Scientific Publications

As I reflect on my time in academia, I'm truly proud of the scientific publications I had the opportunity to contribute to during my journey, culminating with my PhD and postdoctoral work at ETH Zürich. Though my focus has shifted since then, I fondly look back on these accomplishments as a testament to the collaborative spirit that allowed me to learn and grow alongside my esteemed colleagues.

While my career has taken a new direction, I remain deeply grateful for the collaborations that broadened my horizons and enriched my knowledge. I invite you to explore the list of publications that represent not only my academic achievements, but also the invaluable connections forged along the way.

🌟 Supek, F., Bošnjak, M., Škunca, N., & Šmuc, T. (2011). REVIGO summarizes and visualizes long lists of gene ontology terms. PloS One, 6(7), e21800.

Du Plessis, L., Škunca, N., & Dessimoz, C. (2011). The what, where, how and why of gene ontology—a primer for bioinformaticians. Briefings in Bioinformatics, 12(6), 723–735.

Supek, F., Škunca, N., Repar, J., Vlahoviček, K., & Šmuc, T. (2010). Translational selection is ubiquitous in prokaryotes. PLoS Genetics, 6(6), e1001004.

🌟 Škunca, N., Altenhoff, A., & Dessimoz, C. (2012). Quality of computationally inferred gene ontology annotations. PLoS Computational Biology, 8(5), e1002533.

Škunca, N., Bošnjak, M., Kriško, A., Panov, P., Džeroski, S., Šmuc, T., & Supek, F. (2013). Phyletic profiling with cliques of orthologs is enhanced by signatures of paralogy relationships. PLoS Computational Biology, 9(1), e1002852.

Zucko, J., Skunca, N., Curk, T., Zupan, B., Long, P. F., Cullum, J., … Hranueli, D. (2007). Polyketide synthase genes and the natural products potential of Dictyostelium discoideum. Bioinformatics, 23(19), 2543–2549.

Radivojac, P., Clark, W. T., Oron, T. R., Schnoes, A. M., Wittkop, T., Sokolov, A., … Others. (2013). A large-scale evaluation of computational protein function prediction. Nature Methods, 10(3), 221–227.

🌟 Škunca, N., Supek, F., Panov, P., Džeroski, S., & Šmuc, T. (2008). Functional annotation of orthologous groups by using hierarchical multi label classification. Journal of the Royal Society Interface, 5(19), 151–170.

Hranueli, D., Starčević, A., Ýučko, J., Diminić, J., Škunca, N., Ýeljeznak, V., … Pavlinušić, D. (2008). Oblikovanje novih prirodnih spojeva u uvjetima in silico. Kemija u Industriji: Časopis Kemičara i Kemijskih Inženjera Hrvatske, 57(5), 245–256.

Dessimoz, C., Škunca, N., & Thomas, P. D. (2013). CAFA and the open world of protein function predictions. Trends in Genetics, 29(11), 609–610.

🌟 Skunca, Nives, Thomas, P. D., & Dessimoz, C. (n.d.). Assessing protein function predictions in light of the Open World Assumption. Automated Function Prediction SIG, 10, 221–227.

Altenhoff, A. M., Škunca, N., Glover, N., Train, C.-M., Sueki, A., Piližota, I., … Others. (2015). The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. Nucleic Acids Research, 43(D1), D240–D249.

🌟 Škunca, N., & Dessimoz, C. (2015). Phylogenetic profiling: how much input data is enough? PloS One, 10(2), e0114701.

Egger, B., Lapraz, F., Tomiczek, B., Müller, S., Dessimoz, C., Girstmair, J., … Others. (2015). A transcriptomic-phylogenomic analysis of the evolutionary relationships of flatworms. Current Biology, 25(10), 1347–1353.

Ravenhall, M., Škunca, N., Lassalle, F., & Dessimoz, C. (2015). Inferring horizontal gene transfer. PLoS Computational Biology, 11(5), e1004095.

Škunca, N. (2014). Computational prediction of gene function under the Open World Assumption. ETH Zurich.

Jiang, Y., Oron, T. R., Clark, W. T., Bankapur, A. R., D’Andrea, D., Lepore, R., … Others. (2016). An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology, 17(1), 1–19.

Bastian, F. B., Chibucos, M. C., Gaudet, P., Giglio, M., Holliday, G. L., Huang, H., … Others. (2015). The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations. Database, 2015.

Gaudet, P., Škunca, N., Hu, J. C., & Dessimoz, C. (2017). Primer on the gene ontology. The Gene Ontology Handbook, 25–37.

Supek, F., & Škunca, N. (2016). Visualizing gene ontology annotations. ArXiv Preprint ArXiv:1602. 07103.

of Bioinformatics Members, S. S. I. (2016). The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases. Nucleic Acids Research, 44(D1), D27–D37.

Peng, X., Alföldi, J., Gori, K., Eisfeld, A. J., Tyler, S. R., Tisoncik-Go, J., … Others. (2014). The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease. Nature Biotechnology, 32(12), 1250–1255.

🌟 Dessimoz, C., & Škunca, N. (2017). The gene ontology handbook. Springer Nature.

Škunca, N., Roberts, R. J., & Steffen, M. (2017). Evaluating computational gene ontology annotations. The Gene Ontology Handbook, 97–109.

Supek, F., & Škunca, N. (2017). Visualizing go annotations. The Gene Ontology Handbook, 207–220.

Škunca, N. (2006). Analiza gena PKS u genomu amebe Dictyostelium discoideum. University of Zagreb. Faculty of Food Technology and Biotechnology ….

Peng, X., Alföldi, J., Gori, K., Eisfeld, A. J., Tyler, S. R., Tisoncik-Go, J., … Others. (n.d.). the draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory.

Jiang, Y., Oron, T. R., Clark, W. T., Bankapur, A. R., D’Andrea, D., Lepore, R., … Others. (n.d.). Availability: This version is available at: http://porto. polito. it/2649752/since: September 2016.

Hastings, J. (2017). The Gene Ontology Handbook. Springer.

🌟 Altenhoff, A., Dessimoz, C., & Others. (2012). Quality of Computationally Inferred Gene Ontology Annotations. PLoS Computational Biology, 8(5).