Three-dimensional visualization of protein interaction networks

Computers in Biology and Medicine

Volumn 34, Issue 2, 2004, Pages 127-139

  Han, Kyungsook ^a   Byun, Yanga ^a  

^a Inha University   (South Korea)

Author keywords

Graph layout; Protein protein interactions; Visualization

Indexed keywords

ALGORITHMS; BIOMEDICAL ENGINEERING; GRAPH THEORY; MATHEMATICAL MODELS; VISUALIZATION;

PROTEIN INTERACTION NETWORKS; TERMINAL NODES;

PROTEINS;

ALGORITHM; ARTICLE; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN INTERACTION; THREE DIMENSIONAL IMAGING;

EID: 1242338032     PISSN: 00104825     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0010-4825(03)00045-3     Document Type: Article

References (12)

1. Ito T., Tashiro K., Muta S., Ozawa R., Chiba T., Nishizawa M., Yamamoto K., Kuhara S., Sakaki Y. Toward a protein-protein interaction network of the budding yeast. a comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins Proc. Natl. Acad. Sci. USA. 97(3):2000;1143-1147.
2. Uetz P., Giot L., Cagney G.et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 403:2000;623-627.
3. Park J., Lappe M., Teichmann S.A. Mapping protein family interactions. intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast J. Mol. Biol. 307:2001;929-938.
4. Xenarios I., Fernandez E., Salwinski L., Duan X.J., Thompson M.J., Marcotte E.M., Eisenberg D. DIP: the database of interacting proteins: 2001 update. Nucleic Acids Res. 29(1):2001;239-241.
5. Schwikowski B., Uetz P., Fields S. A network of protein-protein interactions in yeast. Nat. Biotechnol. 18(12):2000;1257-1261.
6. Tucker C.L., Gera J.F., Uetz P. Towards an understanding of complex protein networks. Trends Cell Biol. 11(3):2001;102-106.
7. Mrowka R. A java applet for visualizing protein-protein interaction. Bioinformatics. 17(7):2001;669-670.
8. Gavin A.-C., Bosche M., Krause R.et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 415(6868):2002;141-147.
9. Kamada T., Kawai S. An algorithm for drawing general undirected graphs. Inform. Process. Lett. 31:1989;7-15.
10. M. Himsolt, GML: graph modeling language, http://www.uni-passau.de/ Graphlet/GML , 1997.
11. Batagelj V., Mrvar A. Pajek - analysis and visualization of large networks. Lecture Notes Comput. Sci. 2265:2001;477-478.
12. Fruchterman T.M.J., Reingold E.M. Graph drawing by force-directed placement. Software-Practice Experience. 21(11):1991;1129-1164 Kyungsook Han received the B.S. degree from Seoul National University in 1983, the M.S. degree in computer science from KAIST in 1985, another M.S. degree in computer science from the University of Minnesota at Minneapolis in 1989, and the Ph.D. degree in computer science from Rutgers - the State University of New Jersey at New Brunswick in 1994. She is an associate professor of computer science at Inha University, where she teaches and conducts research in the area of computer graphics and bioinformatics. Her research interests include visualization of biological data, particularly visualization of protein interaction networks and RNA structures. Yanga Byun is currently an undergraduate student in automation engineering at Inha University. For the past 2 years, she has participated in research projects led by Professor Han. Her research interests include visualization of protein interaction networks and RNA structures, and graph drawing in general.