Education
Phd in Bioinformatics, 2013-2016
Institute of Molecular Life Sciences; Prof. Christian von Mering group, University of Zurich, Zurich, Switzerland
Msc in Computer Science, 2001-2008
Faculty of Computer and Information Science; University of Ljubljana, Ljubljana, Slovenia

Research
Latest Research, 2013-present
Analysis of 3rd generation long-read datasets (Nanopore) to extract alternative polyadenylation and alternative splicing information and look at how both processes interconnect; the Nanopore whole transcript reads provide novel opportunities for studying post-transcriptional processing
post-transcriptional analysis (alternative polyadenylation, alternative splicing, motif analysis) on NGS data (human, mouse, fly) in collaboration with UCL, London, UK; Francis Crick Institute, London, UK; Center for Cancer Research, NIH, USA; Lexogen, Vienna, Austria;
development of post-transcriptional research platform expressRNA.org
RNA-protein binding (iCLIP protocol) analytics in collaboration with MRC Laboratory of Molecular Biology, Cambridge, UK and University College London, London, UK
Early Work in Bioinformatics, 2008-2013
iCLIP analytics in collaboration with MRC LMB, Cambridge, UK
RNA-seq and ChIP-seq analytics in collaboration with Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
comparative genomics of fungal plant pathogens using NGS data of DNA/RNA samples in collaboration with Biotechnical Faculty, Ljubljana, Slovenia

Professional
Experience
University of Zurich, 2013-present, UZH home page
scientific software developer: analysis pipelines, interactive web applications using Javascript (client-side) and Apache+Python+Mysql (server-side), database integration
analysis of high-throughput sequence datasets (iCLIP, RNA-seq, 3’-end-seq)
modelling of post-transcriptional processes (alternative splicing and polyadenylation)
novel algorithms for regulatory motif discovery from RNA-seq datasets
University of Ljubljana, 2008-2013
data analyst and scientific programmer (Python, Adobe Flash, Mysql)
@ Bioinformatics Laboratory, Faculty of Computer and Information Science, University of Ljubljana, Slovenia
Company Software Development, 2005-2008
software engineer at SAOP, Nova Gorica, Slovenia (Delphi, PHP, ASP.net)
medical software engineering, Generationbyte, Italy (ASP.net, Delphi)
developing an interactive platform for on-line education and learning, Inter-es, Slovenia (Adobe Flex, Java)

Software
Scientific Online Research Platforms
expressRNA
Post-transcriptional integrative analytics, combining RNA-protein binding with motif signals.
Published: Rot et al., 2017
RNAmotifs2
Cluster branch of the RNAmotifs software, upgraded to look for regulatory motif clusters.
SNPsyn
GWAS SNP-SNP interaction web analytics.
Published: Curk et al., 2011
dictyExpress v1
Gene expression profile analytics.
Published: Rot et al., 2009

Life
Stays Abroad
April 2013 - present: Living in Zurich, Switzerland
December 2012: 1 month visit at Baylor College of Medicine (BCM), Houston, USA
April - June 2011: 3 months visit at Laboratory of Molecular Biology (LMB), Cambridge, UK
September 2005 - July 2006: 2 semester Erasmus student exchange at Czech Technical University (CTU), Prague, Czech Republic
Languages
Slovenian (native), English (fluent), Italian (fluent), French (intermediate), Croatian and Serbian (colloquial), German (beginner)
Python, R, Javascript, JQuery, HTML, CSS, C/C++, SQL, Matlab, Shell scripting, Unix and Windows administration
Hobbies
2016 - present: flute player with Musikverein Harmonie Schwamendingen, Zurich, Switzerland
Sailing, Yoga, Running, Meditation, Photography

Publications
Papers
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
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 (2011) 39, W444–9
Tollervey, J. R., Wang, Z., Hortobagyi, T., Witten, J. T., Zarnack, K., Kayikci, M., Clark, T. A., Schweitzer, A. C., Rot, G., Curk, T., Zupan, B., Rogelj, B., Shaw, C. E. & Ule, J.
Analysis of alternative splicing associated with aging and neurodegeneration in the human brain.
Genome Research (2011), 21, 1572–82
Tollervey, J. R., Curk, T., Rogelj, B., Briese, M., Cereda, M., Kayikci, M., Konig, J., Hortobagyi, T., Nishimura, A. L., Zupunski, V., Patani, R., Chandran, S., Rot, G., Zupan, B., Shaw, C. E. & Ule, J.
Characterizing the RNA targets and position-dependent splicing regulation by TDP-43.
Nature Neuroscience (2011) 14, 452–8
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
Parikh, A., Miranda, E. R., Katoh-Kurasawa, M., Fuller, D., Rot, G., Zagar, L., Curk, T., Sucgang, R., Chen, R., Zupan, B., Loomis, W. F., Kuspa, A. & Shaulsky, G.
Conserved developmental transcriptomes in evolutionarily divergent species.
Genome Biology (2010) 11, R35
Wang, Z., Kayikci, M., Briese, M., Zarnack, K., Luscombe, N. M., Rot, G., Zupan, B., Curk, T. & Ule, J.
iCLIP predicts the dual splicing effects of TIA-RNA interactions.
PLoS Biology (2010) 8
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-based interface.
BMC Bioinformatics (2009) 10, 265
Book Chapters
Miranda, E. R., Rot, G., Toplak, M., Santhanam, B., Curk, T., Shaulsky, G. & Zupan, B.
Transcriptional Profiling of Dictyostelium with RNA Sequencing.
Eichinger, L. & Rivero, F., 139– 171, Humana Press, Totowa, NJ, 2013
Phd Thesis
Rot, G. Integrative Approaches for Studying Regulatory Principles of Alternative Polyadenylation.
Committee: von Mering, C., Ule, J., Curk, T., Ciaudo, C., Robinson, M.
University of Zurich, Zurich, Switzerland. 17th August 2016
Last updated: 20171222; Comment platform by Disqus