PathBLAST Publications

Publication Method Application
Kelley, B. P., Sharan, R., Karp, R., Sittler, E. T., Root, D. E., Stockwell, B. R., and Ideker, T. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc Natl Acad Sci U S A 100, 11394-9 (2003). Original proof of concept. Identification of paths. Yeast vs. H. Pylori
Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data (with Trey Ideker, Brian Kelley, Ron Shamir and Richard Karp). Proceedings: RECOMB 2004, pp. 282-289; Journal: Journal of Computational Biology 12, pp. 835-846, 2005 Improved scoring and identification of protein complexes.  
Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks (with Jacob Scott, Trey Ideker and Richard Karp) Proceedings: RECOMB 2005, pp. 1-13. Improved scoring and identification of protein pathways.  
Kelley, B. P., Yuan, B., Lewitter, F., Sharan, R., Stockwell, B. R., and Ideker T. PathBLAST: a tool for alignment of protein interaction networks. Nucleic Acids Res.32(Web Server issue):W83-8. 2004 PathBLAST web server.  
Sharan, R., Suthram, S., Kelley, R. M., Kuhn, T., McCuine, S., Uetz, P., Sittler, T., Karp, R. M., and Ideker, T. Conserved patterns of protein interaction in multiple species. Proc Natl Acad Sci U S A. 8:102(6) 1974-79 (2005). 3-way alignments Yeast vs. Worm vs. Fly
Kelley, R. and Ideker, T. Systematic interpretation of genetic interactions using protein networks. Nature Biotechnology 23(5):561-566 (2005)   Yeast physical vs. genetic interpretation
The Plasmodium protein network diverges from those of other eukaryotes. Silpa Suthram, Taylor Sittler, Trey Ideker. Nature 438, 108-112 (03 Nov 2005)   Plasmodium vs. other eukaryotes