We have developed iCount - an open-source and freely available computational pipeline. The system allows users to perform comprehensive and complex data analyses of ChIP-Seq, RNA-Seq and iCLIP experiments for the study of protein-RNA interactions. Over 30 research groups from institutions across the world are currently using our laboratory installation of iCount to study protein-RNA interactions of approximately 60 proteins and their role in alternative splicing. We have presented iCount at one of the most important conferences devoted to computational biology (ECCB10).
F.06 Development of a new product
COBISS.SI-ID: 7925076We have developed iDiscover, an intelligent assistant for comprehensive analysis of transcriptome data. The system guides the user towards most interesting results of analysis and thus supports the user in forming new hypotheses on regulation of transcription. It connects to iCount, which allows users to perform complex and comprehensive analyses of ChIP-Seq, RNA-Seq and iCLIP experiments for the study of protein-RNA interactions. By automatically comparing and sifting through the results of analyses present in iCount’s on few thousands of experiments, it identifies general patterns typical of larger subgroups of data as well as experiment-specific relations among transcriptome elements. We have presented iDiscover at one of the most important conferences devoted to computational biology (ISMB ECCB 2011).
F.06 Development of a new product
COBISS.SI-ID: 8501076I have delivered a lecture to 40 doctoral students at the IRTG (International Research Training Group) workshop, which was a satellite to the TRR81-Symposium “Chromatin Changes in Differentiation and Malignancies” and prepared the students for the symposium lectures. I have presented the workflow and methodologies for the analysis of protein-RNA interaction data. I have also presented the iCount and iDiscover programs that we have developed in this project. The presentation included also a practical, hands-on part.
F.18 Transfer of new know-how to direct users (seminars, fora, conferences)
COBISS.SI-ID: 8594260Following an invited lecture on the bioinformatics for the analysis of protein-RNA interactions, which were developed in Slovenija in collaboration with Jernej Ule’s laboratory at MRC LMB, Cambridge, UK, researcher Tomaž Curk, PhD, received an initiation for a longer visit of Matthias Hentze’s laboratory at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany. The ten-month visit started in September 2012. During the stay, Curk will develop new computational methods for the identification of interaction sites on proteins and also to plan long-term research collaboration.
B.06 Other
COBISS.SI-ID: 9028436