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Items: 1 to 20 of 99

1.

Inference and validation of predictive gene networks from biomedical literature and gene expression data.

Olsen C, Fleming K, Prendergast N, Rubio R, Emmert-Streib F, Bontempi G, Haibe-Kains B, Quackenbush J.

Genomics. 2014 May-Jun;103(5-6):329-36. doi: 10.1016/j.ygeno.2014.03.004. Epub 2014 Mar 29.

2.

Relevance of different prior knowledge sources for inferring gene interaction networks.

Olsen C, Bontempi G, Emmert-Streib F, Quackenbush J, Haibe-Kains B.

Front Genet. 2014 Jun 24;5:177. doi: 10.3389/fgene.2014.00177. eCollection 2014.

3.

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
4.

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.

5.

Probabilistic inference and ranking of gene regulatory pathways as a shortest-path problem.

Jensen JD, Jensen DM, Clement MJ, Snell QO.

BMC Bioinformatics. 2013;14 Suppl 13:S5. doi: 10.1186/1471-2105-14-S13-S5. Epub 2013 Oct 1.

6.

Inferring the perturbed microRNA regulatory networks from gene expression data using a network propagation based method.

Wang T, Gu J, Li Y.

BMC Bioinformatics. 2014 Jul 29;15:255. doi: 10.1186/1471-2105-15-255.

7.

Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks.

Marbach D, Roy S, Ay F, Meyer PE, Candeias R, Kahveci T, Bristow CA, Kellis M.

Genome Res. 2012 Jul;22(7):1334-49. doi: 10.1101/gr.127191.111. Epub 2012 Mar 28.

8.

Inference of dynamical gene-regulatory networks based on time-resolved multi-stimuli multi-experiment data applying NetGenerator V2.0.

Weber M, Henkel SG, Vlaic S, Guthke R, van Zoelen EJ, Driesch D.

BMC Syst Biol. 2013 Jan 2;7:1. doi: 10.1186/1752-0509-7-1.

9.

Ensemble inference and inferability of gene regulatory networks.

Ud-Dean SM, Gunawan R.

PLoS One. 2014 Aug 5;9(8):e103812. doi: 10.1371/journal.pone.0103812. eCollection 2014.

10.
11.

Revealing strengths and weaknesses of methods for gene network inference.

Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, Stolovitzky G.

Proc Natl Acad Sci U S A. 2010 Apr 6;107(14):6286-91. doi: 10.1073/pnas.0913357107. Epub 2010 Mar 22.

12.

Large-scale modeling of condition-specific gene regulatory networks by information integration and inference.

Ellwanger DC, Leonhardt JF, Mewes HW.

Nucleic Acids Res. 2014 Dec 1;42(21). doi: 10.1093/nar/gku916. Epub 2014 Oct 7.

13.

An integrative network inference approach to predict mechanisms of cancer chemoresistance.

Lecca P.

Integr Biol (Camb). 2013 Mar;5(3):458-73. doi: 10.1039/c2ib20205k.

PMID:
23340828
14.

Using shRNA experiments to validate gene regulatory networks.

Olsen C, Fleming K, Prendergast N, Rubio R, Emmert-Streib F, Bontempi G, Quackenbush J, Haibe-Kains B.

Genom Data. 2015 Apr 1;4:123-6. doi: 10.1016/j.gdata.2015.03.011. eCollection 2015 Jun.

15.

A network-based, integrative study to identify core biological pathways that drive breast cancer clinical subtypes.

Dutta B, Pusztai L, Qi Y, André F, Lazar V, Bianchini G, Ueno N, Agarwal R, Wang B, Shiang CY, Hortobagyi GN, Mills GB, Symmans WF, Balázsi G.

Br J Cancer. 2012 Mar 13;106(6):1107-16. doi: 10.1038/bjc.2011.584. Epub 2012 Feb 16.

16.

Joint network and node selection for pathway-based genomic data analysis.

Zhe S, Naqvi SA, Yang Y, Qi Y.

Bioinformatics. 2013 Aug 15;29(16):1987-96. doi: 10.1093/bioinformatics/btt335. Epub 2013 Jun 8.

17.

Function approximation approach to the inference of reduced NGnet models of genetic networks.

Kimura S, Sonoda K, Yamane S, Maeda H, Matsumura K, Hatakeyama M.

BMC Bioinformatics. 2008 Jan 14;9:23. doi: 10.1186/1471-2105-9-23.

18.

Gene prioritization for livestock diseases by data integration.

Jiang L, Sørensen P, Thomsen B, Edwards SM, Skarman A, Røntved CM, Lund MS, Workman CT.

Physiol Genomics. 2012 Mar 1;44(5):305-17. doi: 10.1152/physiolgenomics.00047.2011. Epub 2012 Jan 10.

19.

Gene network inference and visualization tools for biologists: application to new human transcriptome datasets.

Hurley D, Araki H, Tamada Y, Dunmore B, Sanders D, Humphreys S, Affara M, Imoto S, Yasuda K, Tomiyasu Y, Tashiro K, Savoie C, Cho V, Smith S, Kuhara S, Miyano S, Charnock-Jones DS, Crampin EJ, Print CG.

Nucleic Acids Res. 2012 Mar;40(6):2377-98. doi: 10.1093/nar/gkr902. Epub 2011 Nov 24.

20.

Inference of radio-responsive gene regulatory networks using the graphical lasso algorithm.

Oh JH, Deasy JO.

BMC Bioinformatics. 2014;15 Suppl 7:S5. doi: 10.1186/1471-2105-15-S7-S5. Epub 2014 May 28.

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