Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks

Nadezhda T Doncheva (Corresponding author), John H Morris, Henrietta Holze, Rebecca Kirsch, Katerina C Nastou, Yesid Cuesta-Astroz, Thomas Rattei, Damian Szklarczyk, Christian von Mering, Lars J Jensen (Corresponding author)

Publications: Contribution to journalArticlePeer Reviewed


Biological networks are often used to represent complex biological systems, which can contain several types of entities. Analysis and visualization of such networks is supported by the Cytoscape software tool and its many apps. While earlier versions of stringApp focused on providing intraspecies protein-protein interactions from the STRING database, the new stringApp 2.0 greatly improves the support for heterogeneous networks. Here, we highlight new functionality that makes it possible to create networks that contain proteins and interactions from STRING as well as other biological entities and associations from other sources. We exemplify this by complementing a published SARS-CoV-2 interactome with interactions from STRING. We have also extended stringApp with new data and query functionality for protein-protein interactions between eukaryotic parasites and their hosts. We show how this can be used to retrieve and visualize a cross-species network for a malaria parasite, its host, and its vector. Finally, the latest stringApp version has an improved user interface, allows retrieval of both functional associations and physical interactions, and supports group-wise enrichment analysis of different parts of a network to aid biological interpretation. stringApp is freely available at

Original languageEnglish
Pages (from-to)637-646
Number of pages10
JournalJournal of Proteome Research
Issue number2
Publication statusPublished - 3 Feb 2023

Austrian Fields of Science 2012

  • 106026 Ecosystem research
  • 106022 Microbiology


  • Humans
  • COVID-19
  • SARS-CoV-2
  • Software
  • Proteins
  • Eukaryota
  • heterogeneous networks
  • omics data
  • Cytoscape
  • enrichment analysis
  • stringApp
  • virus−host
  • cross-species interactions
  • host−parasite

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