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Items: 1 to 20 of 226

1.

Metabolic constraint-based refinement of transcriptional regulatory networks.

Chandrasekaran S, Price ND.

PLoS Comput Biol. 2013;9(12):e1003370. doi: 10.1371/journal.pcbi.1003370. Epub 2013 Dec 5.

2.

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis.

Chandrasekaran S, Price ND.

Proc Natl Acad Sci U S A. 2010 Oct 12;107(41):17845-50. doi: 10.1073/pnas.1005139107. Epub 2010 Sep 27.

3.

Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p.

Moxley JF, Jewett MC, Antoniewicz MR, Villas-Boas SG, Alper H, Wheeler RT, Tong L, Hinnebusch AG, Ideker T, Nielsen J, Stephanopoulos G.

Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6477-82. doi: 10.1073/pnas.0811091106. Epub 2009 Apr 3.

4.

Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae.

Herrgård MJ, Lee BS, Portnoy V, Palsson BØ.

Genome Res. 2006 May;16(5):627-35. Epub 2006 Apr 10.

5.
6.

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.

7.

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.

8.

Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models.

Faria JP, Overbeek R, Xia F, Rocha M, Rocha I, Henry CS.

Brief Bioinform. 2014 Jul;15(4):592-611.

9.

An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models.

Barua D, Kim J, Reed JL.

PLoS Comput Biol. 2010 Oct 28;6(10):e1000970. doi: 10.1371/journal.pcbi.1000970.

10.

Gene expression network reconstruction by convex feature selection when incorporating genetic perturbations.

Logsdon BA, Mezey J.

PLoS Comput Biol. 2010 Dec 2;6(12):e1001014. doi: 10.1371/journal.pcbi.1001014.

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.

12.

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.

13.

Genome-level transcription data of Yersinia pestis analyzed with a new metabolic constraint-based approach.

Navid A, Almaas E.

BMC Syst Biol. 2012 Dec 6;6:150. doi: 10.1186/1752-0509-6-150.

14.

Identification of context-specific gene regulatory networks with GEMULA--gene expression modeling using LAsso.

Geeven G, van Kesteren RE, Smit AB, de Gunst MC.

Bioinformatics. 2012 Jan 15;28(2):214-21. doi: 10.1093/bioinformatics/btr641. Epub 2011 Nov 21.

15.
16.

Methods to reconstruct and compare transcriptional regulatory networks.

Babu MM, Lang B, Aravind L.

Methods Mol Biol. 2009;541:163-80. doi: 10.1007/978-1-59745-243-4_8. Review.

PMID:
19381525
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.

Inferring transcriptional gene regulation network of starch metabolism in Arabidopsis thaliana leaves using graphical Gaussian model.

Ingkasuwan P, Netrphan S, Prasitwattanaseree S, Tanticharoen M, Bhumiratana S, Meechai A, Chaijaruwanich J, Takahashi H, Cheevadhanarak S.

BMC Syst Biol. 2012 Aug 16;6:100. doi: 10.1186/1752-0509-6-100.

19.

TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks.

Jensen PA, Lutz KA, Papin JA.

BMC Syst Biol. 2011 Sep 23;5:147. doi: 10.1186/1752-0509-5-147.

20.

Identifying functional gene regulatory network phenotypes underlying single cell transcriptional variability.

Park J, Ogunnaike B, Schwaber J, Vadigepalli R.

Prog Biophys Mol Biol. 2015 Jan;117(1):87-98. doi: 10.1016/j.pbiomolbio.2014.11.004. Epub 2014 Nov 27.

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