05 Postdoctoral Fellowship at European Molecular Biology Laboratory (EMBL), Germany

EMBL seeks a postdoctoral researcher in the context of the new transversal research theme Planetary Biology which aims to understand, from the molecular to the population level, how micro- and macroorganisms respond to each other and to their environment and what the effects are that they and their relationships have on their ecosystems. The TREC (Transversing European Coastlines) project is a large and highly collaborative endeavor that EMBL is coordinating together with other EMBL member states’ scientists and institutions. This flagship project aims to sample and study the coastal land-water interface along the European coastlines to monitor the local and global human footprint on oceans, seas, and estuaries, with regard to urbanization, agriculture, coastal exploitation, various forms of contamination as well as impacts of climate change. The postdoctoral researcher will assist in the preparatory phase of TREC by assembling historical data from satellites, validate the water quality retrievals and, once TREC is underway, participate in some data collection activities, and generation of match-ups with satellites.

You will be involved in as well as provide support in the set up, implementation and optimization of computational methods that bridge and integrate between various large-scale spatial molecular measurements which includes: spatial omics, mechanical measurements of tissue stiffness, and single cell methods to resolve spatial data to individual cell layers. The scope of work will encompass data management of large-scale spatial molecular and mechanical data, QC, segmentation and processing, and all levels of analysis in collaboration with scientists in the Diz-Muñoz and Korbel groups. The role provides opportunities to train others in courses and through one-to-one support/training interactions.

Immune checkpoint blockade (ICB) therapy has revolutionised the treatment landscape for multiple cancer types. However, long-lasting responses are only observed in some patients. Although several genetic features of tumours have been linked with higher response rates, such as a high tumour mutational burden, we currently lack critical knowledge about what factors underpin variable responses to ICB. A major challenge for the identification of predictive biomarkers and resistance mechanisms to ICB has been the lack of well-powered molecular profiling data sets matched with ICB response information and clinical covariates. In this project, we aim to harness a large collection of ICB clinical trial data sets consisting of matched whole-exome/panel sequencing, RNA-Seq, and longitudinal cell-free DNA panel sequencing data matched with ICB response information for tumour samples collected before and after ICB treatment  to (1) generate multi-omic predictors of ICB response for multiple cancer types; (2) identify tumour intrinsic and extrinsic mechanisms of primary and acquired resistance to ICB; and (3) determine the patterns of clonal evolution in tumours during ICB treatment and whether such patterns predict response to ICB.

As part of the 3-year DFG-funded Priority Program “Molecular mechanisms of functional phase separation” (https://www.spp2191.com/) the Duss and Mahamid groups are looking to recruit a highly motivated and cross-disciplinary postdoctoral researcher to study mechanisms of bacterial ribosomal RNA transcription condensates by combining biochemistry, single-molecule fluorescence microscopy, and cryo-electron tomography.

We are seeking highly motivated computational biologists to join the research group of Peer Bork within the Structural and Computational Biology Unit as a postdoctoral fellow. This bioinformatics group works on a wide range of topics with a current focus on microbiome analysis in ecosystems like the human gut and the ocean. Within the TREC (Traversing European Coastlines) project, we are gathering microbiome data from soil and ocean samples.