GraphCrunch statistics

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Citations per year

Number of citations per year for the bioinformatics software tool GraphCrunch

Tool usage distribution map

This map represents all the scientific publications referring to GraphCrunch per scientific context
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Associated diseases


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GraphCrunch specifications


Unique identifier OMICS_15579
Name GraphCrunch
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License GNU General Public License version 3.0
Computer skills Medium
Version 2.1.1
Stability Stable
Perl, Xdialog
Source code URL
Maintained Yes




No version available



  • person_outline Natasa Przulj

Publications for GraphCrunch

GraphCrunch citations


Modular Organization of Residue Level Contacts Shapes the Selection Pressure on Individual Amino Acid Sites of Ribosomal Proteins

Genome Biol Evol
PMCID: 5388290
PMID: 28338825
DOI: 10.1093/gbe/evx036

[…] m networks—where graphlets are small substructures of large networks ()—relative graphlet frequency distance (RGF-distance) and graphlet degree distribution agreement (GDD-agreement), estimated using GraphCrunch software package (). A high GDD-agreement and low RGF-distance denote a strong structural similarity between the original network and the random model.GDD-agreement and RGF-distance-based […]


Combinatorial algorithm for counting small induced graphs and orbits

PLoS One
PMCID: 5300269
PMID: 28182743
DOI: 10.1371/journal.pone.0171428

[…] om Erdős-Rényi graphs.We measured the time needed for counting node- and edge-orbits with the Orca algorithm and compared it to a bruteforce enumeration. For the latter we used an implementation from GraphCrunch. Orca outperforms exhaustive enumeration by an order of magnitude (Tables and ). The running times for counting node-orbits and edge-orbits are practically the same in the case of countin […]


An Examination of Not For Profit Stakeholder Networks for Relationship Management: A Small Scale Analysis on Social Media

PLoS One
PMCID: 5053609
PMID: 27711236
DOI: 10.1371/journal.pone.0163914

[…] As discussed, the output from the pairwise network comparison implemented with GraphCrunch 2 allows us to report, among other measures, GDD agreement (arithmetic mean), and RGF distance, to assess local-level topological similarity—along with Pearson and Spearman correlations of […]


Wnt signal transduction pathways: modules, development and evolution

BMC Syst Biol
PMCID: 4977476
PMID: 27490822
DOI: 10.1186/s12918-016-0299-7

[…] as been the topological similarity between the two species-specific pathways. SP(x,y) has been calculated by the GRAph ALigner algorithm (GRAAL) developed by Kuchaiev et al. [] and implemented in the GraphCrunch2 software []. SP(x,y) is nothing but Edge Correctness (EC) value between a pair of species-specific Wnt STPs. Edge correctness is the percentage of edges in the first graph that are aligne […]


Distinctive Behaviors of Druggable Proteins in Cellular Networks

PLoS Comput Biol
PMCID: 4689399
PMID: 26699810
DOI: 10.1371/journal.pcbi.1004597

[…] protein’s neighbors are in the same community and therefore the protein favors intra-community communication while a low VM number indicates the protein favors inter-community communication. We used GraphCrunch [] to calculate subgraphs previously described as a means of fragmenting networks into smaller graphlets [] (Fig B in ). The nodes within these graphlets can be classified into ‘isomorphis […]


Exploring the structure and function of temporal networks with dynamic graphlets

PMCID: 4765862
PMID: 26072480
DOI: 10.1093/bioinformatics/btv227

[…] mporal network as well as for each individual node. To obtain static or static-temporal graphlet counts of the entire aggregated network or of individual temporal snapshots, respectively, one can use GraphCrunch (; ).As different input parameter values may be optimal for different network types (e.g. networks from different domains), we recommend testing several different combinations, as permitte […]

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GraphCrunch institution(s)
Department of Computing, Imperial College, London, UK; Department of Computer Science, University of California, Irvine, CA, USA
GraphCrunch funding source(s)
This project was supported by NSF CAREER IIS- 0644424 and NSF CDI OIA-1028394 grants.

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