Visualization

Methods in Molecular Biology

Volumn 453, Issue , 2008, Pages 441-450

  Schreiber, Falk ^a,b  

^a LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

^b MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

Author keywords

Data exploration; Force directed layout; Graph drawing; Heatmaps; Visualization

Indexed keywords

EID: 84934442697     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-60327-429-6_23     Document Type: Article

References (30)

1. Tsai, C. S. (2003) Introduction to Computational Biochemistry. Wiley-Liss, New York.
2. Can, T., Wang, Y., Wang, Y.-F., et al. (2003) FPV: fast protein visualization using Java3D. Bioinformatics 19, 913-922.
3. Helt, G. A., Lewis, S., Loraine, A. E., et al. (1998) BioViews: Java-based tools for genomic data visualization. Genome Res 8, 291-305.
4. Kerkhoven, R., van Enckevort, F. H. J., Boekhorst, J., et al. (2004) Visualization for genomics: the microbial genome viewer. Bioinformatics 20, 1812-1814.
5. Andrews, D. F. (1972) Plots of highdimensional data. Biometrics 29, 125-136.
6. Inselberg, A., Dimsdale, B. (1990) Parallel coordinates: a tool for visualizing multidimensional geometry. Proc Visual '90, 361-370.
7. Eisen, M. B., Spellman, P. T., Brown, P. O., et al. (1998). Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95, 14863-14868.
8. Baehrecke, E. H., Dang, N., Babaria, K., et al. (2004) Visualization and analysis of microarray and gene ontology data with treemaps. BMC Bioinformatics 5, 84.
9. Hughes, T., Hyun, Y., Liberles, D. (2004) Visualising very large phylogenetic trees in three dimensional hyperbolic space. BMC Bioinformatics 5, 48.
10. Rost U., Bornberg-Bauer, E. (2002) Tree-Wiz: interactive exploration of huge trees. Bioinformatics 18, 109-114.
11. Schreiber, F. (1992) High quality visualization of biochemical pathways in BioPath. In Silico Biol 2, 59-73.
12. Sirava, M., Schäfer, T., Eiglsperger, M., et al. (2002) BioMiner: modeling, analyzing, and visualizing biochemical pathways and networks. Bioinformatics 18, S219-S230.
13. Molw PDB Viewer 4.0. http://www.cris.com/̃Molimage/.
14. Junker, B. H., Klukas, C., Schreiber, F. (2006) VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics 7, 109.
15. Forster, M., Pick, A., Raitner, M., et al. (2002) The System Architecture of the BioPath system. In Silico Biol 2, 415-426.
16. Duggan, D., Bittner, B., Chen, Y., et al. (1999) Expression profiling using cDNA microarrays. Nat Genet 21, 11-19.
17. MacBeath, G. (2002) Protein microarrays and proteomics. Nat Genet 32, 526-532.
18. Villas-Boas, S. G., Mas, S., Akesson, M., et al. (2005) Mass spectrometry in metabolome analysis. Mass Spectrom Rev 24, 613-646.
19. R. http://www.r-project.org/.
20. Ito, T., Chiba, T., Ozawa, R., et al. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc Natl Acad Sci U S A 98, 4569-4574.
21. CentiBin. http://centibin.ipk-gatersleben.de/.
22. Bar-Joseph, Z., Gifford, D. K., Jaakkola, T. S. (2001) Fast optimal leaf ordering for hierarchical clustering. Bioinformatics 17, S22-S29.
23. Biedl, T., Brejová, B., Demaine, E. D., et al. (2001) Optimal arrangement of leaves in the tree representing hierarchical clustering of gene expression data. Technical report 2001-14, Dept. of Computer Science, University of Waterloo.
24. Di Battista, G., Eades, P., Tamassia, R., et al. (1999) Graph Drawing. Prentice-Hall, Upper Saddle River, New Jersey.
25. Eades, P. (1984) A heuristic for graph drawing. Congressus Numerantium 42, 149-160.
26. Fruchterman, T., Reingold, E. (1991) Graph drawing by force-directed placement. Software Pract Exper 21, 1129-1164.
27. Kamada, T., Kawai, S. (1989) An algorithm for drawing general undirected graphs. Inf Proc Letts 31, 7-15.
28. Sugiyama, K., Misue, K. (1995) Graph drawing by magnetic spring model. J Vis Lang Comput 6, 217-231.
29. JUNG. http://jung.sourceforge.net/.
30. Gravisto. http://www.gravisto.org/.