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

The Krebs Lab is seeking for a postdoctoral researcher with a strong background in mathematical modelling to join an interdisciplinary project focused on uncovering the role of energy expenditure in gene regulation, particularly with respect to transcription factors. The candidate is expected to develop the projects together with experimentalists. This project combines single-molecule and single-cell techniques, high-throughput genetic perturbations, and mathematical modelling of cis-regulatory element kinetics. The successful candidates will work develop novel graph-theoretic mathematical approaches in tight collaboration with the group of Jeremy Gunawardena. The research will be supported by EMBL’s computational and high-end sequencing facilities, and the candidates will be expected to integrate the Theory@EMBL community.

The EMBL-EBI–AstraZeneca Postdoctoral (EAZPOD) Programme builds on the collaborative relationship between EMBL-EBI and AstraZeneca, offering projects that push the boundaries of cutting-edge computational biology in oncology.

For 2024, the following project areas are available, for more information on the projects please view the EAZPOD page:

1. Dissecting the multicellular coordinated processes of cancer cell persistence from single-cell data

• Partners: Julio Saez-Rodriguez and Ricardo Ramirez Flores (EMBL-EBI) and Pedro Moreno and Martin Miller (AstraZeneca)

2. DELPHI: Drug-Disease Interactions and Clinical Trial Applications

• Partners: Ewan Birney and Tom Fitzgerald (EMBL-EBI) and Martin Miller (AstraZeneca)

The goal of the Saez Rodriguez group is to acquire a functional understanding of the deregulation of signalling networks in disease and to apply this knowledge to develop novel therapeutics. We focus on cancer, auto-immune and fibrotic disease. Towards this goal, we integrate big (‘Omics’) data with mechanistic molecular knowledge into statistical and machine learning methods, and we share our tools as free open-source packages.

You will work in an international team together with experimentalists and other computational scientists to develop and apply tailored computational methods that are designed to fully exploit clinical and organoid data obtained as part of a transnational project. This project investigates the epigenetic changes during the progression of human metastatic colorectal cancer (CC), and aims to leverage ctDNA status to personalise the post-surgical care of early-stage CC.

We are looking for an extremely motivated candidate who will take on this cutting-edge project, which has translational potential. The successful candidate will learn, from a current senior team member, how to setup the 3D culture of an in vitro maternal-fetal interface on-chip. The candidate will become adept at employing the model and all associated assays and analysis techniques. As part of a collaboration with local clinical researchers, the candidate will isolate primary-derived trophoblast cells from explanted placenta for incorporation and optimization on-chip. Once optimized, the model will be used to explore a range of questions related to sex differences, exposures, and infection. For the latter part of the project, a collaborative aim is to explore malaria infection in the placenta model, in partnership with Bernabeu group at EMBL Barcelona.

We are looking for a postdoctoral researcher to work on a project using human organoid models to understand how hypoxia, nicotine, and genetic perturbations influence the plasticity of pulmonary neuroendocrine cells and their susceptibility to cancer. Ultimately, we aim to generate genetically engineered human organoid models of neuroendocrine cancer. The project will involve international collaborations with clinicians and environmental epidemiologists as well as the generation and analysis of single cell -omics datasets. Many details of the project can be tailored to fit the candidate’s particular expertise and interests. This specific position is for a 3-year appointment with the possibility and expectation for renewal.

The successful candidate will be intrinsically motivated, and will lead their own project, contribute to other projects on a collaborative basis (both in the lab and with external collaborators) and may guide PhD and Masters students in their research. Importantly, the candidate will contribute to shaping the environment and research of a young and growing research team.