IsoRank 2008 / IsoRankN 2009 – Global Alignment of multiple PPI Networks / on Spectral methods

IsoRank 2008 / IsoRankN 2009


IsoRank is an algorithm for global alignment of multiple protein-protein interaction (PPI) networks. The intuition is that a protein in one PPI network is a good match for a protein in another network if the former’s neighbors are good matches for the latter’s neighbors.

IsoRankN (IsoRank-Nibble) is 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.


Bonnie Berger‘s group at MIT.




  • Linux


IsoRank / IsoRankN



Global alignment of multiple protein interaction networks with application to functional orthology detection.
Singh R, Xu J, Berger B.
Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):12763-8. doi: 10.1073/pnas.0806627105.

IsoRankN: spectral methods for global alignment of multiple protein networks.
Liao CS, Lu K, Baym M, Singh R, Berger B.
Bioinformatics. 2009 Jun 15;25(12):i253-8. doi: 10.1093/bioinformatics/btp203.