Gregor Rot

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

I am a Computer Scientist and Bioinformatician, mostly working on computational analysis of RNA and crafting useful and beautiful web applications along the way, to easily share and discuss results of analysis with fellow scientists.

An example web application we developed is the collaborative platform expressRNA, which integrates protein-RNA binding iCLIP with regulatory (exon and polyA site) information from high-throughput sequencing datasets (RNA-seq, 3'-end targeted RNA-seq). This allows us to study how protein-RNA binding regulates inclusion or exclusion of features (alternative splicing in case of exons and alternative polyadenylation in case of polyA sites).

Feel free to contact me in case you are interested in establishing 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



Research

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 and Prof. Jernej Ule and his group at the Francis Crick Institute, London, UK.

Phd times were very intense and interesting times, during which the scientific support and kindness of several people allowed me to establish many fruitful collaborations with fellow scientists around the world.
April 2013 - August 2016

Masters in Computer Science

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

I am fascinated with computers, i see them as machines that can be used to solve and answer various questions across fields. I like the algorithmic / programming aspects of computer science and also the theoretical computability questions. I wrote a short article in Slovenian on Alan Turing at the time (On Computability of Love) and was impressed by Chomsky hierarchy.

I then moved on to more practical questions in biology and became a bioinformatician towards the end of my studies. I realized that i am having a blast doing data analysis in collaboration with experimental biologists.

2001 - 2008

Software

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

Research Platforms
expressRNA: post-transcriptional open-source integrative analytics platform, combining protein-RNA binding datasets with feature selection (from RNA-seq) and motif signals. I developed this platform during my Phd and i am keeping it alive, also using my own personal funding. Currently, we are extending it to allow upload of long-read sequencing data (Nanopore, PacBio). Additionally, we plan to include single-cell RNA-seq alternative polyadenylation analysis, since 10xGenomics data is 3'-end targeted, which allows for detailed studies of RNA 3'-end regulation.

RNAmotifs2: an independent Python package, the cluster version of the RNAmotifs software (extended to look for regulatory motif clusters). The software is integrated with expressRNA and for now doesn't have a web interface of it's own.

SNPsyn: a Flash interface to the GWAS SNP-SNP interaction web analytics software. It allows the upload of SNP data with phenotype to then compute synergistic SNP pairs which explain the phenotype.

dictyExpress: gene expression profile analytics of Dictyostelium discoideum, a very interesting (and social!) amoeba. The initial version of this software (Rot et al., 2009) was one of the first interfaces of this kind (Flash), which allowed the exploratory analysis of gene expression profiles from RNA-seq data.

Lessons Learned
If i look back at my path with scientific software development, i would say that probably the best way for research labs to share analysis and results (apart from publications) is in developing intuitive online apps and well documented+portable software. This takes a lot of time but gives visibility and is important for the research community.

Interests

I always liked computers, the machines that run algorithms. Not like in life, the output is predictable from the input (and you can always re-run).

In primary school, my brother started a computer class with ZX Spectrums and soon i was hooked. In no time we were "fighting" at home for a Commodore 64 and later for a PC 286 with 40 MB of hard drive and i think 1MB of RAM. Later i somehow got access to the computer room at the gymnasium with a 64 Kbit/s internet connection. I setup the first Linux webserver there and spent countless hours programming. Meanwhile the gymnasium also sparked additional interests, especially in biology and philosophy and gave me a very broad education.

At the end of my CS studies i got very lucky again since computer science and biology somehow magically combined via bioinformatics (not really magically, more like thanks to the revolution in next-generation sequencing), and i learned to balance the philosophical why? with the technical how?.

When away from computers, reading books calms me down, running helps me put things into perspective and fitness is just the best. A long time passion is portrait photography.