Nikolaus Fortelny

PhD Student co-supervised by Paul Pavlidis

Graduation 2016

Centre for Blood Researchnikolaus
University of British Columbia
2350 Health Sciences Mall
Vancouver, BC, V6T 1Z3, Canada

Lab: #4.420; Bench 12
Phone: +1-604-822-3561 (lab)
Email: nikolaus.fortelny{AT}

LinkedIn ResearchGate


Research Interests:

PBIOLOGY-D-13-03591 Cover ArtI am interested in the workings of systems, in particular biological systems. I believe that, in order to understand the complex, systems-like behavior of organisms, computational integration of data has to go hand in hand with biochemistry for data generation and validation. Aiming to combine these approaches, I try to characterize the “protease web”, a biological network of proteases and protease inhibitors active in- and outside of human cells. Through this network, proteases can alter the activity of other proteases in vivo and thus influence cleavage of a large number of indirect substrates in addition to their direct substrates. I use graph modeling and data-mining to analyze this network and to compare it to other networks of proteins or genes. To enable biochemical validation, I aim to predict testable proteolytic pathways in vivo, through the analysis software PathFINDer, which is implemented as part of our TopFIND database. Building on the protease web analysis, I am also interested in facilitating general analysis of proteomic data, in particular protein termini (e.g. through the program TopFINDer).

Global (network-like) interactions between proteases and their inhibitors

  • Modeling cleavage and inhibition interactions in the protease web
  • (Co-)expression of protease and inhibitors and their isoforms
  • Using co-expression data to predict interactions in the protease web
  • General protein-protein interactions networks

Analysis and interpretation of protein termini (the terminome)

  • Pre- and post-translational processes that shape the terminome (alternative splicing, alternative translation, cleavage,…)
  • Intersection of the terminome with the protease web (identifying paths in the protease web that connect proteases to indirect substrates)
  • Development of TopFIND database and analysis tools to store and interpret protein termini related data



  • PhD in Biochemistry at UBC Vancouver (in the process)
  • M.Sc. in Bioinformatics and Proteomics, University of Geneva, Switzerland (thesis)
  • B.Sc. in Molecular Biology, University of Vienna, Austria

Other interests:

  • Bringing scientific concepts to the high-school classroom by mentoring and judging at the Let’s Talk Science – Science Fair
  • Out- and in-reach to students, faculty, and high-school students at UBC through the  Graduate student association
  • Teaching biochemistry to undergrads (UBC course BIOC302) and bioinformatics to graduate students (UBC course GSAT501)

CIMG6893 garibaldi