Postdoctoral Fellowship

Contract Duration-Is this renewable to 9 years?:

Yes, but only if new funding from other sources will be available.

Contract Duration-Length of Time (years/months):

3 years

About the team/job

About the project: SYMPHONY is a collaboration between the Wellcome Sanger Institute, EMBL and multiple industry partners through the Open Targets (https://www.opentargets.org) consortium. It uses extensive combinatorial CRISPR screening of cancer cell lines to identify and characterize new therapeutic target combinations for lung cancer. Modern cancer therapies often deploy multiple agents to simultaneously target multiple cancer-associated vulnerabilities of malignant cells, or they exploit vulnerabilities that only exist in the context of cancer mutations but not in non-malignant cells. The previous Open Targets project “Encore” used combinatorial CRISPR in KRAS-mutant colorectal cancer and triple negative breast cancer. Here, we extend the approach to lung cancer, the malignancy associated with the largest number of deaths world-wide, with increasing frequency in some groups, incl. women, and presenting an enormous unmet clinical need. The basic genetics of lung cancer is well studied, with activating mutations in KRAS and EGFR, and loss-of-function mutations in TP53, NF1 and STK11 dominating the landscape. In this project, we leverage the unique CRISPR screening platform of the Wellcome Sanger Institute, the computational expertise of EMBL and the drug development and cancer model expertise of the pharma partners to identify and characterize new therapeutic target combinations for lung cancer. About the team: The research group of Wolfgang Huber at EMBL develops statistical data analysis and machine learning methods for modern biotechnologies, applies them to biological and biomedical discovery, and translates them into reusable tools by engaging in open source software communities. The interdisciplinary and international team closely collaborates with researchers in cancer research and biotechnology. 

Your role

You will be the lead-computational scientist for the overall SYMPHONY project, performing discovery-oriented research on the large datasets acquired and generated by the consortium, developing new methodology, and advising partners on approaches and tools. To support these activities, you will also engage in critical method assessment and benchmarking, in collaborative data management, including visualization and QA/QC, and in integrative analysis of consortium data with other, extant data. The primary data type will be barcoded sequencing libraries to determine fitness or viability phenotypes of the many CRISPR-induced mutant genotypes under study. An exciting aspect of the project is the “Car-Pool-Seq” system, which can co-disrupt gene pairs and capture the functional consequences by measuring gene expression responses at single-cell resolution. The systematic perturbation of thousands of genes across dozens of lung cancer models will enable understanding of how genes interact to sustain cancer cell viability and provide novel starting points for therapy development. 

You have

a PhD or equivalent qualification in a quantitative discipline (e.g., bioinformatics, mathematics, statistics, physics, computer science). Your expertise includes statistics and probabilistic modeling of high-dimensional data, machine learning, scientific computing (R, Python or equivalent) and data visualization. We also welcome applications from candidates with little or no background in biology, and a keen interest to learn. You are excited both by computational methodology and by making or contributing to scientific discoveries. You are interested in interdisciplinary science, enjoy collaborative work and like to communicate concepts and results to other scientists. In your application, please include (links to) samples of your prior work, such as GitHub repositories, quarto reports, thesis documents. 

You might also have

A background in biological data science, and/or experience with R package development, interactive visualization, reproducible research and open science technologies. 

Why join us

EMBL is an inclusive, equal opportunity employer offering attractive conditions and benefits appropriate to an international research organization with a collegial and family-friendly working environment. The remuneration package comprises a competitive salary, a comprehensive pension scheme, medical, educational and other social benefits, as well as financial support for relocation, including your family and the availability of an excellent child care facility on campus. EMBL has a large, thriving community of computational biologists, working in close collaboration with experimental scientists and with strong links to other local and international scientists and institutions. 

What else you need to know

We are Europe’s flagship research laboratory for the life sciences – an intergovernmental organization doing scientific research in disciplines including molecular biology, physics, chemistry and computer science. We are an international, innovative and interdisciplinary institution with more than 1600 employees from more than 60 nations, operating across six sites in Heidelberg, Barcelona, Cambridge, Grenoble, Hamburg, and Rome. Our mission is to offer vital services in training scientists, students and visitors at all levels; to develop new instruments and methods in the life sciences and actively engage in technology transfer activities, and to integrate European life science research. Please note that appointments on fixed term contracts can be renewed, depending on circumstances at the time of the review.

To apply, click the 'Apply' button.