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Items: 1 to 20 of 106

1.

FragViz: visualization of fragmented networks.

Stajdohar M, Mramor M, Zupan B, Demšar J.

BMC Bioinformatics. 2010 Sep 22;11:475. doi: 10.1186/1471-2105-11-475.

2.

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.

3.

A generic algorithm for layout of biological networks.

Schreiber F, Dwyer T, Marriott K, Wybrow M.

BMC Bioinformatics. 2009 Nov 12;10:375. doi: 10.1186/1471-2105-10-375.

4.

DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts.

Czerwinska U, Calzone L, Barillot E, Zinovyev A.

BMC Syst Biol. 2015 Aug 14;9:46. doi: 10.1186/s12918-015-0189-4.

5.

LucidDraw: efficiently visualizing complex biochemical networks within MATLAB.

He S, Mei J, Shi G, Wang Z, Li W.

BMC Bioinformatics. 2010 Jan 15;11:31. doi: 10.1186/1471-2105-11-31.

6.

Inference of dynamic networks using time-course data.

Kim Y, Han S, Choi S, Hwang D.

Brief Bioinform. 2014 Mar;15(2):212-28. doi: 10.1093/bib/bbt028. Epub 2013 May 21. Review.

PMID:
23698724
7.

NAIL, a software toolset for inferring, analyzing and visualizing regulatory networks.

Hurley DG, Cursons J, Wang YK, Budden DM, Print CG, Crampin EJ.

Bioinformatics. 2015 Jan 15;31(2):277-8. doi: 10.1093/bioinformatics/btu612. Epub 2014 Sep 21. Erratum in: Bioinformatics. 2015 Jul 1;31(13):2015-240.

PMID:
25246431
8.

Disease gene prioritization by integrating tissue-specific molecular networks using a robust multi-network model.

Ni J, Koyuturk M, Tong H, Haines J, Xu R, Zhang X.

BMC Bioinformatics. 2016 Nov 10;17(1):453.

9.

HOLA: Human-like Orthogonal Network Layout.

Kieffer S, Dwyer T, Marriott K, Wybrow M.

IEEE Trans Vis Comput Graph. 2016 Jan;22(1):349-58. doi: 10.1109/TVCG.2015.2467451. Epub 2015 Aug 12.

PMID:
26390483
10.

Improving gene regulatory network inference using network topology information.

Nair A, Chetty M, Wangikar PP.

Mol Biosyst. 2015 Sep;11(9):2449-63. doi: 10.1039/c5mb00122f. Epub 2015 Jul 1.

PMID:
26126758
11.

Designing a parallel evolutionary algorithm for inferring gene networks on the cloud computing environment.

Lee WP, Hsiao YT, Hwang WC.

BMC Syst Biol. 2014 Jan 16;8:5. doi: 10.1186/1752-0509-8-5.

12.

GeneNet Toolbox for MATLAB: a flexible platform for the analysis of gene connectivity in biological networks.

Taylor A, Steinberg J, Andrews TS, Webber C.

Bioinformatics. 2015 Feb 1;31(3):442-4. doi: 10.1093/bioinformatics/btu669. Epub 2014 Oct 14.

13.

MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization.

Blum T, Kohlbacher O.

Bioinformatics. 2008 Sep 15;24(18):2108-9. doi: 10.1093/bioinformatics/btn360. Epub 2008 Jul 16.

14.

SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks.

Westenberg MA, Roerdink JB, Kuipers OP, van Hijum SA.

Bioinformatics. 2010 Nov 15;26(22):2922-3. doi: 10.1093/bioinformatics/btq535. Epub 2010 Sep 21.

15.

Bridge and brick network motifs: identifying significant building blocks from complex biological systems.

Huang CY, Cheng CY, Sun CT.

Artif Intell Med. 2007 Oct;41(2):117-27. Epub 2007 Sep 7.

PMID:
17825540
16.

MOVE: a multi-level ontology-based visualization and exploration framework for genomic networks.

Bosman DW, Blom EJ, Ogao PJ, Kuipers OP, Roerdink JB.

In Silico Biol. 2007;7(1):35-59.

PMID:
17688427
17.

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.

18.

OptFlux: an open-source software platform for in silico metabolic engineering.

Rocha I, Maia P, Evangelista P, Vilaça P, Soares S, Pinto JP, Nielsen J, Patil KR, Ferreira EC, Rocha M.

BMC Syst Biol. 2010 Apr 19;4:45. doi: 10.1186/1752-0509-4-45.

19.

Inferring regulatory networks.

Li H, Xuan J, Wang Y, Zhan M.

Front Biosci. 2008 Jan 1;13:263-75. Review.

PMID:
17981545
20.

Igloo-Plot: a tool for visualization of multidimensional datasets.

Kuntal BK, Ghosh TS, Mande SS.

Genomics. 2014 Jan;103(1):11-20. doi: 10.1016/j.ygeno.2014.01.004. Epub 2014 Jan 17.

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