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Items: 1 to 20 of 85

1.

A survey of visualization tools for biological network analysis.

Pavlopoulos GA, Wegener AL, Schneider R.

BioData Min. 2008 Nov 28;1:12. doi: 10.1186/1756-0381-1-12.

2.

A reference guide for tree analysis and visualization.

Pavlopoulos GA, Soldatos TG, Barbosa-Silva A, Schneider R.

BioData Min. 2010 Feb 22;3(1):1. doi: 10.1186/1756-0381-3-1.

3.

Graphle: Interactive exploration of large, dense graphs.

Huttenhower C, Mehmood SO, Troyanskaya OG.

BMC Bioinformatics. 2009 Dec 14;10:417. doi: 10.1186/1471-2105-10-417.

4.

ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining.

Huan T, Sivachenko AY, Harrison SH, Chen JY.

BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S5. doi: 10.1186/1471-2105-9-S9-S5.

5.

Linking Cytoscape and the corynebacterial reference database CoryneRegNet.

Baumbach J, Apeltsin L.

BMC Genomics. 2008 Apr 21;9:184. doi: 10.1186/1471-2164-9-184.

6.

In situ exploration of large dynamic networks.

Hadlak S, Schulz HJ, Schumann H.

IEEE Trans Vis Comput Graph. 2011 Dec;17(12):2334-43. doi: 10.1109/TVCG.2011.213.

PMID:
22034354
7.

Cytoscape: software for visualization and analysis of biological networks.

Kohl M, Wiese S, Warscheid B.

Methods Mol Biol. 2011;696:291-303. doi: 10.1007/978-1-60761-987-1_18.

PMID:
21063955
8.

BisoGenet: a new tool for gene network building, visualization and analysis.

Martin A, Ochagavia ME, Rabasa LC, Miranda J, Fernandez-de-Cossio J, Bringas R.

BMC Bioinformatics. 2010 Feb 17;11:91. doi: 10.1186/1471-2105-11-91.

9.

BioGraphE: high-performance bionetwork analysis using the Biological Graph Environment.

Chin G Jr, Chavarria DG, Nakamura GC, Sofia HJ.

BMC Bioinformatics. 2008 May 28;9 Suppl 6:S6. doi: 10.1186/1471-2105-9-S6-S6.

10.

MGV: a generic graph viewer for comparative omics data.

Symons S, Nieselt K.

Bioinformatics. 2011 Aug 15;27(16):2248-55. doi: 10.1093/bioinformatics/btr351.

PMID:
21666268
11.

Medusa: A tool for exploring and clustering biological networks.

Pavlopoulos GA, Hooper SD, Sifrim A, Schneider R, Aerts J.

BMC Res Notes. 2011 Oct 6;4:384. doi: 10.1186/1756-0500-4-384.

12.

Key-Node-Separated Graph Clustering and Layouts for Human Relationship Graph Visualization.

Itoh T, Klein K.

IEEE Comput Graph Appl. 2015 Nov-Dec;35(6):30-40. doi: 10.1109/MCG.2015.115.

PMID:
26415161
13.

Clust&See: a Cytoscape plugin for the identification, visualization and manipulation of network clusters.

Spinelli L, Gambette P, Chapple CE, Robisson B, Baudot A, Garreta H, Tichit L, Guénoche A, Brun C.

Biosystems. 2013 Aug;113(2):91-5. doi: 10.1016/j.biosystems.2013.05.010.

14.

VirtualPlant: a software platform to support systems biology research.

Katari MS, Nowicki SD, Aceituno FF, Nero D, Kelfer J, Thompson LP, Cabello JM, Davidson RS, Goldberg AP, Shasha DE, Coruzzi GM, Gutiérrez RA.

Plant Physiol. 2010 Feb;152(2):500-15. doi: 10.1104/pp.109.147025.

15.

A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data.

Bhadra S, Bhattacharyya C, Chandra NR, Mian IS.

Algorithms Mol Biol. 2009 Feb 24;4:5. doi: 10.1186/1748-7188-4-5.

16.

CytoITMprobe: a network information flow plugin for Cytoscape.

Stojmirović A, Bliskovsky A, Yu YK.

BMC Res Notes. 2012 May 15;5:237. doi: 10.1186/1756-0500-5-237.

17.

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.

Pavlopoulos GA, Malliarakis D, Papanikolaou N, Theodosiou T, Enright AJ, Iliopoulos I.

Gigascience. 2015 Aug 25;4:38. doi: 10.1186/s13742-015-0077-2. Review.

18.

Visualization and analytics tools for infectious disease epidemiology: a systematic review.

Carroll LN, Au AP, Detwiler LT, Fu TC, Painter IS, Abernethy NF.

J Biomed Inform. 2014 Oct;51:287-98. doi: 10.1016/j.jbi.2014.04.006. Review.

19.

Generalized lattice graphs for 2D-visualization of biological information.

González-Díaz H, Pérez-Montoto LG, Duardo-Sanchez A, Paniagua E, Vázquez-Prieto S, Vilas R, Dea-Ayuela MA, Bolas-Fernández F, Munteanu CR, Dorado J, Costas J, Ubeira FM.

J Theor Biol. 2009 Nov 7;261(1):136-47. doi: 10.1016/j.jtbi.2009.07.029.

PMID:
19646452
20.

A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila.

Pacifico S, Liu G, Guest S, Parrish JR, Fotouhi F, Finley RL Jr.

BMC Bioinformatics. 2006 Apr 7;7:195.

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