Gregor Rot

University of Zurich · Institute of Molecular Life Sciences · Winterthurerstrasse 190, 8057 Zurich, Switzerland · +41 44 63 53148 · gregor.rot@gmail.com

Computer scientist and bioinformatics enthusiast, working in computational research of RNA processing. Our collaborative platform expressRNA integrates RNA-protein binding iCLIP with other high-throughput sequencing signals (3'-end targeted, whole transcriptome) to study alternative polyadenylation and alternative splicing. On top of that, I especially love crafting useful and beautiful explorative scientific web applications.

Contact me to establish new research collaborations.

Ta svet je lep, če nekomu nekaj daš. Ta svet je lep, če nekoga rad imaš, če stisneš roko komu, ki ga kaj boli. Ta svet je lep, če si človek do ljudi.
Tone Pavček



Experience

Postdoc

University of Zurich, Institute of Molecular Life Sciences

Continuing work on expressRNA and helping develop microbeAtlas, an interactive fast interface to the analysis of more than 1M metagenomic samples.

February 2018 - Present

Phd Student

University of Zurich, Institute of Molecular Life Sciences

During my Phd i developed integrative approaches to study post-transcriptional modifications, by combining regulatory information with RNA-protein binding CLIP data. Main publications from this period:

Rot, G., Wang, Z., Huppertz, I., Modic, M., Lenče, T., Hallegger, M., Haberman, N., Curk, T., von Mering, C., Ule, J.
High-resolution RNA maps suggest common principles of splicing and polyadenylation regulation by TDP-43
Cell Rep (2017) 9, 1056–1067

Cereda, M., Pozzoli, U., Rot, G., Juvan, P., Schweitzer, A., Clark, T., Ule, J.
RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing
Genome Biology (2014) 15, R20

April 2013 - August 2016

Scientific Software Developer

University of Ljubljana, Faculty of Computer and Information Science

Worked on several bioinformatics projects. We developed dictyExpress, at the time the most advanced online web application for gene expression profile exploratory analytics with basic on-the-fly bioinformatics (clustering, GO enrichment analysis). Co-developed the first analysis pipeline for iCLIP RNA-protein binding data and started working on analysis of post-transcriptional modifications. Main publications from this period:

Konig, J., Zarnack, K., Rot, G., Curk, T., Kayikci, M., Zupan, B., Turner, D. J., Luscombe, N. M. & Ule, J.
iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
Nature Structural & Molecular Biology (2010) 17, 909–15

Rogelj, B., Easton, L. E., Bogu, G. K., Stanton, L. W., Rot, G., Curk, T., Zupan, B., Sugimoto, Y., Modic, M., Haberman, N., Tollervey, J., Fujii, R., Takumi, T., Shaw, C. E. & Ule, J.
Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain
Nature Scientific Reports (2012) 2, 603

Curk, T., Rot, G., Zupan, B.
SNPsyn: detection and exploration of SNP-SNP interactions
Nucleic Acids Research 39, W444–9, 2011

Rot, G., Parikh, A., Curk, T., Kuspa, A., Shaulsky, G. & Zupan, B.
dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web interface
BMC Bioinformatics (2009) 10, 265

mid 2008 - beginning 2013

Education

Phd in Bioinformatics

University of Zurich, Institute of Molecular Life Sciences, Switzerland
Phd position in Bioinformatics with Prof. Christian von Mering at the Institute of Molecular LIfe Sciences, University of Zurich
April 2013 - August 2016

Masters in Computer Science

University of Ljubljana, Faculty of Computer and Information Science, Slovenia

In the second year i choose the software research study branch and was very fascinated with how theoretical computer science (Chomsky, Turing) is connected with philosophy.

2001 - 2008

Software

Languages
  • Python, R, Javascript, JQuery, Html5, CSS, C/C++, SQL
  • Slovenian, English, Italian, French, Serbian & Croatian

Research Platforms
expressRNA: post-transcriptional integrative analytics, combining RNA-protein binding with motif signals

RNAmotifs2: Cluster branch of the RNAmotifs software, upgraded to look for regulatory motif clusters

SNPsyn: GWAS SNP-SNP interaction web analytics

dictyExpress: Gene expression profile analytics

Interests

I started to be interested in computers in primary school, mainly because my brother started a computer class with ZX Spectrums. Soon we were "fighting" at home for time on a Commodore 64 and later for a PC 286 with 40 MB of hard drive and i think 1MB of RAM. Then the high-school gymnasium in my home town sparked additional interests in biology and philosophy and gave me a broad anthropological education, and also a 64 Kbit/s link to the internet. At the end of college i got very lucky again since computer science and biology somehow magically combined via bioinformatics, and i learned to balance the philosophical why? with the technical how?.

Apart from computers and bioinformatics, a friend once called me an ad-hoc philosopher ;-). I like reading books, moving (running + fitness) and latelly i am getting more into meditation and hiking. A long time passion is portrait photography (however other people sometimes get annoyed by me taking photos, wonder why :-)