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  • Petar Glažar (BSc thesis, 2011) "Contextual analysis and visualization of high- throughput data"
  • Jelena Tica (MSc thesis, 2011) "Computational analysis of plasma glycome and genotypes in human population"
  • Vedran Franke (BSc thesis, 2010) "Predicting protein-protein interactions from primary structure using a random forest classifier"
  • Maša Milošević (BSc thesis, 2009) "Analysis of metagenomes in extreme environments"
  • Ozren Stojanović (BSc thesis, 2008) "Computational analysis of exonic splicing regulators"
  • Morana Vitezić (BSc thesis, 2008) "Codon usage bias applied to molecular evolution"
  • Tina Kokan (BSc thesis, 2007) "Computational analysis of the location of highly curved DNA regions in human genome"
  • Tamara Milošević (BSc thesis, 2006) "Computational study of DNA recombinatinal repair evolution"
  • Marija Buljan (BSc thesis, 2006) "Horizontal gene transfer in metagenomes"
  • Rosa Karlić (BSc thesis, 2006) "Computational classification of protein folds"
  • Sonja Čubrilo (BSc thesis, 2006) "Analysis of DNA curvature in human genome"
  • Nenad Bartoniček (BSc thesis, 2004) "MADNet - Microarray Database Network, Web server for analysis and interactive display of microarray experiments"
  • Fran Supek (BSc thesis, 2004) "INCA -A computer program for codon usage analysis and its application to prokaryotic genomes"