Bisociative Knowledge Discovery for Microarray Data Analysis. - Igor Mozetic; Nada Lavrac; Vid Podpecan; Petra Kralj Novak; Helena Motaln; Marko Petek; Kristina Gruden; Hannu Toivonen; Kimmo Kulovesi (ICCC, 2010)

SegMine workflows for semantic microarray data analysis in Orange4WS. - Vid Podpecan; Nada Lavrac; Igor Mozetic; Petra Kralj Novak; Igor Trajkovski; Laura Langohr; Kimmo Kulovesi; Hannu Toivonen; Marko Petek; Helena Motaln; Kristina Gruden (BMC Bioinform., 2011)

Constraint-driven optimization of plant defense model parameters. - Dragana Miljkovic; Matjaz Depolli; Igor Mozetic; Nada Lavrac; Tjasa Stare; Marko Petek; Kristina Gruden (BIBM Workshops, 2012)

Contrast Mining from Interesting Subgroups. - Laura Langohr; Vid Podpecan; Marko Petek; Igor Mozetic; Kristina Gruden (Bisociative Knowledge Discovery, 2012)

Modelling a Biological System: Network Creation by Triplet Extraction from Biological Literature. - Dragana Miljkovic; Vid Podpecan; Miha Grcar; Kristina Gruden; Tjasa Stare; Marko Petek; Igor Mozetic; Nada Lavrac (Bisociative Knowledge Discovery, 2012)

Semantic Subgroup Discovery and Cross-Context Linking for Microarray Data Analysis. - Igor Mozetic; Nada Lavrac; Vid Podpecan; Petra Kralj Novak; Helena Motaln; Marko Petek; Kristina Gruden; Hannu Toivonen; Kimmo Kulovesi (Bisociative Knowledge Discovery, 2012)

Integrating semantic transcriptomic data analysis and knowledge extraction from biological literature. - Vid Podpecan; Dragana Miljkovic; Marko Petek; Tjasa Stare; Kristina Gruden; Igor Mozetic; Nada Lavrac (BIBM, 2013)

Incremental revision of biological networks from texts. - Dragana Miljkovic; Vid Podpecan; Tjasa Stare; Igor Mozetic; Kristina Gruden; Nada Lavrac (IWBBIO, 2013)

The GMOseek matrix: a decision support tool for optimizing the detection of genetically modified plants. - Annette Block; Frédéric Debode; Lutz Grohmann; Julie Hulin; Isabel Taverniers; Linda Kluga; Elodie Barbau-Piednoir; Sylvia Broeders; Ingrid Huber; Marc Van den Bulcke; Petra Heinze; Gilbert Berben; et al. (BMC Bioinform., 2013)

Contrasting Subgroup Discovery. - Laura Langohr; Vid Podpecan; Marko Petek; Igor Mozetic; Kristina Gruden; Nada Lavrac; Hannu Toivonen (Comput. J., 2013)

GMOseek: a user friendly tool for optimized GMO testing. - Dany Morisset; Petra Kralj Novak; Darko Zupanic; Kristina Gruden; Nada Lavrac; Jana Zel (BMC Bioinform., 2014)

Plant defence model revisions through iterative minimisation of constraint violations. - Dragana Miljkovic; Matjaz Depolli; Tjasa Stare; Igor Mozetic; Marko Petek; Kristina Gruden; Nada Lavrac (Int. J. Comput. Biol. Drug Des., 2014)

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)

quantGenius: implementation of a decision support system for qPCR-based gene quantification. - Spela Baebler; Miha Svalina; Marko Petek; Katja Stare; Ana Rotter; Marusa Pompe-Novak; Kristina Gruden (BMC Bioinform., 2017)

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

Discovery of Relevant Response in Infected Potato Plants from Time Series of Gene Expression Data. - Dragan Gamberger; Tjasa Stare; Dragana Miljkovic; Kristina Gruden; Nada Lavrac (Mach. Learn. Knowl. Extr., 2019)

The need for standardisation in life science research - an approach to excellence and trust. - Susanne Hollmann; Andreas Kremer; Spela Baebler; Christophe Trefois; Kristina Gruden; Witold R. Rudnicki; Weida Tong; Aleksandra Gruca; Erik Bongcam-Rudloff; Chris T. A. Evelo; Alina S. Nechyporenko; Marcus Frohme; et al. (F1000Research, 2020)

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)