Nikolaus Fortelny
PhD Student co-supervised by Paul Pavlidis
Graduation 2016
Centre for Blood Research
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}alumni.ubc.ca
Research Interests:
I 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
Publications
- Nikolaus Fortelny, Paul Pavlidis, and Christopher M. Overall (2015) The path of no return – Truncated protein N-termini and current ignorance of their genesis. PROTEOMICS, DOI: 10.1002/pmic.201500043
- Nikolaus Fortelny, Jennifer Cox, Reinhild Kappfelhoff, Amanda E. Starr, Philipp F. Lange, Paul Pavlidis, Christopher M. Overall (2014). Network Analyses Reveal Pervasive Functional Regulation Between Proteases in the Human Protease Web. PLoS Biology, 12(5):e1001869. PMID: 24865846.
- Nikolaus Fortelny, Sharon Yang, Paul Pavlidis, Philipp F. Lange* and Christopher M. Overall* (2014) Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events. Nucl. Acids Res. 43 (D1) D290-D297
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Anna Prudova, Katherine Serrano, Ulrich Eckhard, Nikolaus Fortelny, Dana V. Devine, and Christopher M. Overall (2014). TAILS N-terminomics of human platelets reveals pervasive metalloproteinase dependent proteolytic processing in storage. Blood, blood-2014-04-569640
Education:
- 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)
