PhD Position in Machine Learning for Single-Cell Genomics (f/m/x) Full-time

PhD Position in Machine Learning for Single-Cell Genomics (f/m/x)

At Helmholtz Munich, we develop groundbreaking solutions for a healthier society in a rapidly changing world. We believe that diverse perspectives drive innovation. Through strong partnerships, we accelerate the transfer of new ideas from the lab to real-life applications, improving lives.

The Cortés López Lab at Helmholtz Munich, embedded in the Computational Health Center and closely integrated with LMU 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.

Your Profile

• 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.

Benefits

• Career Development: Postdoc program, scientific training & career center with tailored offers
• Scientific Resources: State-of-the-art infrastructure 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

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.”

If you have any questions, feel free to contact Mariela Cortés López, who will be happy to help.

Our recruiting is decentralized – your application will be reviewed directly by the specialist department in which you could work in the future.

Please send your application only via our online application tool and with the following documents:

• Contact details for at least two referees
• CV
• 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 by the time you start work at the latest.

We are committed to promoting a culture of diversity and welcome applications from talented people regardless of gender, cultural background, nationality, ethnicity, sexual identity, physical abilities, religion or age. Qualified applicants with physical disabilities will be given preference.