Sat, 26 Jul 2008 16:58:34 BST CiteULike: AbnerCYH Segal http://www.citeulike.org/user/AbnerCYH/author/Segal CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/AbnerCYH/article/2580569 <i>BMC Bioinformatics, Vol. 7 (2006), 199.</i><br /><br />Background Sequence comparison is one of the most prominent tools in biological research, and is instrumental in studying gene function and evolution. The rapid development of high-throughput technologies for measuring protein interactions calls for extending this fundamental operation to the level of pathways in protein networks. Results We present a comprehensive framework for protein network searches using pathway queries. Given a linear query pathway and a network of interest, our algorithm, QPath, efficiently searches the network for homologous pathways, allowing both insertions and deletions of proteins in the identified pathways. Matched pathways are automatically scored according to their variation from the query pathway in terms of the protein insertions and deletions they employ, the sequence similarity of their constituent proteins to the query proteins, and the reliability of their constituent interactions. We applied QPath to systematically infer protein pathways in fly using an extensive collection of 271 putative pathways from yeast. QPath identified 69 conserved pathways whose members were both functionally enriched and coherently expressed. The resulting pathways tended to preserve the function of the original query pathways, allowing us to derive a first annotated map of conserved protein pathways in fly. Conclusion Pathway homology searches using QPath provide a powerful approach for identifying biologically significant pathways and inferring their function. The growing amounts of protein interactions in public databases underscore the importance of our network querying framework for mining protein network data. QPath: a method for querying pathways in a protein-protein interaction network Tomer Shlomi Daniel Segal Eytan Ruppin Roded Sharan doi:10.1186/1471-2105-7-199 BMC Bioinformatics, Vol. 7 (2006), 199. 2008-03-24T14:05:40-00:00 2006 BMC Bioinformatics 7 199 algorithms biology complex graph http://www.citeulike.org/user/AbnerCYH/article/1726165 <i>ACM Trans. Sen. Netw., Vol. 2, No. 3. (August 2006), pp. 444-453.</i> A simple improved distributed algorithm for minimum CDS in unit disk graphs Stefan Funke Alexander Kesselman Ulrich Meyer Michael Segal doi:10.1145/1167935.1167941 ACM Trans. Sen. Netw., Vol. 2, No. 3. (August 2006), pp. 444-453. 2007-10-04T07:02:52-00:00 2006 ACM Trans. Sen. Netw. 1550-4859 2 3 444 453 ACM Press algorithms geometries graph