Journal of the ACM (JACM)
Approximation Algorithms for Some Parameterized Counting Problems
ISAAC '02 Proceedings of the 13th International Symposium on Algorithms and Computation
The Parameterized Complexity of Counting Problems
SIAM Journal on Computing
Modeling interactome: scale-free or geometric?
Bioinformatics
Monte-Carlo algorithms for enumeration and reliability problems
SFCS '83 Proceedings of the 24th Annual Symposium on Foundations of Computer Science
Algorithm Engineering for Color-Coding with Applications to Signaling Pathway Detection
Algorithmica - Parameterized and Exact Algorithms
Finding, minimizing, and counting weighted subgraphs
Proceedings of the forty-first annual ACM symposium on Theory of computing
QNet: a tool for querying protein interaction networks
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
Network motif discovery using subgraph enumeration and symmetry-breaking
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
Balanced families of perfect hash functions and their applications
ICALP'07 Proceedings of the 34th international conference on Automata, Languages and Programming
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A current major challenge in systems biology is to compute statistics on biomolecular network motifs, since this can reveal significant systemic differences between organisms. We extend the "color coding" technique to weighted edge networks and apply it to PPI networks where edges are weighted by probabilistic confidence scores, as provided by the STRING database. This is a substantial improvement over the previously available studies on, still heavily noisy, binary-edge-weight data. Following up on such a study, we compute the expected number of occurrences of non-induced subtrees with k ≤ 9 vertices. Beyond the previously reported differences between unicellular and multicellular organisms, we reveal major differences between prokaryotes and unicellular eukaryotes. This establishes, for the first time on a statistically sound data basis, that evolutionary distance can be monitored in terms of elevated systemic arrangements.