Biotechnological Hub of the NIB (BTH-NIB)

The purpose of the investment project BTH-NIB is the assurance of the appropriate infrastructural conditions for the use of research and developmental opportunities in the fields of operation of the NIB.

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Dr. Denis Kutnjak

Working place: Scientific Associate

Telephone number: +386 (0)59 23 28 30
Department: Department of Biotechnology and Systems Biology

Denis Kutnjak is employed at the National Institute of Biology (NIB), Department of Biotechnology and Systems Biology, Ljubljana, Slovenia, from 2012 on, currently as a Scientific Associate. From 2021 on, he is leading a research unit Microbiology within the Department.

His research interests include studies on diversity, evolution and epidemiology of viruses. He uses modern and classical virological tools to study viromes of plants, animals and environmental samples. He is specialized in the use of high-throughput sequencing and bioinformatics in virology and is transferring those skills also into other fields, such as virus diagnostics in plants and wastewater, as well as into studies focusing on environmental DNA.

Education and work experience

Denis Kutnjak finished his undergraduate studies in Biology at the Biotechnical Faculty of the University of Ljubljana, Slovenia in 2012. He conducted laboratory part and prepare his graduation thesis during the visit at the Institute of Botany of the University of Innsbruck, Austria (Prof. Božo Frajman, PhD), where he was later shortly employed as a project collaborator, working on plants' phylogenetics, phylogeography and conservation genetics.

In 2012, he started his PhD studies at the Jožef Stefan International Postgraduate School, Ljubljana, Slovenia (Nanosciences and Nanotechnologies), where he defended his PhD thesis in 2016. He did his PhD under the supervision of Prof. Maja Ravnikar, PhD. His research was focused on the use of high-throughput sequencing technologies for discovery and diversity studies of viruses. During his PhD, in 2012, he visited the International Potato Center (CIP), Lima, Peru (Jan F. Kreuze, PhD), and in 2016, the Institute for Plant Molecular and Cellular Biology, Valencia, Spain (Prof. Santiago F. Elena, PhD).

After the completion of his PhD studies, he continued his work in the fields of biology, diversity studies and evolution of plant viruses, introduction of modern methods for the detection of viruses in the diagnostic lab and studies of viromes from diverse sample types. In 2019 and 2020 he conducted a postdoctoral research stay at the Institute for Integrative Systems Biology (I2SysBio) in Valencia, Spain (Prof. Santiago F. Elena, PhD), where he studied the dynamics of viral populations in different transmission modes and priming effects of non-concurrent viral infections in plants. During SARS-CoV-2 pandemics, he was actively involved in the establishment and implementation of SARS-CoV-2 monitoring in wastewaters.

Selected publications:

PECMAN Anja, ADAMS Ian, GUTIÉRREZ-AGUIRRE Ion, FOX Adrian, BOONHAM Neil, RAVNIKAR Maja and KUTNJAK Denis. Systematic Comparison of Nanopore and Illumina Sequencing for the Detection of Plant Viruses and Viroids Using Total RNA Sequencing Approach. Front. Microbiol. 2022, 13:883921. DOI:

GREGORIČ, Matjaž, KUTNJAK, Denis, BAČNIK, Katarina, GOSTINČAR, Cene, PECMAN, Anja, RAVNIKAR, Maja, & KUNTNER, Matjaž. Spider webs as eDNA samplers: Biodiversity assessment across the tree of life. Molecular Ecology Resources, 2022, 00, 1–12. DOI:

RIVAREZ, Mark Paul Selda, VUČUROVIĆ, Ana, MEHLE, Nataša, RAVNIKAR, Maja, KUTNJAK, Denis. Global advances in tomato virome research : current status and the impact of high-throughput sequencing. Frontiers in microbiology. 2021, vol. 12, str. 1-22. ISSN 1664-302X., DOI: 10.3389/fmicb.2021.671925.

SILVA, Washington da, KUTNJAK, Denis, XU, Yi, XU, Yimin, GIOVANNONI, James, ELENA, Santiago F., GRAY, Stewart. Transmission modes affect the population structure of potato virus Y in potato. PLOS pathogens. 23 Jun. 2020, 16, 6, str. e1008608, 1-23, ilustr. ISSN 1553-7366., DOI: 10.1371/journal.ppat.1008608.

BAČNIK, Katarina, KUTNJAK, Denis, PECMAN, Anja, MEHLE, Nataša, TUŠEK-ŽNIDARIČ, Magda, GUTIÉRREZ-AGUIRRE, Ion, RAVNIKAR, Maja. Viromics and infectivity analysis reveal the release of infective plant viruses from wastewater into the environment. Water research. 2020, vol. 177, str. 1-11. ISSN 0043-1354. DOI: 10.1016/j.watres.2020.115628.

PECMAN, Anja, KUTNJAK, Denis, GUTIÉRREZ-AGUIRRE, Ion, ADAMS, Ian, FOX, Adrian, BOONHAM, Neil, RAVNIKAR, Maja. Next generation sequencing for detection and discovery of plant viruses and viroids : comparison of two approaches. Frontiers in microbiology. 2017, vol. 8, str. 1-10. ISSN 1664-302X., DOI: 10.3389/fmicb.2017.01998.

KUTNJAK, Denis, ELENA, Santiago F., RAVNIKAR, Maja. Time-sampled population sequencing reveals the interplay of selection and genetic drift in experimental evolution of Potato virus Y. Journal of virology. 2017, vol. 91, iss. 16, str. 1-17. ISSN 0022-538X. DOI: 10.1128/JVI .00690-17.

KUTNJAK, Denis, KUTTNER, Michael, NIKETIĆ, Marjan, DULLINGER, Stefan, SCHÖNSWETTER, Peter, FRAJMAN, Božo. Escaping to the summits : phylogeography and predicted range dynamics of Cerastium dinaricum, an endangered high mountain plant endemic to the western Balkan Peninsula. Molecular phylogenetics and evolution. 2014, vol. 78, str. 365-374. ISSN 1055-7903., DOI: 10.1016/j.ympev.2014.05.015.

Link to bibliography (Google Scholar):