Dr. Denis Kutnjak

Working place: Research Assistant

Department: Department of Biotechnology and Systems Biology

My past and current research focuses on topics of plant biology and virology, evolution and phylogenetics, high-throughput sequencing and bioinformatics. At the start of my research career (2011-2012) I was involved in the EU-funded Plus project BALKBIODIV (“Insights into the plant diversity of the Balkan Peninsula”) at the University of Innsbruck, Austria, focusing on a phylogenetics, phylogeography and conservation genetics of the indigenous plant species on the Balkan Penninsula. As a PhD candidate (2012-2016) I was focusing on several aspects of high-throughput sequencing use in plant virology and broader. I was involved in the discovery of the new strain of potato virus X, characterization of the population structure of potato virus Y within the plants and finally its dynamics during the experimental evolution in different hosts. My work was tightly connected to the Slovenian Research Agency project L4-5525 “Epidemiology and Biodiversity Studies of Plant Pathogens.” Besides these topics, I collaborated in several other projects, e.g., in the characterization of the new orthoreovirus species in human (in collaboration with the Faculty of Medicine, University of Ljubljana) and the forensics metagenomics project (ordered by District Court in Ljubljana of the Republic of Slovenia).

Experimental evolution of potato virus Y in different genotypes of potato

Currently, I am involved in several research projects within NIB. In a postdoctoral project, funded by Slovenian Research Agency (“The role of epigenetic imprinting in temporally separated multiple virus infections in plants”) I am looking into mechanisms of plant stress memory in collaboration with Evolutionary Systems Virology Group from the Institute for Integrative Systems Biology, Valencia, Spain. In the frame of ARIMNet2 project EMERAMB (“Emergent viruses and virus vectors in Mediterranean Basin crops”) we are conducting a research on the effect of mixed infections of plant viruses on the viral evolution and developing tools for characterization of virome in environmental water samples using high-throughput sequencing. In the frame of Slovenian Smart Specialization project, I am employing metagenomics approaches to characterize the metagenomes of important production cell lines in pharmaceutical area. I am also involved in the plant virus diagnostic work, developing high-throughput sequencing-based diagnostics for plant viruses. I am collaborating in several other projects at the national and international level, e.g., with the Institute of Microbiology and Immunology (Faculty of Medicine, University of Ljubljana), on human DNA viruses sequencing using Oxford Nanopore MinIon sequencer and with the Jovan Hadži Institute of Biology (Slovenian Academy of Sciences and Arts), on metabarcoding and environmental DNA sequencing from spiders' webs.

Disseminating the results together with students and supervisors


2016        PhD (Nanoscience and nanotechnologies)
Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
Title: Discovery and diversity studies of viruses with next generation sequencing
2012        Diploma (Biology)
Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
Title: Phylogeography and conservation genetics of Cerastium dinaricum


2017-        Research Assistant
National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia
Main topics:
  •  variability of plant virus populations
  •  molecular characterization of new viruses and viral strains using new sequencing technologies
  • characterization of viral metagenomes from environmental samples
  • characterization of plant microbiome
  • design and conduction of experiments
  • bioinformatics and in-silico sequence analysis


2012-2016    Young researcher (PhD candidate)
National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia
2012             Project collaborator
Institute of Botany University of Innsbruck, Innsbruck, Austria


2017    1st prize from the Slovenian Microbiological Society at the competition of PhD dissertations from the microbiology field defended from  2014 to 2016
2014    young researcher presentation award, 6th Monolith Summer School & Symposium 2014, Portorož, Slovenia
2014    poster presentation award, Workshop SeqAhead: NGS current challenges and data analysis for plant researchers, The Genome Analysis Centre (TGAC), Norwich, UK
2012    Prešeren award of Biotechnical Faculty for the Diploma thesis, Ljubljana, Slovenia


Currently co-supervising two MsC (Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia) and two PhD students (Jožef Stefan International Postgraduate School, Ljubljana, Slovenia).


Reviewer for several scientific journals, including Scentific Reports, Journal of Virology, Annals of Applied Biology,  Journal of Virological Methods and Jorunal of Plant Pathology.
Management committee substitute in the EU-funded COST FA1407 project (Application of next generation sequencing for the study and diagnosis of plant viral diseases in agriculture).


Member of:
Slovenian Microbiology Society (SMD),
Slovenian Society of Plant Biology (SDBR),
American Society for Microbiology (ASM) and
representative of the institute at the International Alliance for Biological Standardization (IABS).


2016-2017, 2019    Prof. Dr. Santiago Elena, population genetics and experimental evolution of plant virus populations, Instituto de Biologia Molecular y Celular de Plantas, Universitat Politecnica de Valencia, Spain

2012-2013    Dr. Jan Kreuze, small RNA sequencing for detection of plant viruses, International Potato Center (CIP), Lima, Peru

Link to bibliography (Google Scholar):