IsoRank statistics

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Citations per year

Number of citations per year for the bioinformatics software tool IsoRank
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Tool usage distribution map

This map represents all the scientific publications referring to IsoRank per scientific context
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Protocols

IsoRank specifications

Information


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

Versioning


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Publication for IsoRank

IsoRank citations

 (29)
call_split

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

2017
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 […]

call_split

Unified Alignment of Protein Protein Interaction Networks

2017
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 […]

library_books

Net2Align: An Algorithm For Pairwise Global Alignment of Biological Networks

2016
Bioinformation
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 […]

library_books

Learning from Co expression Networks: Possibilities and Challenges

2016
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 […]

library_books

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

2016
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− […]

call_split

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

2016
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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