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IsoRank specifications


Unique identifier OMICS_05091
Name IsoRank
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available

Publication for IsoRank

IsoRank citations


CUFID query: accurate network querying through random walk based network flow estimation

BMC Bioinformatics
PMCID: 5751815
PMID: 29297279
DOI: 10.1186/s12859-017-1899-y
call_split See protocol

[…] ode insertions/deletions. Furthermore, random walk based approaches are typically computationally efficient because the real-world biological networks generally have sparse interactions. For example, IsoRank [] and IsoRankN [] adopt the Google’s PageRank algorithm [] in order to estimate node correspondence scores. It performs a random walk over the Kronecker product between two networks, and util […]


Unified Alignment of Protein Protein Interaction Networks

Sci Rep
PMCID: 5430463
PMID: 28424527
DOI: 10.1038/s41598-017-01085-9
call_split See protocol

[…] each this upper-limit of 100 alignments. On average, it generates 85 alignments per network pair. Hence, in total, for our 16 pairs of networks, our study contains 2,770 alignments. We do not include ISORANK, MI-GRAAL, GHOST, or NETAL in this study, as they fail to produce alignments for all of the pairs of networks that we consider. We also do not include DUALALIGNER, as it requires GO annotation […]


Net2Align: An Algorithm For Pairwise Global Alignment of Biological Networks

PMCID: 5357568
PMID: 28356678
DOI: 10.6026/97320630012408

[…] conserved modules, local alignment can be ambivalent. However, global alignment provides a unique approach where each node in one network is mapped across each node in another network. In particular, ISORANK [] aimed to provide maximum overall match between two networks. It used a heuristic by assigning a score to the aligning pair where 2 nodes are considered a match if their neighbors also match […]


Learning from Co expression Networks: Possibilities and Challenges

Front Plant Sci
PMCID: 4825623
PMID: 27092161
DOI: 10.3389/fpls.2016.00444

[…] cies co-clustering approach (COMODO). Network comparisons can be done at the global scale or focused on specific gene modules. In a global approach, Ficklin and Feltus () used an alignment algorithm, IsoRank, that incorporates both gene homology and network topology to compare networks in rice and maize. They identified aligned modules enriched for similar functional terms, suggesting their potent […]


Stochastic block coordinate Frank Wolfe algorithm for large scale biological network alignment

EURASIP J Bioinform Syst Biol
PMCID: 4826425
PMID: 27110234
DOI: 10.1186/s13637-016-0041-1

[…] At each iteration, the most computationally expensive operations are the updates of p k and q k (lines 7 and 10 of SBCFW-IsoRank) and the calculation of the partial gradient ∇i f(x k) (line 7 of SBCFW-IsoRank).The calculation of p k and q k are similar. From line 10 of Algorithm 2, we know (19)pk=Exk=Exk−1+γk−1sk−1−xk− […]


New strategy for drug discovery by large scale association analysis of molecular networks of different species

Sci Rep
PMCID: 4766474
PMID: 26912056
DOI: 10.1038/srep21872
call_split See protocol

[…] -known measures reflecting information content similarity for enzyme pairs and SIMCOMP for compound pairs.The topological similarities of the subnetworks were calculated by following the intuition of IsoRank that if the subnetwork Ri is mapped to Rj, their neighbors in the corresponding pathways should also be similar. The topological similarity was then used to favor mappings of subnetworks that […]


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IsoRank institution(s)
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA

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