Doc. Dr. Jernej Zupanc

[ email | bibliography | personal page ]

Jernej was a postdoc at Bionanoteam (2011-2012). This page remains as a research CV.

I develop image processing and data analysis solutions for life sciences. From research to application, from microscopy to synchrotron data, from pixels to plots.

Majority of my scientific work has been aimed towards developing a method for assessing whether nanoparticles interact with lipid membranes. Various steps of this biosensor-based method that is still being developed at Bionanoteam have been published in a number of papers, but for a quick grasp, one can skim over my PhD thesis. The thesis also contains an introduction into large-scale/virtual/computational microscopy.

My research interests are also in:

  • bioimage informatics,
  • large scale microscopy,
  • soft computing,
  • data analysis,
  • computer vision.

I hold a PhD in Computer Science (2011) from the Faculty of Computer and Information Science, University of Ljubljana, Slovenia.

Awards, honors, and grants:

  • (2012) Most important Slovenian scientific contribution in the domain: Technology driven physics for year 2011, ARRS – Slovenian Research Agency
  • (2011) Dean’s Award, Faculty of Computer and Information Science, University of Ljubljana
  • (2010) WFS – World Federation of Scientists Scholarship [ ceremony ]
  • (2010) SLO – USA Bilateral research project. Two year grant for research visits [ BI-US/11-12/017 ]
  • (2010) UNESCO grant for participation in Euroscience Open Forum in Torino, Italy
  • (2009) Fulbright Scholarship, Boston, USA (2009/2010)
  • (2007) Best Student Paper award, International conference DSI 2007 [ site ]

International activities:

Reviewer for:

FTIR microscopy reveals distinct biomolecular profile of crustacean digestive glands upon subtoxic exposure to ZnO nanoparticles
Romih T, Jemec A, Novak S, Vaccari L, Ferraris P, Šimon M, Kos M, Susič R, Kogej K, Zupanc J, Drobne D
[ pdf ] [ site ] Nanotoxicology

Lipid Vesicle Shape Analysis from Populations Using Light Video Microscopy and Computer Vision
Zupanc J, Drašler D, Boljte S, Kralj-Iglič V, Iglič A, Erdogmus D, Drobne D
[ pdf ] [ site ] PLoS One

Effects of magnetic cobalt ferrite nanoparticles on biological and artificial lipid membranes
Drašler B, Drobne D, Novak S, Valant J, Boljte S, Otrin L, Rappolt M, Sartori B, Iglič A, Kralj-Iglič V, Šuštar V, Makovec D, Gyergyek S, Hočevar M, Godec M, Zupanc J
[ pdf ] [ site ] International Journal of Nanomedicine

Cellular Internalization of Dissolved Cobalt Ions from Ingested CoFe2O4 Nanoparticles: In Vivo Experimental Evidence
Novak S, Drobne D, Golobič M, Zupanc J, Romih T, Gianoncelli A, Kiskinova M, Kaulich B, Pelicon P, Vavpetič P, Jeromel L, Ogrinc N, Makovec D
[ pdf ] [ site ] Environmental Science & Technology

Effect of engineered TiO2 and ZnO nanoparticles on erythrocytes, platelet-rich plasma and giant unilamelar phospholipid vesicles
Šimundić M, Drašler B, Šuštar V, Zupanc J, Štukelj R, Makovec D, Erdogmus D, Hagerstrand H, Drobne D, and Kralj-Iglič V
[ pdf ] [ site ] BMC Veterinary Research

Experimental evidence for the interaction of C-60 fullerene with lipid vesicle membranes
Zupanc J, Drobne D, Drašler B, Valant J, Iglič A, Kralj-Iglič V, Makovec D, Rappolt M, Sartori B, Kogej K
[ pdf ] [ site ] Carbon

Markov Random Field Model for Segmenting Large Populations of Lipid Vesicles from Micrographs
Zupanc J, Drobne D, Ster B
[ pdf ] [ site ] Journal of Liposome Research

Biological Reactivity of Nanoparticles: Mosaics from Optical Microscopy Videos of Giant Lipid Vesicles
Zupanc J, Drobne D, Erdogmus D, Bas E, Valant J, Dobnikar A
[ pdf ] [ site ] Journal of Biomedical Optics

A new approach to analyse effects of nanoparticles on lipid vesicles
Zupanc J, Valant J, Drobne D, Kralj-Iglič V, Iglič A
[ pdf ] [ site ] International Journal of Biomedical Nanoscience and Nanotechnology