An Introduction to Metabolic Networks and Their Structural Analysis
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
On-line exact shortest distance query processing
Proceedings of the 12th International Conference on Extending Database Technology: Advances in Database Technology
Path finding approaches and metabolic pathways
Discrete Applied Mathematics
Linked Metabolites: A tool for the construction of directed metabolic graphs
Computers in Biology and Medicine
Advanced querying interface for biochemical network databases
Proceedings of the 2010 ACM Symposium on Applied Computing
Identifying Necessary Reactions in Metabolic Pathways by Minimal Model Generation
Proceedings of the 2010 conference on ECAI 2010: 19th European Conference on Artificial Intelligence
Identifying branched metabolic pathways by merging linear metabolic pathways
RECOMB'11 Proceedings of the 15th Annual international conference on Research in computational molecular biology
Shortest-path queries for complex networks: exploiting low tree-width outside the core
Proceedings of the 15th International Conference on Extending Database Technology
The exact distance to destination in undirected world
The VLDB Journal — The International Journal on Very Large Data Bases
Fast exact shortest-path distance queries on large networks by pruned landmark labeling
Proceedings of the 2013 ACM SIGMOD International Conference on Management of Data
Shortest-path queries in static networks
ACM Computing Surveys (CSUR)
Proceedings of the 23rd international conference on World wide web
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Motivation: Pathway Hunter Tool (PHT), is a fast, robust and user-friendly tool to analyse the shortest paths in metabolic pathways. The user can perform shortest path analysis for one or more organisms or can build virtual organisms (networks) using enzymes. Using PHT, the user can also calculate the average shortest path (Jungnickel, 2002 Graphs, Network and Algorithm. Springer-Verlag, Berlin), average alternate path and the top 10 hubs in the metabolic network. The comparative study of metabolic connectivity and observing the cross talk between metabolic pathways among various sequenced genomes is possible. Results: A new algorithm for finding the biochemically valid connectivity between metabolites in a metabolic network was developed and implemented. A predefined manual assignment of side metabolites (like ATP, ADP, water, CO2 etc.) and main metabolites is not necessary as the new concept uses chemical structure information (global and local similarity) between metabolites for identification of the shortest path. Availability: PHT is accessible at http://www.pht.uni-koeln.de Contact: d.schomburg@uni-koeln.de