| 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. | |
| Effcient 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 |