Machine Learning for Single-Cell Genomics

The Cortés López Lab at Helmholtz Munich, embedded in the Computational Health Center and closely integrated with LMU Children's Hospital (Dr. von Hauner Children's Hospital), investigates how RNA regulation and alternative splicing shape cellular plasticity in development and disease. By combining long-read and single-cell transcriptomics with multimodal data integration and AI-based modeling, we aim to uncover RNA programs that drive pediatric health and disease.

The project is embedded in the German Center for Child and Adolescent Health (DZKJ) and provides direct access to clinically annotated pediatric samples and patient-derived experimental models. This unique integration of genomics, computation, and clinical expertise ensures both mechanistic depth and strong medical relevance.

We are seeking a highly motivated PhD student (f/m/x) in Machine Learning / Computational Biology to join this interdisciplinary research program.

Your tasks

• Investigate RNA splicing regulation in developmental and pediatric disease contexts within a collaborative, translational research environment.
• Work closely across experimental and computational disciplines to iteratively refine study design and translate findings into biologically meaningful insights.
• Develop pipelines for isoform-resolved analysis of short- and long-read single-cell RNA-seq data.
• Integrate multimodal datasets across developmental stages, tissues, and disease states.
• Build statistical and machine-learning models to infer RNA regulatory networks and developmental splicing programs, translating results into experimentally testable hypotheses., If you fulfill all the requirements, you may be eligible for a salary grade of up to E 13 50%. Social benefits are based on the Collective Wage Agreement for Public-Sector Employees (TVöD). The position has an (initial) fixed term of 3 years but may be extended under certain circumstances. Managing Director Mike Frieser:

"We believe that diversity is the key to groundbreaking research and innovative solutions. Our flexible working models and remote options create a supportive environment for balancing work and family life. For us, contributing to a healthier society in such an inspiring workplace is truly meaningful."

• Master's degree in Computational Biology, Bioinformatics, Computer Science, Physics, or a related quantitative discipline.
• Strong interest in RNA biology, development, and pediatric disease research.
• Strong programming skills (Python/R and/or Rust) and experience with reproducible workflows (Nextflow, Snakemake, WDL, Git, containers).
• Excellent communication skills and ability to work collaboratively in a multidisciplinary team.
• Scientific curiosity, initiative, and motivation to thrive in a translational research environment.

Desirable qualification

• Familiarity with HPC environments and willingness to apply machine learning/deep learning frameworks (e.g. PyTorch); experience in single-cell analysis or machine learning is advantageous., + A short motivation letter

• A short motivation letter

If you have obtained a university degree abroad, we will require further documents from you regarding the comparability of your degree. Please request the Statement of Comparability for Foreign Higher Education Qualifications as early as possible.

• Career Development: Postdoc program, scientific training & career center with tailored offers
• Scientific Resources: State-of-the-art infrastruture and Core Facilities
• Recreation: 30 days annual leave, flexi days, plus public holidays
• International Staff Service: Support with the relocation and integration process in Germany
• Health Promotion: Sports, company doctor, mental health initiatives