Postdoctoral Researcher in AI for Single-cell Epigenomics (m/f/d)

The Max Delbrück Center for Molecular Medicine in the Helmholtz Association aims to transform tomorrow’s medicine through our discoveries of today. At locations in Berlin-Buch, Berlin-Mitte, Heidelberg and Mannheim, our researchers harness interdisciplinary collaboration to decipher the complexities of disease at the systems level – from molecules and cells to organs and the entire organism. Through academic, clinical, and industry partnerships, as well as global networks, we strive to translate biological discoveries into applications that enable the early detection of deviations from health, personalize treatment, and ultimately prevent disease. First founded in 1992, the Max Delbrück Center today inspires and nurtures a diverse talent pool of 1,800 people from over 70 countries. We are 90 percent funded by the German federal government and 10 percent by the state of Berlin.

We are looking for a highly motivated postdoctoral researcher to join the Computational and Developmental Biology group at the Max Delbrück Center for Molecular Medicine (MDC) in Berlin. Our interdisciplinary team develops innovative computational approaches to reconstruct tissue trajectories from multimodal single-cell and spatial omics data and to uncover the regulatory mechanisms driving cellular differentiation during vertebrate embryonic development. In this project, you will develop quantitative machine learning models to study how different layers of epigenetic regulation shape cell fate decisions. In close collaboration with experimental groups, you will work with large-scale multiome datasets from mouse and zebrafish embryos, including single-cell measurements of chromatin accessibility, promoter activity, histone modifications, and chromatin topology.

Job Description

During your daily work, you will:

• develop sequence-to-function deep learning models (e.g. Borzoi-, Enformer-, or AlphaGenome-style) to predict single-cell chromatin accessibility, histone modifications, higher-order chromatin organization, and gene expression in mouse and zebrafish embryos
• design and perform large-scale in silico perturbation experiments, including motif ablation, virtual transcription factor knock-outs, and regulatory-element screening, to generate mechanistic hypotheses
• analyse experimental perturbation datasets from in-house projects and collaborations, including perturbations of histone modifiers and developmental signalling pathways such as Nodal, BMP, FGF, WNT, and retinoic acid
• compare mouse and zebrafish embryogenesis to identify conserved and species-specific regulatory programs
• collaborate closely with experimental researchers to design validation experiments and refine predictive models
• contribute actively to a highly interdisciplinary and collaborative environment of computational and experimental biologists

Requirements

• PhD (or MSc with several years of working experience) in computational or natural sciences with a strong computational / quantitative focus
• Strong programming skills in Python or R; experience with a modern deep-learning framework; experience in building efficient and reusable software is a plus
• Solid background in machine learning
• Experience with the analysis of high-throughput sequencing data (single-cell RNA-seq, ATAC-seq, multiome) is highly desirable
• Interest in genomics, gene regulation and/or developmental biology
• Ability to work both independently and collaboratively in an interdisciplinary team

We offer

• international working environment with communication in English and German
• interesting career opportunities and a range of opportunities for further qualification and training
• Compatibility of family and career certified by the workandfamily audit (“berufundfamilie audit”)
• Support for "New Berliners" through the MDC Welcome & Family Office

You also benefit from:

• a remuneration in accordance with the collective agreement for the federal public service (TVöD-Bund), including additional company pension schemes
• a secure job
• flexible working hours and childcare support
• the possibility of mobile working
• an idyllic green campus, which is easily accessible by bicycle, public transport or car
• free use of Nextbike from the Buch S-Bahn station to the campus
• Subsidy for the job ticket as well as discounts in the campus canteen
• On-campus health and fitness center
• additional health benefits such as flu vaccination, eye test, ergonomics advice at the workplace