.

13.

On modeling and state estimation for genetic regulatory networks with polytopic uncertainties.

Wang Z, Wu H, Liang J, Cao J, Liu X.

IEEE Trans Nanobioscience. 2013 Mar;12(1):13-20. doi: 10.1109/TNB.2012.2215626. Epub 2012 Sep 14.

PMID:
22997273
14.

SMARTS: reconstructing disease response networks from multiple individuals using time series gene expression data.

Wise A, Bar-Joseph Z.

Bioinformatics. 2015 Apr 15;31(8):1250-7. doi: 10.1093/bioinformatics/btu800. Epub 2014 Dec 4.

15.

Parameter estimation using Simulated Annealing for S-system models of biochemical networks.

Gonzalez OR, Küper C, Jung K, Naval PC Jr, Mendoza E.

Bioinformatics. 2007 Feb 15;23(4):480-6. Epub 2006 Oct 11.

PMID:
17038344
16.

Systems biology strikes gold.

Camacho DM, Collins JJ.

Cell. 2009 Apr 3;137(1):24-6. doi: 10.1016/j.cell.2009.03.032.

17.

Functional data analysis for identifying nonlinear models of gene regulatory networks.

Summer G, Perkins TJ.

BMC Genomics. 2010 Dec 2;11 Suppl 4:S18. doi: 10.1186/1471-2164-11-S4-S18.

18.

Simultaneous learning of instantaneous and time-delayed genetic interactions using novel information theoretic scoring technique.

Morshed N, Chetty M, Nguyen XV.

BMC Syst Biol. 2012 Jun 12;6:62. doi: 10.1186/1752-0509-6-62.

19.

Linear fuzzy gene network models obtained from microarray data by exhaustive search.

Sokhansanj BA, Fitch JP, Quong JN, Quong AA.

BMC Bioinformatics. 2004 Aug 10;5:108.

20.

GeNOSA: inferring and experimentally supporting quantitative gene regulatory networks in prokaryotes.

Chen YH, Yang CD, Tseng CP, Huang HD, Ho SY.

Bioinformatics. 2015 Jul 1;31(13):2151-8. doi: 10.1093/bioinformatics/btv075. Epub 2015 Feb 24.

PMID:
25717191

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