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Items: 1 to 20 of 125

1.

Inferring latent gene regulatory network kinetics.

González J, Vujačić I, Wit E.

Stat Appl Genet Mol Biol. 2013 Mar 26;12(1):109-27. doi: 10.1515/sagmb-2012-0006.

PMID:
23744300
2.

Inferring microRNA and transcription factor regulatory networks in heterogeneous data.

Le TD, Liu L, Liu B, Tsykin A, Goodall GJ, Satou K, Li J.

BMC Bioinformatics. 2013 Mar 11;14:92. doi: 10.1186/1471-2105-14-92.

3.

Inference of gene regulatory networks incorporating multi-source biological knowledge via a state space model with L1 regularization.

Hasegawa T, Yamaguchi R, Nagasaki M, Miyano S, Imoto S.

PLoS One. 2014 Aug 27;9(8):e105942. doi: 10.1371/journal.pone.0105942. eCollection 2014.

4.

A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data.

Thomas R, Paredes CJ, Mehrotra S, Hatzimanikatis V, Papoutsakis ET.

BMC Bioinformatics. 2007 Jun 29;8:228.

5.

Statistical reconstruction of transcription factor activity using Michaelis-Menten kinetics.

Khanin R, Vinciotti V, Mersinias V, Smith CP, Wit E.

Biometrics. 2007 Sep;63(3):816-23.

PMID:
17825013
6.

Estimating dynamic models for gene regulation networks.

Cao J, Zhao H.

Bioinformatics. 2008 Jul 15;24(14):1619-24. doi: 10.1093/bioinformatics/btn246. Epub 2008 May 27.

7.

Reconstruction of transcriptional network from microarray data using combined mutual information and network-assisted regression.

Wang XD, Qi YX, Jiang ZL.

IET Syst Biol. 2011 Mar;5(2):95-102. doi: 10.1049/iet-syb.2010.0041.

PMID:
21405197
8.

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.

9.

Identification of biochemical networks by S-tree based genetic programming.

Cho DY, Cho KH, Zhang BT.

Bioinformatics. 2006 Jul 1;22(13):1631-40. Epub 2006 Apr 3.

10.

Modeling gene regulation networks using ordinary differential equations.

Cao J, Qi X, Zhao H.

Methods Mol Biol. 2012;802:185-97. doi: 10.1007/978-1-61779-400-1_12.

PMID:
22130881
11.

Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities.

Fu Y, Jarboe LR, Dickerson JA.

BMC Bioinformatics. 2011 Jun 13;12:233. doi: 10.1186/1471-2105-12-233.

12.

Trimming of mammalian transcriptional networks using network component analysis.

Tran LM, Hyduke DR, Liao JC.

BMC Bioinformatics. 2010 Oct 13;11:511. doi: 10.1186/1471-2105-11-511.

13.

Modeling gene expression regulatory networks with the sparse vector autoregressive model.

Fujita A, Sato JR, Garay-Malpartida HM, Yamaguchi R, Miyano S, Sogayar MC, Ferreira CE.

BMC Syst Biol. 2007 Aug 30;1:39.

14.

Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli.

Wang RS, Jin G, Zhang XS, Chen L.

BMC Bioinformatics. 2009 Apr 29;10 Suppl 4:S6. doi: 10.1186/1471-2105-10-S4-S6.

15.

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.

16.

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.

17.

Transcriptional regulatory networks via gene ontology and expression data.

Tuncay K, Ensman L, Sun J, Haidar AA, Stanley F, Trelinski M, Ortoleva P.

In Silico Biol. 2007;7(1):21-34.

PMID:
17688426
18.

Reverse engineering gene regulatory network from microarray data using linear time-variant model.

Kabir M, Noman N, Iba H.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S56. doi: 10.1186/1471-2105-11-S1-S56.

19.

Weighted-LASSO for structured network inference from time course data.

Charbonnier C, Chiquet J, Ambroise C.

Stat Appl Genet Mol Biol. 2010;9:Article 15. doi: 10.2202/1544-6115.1519. Epub 2010 Feb 1.

PMID:
20196750
20.

Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics.

Ronen M, Rosenberg R, Shraiman BI, Alon U.

Proc Natl Acad Sci U S A. 2002 Aug 6;99(16):10555-60. Epub 2002 Jul 26.

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