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Items: 1 to 20 of 54

1.

Structural analysis to determine the core of hypoxia response network.

Heiner M, Sriram K.

PLoS One. 2010 Jan 19;5(1):e8600. doi: 10.1371/journal.pone.0008600.

2.

The signaling petri net-based simulator: a non-parametric strategy for characterizing the dynamics of cell-specific signaling networks.

Ruths D, Muller M, Tseng JT, Nakhleh L, Ram PT.

PLoS Comput Biol. 2008 Feb 29;4(2):e1000005. doi: 10.1371/journal.pcbi.1000005.

3.

Exhaustive analysis of the modular structure of the spliceosomal assembly network: a Petri net approach.

Bortfeldt RH, Schuster S, Koch I.

In Silico Biol. 2010;10(1):89-123. doi: 10.3233/ISB-2010-0419.

PMID:
22430224
4.

Exhaustive analysis of the modular structure of the spliceosomal assembly network: a petri net approach.

Bortfeldt RH, Schuster S, Koch I.

Stud Health Technol Inform. 2011;162:244-78.

PMID:
21685576
5.

Structure discovery in PPI networks using pattern-based network decomposition.

Bachman P, Liu Y.

Bioinformatics. 2009 Jul 15;25(14):1814-21. doi: 10.1093/bioinformatics/btp297. Epub 2009 May 15.

PMID:
19447784
6.

VAN: an R package for identifying biologically perturbed networks via differential variability analysis.

Jayaswal V, Schramm SJ, Mann GJ, Wilkins MR, Yang YH.

BMC Res Notes. 2013 Oct 25;6:430. doi: 10.1186/1756-0500-6-430.

7.

Application of Petri net based analysis techniques to signal transduction pathways.

Sackmann A, Heiner M, Koch I.

BMC Bioinformatics. 2006 Nov 2;7:482.

8.

Quasi-Steady-State Analysis based on Structural Modules and Timed Petri Net Predict System's Dynamics: The Life Cycle of the Insulin Receptor.

Scheidel J, Lindauer K, Ackermann J, Koch I.

Metabolites. 2015 Dec 17;5(4):766-93. doi: 10.3390/metabo5040766.

9.

Propagation of kinetic uncertainties through a canonical topology of the TLR4 signaling network in different regions of biochemical reaction space.

Gutiérrez J, St Laurent G 3rd, Urcuqui-Inchima S.

Theor Biol Med Model. 2010 Mar 15;7:7. doi: 10.1186/1742-4682-7-7.

10.

Identification of functional hubs and modules by converting interactome networks into hierarchical ordering of proteins.

Cho YR, Zhang A.

BMC Bioinformatics. 2010 Apr 29;11 Suppl 3:S3. doi: 10.1186/1471-2105-11-S3-S3.

11.

Pathway switching explains the sharp response characteristic of hypoxia response network.

Yu Y, Wang G, Simha R, Peng W, Turano F, Zeng C.

PLoS Comput Biol. 2007 Aug;3(8):e171. Epub 2007 Jul 20.

12.

Network visualization and network analysis.

Nikiforova VJ, Willmitzer L.

EXS. 2007;97:245-75. Review.

PMID:
17432271
14.

Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data.

Li M, Wu X, Wang J, Pan Y.

BMC Bioinformatics. 2012 May 23;13:109. doi: 10.1186/1471-2105-13-109.

15.

LucidDraw: efficiently visualizing complex biochemical networks within MATLAB.

He S, Mei J, Shi G, Wang Z, Li W.

BMC Bioinformatics. 2010 Jan 15;11:31. doi: 10.1186/1471-2105-11-31.

16.

Integrative identification of core genetic regulatory modules via a structural model-based clustering method.

Tang B, Chen SS, Jin VX.

Int J Comput Biol Drug Des. 2011;4(2):127-46. doi: 10.1504/IJCBDD.2011.041007. Epub 2011 Jun 28.

PMID:
21712564
17.

The connectivity structure, giant strong component and centrality of metabolic networks.

Ma HW, Zeng AP.

Bioinformatics. 2003 Jul 22;19(11):1423-30.

PMID:
12874056
18.

Efficient and accurate Greedy Search Methods for mining functional modules in protein interaction networks.

He J, Li C, Ye B, Zhong W.

BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S19. doi: 10.1186/1471-2105-13-S10-S19.

19.

JAK/STAT signalling--an executable model assembled from molecule-centred modules demonstrating a module-oriented database concept for systems and synthetic biology.

Blätke MA, Dittrich A, Rohr C, Heiner M, Schaper F, Marwan W.

Mol Biosyst. 2013 Jun;9(6):1290-307. doi: 10.1039/c3mb25593j. Epub 2013 Feb 26.

PMID:
23443149
20.

An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia.

Benita Y, Kikuchi H, Smith AD, Zhang MQ, Chung DC, Xavier RJ.

Nucleic Acids Res. 2009 Aug;37(14):4587-602. doi: 10.1093/nar/gkp425. Epub 2009 Jun 2.

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