Postdoctoral Researcher / Research Engineer in Cancer Single-Cell and Spatial Bioinformatics

We are looking for an enthusiastic postdoctoral researcher or PhD-qualified research engineer to join our Computational Biology and Bioinformatics team at IBGC (CNRS, Bordeaux), led by Dr Macha Nikolski.

Our INCa PLBIO-funded project investigates the interplay between cancer stem cells and immunosuppressive myeloid cells in liver cancer (hepatocellular carcinoma). We seek to understand how myeloid cells promote the acquisition or maintenance of cancer stem cell properties, and how cancer cells, in turn, influence myeloid cell behaviour. A central question is how epigenetic regulation and the spatial organisation of the tumour microenvironment shape this reciprocal communication.

The hired person will analyse and integrate single-cell RNA-seq, single-cell epigenomics (scChIP-seq profiling H3K4me3 and H3K27me3), and spatial transcriptomics (Visium, Xenium and ATERA) from human tumour samples. These datasets will be complemented by bulk RNA-seq and proteomics from experimental co-cultures, providing a way to connect observations in patient tissues with molecular changes induced by cell–cell interactions.

The end goal is to link cellular states, chromatin profiles and spatial niches to identify candidate signalling pathways underlying cancer cell plasticity and immune suppression. This will involve characterising cellular heterogeneity, mapping spatial relationships, inferring cell–cell communication and integrating evidence across modalities. Computational findings will guide the selection of candidate mediators for functional testing in experimental models, in close collaboration with biologists.

Your profile

You hold a PhD in bioinformatics, computational biology or a related discipline, with strong R and/or Python skills and demonstrated experience in single-cell transcriptomics. We value scientific autonomy, sound statistical judgement, reproducible analysis practices and an interest in connecting computational findings to biological mechanisms. Experience in spatial transcriptomics, epigenomics or cell–cell communication analysis would be an plus; expertise in all these areas is not expected. Good written and spoken English is required.

How to apply

Send your CV and motivation letter to macha.nikolski@u-bordeaux.fr and domitille.chalopin-fillot@u-bordeaux.fr