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Results: 1 to 20 of 97

1.

Gene regulatory networks in plants: learning causality from time and perturbation.

Krouk G, Lingeman J, Colon AM, Coruzzi G, Shasha D.

Genome Biol. 2013 Jun 27;14(6):123. doi: 10.1186/gb-2013-14-6-123.

PMID:
23805876
[PubMed - in process]
Free PMC Article
2.

Inferring gene networks from steady-state response to single-gene perturbations.

Brazhnik P.

J Theor Biol. 2005 Dec 21;237(4):427-40. Epub 2005 Jun 22.

PMID:
15975609
[PubMed - indexed for MEDLINE]
3.

Gradient descent optimization in gene regulatory pathways.

Das M, Mukhopadhyay S, De RK.

PLoS One. 2010 Sep 3;5(9):e12475. doi: 10.1371/journal.pone.0012475.

PMID:
20838430
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Inference of gene regulatory networks with sparse structural equation models exploiting genetic perturbations.

Cai X, Bazerque JA, Giannakis GB.

PLoS Comput Biol. 2013;9(5):e1003068. doi: 10.1371/journal.pcbi.1003068. Epub 2013 May 23.

PMID:
23717196
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Learning gene networks under SNP perturbations using eQTL datasets.

Zhang L, Kim S.

PLoS Comput Biol. 2014 Feb 27;10(2):e1003420. doi: 10.1371/journal.pcbi.1003420. eCollection 2014 Feb. Erratum in: PLoS Comput Biol. 2014 Apr;10(4):e1003608.

PMID:
24586125
[PubMed - in process]
Free PMC Article
6.

Autoregressive models for gene regulatory network inference: sparsity, stability and causality issues.

Michailidis G, d'Alché-Buc F.

Math Biosci. 2013 Dec;246(2):326-34. doi: 10.1016/j.mbs.2013.10.003. Epub 2013 Oct 28. Review.

PMID:
24176667
[PubMed - indexed for MEDLINE]
7.

Identifying interactions in the time and frequency domains in local and global networks - A Granger Causality Approach.

Zou C, Ladroue C, Guo S, Feng J.

BMC Bioinformatics. 2010 Jun 21;11:337. doi: 10.1186/1471-2105-11-337.

PMID:
20565962
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Computational and experimental approaches for modeling gene regulatory networks.

Goutsias J, Lee NH.

Curr Pharm Des. 2007;13(14):1415-36. Review.

PMID:
17504165
[PubMed - indexed for MEDLINE]
9.

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.

PMID:
23924435
[PubMed - indexed for MEDLINE]
Free Article
10.

Moving toward a system genetics view of disease.

Sieberts SK, Schadt EE.

Mamm Genome. 2007 Jul;18(6-7):389-401. Epub 2007 Jul 26. Review.

PMID:
17653589
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Editorial: protein systems biology: method, regulation, and network.

Chen Q, Chen M.

Curr Protein Pept Sci. 2014;15(6):519-21.

PMID:
25135673
[PubMed - in process]
12.

Predicting genetic regulatory response using classification.

Middendorf M, Kundaje A, Wiggins C, Freund Y, Leslie C.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i232-40.

PMID:
15262804
[PubMed - indexed for MEDLINE]
Free Article
13.

On the processing of metabolic information through metabolite-gene communication networks: an approach for modelling causality.

Szymanski J, Bielecka M, Carrari F, Fernie AR, Hoefgen R, Nikiforova VJ.

Phytochemistry. 2007 Aug-Sep;68(16-18):2163-75. Epub 2007 Jun 4.

PMID:
17544461
[PubMed - indexed for MEDLINE]
14.

Inferring microRNA-mRNA causal regulatory relationships from expression data.

Le TD, Liu L, Tsykin A, Goodall GJ, Liu B, Sun BY, Li J.

Bioinformatics. 2013 Mar 15;29(6):765-71. doi: 10.1093/bioinformatics/btt048. Epub 2013 Jan 30.

PMID:
23365408
[PubMed - indexed for MEDLINE]
Free Article
15.

Gene perturbation and intervention in probabilistic Boolean networks.

Shmulevich I, Dougherty ER, Zhang W.

Bioinformatics. 2002 Oct;18(10):1319-31.

PMID:
12376376
[PubMed - indexed for MEDLINE]
Free Article
16.

M-matrix-based stability conditions for genetic regulatory networks with time-varying delays and noise perturbations.

Tian LP, Shi ZK, Liu LZ, Wu FX.

IET Syst Biol. 2013 Oct;7(5):214-22. doi: 10.1049/iet-syb.2012.0051.

PMID:
24067422
[PubMed - indexed for MEDLINE]
17.

Using stochastic causal trees to augment Bayesian networks for modeling eQTL datasets.

Chipman KC, Singh AK.

BMC Bioinformatics. 2011 Jan 6;12:7. doi: 10.1186/1471-2105-12-7.

PMID:
21211042
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Construction of regulatory networks using expression time-series data of a genotyped population.

Yeung KY, Dombek KM, Lo K, Mittler JE, Zhu J, Schadt EE, Bumgarner RE, Raftery AE.

Proc Natl Acad Sci U S A. 2011 Nov 29;108(48):19436-41. doi: 10.1073/pnas.1116442108. Epub 2011 Nov 14.

PMID:
22084118
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Organization principles in genetic interaction networks.

Jacobs C, Segrè D.

Adv Exp Med Biol. 2012;751:53-78. doi: 10.1007/978-1-4614-3567-9_3. Review.

PMID:
22821453
[PubMed - indexed for MEDLINE]
20.

Back to the biology in systems biology: what can we learn from biomolecular networks?

Huang S.

Brief Funct Genomic Proteomic. 2004 Feb;2(4):279-97. Review.

PMID:
15163364
[PubMed - indexed for MEDLINE]
Free Article

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