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Postdoc position to develop predictive models of protein synthesis

The Biozentrum of the University of Basel is one of the leading institutes worldwide for molecular and biomedical basic research and teaching. It is home to more than 30 research groups with scientists from over 40 countries. Research at the Biozentrum focuses on the areas of Cell Growth & Development, Infection Biology, Neurobiology, Structural Biology & Biophysics and Computational & Systems Biology. With its more than 500 employees, the Biozentrum is the largest department at the University of Basel’s Faculty of Science.

A postdoc position is available in the research group of  Prof. Zavolan  at the Biozentrum, University of Basel to develop predictive models of protein synthesis in eukaryotic cells.

Our computational biology group, which is part of the Biozentrum and the Swiss Institute of Bioinformatics, is composed of experimental and theoretical scientists that study various aspects of cell fate determination, in relation to aging and diseases. Recently, protein synthesis by the ribosome has attracted renewed attention, with the discovery that a variety or RNA-binding proteins can modulate translation of individual mRNAs in time and space. Our group has identified a number of ribosomal proteins with cell type-specific expression, due either to transcription regulatory events or to copy number variations (in cancers). We have further developed an approach to estimate the rates of translation initiation and elongation for individual transcripts, which allows us to study the variation in these rates between cell types. Moreover, we developed approaches to identify the transcript isoforms that are expressed and undergo varying translation in various cell types, up to the level of single cells. The project aims to apply this approach to various mammalian systems.

References

  1. Guimaraes JC, Zavolan M. Patterns of ribosomal protein expression specify normal and malignant human cells. Genome Biol. 2016 Nov 24;17(1):236.
  2. Mittal N, Guimaraes JC, Gross T, Schmidt A, Vina-Vilaseca A, Nedialkova DD, Aeschimann F, Leidel SA, Spang A, Zavolan M. The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan. Nat Commun. 2017 Sep 6;8(1):457.
  3. Essig K, Kronbeck N, Guimaraes JC, Lohs C, Schlundt A, Hoffmann A, Behrens G, Brenner S, Kowalska J, Lopez-Rodriguez C, Jemielity J, Holtmann H, Reiche K, Hackermüller J, Sattler M, Zavolan M, Heissmeyer V. Roquin targets mRNAs in a 3'-UTR-specific manner by different modes of regulation. Nat Commun. 2018 Sep 19;9(1):3810.
  4. Essig K, Hu D, Guimaraes JC, Alterauge D, Edelmann S, Raj T, Kranich J, Behrens G, Heiseke A, Floess S, Klein J, Maiser A, Marschall S, Hrabĕ de Angelis M, Leonhardt H, Calkhoven CF, Noessner E, Brocker T, Huehn J, Krug AB, Zavolan M, Baumjohann D, Heissmeyer V. Roquin Suppresses the PI3K-mTOR Signaling Pathway to Inhibit T Helper Cell Differentiation and Conversion of Treg to Tfr Cells. Immunity. 2017 Dec 19;47(6):1067-1082.

Your profile
We are looking for highly motivated candidates with at basic knowledge of molecular biology and a strong quantitative background, i.e. in physics, mathematics, computer science or computational biology. Candidates should have experience in computational model development and programming, and be familiar with high-throughput biological data analysis (transcriptomics, ribosome footprinting etc.).

We offer
The salary is generous and is set according to the guidelines of the Swiss National Science Foundation. The duration of the project is initially set to be 18 months, but can be extended. Basel is a very international city and a center of life science research, with over 900 life science research companies in the area, including Novartis and Roche. The Biozentrum of the University of Basel is one of the leading institutes worldwide for molecular and biomedical basic research and teaching. It is home to more than 30 research groups with scientists from over 40 countries. Research at the Biozentrum focuses on the areas of Cell Growth & Development, Infection Biology, Neurobiology, Structural Biology & Biophysics and Computational & Systems Biology. With its more than 500 employees, the Biozentrum is the largest department at the University of Basel’s Faculty of Science. Several other academic institutions are also in the city, including the Friedrich Miescher Institute, the ETH Zurich Biosystems Science and Engineering Department, and the Swiss Tropical Institute. The city is less than 5km from both France and Germany and an hour and a half from the Swiss Alps.

Application / Contact
Please send your completed application as a single pdf-file - including application letter, a statement of research interests, CV, diplomas and contact information of at least two referees – to the following e-mail address (also for informal information)

mihaela.zavolan(at)unibasto make life hard for spam bots.ch

Prof. Mihaela Zavolan
Biozentrum, Universität Basel
SIB - Swiss Institute of Bioinformatics
Klingelbergstrasse 50-70
4056 Basel Switzerland