The what, where, how and why of gene ontology - a primer for bioinformaticians. - Louis du Plessis; Nives Skunca; Christophe Dessimoz (Briefings Bioinform., 2011)

Quality of Computationally Inferred Gene Ontology Annotations. - Nives Skunca; Adrian M. Altenhoff; Christophe Dessimoz (PLoS Comput. Biol., 2012)

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)

The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations. - Frederic B. Bastian; Marcus C. Chibucos; Pascale Gaudet; Michelle G. Giglio; Gemma L. Holliday; Hong Huang; Suzanna E. Lewis; Anne Niknejad; Sandra E. Orchard; Sylvain Poux; Nives Skunca; Marc Robinson-Rechavi (Database J. Biol. Databases Curation, 2015)

The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. - Adrian M. Altenhoff; Nives Skunca; Natasha M. Glover; Clément-Marie Train; Anna Sueki; Ivana Pilizota; Kevin Gori; Bartlomiej Tomiczek; Steven Müller; Henning Redestig; Gaston H. Gonnet; Christophe Dessimoz (Nucleic Acids Res., 2015)

Inferring Horizontal Gene Transfer. - Matt Ravenhall; Nives Skunca; Florent Lassalle; Christophe Dessimoz (PLoS Comput. Biol., 2015)