Selected Publications
Complete publications at Google Scholar

 Currently I am continuing work on expressRNA and helping develop microbeAtlas, an interactive fast interface to the analysis of more than 1M metagenomic samples. I also try to maintain several collaborations on RNA bioinformatics. Main publications from this period are:

Miha Modic, Markus Grosch, Gregor Rot, Silvia Schirge, Tjaša Lepko, Tomohiro Yamazaki, Flora C.Y. Lee, Ejona Rusha, Dmitry Shaposhnikov, Michael Palo, Juliane Merl-Pham, Davide Cacchiarelli, Boris Rogelj, Stefanie M. Hauck, Christian von Mering, Alexander Meissner, Heiko Lickert, Tetsuro Hirose, Jernej Ule, Micha Drukker
Cross-Regulation Between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition

 During my Phd I developed integrative approaches to study post-transcriptional modifications. We combined regulatory information with RNA-protein binding iCLIP data. In this way, we can visualize and represent regulatory information on exon/polyA site usage in relation to RNA-protein binding. You can read more about this and other work in these publications:

Gregor Rot, Zhen Wang, Ina Huppertz, Miha Modic, Tina Lenče, Martina Hallegger, Nejc Haberman, Tomaž Curk, Christian von Mering, Jernej Ule
High-resolution RNA maps suggest common principles of splicing and polyadenylation regulation by TDP-43
Cell Rep (2017)
Matteo Cereda, Uberto Pozzoli, Gregor Rot, Peter Juvan, Anthony Schweitzer, Tyson Clark, Jernej Ule
RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing
Genome Biology (2014)

 In May 2008 I started working on several bioinformatics projects at the Faculty of Computer and Information Science in Ljubljana. We developed dictyExpress, probably the most advanced web application for gene expression profile analytics (clustering, GO enrichment analysis) at the time. I co-developed the first analysis pipeline for iCLIP RNA-protein binding data and started working on analysis of post-transcriptional modifications. Publications from this period include:

Julian Konig, Kathi Zarnack, Gregor Rot, Tomaž Curk, Melis Kayikci, Blaž Zupan, Daniel J Turner, Nicholas M Luscombe, & Jernej Ule
iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
Nature Structural & Molecular Biology (2010)
Boris Rogelj, Laura E. Easton, Gireesh K. Bogu, Lawrence W. Stanton, Gregor Rot, Tomaž Curk, Blaž Zupan, Yoichiro Sugimoto, Miha Modic, Nejc Haberman, James Tollervey, Ritsuko Fujii, Toru Takumi, Christopher E. Shaw, Jernej Ule
Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain
Nature Scientific Reports (2012)
Tomaž Curk, Gregor Rot, Blaž Zupan
SNPsyn: detection and exploration of SNP-SNP interactions
Nucleic Acids Research (2011)
Gregor Rot, Anup Parikh, Tomaž Curk, Adam Kuspa, Gad Shaulsky, Blaž Zupan
dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web interface