The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks

Marouen Ben Guebila, Tian Wang, Camila M. Lopes-Ramos, Viola Fanfani, Des Weighill, Rebekka Burkholz, Daniel Schlauch, Joseph N. Paulson, Michael Altenbuchinger, Katherine H. Shutta, Abhijeet R. Sonawane, James Lim, Genis Calderer, David G.P. van IJzendoorn, Daniel Morgan, Alessandro Marin, Cho Yi Chen, Qi Song, Enakshi Saha, Dawn L. DeMeoMegha Padi, John Platig, Marieke L. Kuijjer, Kimberly Glass, John Quackenbush

Research output: Contribution to journalArticlepeer-review


Inference and analysis of gene regulatory networks (GRNs) require software that integrates multi-omic data from various sources. The Network Zoo (netZoo; is a collection of open-source methods to infer GRNs, conduct differential network analyses, estimate community structure, and explore the transitions between biological states. The netZoo builds on our ongoing development of network methods, harmonizing the implementations in various computing languages and between methods to allow better integration of these tools into analytical pipelines. We demonstrate the utility using multi-omic data from the Cancer Cell Line Encyclopedia. We will continue to expand the netZoo to incorporate additional methods.

Original languageEnglish (US)
Article number45
JournalGenome biology
Issue number1
StatePublished - Dec 2023


  • Gene regulation
  • Multi-omic analysis
  • Network biology
  • Open-source software

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology


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