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Results: 1 to 20 of 346

1.

Hub-centered gene network reconstruction using automatic relevance determination.

Böck M, Ogishima S, Tanaka H, Kramer S, Kaderali L.

PLoS One. 2012;7(5):e35077. doi: 10.1371/journal.pone.0035077. Epub 2012 May 3.

PMID:
22570688
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Reconstructing nonlinear dynamic models of gene regulation using stochastic sampling.

Mazur J, Ritter D, Reinelt G, Kaderali L.

BMC Bioinformatics. 2009 Dec 28;10:448. doi: 10.1186/1471-2105-10-448.

PMID:
20038296
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

A copula method for modeling directional dependence of genes.

Kim JM, Jung YS, Sungur EA, Han KH, Park C, Sohn I.

BMC Bioinformatics. 2008 May 1;9:225. doi: 10.1186/1471-2105-9-225.

PMID:
18447957
[PubMed - indexed for MEDLINE]
Free PMC Article
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
[PubMed - indexed for MEDLINE]
5.

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.

PMID:
19594874
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
20338053
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Unraveling gene regulatory networks from time-resolved gene expression data - a measures comparison study.

Hempel S, Koseska A, Nikoloski Z, Kurths J.

BMC Bioinformatics. 2011 Jul 19;12:292. doi: 10.1186/1471-2105-12-292.

PMID:
21771321
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Fitting Boolean networks from steady state perturbation data.

Almudevar A, McCall MN, McMurray H, Land H.

Stat Appl Genet Mol Biol. 2011 Oct 5;10(1). pii: /j/sagmb.2011.10.issue-1/1544-6115.1727/1544-6115.1727.xml. doi: 10.2202/1544-6115.1727.

PMID:
23089817
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Reconstructing directed signed gene regulatory network from microarray data.

Qiu P, Plevritis SK.

IEEE Trans Biomed Eng. 2011 Dec;58(12):3518-21. doi: 10.1109/TBME.2011.2163188. Epub 2011 Jul 29.

PMID:
21803675
[PubMed - indexed for MEDLINE]
10.

Analysis of combinatorial regulation: scaling of partnerships between regulators with the number of governed targets.

Bhardwaj N, Carson MB, Abyzov A, Yan KK, Lu H, Gerstein MB.

PLoS Comput Biol. 2010 May 27;6(5):e1000755. doi: 10.1371/journal.pcbi.1000755.

PMID:
20523742
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
20030818
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Improvements in the reconstruction of time-varying gene regulatory networks: dynamic programming and regularization by information sharing among genes.

Grzegorczyk M, Husmeier D.

Bioinformatics. 2011 Mar 1;27(5):693-9. doi: 10.1093/bioinformatics/btq711. Epub 2010 Dec 21.

PMID:
21177328
[PubMed - indexed for MEDLINE]
Free Article
13.

A duplication growth model of gene expression networks.

Bhan A, Galas DJ, Dewey TG.

Bioinformatics. 2002 Nov;18(11):1486-93.

PMID:
12424120
[PubMed - indexed for MEDLINE]
Free Article
14.

A new multiple regression approach for the construction of genetic regulatory networks.

Zhang SQ, Ching WK, Tsing NK, Leung HY, Guo D.

Artif Intell Med. 2010 Feb-Mar;48(2-3):153-60. doi: 10.1016/j.artmed.2009.11.001. Epub 2009 Dec 5.

PMID:
19963359
[PubMed - indexed for MEDLINE]
15.

A scale-free structure prior for graphical models with applications in functional genomics.

Sheridan P, Kamimura T, Shimodaira H.

PLoS One. 2010 Nov 5;5(11):e13580. doi: 10.1371/journal.pone.0013580.

PMID:
21079769
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Identification of genetic network dynamics with unate structure.

Porreca R, Cinquemani E, Lygeros J, Ferrari-Trecate G.

Bioinformatics. 2010 May 1;26(9):1239-45. doi: 10.1093/bioinformatics/btq120. Epub 2010 Mar 19.

PMID:
20305266
[PubMed - indexed for MEDLINE]
Free Article
17.

Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle.

Wu WS, Li WH, Chen BS.

BMC Bioinformatics. 2006 Sep 29;7:421.

PMID:
17010188
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge.

Geier F, Timmer J, Fleck C.

BMC Syst Biol. 2007 Feb 2;1:11.

PMID:
17408501
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context.

Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A.

BMC Bioinformatics. 2006 Mar 20;7 Suppl 1:S7.

PMID:
16723010
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

PMID:
24669835
[PubMed - indexed for MEDLINE]
Free PMC Article
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