INCA: synonymous codon usage analysis and clustering by means of self-organizing map. - Fran Supek; Kristian Vlahovicek (Bioinform., 2004)

Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity. - Fran Supek; Kristian Vlahovicek (BMC Bioinform., 2005)

Correction: Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity. - Fran Supek; Kristian Vlahovicek (BMC Bioinform., 2010)

Nucleoid-Associated Proteins Affect Mutation Dynamics in E. coli in a Growth Phase-Specific Manner. - Tobias Warnecke; Fran Supek; Ben Lehner (PLoS Comput. Biol., 2012)

Semi-Supervised Learning for Quantitative Structure-Activity Modeling. - Jurica Levatic; Saso Dzeroski; Fran Supek; Tomislav Smuc (Informatica (Slovenia), 2013)

Phyletic Profiling with Cliques of Orthologs Is Enhanced by Signatures of Paralogy Relationships. - Nives Skunca; Matko Bosnjak; Anita Krisko; Pance Panov; Saso Dzeroski; Tomislav Smuc; Fran Supek (PLoS Comput. Biol., 2013)

Extensive complementarity between gene function prediction methods. - Vedrana Vidulin; Tomislav Smuc; Fran Supek (Bioinform., 2016)

Phenotype Inference from Text and Genomic Data. - Maria Brbic; Matija Piskorec; Vedrana Vidulin; Anita Krisko; Tomislav Smuc; Fran Supek (ECML/PKDD (3), 2017)

Phenotype Prediction with Semi-supervised Classification Trees. - Jurica Levatic; Maria Brbic; Tomaz Stepisnik Perdih; Dragi Kocev; Vedrana Vidulin; Tomislav Smuc; Fran Supek; Saso Dzeroski (NFMCP@PKDD/ECML, 2017)

Passenger mutations accurately classify human tumors. - Marina Salvadores; David Mas-Ponte; Fran Supek (PLoS Comput. Biol., 2019)