University of Basel (Unibas)
Type of contract
Understanding how a fertilized egg develops into a complex multicellular organism is one of the most fascinating topics in biology.
The current challenge is to understand how genes function as part of gene regulatory networks (GRNs) that control the proliferation and patterning of progenitor and stem cells during embryonic development. Our group uses the mouse limb bud as a paradigm to study the transcriptional and epigenetic mechanisms controlling gene expression during organogenesis. To this aim, we combine genetic, molecular, and cellular analysis with bioinformatics and computational biology (http://www.devgenbasel.com). These studies allow us to gain insights into the GRNs that provide embryonic development with robustness and study the molecular changes underlying evolutionary diversification of limb development.
The successful candidate will join our ongoing SNF-funded research projects and closely interact with the experimentalists in the group. This should generate significant synergies, which increases the chance of innovative research and publications (see below). In particular, the bioinformatics postdoctoral fellow will be involved in novel studies from the moment of study design in collaboration with the wet lab scientists. To study the interactions among transcription factors that control the expression of shared target gene networks, we are setting up Rapid Immunoprecipitation Mass spectrometry of Endogenous protein (RIME) for key epitope-tagged transcription factors. This will require the establishment of standards and a bioinformatics pipeline in close collaboration with the experimentalists. In follow-up studies candidate interaction partners will be verified which requires further omics studies, GRN construction, and network analysis.
A second main focus of our research is a state-of-the-art comparative analysis of large-scale omics datasets such as total and single-cell RNA-seq generated from limb buds from mice and other species. To gain insight into differential transcriptional regulation, RNA-seq analysis is combined with chromatin structure and epigenetic marker analysis using ChIP-seq, capture-HiC, total and single-cell ATAC-seq, and available datasets from other resources. This will allow us to gain insight into systems robustness and the plasticity underlying diversification and is complementary to proteomics studies. Finally, the bioinformatician is the group’s liaison to the Departmental Bioinformatics Core Facility. He/she also supervises the group’s data storage and project hubs at the University of Basel SciCore Center (http://scicore.unibas.ch).
A stimulating research environment in an internationally renowned research team at the Department of Biomedicine at the University of Basel with a track record of innovative research that incorporates bioinformatics and computational approaches: Lopez-Rios et al. 2014, Nature 511, 46-51; Reinhardt et al. 2019, Development 146, dev173328; Malkmus et al. 2021, Nature Comm 12, 5557; Jhanwar et al. 2021, Nature Comm 12, 5685. The position also provides excellent career development opportunities for achieving scientific independence. The University of Basel is an equal opportunity employer that offers competitive salaries and a very attractive work environment.
We are looking for a highly motivated person with a Ph.D. in bioinformatics/computational biology or a closely related field that considers our group an excellent opportunity for innovative and out-of-the-box research. The candidate has experience in the analysis of omics datasets, excellent statistical knowledge, and programming skills in writing custom code (using e.g. R/Bioconductor; Phyton and/or C). In addition, the successful candidate must have already published and have the ambition to create synergies with experimentalists and develop his/her own ideas in the framework of the groups' research.
Start date: immediately or as agreed
Application deadline: 28 Feb 2022