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Items: 1 to 20 of 103

1.

A computational framework for gene regulatory network inference that combines multiple methods and datasets.

Gupta R, Stincone A, Antczak P, Durant S, Bicknell R, Bikfalvi A, Falciani F.

BMC Syst Biol. 2011 Apr 13;5:52. doi: 10.1186/1752-0509-5-52.

2.

An algebra-based method for inferring gene regulatory networks.

Vera-Licona P, Jarrah A, Garcia-Puente LD, McGee J, Laubenbacher R.

BMC Syst Biol. 2014 Mar 26;8:37. doi: 10.1186/1752-0509-8-37.

3.

RMaNI: Regulatory Module Network Inference framework.

Madhamshettiwar PB, Maetschke SR, Davis MJ, Ragan MA.

BMC Bioinformatics. 2013;14 Suppl 16:S14. doi: 10.1186/1471-2105-14-S16-S14. Epub 2013 Oct 22.

4.

Gene expression complex networks: synthesis, identification, and analysis.

Lopes FM, Cesar RM, Costa Lda F.

J Comput Biol. 2011 Oct;18(10):1353-67. doi: 10.1089/cmb.2010.0118. Epub 2011 May 6.

PMID:
21548810
5.

Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a Systems Biology approach.

Linde J, Hortschansky P, Fazius E, Brakhage AA, Guthke R, Haas H.

BMC Syst Biol. 2012 Jan 19;6:6. doi: 10.1186/1752-0509-6-6.

6.

Empirically determining the sample size for large-scale gene network inference algorithms.

Altay G.

IET Syst Biol. 2012 Apr;6(2):35-43. doi: 10.1049/iet-syb.2010.0091.

PMID:
22519356
7.

Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation.

Pinna A, Heise S, Flassig RJ, de la Fuente A, Klamt S.

BMC Syst Biol. 2013 Aug 8;7:73. doi: 10.1186/1752-0509-7-73.

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.

Network inference using steady-state data and Goldbeter-Koshland kinetics. [corrected].

Oates CJ, Hennessy BT, Lu Y, Mills GB, Mukherjee S.

Bioinformatics. 2012 Sep 15;28(18):2342-8. doi: 10.1093/bioinformatics/bts459. Epub 2012 Jul 19. Erratum in: Bioinformatics. 2013 Mar 15;29(6):819.

10.

A network inference workflow applied to virulence-related processes in Salmonella typhimurium.

Taylor RC, Singhal M, Weller J, Khoshnevis S, Shi L, McDermott J.

Ann N Y Acad Sci. 2009 Mar;1158:143-58. doi: 10.1111/j.1749-6632.2008.03762.x.

PMID:
19348639
11.

Reverse engineering module networks by PSO-RNN hybrid modeling.

Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW.

BMC Genomics. 2009 Jul 7;10 Suppl 1:S15. doi: 10.1186/1471-2164-10-S1-S15.

12.

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.

13.

Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis.

Kaleta C, Göhler A, Schuster S, Jahreis K, Guthke R, Nikolajewa S.

BMC Syst Biol. 2010 Aug 18;4:116. doi: 10.1186/1752-0509-4-116.

14.

Inference of gene regulatory networks from time series by Tsallis entropy.

Lopes FM, de Oliveira EA, Cesar RM Jr.

BMC Syst Biol. 2011 May 5;5:61. doi: 10.1186/1752-0509-5-61.

15.

Biological Network Inference and analysis using SEBINI and CABIN.

Taylor R, Singhal M.

Methods Mol Biol. 2009;541:551-76. doi: 10.1007/978-1-59745-243-4_24. Review.

PMID:
19381531
16.

NAIL, a software toolset for inferring, analyzing and visualizing regulatory networks.

Hurley DG, Cursons J, Wang YK, Budden DM, Print CG, Crampin EJ.

Bioinformatics. 2015 Jan 15;31(2):277-8. doi: 10.1093/bioinformatics/btu612. Epub 2014 Sep 21. Erratum in: Bioinformatics. 2015 Jul 1;31(13):2015-240.

PMID:
25246431
17.

Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data.

Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW.

BMC Bioinformatics. 2008 Apr 21;9:203. doi: 10.1186/1471-2105-9-203.

18.

Semi-Supervised Multi-View Learning for Gene Network Reconstruction.

Ceci M, Pio G, Kuzmanovski V, Džeroski S.

PLoS One. 2015 Dec 7;10(12):e0144031. doi: 10.1371/journal.pone.0144031. eCollection 2015.

19.

An integrative, multi-scale, genome-wide model reveals the phenotypic landscape of Escherichia coli.

Carrera J, Estrela R, Luo J, Rai N, Tsoukalas A, Tagkopoulos I.

Mol Syst Biol. 2014 Jul 1;10:735. doi: 10.15252/msb.20145108.

20.

TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach.

Zoppoli P, Morganella S, Ceccarelli M.

BMC Bioinformatics. 2010 Mar 25;11:154. doi: 10.1186/1471-2105-11-154.

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