Graph-based analysis and visualization of experimental results with ONDEX.

Köhler J, Baumbach J, Taubert J, Specht M, Skusa A, Rueegg A, Rawlings C, Verrier P, Philippi S (2006)
Bioinformatics 22(11): 1383-1390.

Journal Article | Published | English

No fulltext has been uploaded

Author
; ; ; ; ; ; ; ;
Publishing Year
ISSN
eISSN
PUB-ID

Cite this

Köhler J, Baumbach J, Taubert J, et al. Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics. 2006;22(11):1383-1390.
Köhler, J., Baumbach, J., Taubert, J., Specht, M., Skusa, A., Rueegg, A., Rawlings, C., et al. (2006). Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics, 22(11), 1383-1390.
Köhler, J., Baumbach, J., Taubert, J., Specht, M., Skusa, A., Rueegg, A., Rawlings, C., Verrier, P., and Philippi, S. (2006). Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics 22, 1383-1390.
Köhler, J., et al., 2006. Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics, 22(11), p 1383-1390.
J. Köhler, et al., “Graph-based analysis and visualization of experimental results with ONDEX.”, Bioinformatics, vol. 22, 2006, pp. 1383-1390.
Köhler, J., Baumbach, J., Taubert, J., Specht, M., Skusa, A., Rueegg, A., Rawlings, C., Verrier, P., Philippi, S.: Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics. 22, 1383-1390 (2006).
Köhler, J., Baumbach, J., Taubert, J., Specht, M., Skusa, Andre, Rueegg, Alexander, Rawlings, Chris, Verrier, Paul, and Philippi, Stephan. “Graph-based analysis and visualization of experimental results with ONDEX.”. Bioinformatics 22.11 (2006): 1383-1390.
This data publication is cited in the following publications:
This publication cites the following data publications:

59 Citations in Europe PMC

Data provided by Europe PubMed Central.

Representing and querying disease networks using graph databases.
Lysenko A, Roznovat IA, Saqi M, Mazein A, Rawlings CJ, Auffray C., BioData Min 9(), 2016
PMID: 27462371
Data integration in biological research: an overview.
Lapatas V, Stefanidakis M, Jimenez RC, Via A, Schneider MV., J Biol Res (Thessalon) 22(1), 2015
PMID: 26336651
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 4(), 2015
PMID: 26309733
Ondex Web: web-based visualization and exploration of heterogeneous biological networks.
Taubert J, Hassani-Pak K, Castells-Brooke N, Rawlings CJ., Bioinformatics 30(7), 2014
PMID: 24363379
Network-based data integration for selecting candidate virulence associated proteins in the cereal infecting fungus Fusarium graminearum.
Lysenko A, Urban M, Bennett L, Tsoka S, Janowska-Sejda E, Rawlings CJ, Hammond-Kosack KE, Saqi M., PLoS ONE 8(7), 2013
PMID: 23861834
Connecting the dots between PubMed abstracts.
Hossain MS, Gresock J, Edmonds Y, Helm R, Potts M, Ramakrishnan N., PLoS ONE 7(1), 2012
PMID: 22235301
Comparative microbial modules resource: generation and visualization of multi-species biclusters.
Kacmarczyk T, Waltman P, Bate A, Eichenberger P, Bonneau R., PLoS Comput. Biol. 7(12), 2011
PMID: 22144874
Customizable views on semantically integrated networks for systems biology.
Weile J, Pocock M, Cockell SJ, Lord P, Dewar JM, Holstein EM, Wilkinson D, Lydall D, Hallinan J, Wipat A., Bioinformatics 27(9), 2011
PMID: 21414991
Challenges in integrating Escherichia coli molecular biology data.
Lourenco A, Carneiro S, Rocha M, Ferreira EC, Rocha I., Brief. Bioinformatics 12(2), 2011
PMID: 21059604

21 References

Data provided by Europe PubMed Central.

Genomic Object Net: II. Modelling biopathways by hybrid functional Petri net with extension.
Doi A, Nagasaki M, Fujita S, Matsuno H, Miyano S., Appl. Bioinformatics 2(3), 2003
PMID: 15130807

durand, current opinion in drug discovery & development 6(3), 2003

AUTHOR UNKNOWN, in silico biology 5(), 2004

AUTHOR UNKNOWN, bspp newsl 42(), 2002
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons.
Remm M, Storm CE, Sonnhammer EL., J. Mol. Biol. 314(5), 2001
PMID: 11743721
KEGG: kyoto encyclopedia of genes and genomes.
Kanehisa M, Goto S., Nucleic Acids Res. 28(1), 2000
PMID: 10592173
PatternHunter: faster and more sensitive homology search.
Ma B, Tromp J, Li M., Bioinformatics 18(3), 2002
PMID: 11934743
Data integration and visualization system for enabling conceptual biology.
Gopalacharyulu PV, Lindfors E, Bounsaythip C, Kivioja T, Yetukuri L, Hollmen J, Oresic M., Bioinformatics 21 Suppl 1(), 2005
PMID: 15961455
PHI-base: a new database for pathogen host interactions.
Winnenburg R, Baldwin TK, Urban M, Rawlings C, Kohler J, Hammond-Kosack KE., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381911
PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways.
Demir E, Babur O, Dogrusoz U, Gursoy A, Nisanci G, Cetin-Atalay R, Ozturk M., Bioinformatics 18(7), 2002
PMID: 12117798
Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress.
Kreps JA, Wu Y, Chang HS, Zhu T, Wang X, Harper JF., Plant Physiol. 130(4), 2002
PMID: 12481097
Osprey: a network visualization system.
Breitkreutz BJ, Stark C, Tyers M., Genome Biol. 4(3), 2003
PMID: 12620107
Integrating biological databases.
Stein LD., Nat. Rev. Genet. 4(5), 2003
PMID: 12728276
AraCyc: a biochemical pathway database for Arabidopsis.
Mueller LA, Zhang P, Rhee SY., Plant Physiol. 132(2), 2003
PMID: 12805578
Pathway studio--the analysis and navigation of molecular networks.
Nikitin A, Egorov S, Daraselia N, Mazo I., Bioinformatics 19(16), 2003
PMID: 14594725
Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T., Genome Res. 13(11), 2003
PMID: 14597658
BRENDA, the enzyme database: updates and major new developments.
Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D., Nucleic Acids Res. 32(Database issue), 2004
PMID: 14681450
MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes.
Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P, Selbig J, Muller LA, Rhee SY, Stitt M., Plant J. 37(6), 2004
PMID: 14996223
Integration of life science databases
KOHLER, Drug Discovery Today BIOSILICO 2(2), 2004
Microarray analysis of nitric oxide responsive transcripts in Arabidopsis.
Parani M, Rudrabhatla S, Myers R, Weirich H, Smith B, Leaman DW, Goldman SL., Plant Biotechnol. J. 2(4), 2004
PMID: 17134397

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 16533819
PubMed | Europe PMC

Search this title in

Google Scholar