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.

Play Video About project      Publication

Assist. Prof. Dr. Špela Baebler

Working place: Senior Research Associate

Telephone number: +386 (0)59 23 28 25
Department: Department of Biotechnology and Systems Biology


1992-1998       University of Ljubljana, Biotechnical faculty, Biology Department
1998-2006       University of Ljubljana, Biotechnical faculty, Interdisciplinary postgraduate study of Biotechnology


1998-2006              National Institute of Biology, Young Researcher
2006-present         National Institute of Biology, Researcher


1) Potato – potato virus Y interaction, systems biology approach 

We are investigating the interaction of potato with its agronomically important viral pathogen, PVY on different (molecular, transcriptome, proteome, sRNA) levels. We have confirmed the role of plant hormone salicylic acid in the hypersensitive resistance response of cv. Rywal (Baebler et al., 2014). Whole genome transcriptome analysis has shown a delayed response in potato plants without salicylic acid and identified potential players of the resistance response. We have also shown that the virus is not limited by the HR lesion, confirming that HR cell death is separated from the resistance mechanisms which lead to PVY restriction in Ny-1 genetic background (Lukan et. al, 2018). Moreover, we have shown that in the salicylic acid-dependent response to PVY (Baebler et al., 2011), small RNAs represent important regulatory layer, connecting development and immune signalling (Križnik et al., 2017).
Figure: Symptom appearance and number of differentially expressed genes (bold, upregulated; regular, downregulated) in virus vs. mock treated plants of cv. Rywal (left) and NahG-Rywal (right). (Baebler et al, 2014)

Selected publications

  • Baebler Š, Witek K, Petek M, Stare K, Tušek-Znidaric M, Pompe-Novak M, Renaut J, Szajko K, Strzelczyk-Zyta D, Marczewski W, et al. 2014. Salicylic acid is an indispensable component of the Ny-1 resistance-gene-mediated response against Potato virus Y infection in potato. Journal of experimental botany 65, 1095–1109.
  • Baebler Š, Stare K, Kovač M, Blejec A, Prezelj N, Stare T, Kogovšek P, Pompe-Novak M, Rosahl S, Ravnikar M, et al. 2011. Dynamics of Responses in Compatible Potato - Potato virus Y Interaction Are Modulated by Salicylic Acid (G Bonaventure, Ed.). PLoS ONE 6, e29009.
  • Križnik M, Petek M, Dobnik D, Ramšak Ž, Baebler Š, Pollmann S, Kreuze J, Žel J, Gruden K. 2017. Salicylic acid perturbs sRNA-gibberellin regulatory network in immune response of potato to Potato virus Y infection. Frontiers in Plant Science, vol. 8, str. 1-14.
  • Lukan T, Baebler Š, Pompe Novak M, Guček K, Zagorščak M, Coll Rius A, Gruden K. 2018. Cell death is not sufficient for the restriction of potato virus Y spread in hypersensitive response-conferred resistance in potato. Frontiers in Plant Science.


2) Development and data analysis tools 

We are focusing on various approaches to omics data analysis, integration and visualization. Recently we have developed GoMapMan (, an open web-accessible resource for gene functional annotations in the plant sciences and quantGenius (, a web application for qPCR data analysis. 

Figure: Scheme of developed resources GoMapMan (left) and quantGenius (right)

Selected publications

  • Baebler Š, Svalina M, Petek M, Stare K, Rotter A, Pompe Novak M, Gruden K. 2017. quantGenius : implementation of a decision support system for qPCR-based gene quantification. BMC Bioinformatics.
  • Ramšak Ž, Baebler Š, Rotter A, Korbar M, Mozetič I, Usadel B, Gruden K. 2014. GoMapMan: integration, consolidation and visualization of plant gene annotations within the MapMan ontology. Nucleic acids research 42, D1167–75.
  • Rotter A, Usadel B, Baebler Š, Stitt M, Gruden K. 2007. Adaptation of the MapMan ontology to biotic stress responses: application in solanaceous species. Plant methods 3, 10.

3) Transcriptomics in pharmaceutical biotehnology and ecotoxicology

Transcriptome analysis was applied in optimization of drug development (Petek et al., 2010), characterisation of pharmaceutical production strains (Kirm et al., 2013), cell line development (Jamnikar et al., 2015) and in response of to environmental residues of cytostatics (Kovacs et al., 2015).

Figure: Left - model of transcriptome response to fosfomycin primary effect in S. aureus (Petek at al., 2010). Right - Histology, DNA damage and gene expression effects of 5-FU in zebrafish after chronic exposure to low doses of the cytostatic 5-fluorouracile (Kovacs et al, 2015) 

Selected publications

  • Jamnikar U, Nikolić P, Belič A, Blas M, Gaser D, Francky A, Laux H, Blejec A, Baebler Š, Gruden K. 2015. Transcriptome study and identification of potential marker genes related to the stable expression of recombinant proteins in CHO clones. BMC biotechnology, 15, 98.
  • Karničar K, Drobnak I, Petek M, Magdevska V, Horvat J, Vidmar, R, Baebler Š, Rotter A, Jamnik P, Fujs Š, Turk B, Fonović M, Gruden K, Kosec G, Petković H. 2016. Integrated omics approaches provide strategies for rapid erythromycin yield increase in Saccharopolyspora erythraea.
  • Kovács R, Csenki Z, Bakos K, Urbányi B, Horvath A, Garaj-Vrhovac V, Gajski G, Gerić M, Negreira N, Lopez De Alda M, Barceló D, Heath E, Kosjek T, Žegura B, Novak M, Zajc I, Baebler Š, Rotter A, Ramšak Ž, Filipič M. Assessment of toxicity and genotoxicity of low doses of 5-fluorouracil in zebrafish (Danio rerio) two-generation study. Water research, 2015, 77, 201-212.
  • Petek M, Baebler Š, Kuzman D, Rotter A, Podlesek Z, Gruden K, Ravnikar M, Urleb U. 2010. Revealing fosfomycin primary effect on Staphylococcus aureus transcriptome: modulation of cell envelope biosynthesis and phosphoenolpyruvate induced starvation. BMC microbiology 10, 159.



  • Co-founder NIB spin-out company BioSistemika d.o.o., organization common NIB-BioSistemika workshops (
  • Science communication: organization of events, TV and radio shows (in Slovene).  


  • SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture, (2018-20120, ERANet Cobiotech project, national coordinator,
  • Fate and effects of cytostatic pharmaceuticals in the environment and the identification of biomarkers for and improved risk assessment on environmental exposure  (Cytothreat; FP7 project, 2011-2014; WP leader,
  • Biotechnology and Plant Sistems Biology (programme, 2015-2020)
  • Spatiotemporal analysis of hypersensitive response to Potato virus Y in potato (2016-2019)
  • Setting up the basis for multiscale systems analysis of potato defence signalling (2014-2017)
  • Analysis of heterogeneous information networks for knowledge discovery in lifesciences (2016-2019)


  • COST Action CA15110, Harmonising standardisation strategies to increase efficiency and competitiveness of European life-science research, management committee member (2016-2019)
  • Centre for Functional Genomics and Biochips, substitute to management committee member
  • Slovenian Society of Plant Biology president
  • NIB business committee  member (2010-2017)
  • External supervisory member of BioApp Interreg project
  • Manuscript reviewer for Molecular Plant-Microbe Interactions, Journal of Experimental Botany, PlosOne, Plant Physiology in Biochemistry,  Journal of Plant Physiology and Central European Journal of Biology


Špela Baebler was born in 1973 in Ljubljana. In 1998 she graduated from the Department of Biology, Biotechnical Faculty, University of Ljubljana. As stipend of the Japanese government, she has studied 6 months at Miyazaki University (Japan). After graduation, she has been working at National Institute of Biology in Ljubljana as a junior researcher. In 1998 she enrolled in a postgraduate program of Biotechnology at the Biotechnical faculty. In 2001 she has completed Master Course with a thesis on plant secondary metabolite production and received Krka award. As a part of her PhD study, she was investigating of gene expression in potato – virus interactions, using microarray and quantitative PCR analysis and defended the thesis 2006. Since then she is continuing her work on the plant – virus interactions focusing on the development of tools that enable easier interpretation oh high-throughput data. Moreover, she is involved in several industrial projects with the main focus of implementing systems biology approaches in pharmaceutical industry. She was work package leader of an FP7 project Cytothreat aimed at identification of environmental risks of cytostatic residues. Currently, she is a national coordinator of an ERANet Cobiotech project SUSPHIRE with a goal to develop bioproduction of alternative plant protection agents. 
She is a co-founder of NIB spin-out company BioSistemika and organizer and lecturer at quantitative PCR workshops, organised in collaboration of NIB and BioSistemika. She teaches at University of Ljubljana and Jožef Stefan postgraduate school and is involved in several science communication activities. She is fluent in English (CAE certificate) and can communicate in French and Japanese.