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.
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
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
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.
|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.|
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 :-)