GoMapMan: integration, consolidation and visualization of plant gene annotations within the MapMan ontology. - Ziva Ramsak; Spela Baebler; Ana Rotter; Matej Korbar; Igor Mozetic; Björn Usadel; Kristina Gruden (Nucleic Acids Res., 2014)

Interactive exploration of heterogeneous biological networks with Biomine Explorer. - Vid Podpecan; Ziva Ramsak; Kristina Gruden; Hannu Toivonen; Nada Lavrac (Bioinform., 2019)

PaintOmics 4: new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases. - Tianyuan Liu; Pedro Salguero; Marko Petek; Carlos Martínez-Mira; Leandro Balzano-Nogueira; Ziva Ramsak; Lauren McIntyre; Kristina Gruden; Sonia Tarazona; Ana Conesa (Nucleic Acids Res., 2022)

DDeMON: Ontology-based function prediction by Deep Learning from Dynamic Multiplex Networks. - Jan Kralj; Blaz Skrlj; Ziva Ramsak; Nada Lavrac; Kristina Gruden (CoRR, 2023)