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Items: 1 to 20 of 183

1.

rBiopaxParser--an R package to parse, modify and visualize BioPAX data.

Kramer F, Bayerlová M, Klemm F, Bleckmann A, Beissbarth T.

Bioinformatics. 2013 Feb 15;29(4):520-2. doi: 10.1093/bioinformatics/bts710.

2.

BioPAX support in CellDesigner.

Mi H, Muruganujan A, Demir E, Matsuoka Y, Funahashi A, Kitano H, Thomas PD.

Bioinformatics. 2011 Dec 15;27(24):3437-8. doi: 10.1093/bioinformatics/btr586.

3.

Building pathway graphs from BioPAX data in R.

Benis N, Schokker D, Kramer F, Smits MA, Suarez-Diez M.

Version 2. F1000Res. 2016 Sep 28 [revised 2016 Jan 1];5:2414.

4.

cPath: open source software for collecting, storing, and querying biological pathways.

Cerami EG, Bader GD, Gross BE, Sander C.

BMC Bioinformatics. 2006 Nov 13;7:497.

5.

KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor.

Zhang JD, Wiemann S.

Bioinformatics. 2009 Jun 1;25(11):1470-1. doi: 10.1093/bioinformatics/btp167.

6.

Building pathway graphs from BioPAX data in R.

Benis N, Schokker D, Kramer F, Smits MA, Suarez-Diez M.

Version 1. F1000Res. 2016 Sep 28;5:2414.

PMID:
27990265
7.

ChiBE: interactive visualization and manipulation of BioPAX pathway models.

Babur O, Dogrusoz U, Demir E, Sander C.

Bioinformatics. 2010 Feb 1;26(3):429-31. doi: 10.1093/bioinformatics/btp665.

8.

VitaPad: visualization tools for the analysis of pathway data.

Holford M, Li N, Nadkarni P, Zhao H.

Bioinformatics. 2005 Apr 15;21(8):1596-602.

9.

BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks.

Zinovyev A, Viara E, Calzone L, Barillot E.

Bioinformatics. 2008 Mar 15;24(6):876-7.

10.

VISIBIOweb: visualization and layout services for BioPAX pathway models.

Dilek A, Belviranli ME, Dogrusoz U.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W150-4. doi: 10.1093/nar/gkq352.

11.

Pathview: an R/Bioconductor package for pathway-based data integration and visualization.

Luo W, Brouwer C.

Bioinformatics. 2013 Jul 15;29(14):1830-1. doi: 10.1093/bioinformatics/btt285.

12.

PAX of mind for pathway researchers.

Luciano JS.

Drug Discov Today. 2005 Jul 1;10(13):937-42. Review.

PMID:
15993813
13.
14.

Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX.

Strömbäck L, Lambrix P.

Bioinformatics. 2005 Dec 15;21(24):4401-7.

15.

synbreed: a framework for the analysis of genomic prediction data using R.

Wimmer V, Albrecht T, Auinger HJ, Schön CC.

Bioinformatics. 2012 Aug 1;28(15):2086-7. doi: 10.1093/bioinformatics/bts335.

16.

Atlas - a data warehouse for integrative bioinformatics.

Shah SP, Huang Y, Xu T, Yuen MM, Ling J, Ouellette BF.

BMC Bioinformatics. 2005 Feb 21;6:34.

17.

JUICE: a data management system that facilitates the analysis of large volumes of information in an EST project workflow.

Latorre M, Silva H, Saba J, Guziolowski C, Vizoso P, Martinez V, Maldonado J, Morales A, Caroca R, Cambiazo V, Campos-Vargas R, Gonzalez M, Orellana A, Retamales J, Meisel LA.

BMC Bioinformatics. 2006 Nov 23;7:513.

18.

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.

19.

An editor for pathway drawing and data visualization in the Biopathways Workbench.

Byrnes RW, Cotter D, Maer A, Li J, Nadeau D, Subramaniam S.

BMC Syst Biol. 2009 Oct 2;3:99. doi: 10.1186/1752-0509-3-99.

20.

BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats.

Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A.

BMC Syst Biol. 2013 Mar 1;7:18. doi: 10.1186/1752-0509-7-18.

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