Gephi statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Gephi

Tool usage distribution map

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

This word cloud represents Gephi usage per disease context

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Gephi specifications


Unique identifier OMICS_16845
Name Gephi
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Medium
Version 0.9.1
Stability Stable
Maintained Yes




No version available


  • person_outline Mathieu Bastian

Gephi citations


MLL fusion driven leukemia requires SETD2 to safeguard genomic integrity

Nat Commun
PMCID: 5959866
PMID: 29777171
DOI: 10.1038/s41467-018-04329-y

[…] esent in at least one complex were used as the background population. p-values were corrected for multiple testing as explained above. Protein interaction networks were visualized using Cytoscape and Gephi. Detailed information about all 960 identified interactors of MLL-fusion proteins is provided in Supplementary Data . […]


Insular threat associations within taxa worldwide

Sci Rep
PMCID: 5913315
PMID: 29686360
DOI: 10.1038/s41598-018-24733-0

[…] the number of insular species threatened by each threat in that region. As above, networks were created using the R packages igraph and rgexf, and network structures were explored and visualized with Gephi software using a Geo Layout, which uses latitude and longitude coordinates to set the node position in the graphic space.For each of the three network types, we estimated the number of species a […]


Meta scale mountain grassland observatories uncover commonalities as well as specific interactions among plant and non rhizosphere soil bacterial communities

Sci Rep
PMCID: 5893626
PMID: 29636506
DOI: 10.1038/s41598-018-24253-x
call_split See protocol

[…] ding to ref., and only coefficients ≥0.6 or ≤−0.6, and FDR-corrected P < 0.05 were kept. Plant-bacterial OTU correlations were visualized in networks produced by the Fruchterman Reingold algorithm in Gephi v.0.8.2. Striking clusters were named according to abundant plant names, or vegetation alliances, if recognizable. A couple of very small plant-bacterial OTU clusters were excluded from further […]


Analysis of lineage specific Alu subfamilies in the genome of the olive baboon, Papio anubis

PMCID: 5858127
PMID: 29560044
DOI: 10.1186/s13100-018-0115-6

[…] EG can be found in Additional file  (Worksheet “Subfamily Counts”). The consensus sequence for each of these 129 Alu subfamilies is available in Additional file . These subfamilies were uploaded into Gephi for visualization (Fig.  with a high resolution PDF available in Additional file ). There are 9 major clusters of Alu elements (assigned a cluster number 1–9) that radiate from a single, central […]


Resolving the complete genome of Kuenenia stuttgartiensis from a membrane bioreactor enrichment using Single Molecule Real Time sequencing

Sci Rep
PMCID: 5854607
PMID: 29545612
DOI: 10.1038/s41598-018-23053-7

[…] subsequently assigned to different metagenome bins based on the coverage depth of the genomic region they aligned too. Coverage cutoffs were set guided by examination of assembly graphs rendered with Gephi 0.8.2 (Supplementary Figure ) and histograms of the coverage depth (Supplementary Figure ). Uncorrected reads aligning to highly covered regions (>110×, 179,021 reads (33.1%) referred to as “hig […]


An Epidemiological Human Disease Network Derived from Disease Co occurrence in Taiwan

Sci Rep
PMCID: 5852024
PMID: 29540710
DOI: 10.1038/s41598-018-21779-y

[…] The patient-disease relationship and disease correlations can be visualised using heatmaps. The overall network structure can be visualised using the software Gephi. In such a plot, diseases that share edges are connected with lines, the size of a node is proportional to its connectivity, and different modules are represented using different colours. Constr […]

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