Postdoc Position to uncover the regulation and functional relevance of RNA processing in determining cellular fate

The Biozentrum of the University of Basel is one of the leading life sciences institutes in the world. It consists of 30 groups and 500 employees that research how molecules and cells create life, spanning the scale from atom to organism. Founded in 1971, the Biozentrum has been the birth place of many fundamental discoveries in biology and medicine, spawning several Nobel Laureates.

A postdoc position is available in the group of Prof. Zavolan at the Biozentrum, University of Basel to uncover the regulation and functional relevance of RNA processing in determining cellular fate.

Project
Currently available technologies enable the determination of entire transcriptomes up the resolution of single cells. Furthermore, work in the past decade has revealed previously unsuspected regulatory programs of isoform expression in relation to physiological states such as proliferation or differentiation. Our group has uncovered some of these programs, driven by specific RNA-binding proteins, e.g. in cancer cells. Taking advantage of the fact that single cell sequencing technologies specifically isolate transcripts with unique 3' ends, in the coming years we plan to develop methods to identify, quantify and functionally evaluate isoforms that result from alternative RNA processing, particularly through alternative polyadenylation. Linking these isoforms to overall patterns of gene expression we further aim to improve the identification of cell types, and from computational models applied to the these data we aim to identify the regulators driving isoform expression in individual cells.

References
1: Herrmann CJ, Schmidt R, Kanitz A, Artimo P, Gruber AJ, Zavolan M. PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3' end sequencing. Nucleic Acids Res. 2019 Oct 16. pii: gkz918. doi: 10.1093/nar/gkz918.
2: Gruber AJ, Zavolan M. Alternative cleavage and polyadenylation in health and disease. Nat Rev Genet. 2019 Oct;20(10):599-614. doi: 10.1038/s41576-019-0145-z.
3: Kanitz A, Syed AP, Kaji K, Zavolan M. Conserved regulation of RNA processing in somatic cell reprogramming. BMC Genomics. 2019 Jan
31;20(1):100. doi: 10.1186/s12864-019-5438-2.
4: Gruber AJ, Gypas F, Riba A, Schmidt R, Zavolan M. Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms. Nat Methods. 2018 Oct;15(10):832-836. doi: 10.1038/s41592-018-0114-z.
5: Gruber AJ, Schmidt R, Ghosh S, Martin G, Gruber AR, van Nimwegen E, Zavolan M. Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC. Genome Biol. 2018 Mar 28;19(1):44. doi: 10.1186/s13059-018-1415-3.

Your profile
We are looking for candidates with knowledge of molecular biology and a strong quantitative background, i.e. in computational biology, computer science, applied mathematics or physics. Candidates should have experience in software development for life sciences and be familiar with high-throughput biological data analysis.

Application / Contact
Please submit your application letter, a statement of research interests, CV,
and the contact information of at least two references to:

Prof. Mihaela Zavolan
Biozentrum Universität Basel SIB - Swiss Institute of Bioinformatics
Klingelbergstrasse 50-70
4056 Basel Switzerland
email: mihaela.zavolan@unibas.ch


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