Combinatorial optimization: algorithms and complexity
Combinatorial optimization: algorithms and complexity
Alignment of metabolic pathways
Bioinformatics
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
Integrated protein interaction networks for 11 microbes
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
Graph algorithms for biological systems analysis
Proceedings of the nineteenth annual ACM-SIAM symposium on Discrete algorithms
A Path Following Algorithm for Graph Matching
ICISP '08 Proceedings of the 3rd international conference on Image and Signal Processing
Dividing Protein Interaction Networks by Growing Orthologous Articulations
PRIB '08 Proceedings of the Third IAPR International Conference on Pattern Recognition in Bioinformatics
GADDI: distance index based subgraph matching in biological networks
Proceedings of the 12th International Conference on Extending Database Technology: Advances in Database Technology
Multiple Alignment of Biological Networks: A Flexible Approach
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
A technique to search for functional similarities in protein-protein interaction networks
International Journal of Data Mining and Bioinformatics
Bimal: bipartite matching alignment for the contact map overlap problem
IJCNN'09 Proceedings of the 2009 international joint conference on Neural Networks
Automatic parameter learning for multiple network alignment
RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology
Dividing protein interaction networks for modular network comparative analysis
Pattern Recognition Letters
Heuristic algorithms in computational molecular biology
Journal of Computer and System Sciences
An Inner-Outer Iteration for Computing PageRank
SIAM Journal on Scientific Computing
Asymmetric Comparison and Querying of Biological Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Computational methods for the prediction of protein-protein interactions
IWCIA'11 Proceedings of the 14th international conference on Combinatorial image analysis
Parsimonious reconstruction of network evolution
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
High efficiency and quality: large graphs matching
Proceedings of the 20th ACM international conference on Information and knowledge management
Scalable multiple global network alignment for biological data
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
SubMAP: aligning metabolic pathways with subnetwork mappings
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
“Master-slave” biological network alignment
ISBRA'10 Proceedings of the 6th international conference on Bioinformatics Research and Applications
Predicting Protein Function by Multi-Label Correlated Semi-Supervised Learning
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Tutorial on biological networks
Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery
Prioritizing disease genes by bi-random walk
PAKDD'12 Proceedings of the 16th Pacific-Asia conference on Advances in Knowledge Discovery and Data Mining - Volume Part II
A multithreaded algorithm for network alignment via approximate matching
SC '12 Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis
Message-Passing Algorithms for Sparse Network Alignment
ACM Transactions on Knowledge Discovery from Data (TKDD)
NABEECO: biological network alignment with bee colony optimization algorithm
Proceedings of the 15th annual conference companion on Genetic and evolutionary computation
Probabilistic Biological Network Alignment
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
High efficiency and quality: large graphs matching
The VLDB Journal — The International Journal on Very Large Data Bases
Inferring anchor links across multiple heterogeneous social networks
Proceedings of the 22nd ACM international conference on Conference on information & knowledge management
Global Network Alignment In The Context Of Aging
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Predicting Protein Functions from Protein Interaction Networks
International Journal of Knowledge Discovery in Bioinformatics
Hi-index | 0.00 |
We describe an algorithm, IsoRank, for global alignment of two protein-protein interaction (PPI) networks. IsoRank aims to maximize the overall match between the two networks; in contrast, much of previous work has focused on the local alignment problem-- identifying many possible alignments, each corresponding to a local region of similarity. IsoRank is guided by the intuition that a protein should be matched with a protein in the other network if and only if the neighbors of the two proteins can also be well matched. We encode this intuition as an eigenvalue problem, in a manner analogous to Google's PageRank method. We use IsoRank to compute the first known global alignment between the S. cerevisiae and D. melanogaster PPI networks. The common subgraph has 1420 edges and describes conserved functional components between the two species. Comparisons of our results with those of a well-known algorithm for local network alignment indicate that the globally optimized alignment resolves ambiguity introduced by multiple local alignments. Finally, we interpret the results of global alignment to identify functional orthologs between yeast and fly; our functional ortholog prediction method is much simpler than a recently proposed approach and yet provides results that are more comprehensive.