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Items: 1 to 20 of 144

1.

An approach for dynamical network reconstruction of simple network motifs.

Nakatsui M, Araki M, Kondo A.

BMC Syst Biol. 2013;7 Suppl 6:S4. doi: 10.1186/1752-0509-7-S6-S4. Epub 2013 Dec 13.

2.

Reverse engineering gene regulatory networks: coupling an optimization algorithm with a parameter identification technique.

Hsiao YT, Lee WP.

BMC Bioinformatics. 2014;15 Suppl 15:S8. doi: 10.1186/1471-2105-15-S15-S8. Epub 2014 Dec 3.

3.

Gene networks reconstruction and time-series prediction from microarray data using recurrent neural fuzzy networks.

Maraziotis IA, Dragomir A, Bezerianos A.

IET Syst Biol. 2007 Jan;1(1):41-50.

PMID:
17370428
4.

An novel frequent probability pattern mining algorithm based on circuit simulation method in uncertain biological networks.

He J, Wang C, Qiu K, Zhong W.

BMC Syst Biol. 2014;8 Suppl 3:S6. doi: 10.1186/1752-0509-8-S3-S6. Epub 2014 Oct 22.

5.

Improved biological network reconstruction using graph Laplacian regularization.

Freschi V.

J Comput Biol. 2011 Aug;18(8):987-96. doi: 10.1089/cmb.2010.0232. Epub 2011 Jun 24.

PMID:
21702693
6.

Designing a parallel evolutionary algorithm for inferring gene networks on the cloud computing environment.

Lee WP, Hsiao YT, Hwang WC.

BMC Syst Biol. 2014 Jan 16;8:5. doi: 10.1186/1752-0509-8-5.

7.

A single source k-shortest paths algorithm to infer regulatory pathways in a gene network.

Shih YK, Parthasarathy S.

Bioinformatics. 2012 Jun 15;28(12):i49-58. doi: 10.1093/bioinformatics/bts212.

8.

IRIS: a method for reverse engineering of regulatory relations in gene networks.

Morganella S, Zoppoli P, Ceccarelli M.

BMC Bioinformatics. 2009 Dec 23;10:444. doi: 10.1186/1471-2105-10-444.

9.

A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs.

Seitzer P, Wilbanks EG, Larsen DJ, Facciotti MT.

BMC Bioinformatics. 2012 Nov 27;13:317. doi: 10.1186/1471-2105-13-317.

10.

An integer optimization algorithm for robust identification of non-linear gene regulatory networks.

Chemmangattuvalappil N, Task K, Banerjee I.

BMC Syst Biol. 2012 Sep 2;6:119.

12.

A group LASSO-based method for robustly inferring gene regulatory networks from multiple time-course datasets.

Liu LZ, Wu FX, Zhang WJ.

BMC Syst Biol. 2014;8 Suppl 3:S1. doi: 10.1186/1752-0509-8-S3-S1. Epub 2014 Oct 22.

13.

Inferring qualitative relations in genetic networks and metabolic pathways.

Akutsu T, Miyano S, Kuhara S.

Bioinformatics. 2000 Aug;16(8):727-34.

PMID:
11099258
14.

An algorithm for network motif discovery in biological networks.

Qin G, Gao L.

Int J Data Min Bioinform. 2012;6(1):1-16.

PMID:
22479815
15.

Inferring large-scale gene regulatory networks using a low-order constraint-based algorithm.

Wang M, Augusto Benedito V, Xuechun Zhao P, Udvardi M.

Mol Biosyst. 2010 Jun;6(6):988-98. doi: 10.1039/b917571g. Epub 2010 Feb 19.

PMID:
20485743
16.

Identification of regulatory structure and kinetic parameters of biochemical networks via mixed-integer dynamic optimization.

Guillén-Gosálbez G, Miró A, Alves R, Sorribas A, Jiménez L.

BMC Syst Biol. 2013 Oct 31;7:113. doi: 10.1186/1752-0509-7-113.

17.

Bridge and brick network motifs: identifying significant building blocks from complex biological systems.

Huang CY, Cheng CY, Sun CT.

Artif Intell Med. 2007 Oct;41(2):117-27. Epub 2007 Sep 7.

PMID:
17825540
18.

RRW: repeated random walks on genome-scale protein networks for local cluster discovery.

Macropol K, Can T, Singh AK.

BMC Bioinformatics. 2009 Sep 9;10:283. doi: 10.1186/1471-2105-10-283.

19.

Simultaneous inference of biological networks of multiple species from genome-wide data and evolutionary information: a semi-supervised approach.

Kashima H, Yamanishi Y, Kato T, Sugiyama M, Tsuda K.

Bioinformatics. 2009 Nov 15;25(22):2962-8. doi: 10.1093/bioinformatics/btp494. Epub 2009 Aug 17.

PMID:
19689962
20.

Inferring robust gene networks from expression data by a sensitivity-based incremental evolution method.

Hsiao YT, Lee WP.

BMC Bioinformatics. 2012 May 8;13 Suppl 7:S8. doi: 10.1186/1471-2105-13-S7-S8.

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