PostDoc Position at the University of Basel – Single-cell and personalized regulatory genomics





Post-doc position in single-cell and personalized regulatory genomics

Biozentrum, of Basel, Switzerland

A post-doctoral position is available in the group of Prof. Erik van Nimwegen at the Biozentrum of the of Basel and Swiss Institute of Bioinformatics.

We are looking for highly motivated individuals with strong mathematical and computational skills that are interested in performing theoretical/computational research in regulatory genomics, especially in the areas of single-cell gene regulation and personalized regulatory networks.

Our research group is highly interdisciplinary, involving both an experimental section where researchers with a background in molecular biology are experimentally studying genome evolution and gene regulation at the single cell level in bacteria, and a theoretical section where researchers with backgrounds in theoretical physics, computer science, and applied mathematics are using techniques from Bayesian probability, evolutionary theory, dynamical systems theory, and stochastic processes, to study the function and evolution of genome-wide regulatory networks in cells. We are particularly interested in uncovering the principles by which genome-wide regulatory networks specify and maintain cell identity in multi-cellular organisms, how cells control and exploit the noise in gene regulatory processes, and how gene regulation evolves. A list of our group’s publications can be found here.

For this position we are looking for candidates interested in developing methods for analysis of the regulatory networks that control cell fate decisions and cell identity in multi-cellular eukaryotes.

Our lab has long worked on developing methods for genome-wide prediction of regulatory sites,e.g Siddhartan et al. 2005, Pachkov et al. 2007, Arnold et al. 2011, Khorshid et al. 2013, and in recent years we have developed several methods for analyzing gene regulatory networks by modeling genome-wide gene expression and chromatin state data in terms of constellations of regulatory sites, e.g. Fantom Consortium 2009, Arnold et al 2012, Balwierz et al. 2014. We are interested in extending these methods to model single-cell regulatory dynamics and cell fate decisions by analysis of single-cell RNA-seq data, and to incorporate the effects of SNPs and other genetic variants on the functioning of gene regulatory networks in mammals. As part of these efforts we are collaborating within the BrainStemX project on mammalian forebrain development. The precise topic of the research project will be determined jointly with the candidate and candidates that display initiative and independence will be given priority.


  • Candidates should have strong mathematical and computational skills, and experience with analysis of next-generation sequencing data
  • Experience in areas such as stochastic processes, dynamical systems theory, and Bayesian statistics is a plus
  • Candidates do not necessarily have to have a biological background but should have a strong desire to directly work with experimental biologists
  • The candidates should have a good knowledge of English
  • German is helpful but not necessary
  • The salary is generous and is set according to the guidelines of the Swiss National Science Foundation
  • The start date will by mutual arrangement

To apply, please send a single pdf containing your application letter, CV, and the names of two references by clicking on the ”Apply for this job” button.

Review of applications will begin immediately.


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. 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.