CytoGEDEVO-global alignment of biological networks with Cytoscape

Maximilian Malek, Rashid Ibragimov, Mario Albrecht, Jan Baumbach

Research output: Contribution to journalArticlepeer-review


MOTIVATION: In the systems biology era, high-throughput omics technologies have enabled the unraveling of the interplay of some biological entities on a large scale (e.g. genes, proteins, metabolites or RNAs). Huge biological networks have emerged, where nodes correspond to these entities and edges between them model their relations. Protein-protein interaction networks, for instance, show the physical interactions of proteins in an organism. The comparison of such networks promises additional insights into protein and cell function as well as knowledge-transfer across species. Several computational approaches have been developed previously to solve the network alignment (NA) problem, but only a few concentrate on the usability of the implemented tools for the evaluation of protein-protein interactions by the end users (biologists and medical researchers).

RESULTS: We have created CytoGEDEVO, a Cytoscape app for visual and user-assisted NA. It extends the previous GEDEVO methodology for global pairwise NAs with new graphical and functional features. Our main focus was on the usability, even by non-programmers and the interpretability of the NA results with Cytoscape.

AVAILABILITY AND IMPLEMENTATION: CytoGEDEVO is publicly available from the Cytoscape app store at In addition, we provide stand-alone command line executables, source code, documentation and step-by-step user instructions at


SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Original languageEnglish
Pages (from-to)1259-61
Number of pages3
Issue number8
Publication statusPublished - 15 Apr 2016
Externally publishedYes


  • Computational Biology/methods
  • Programming Languages
  • Protein Interaction Maps
  • Proteins
  • Software
  • Systems Biology

ASJC Scopus subject areas

  • Computer Science Applications

Fields of Expertise

  • Information, Communication & Computing
  • Human- & Biotechnology

Treatment code (Nähere Zuordnung)

  • Application


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