A Multiple Alignment Algorithm for Metabolic Pathway Analysis Using Enzyme Hierarchy
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
Cluster Graph Modification Problems
WG '02 Revised Papers from the 28th International Workshop on Graph-Theoretic Concepts in Computer Science
Algorithms for inferring cis-regulatory structures and protein interaction networks
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
Finding cliques in protein interaction networks via transitive closure of a weighted graph
Proceedings of the 5th international workshop on Bioinformatics
A parallel edge-betweenness clustering tool for Protein-Protein Interaction networks
International Journal of Data Mining and Bioinformatics
Bounded list injective homomorphism for comparative analysis of protein-protein interaction graphs
Journal of Discrete Algorithms
Finding occurrences of protein complexes in protein-protein interaction graphs
Journal of Discrete Algorithms
Identifying Evolutionarily Conserved Protein Interaction Modules Using GraphHopper
BICoB '09 Proceedings of the 1st International Conference on Bioinformatics and Computational Biology
Maximum Motif Problem in Vertex-Colored Graphs
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Complexity issues in color-preserving graph embeddings
Theoretical Computer Science
Efficient algorithms for node disjoint subgraph homeomorphism determination
DASFAA'08 Proceedings of the 13th international conference on Database systems for advanced applications
Dividing protein interaction networks for modular network comparative analysis
Pattern Recognition Letters
Algorithms and theory of computation handbook
Complexity issues in vertex-colored graph pattern matching
Journal of Discrete Algorithms
Finding approximate and constrained motifs in graphs
CPM'11 Proceedings of the 22nd annual conference on Combinatorial pattern matching
Finding exact and maximum occurrences of protein complexes in protein-protein interaction graphs
MFCS'05 Proceedings of the 30th international conference on Mathematical Foundations of Computer Science
Pairwise local alignment of protein interaction networks guided by models of evolution
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
Assessing significance of connectivity and conservation in protein interaction networks
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Pattern matching in protein-protein interaction graphs
FCT'07 Proceedings of the 16th international conference on Fundamentals of Computation Theory
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Mounting evidence shows that many protein complexes are conserved in evolution. Here we use conservation to find complexes that are common to yeast S. Cerevisiae and bacteria H. pylori. Our analysis combines protein interaction data, that are available for each of the two species, and orthology information based on protein sequence comparison. We develop a detailed probabilistic model for protein complexes in a single species, and a model for the conservation of complexes between two species. Using these models, one can recast the question of finding conserved complexes as a problem of searching for heavy subgraphs in an edge- and node-weighted graph, whose nodes are orthologous protein pairs.We tested this approach on the data currently available for yeast and bacteria and detected 11 significantly conserved complexes. Several of these complexes match very well with prior experimental knowledge on complexes in yeast only, and serve for validation of our methodology. The complexes suggest new functions for a variety of uncharacterized proteins. By identifying a conserved complex whose yeast proteins function predominantly in the nuclear pore complex, we propose that the corresponding bacterial proteins function as a coherent cellular membrane transport system. We also compare our results to two alternative methods for detecting complexes, and demonstrate that our methodology obtains a much higher specificity.