Asymmetric Comparison and Querying of Biological Networks
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Management and analysis of protein-to-protein interaction data
CIBB'10 Proceedings of the 7th international conference on Computational intelligence methods for bioinformatics and biostatistics
Scalable multiple global network alignment for biological data
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
A novel framework for large scale metabolic network alignments by compression
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Topology aware coloring of gene regulatory networks
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
“Master-slave” biological network alignment
ISBRA'10 Proceedings of the 6th international conference on Bioinformatics Research and Applications
Tutorial on biological networks
Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery
The small community phenomenon in networks: models, algorithms and applications
TAMC'12 Proceedings of the 9th Annual international conference on Theory and Applications of Models of Computation
Random walk distances in data clustering and applications
Advances in Data Analysis and Classification
A simple, combinatorial algorithm for solving SDD systems in nearly-linear time
Proceedings of the forty-fifth annual ACM symposium on Theory of computing
Probabilistic Biological Network Alignment
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Color distribution can accelerate network alignment
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Global Network Alignment In The Context Of Aging
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Local topological signatures for network-based prediction of biological function
PRIB'13 Proceedings of the 8th IAPR international conference on Pattern Recognition in Bioinformatics
| Hi-index | 3.84 |
Motivation: With the increasing availability of large protein–protein interaction networks, the question of protein network alignment is becoming central to systems biology. Network alignment is further delineated into two sub-problems: local alignment, to find small conserved motifs across networks, and global alignment, which attempts to find a best mapping between all nodes of the two networks. In this article, our aim is to improve upon existing global alignment results. Better network alignment will enable, among other things, more accurate identification of functional orthologs across species. Results: We introduce IsoRankN (IsoRank-Nibble) a global multiple-network alignment tool based on spectral clustering on the induced graph of pairwise alignment scores. IsoRankN outperforms existing algorithms for global network alignment in coverage and consistency on multiple alignments of the five available eukaryotic networks. Being based on spectral methods, IsoRankN is both error tolerant and computationally efficient. Availability: Our software is available freely for non-commercial purposes on request from: http://isorank.csail.mit.edu/ Contact: bab@mit.edu