Bioinformatics Positions in Gene Expression and Chromatin Epigenetics Analysis

Two Positions in Bioinformatics/Quantitative Biology are available in the research groups of Profs. Filippo Rijli and Helge Grosshans, respectively, at the Friedrich Miescher Institute for Biomedical Research (FMI) in Basel, Switzerland. They will be embedded in the FMI Bioinformatics Platform-Swiss Institute of Bioinformatics and co-supervised by the Head of the FMI Computational group, Dr. Michael Stadler.

The successful candidates will work on the computational analysis of large datasets from high throughput sequencing technologies, providing bioinformatics support for the Rijli and Grosshans groups, respectively. Candidates should have a PhD in Computational Biology, Physics, Computer Sciences, or a related field, or in a relevant biological field with quantitative/computational experience. We expect a track record in analyzing high-throughput sequencing data and a strong interest in gene regulation and epigenetics.

The positions will start July 1st, 2021, or by mutual agreement. Initial contracts will be for 2 years with a planned extension.

Position 1:
Supported by ERC and SNF grants, the Rijli group investigates the role of transcription and epigenetic factors in chromatin regulation during mouse craniofacial and brain circuit development as well as human cartilage regeneration and repair (e.g. see Science 2006, 2013, 2017; Cell Rep 2015, 2017, 2020; Nature Genetics 2021). We are currently mapping chromatin states and generating 3D genome maps of identified neuronal subsets and cranial neural crest cell subpopulations. We aim at gaining a systems-level understanding of the regulatory principles of chromatin modifications in gene regulation by integrating available genetic, epigenetic, and expression data from high throughput sequencing technologies (including single cell and bulk RNAseq, single cell and bulk ATACseq, ChIPseq, promoter capture Hi-C-seq, etc.). The successful candidate will join a computational postdoc and a PhD student already embedded in the Rijli group.

Position 2:
Supported by an ERC Advanced Grant, the Grosshans lab studies temporal patterning through clocks and timers using C. elegans and mammalian cell culture (see for instance Hendriks et al, Mol Cell; Meeuse et al., Mol Syst Biol, Aeschimann et al., Mol Cell). We seek to elucidate the transcriptional and post-transcriptional mechanisms that generate oscillations and other dynamic patterns of gene expression underlying developmental timekeeping. The successful candidate will join an interdisciplinary team of experimentalists and theoreticians and analyse single-cell, single-worm and bulk RNA sequencing, ribosome profiling, ATAC-seq and ChIP-seq datasets. Experience with the analysis of time series data is a plus.

Applications should be submitted electronically at

and include a CV, research experience and interests, and the names and e-mail addresses of three referees. Candidate selection for interviews will begin June 1st, 2021. By default, applications will be evaluated for both positions; candidates that wish to apply for specifically only one of the two positions are asked to indicate this in the “Comment” box in the online application.

For informal inquiries please contact:
Prof. Helge Grosshans
Prof. Filippo Rijli
Dr. Michael Stadler