FragViz: visualization of fragmented networks. - Miha Stajdohar; Minca Mramor; Blaz Zupan; Janez Demsar (BMC Bioinform., 2010)

Orange: data mining toolbox in python. - Janez Demsar; Tomaz Curk; Ales Erjavec; Crtomir Gorup; Tomaz Hocevar; Mitar Milutinovic; Martin Mozina; Matija Polajnar; Marko Toplak; Anze Staric; Miha Stajdohar; Lan Umek; et al. (J. Mach. Learn. Res., 2013)

dictyExpress: a web-based platform for sequence data management and analytics in Dictyostelium and beyond. - Miha Stajdohar; Rafael D. Rosengarten; Janez Kokosar; Luka Jeran; Domen Blenkus; Gad Shaulsky; Blaz Zupan (BMC Bioinform., 2017)

Large scale gene set ranking for survival-related gene sets. - Martin Spendl; Jaka Kokosar; Ela Praznik; Luka Ausec; Miha Stajdohar; Blaz Zupan (Artif. Intell. Medicine, 2025)