PhD position in Bioinformatics

The Institute of Mathematics and Computer Science , Bioinformatics Group, of the Faculty of Mathematics and Natural Sciences at the University of Greifswald, is seeking to fill a part-time position (75%) subject to funding availability, likely starting as soon as possible , for a fixed term of 3 years .

research assistant

The position is to be filled. Remuneration is based on pay grade 13 TV-L Wissenschaft (Collective Agreement for Public Service Employees in the State of Hesse, Academic Staff). 

Deep learning is currently revolutionizing genome annotation. For example, our new deep-learning-based gene prediction program, Tiberius, achieves an accuracy comparable to our annotation pipeline, BRAKER3, even without the use of RNA-Seq data. Building on these results and codebases, the successful candidate will work on a research project in bioinformatics and machine learning, focusing on the inference of alternative splice forms using deep learning methods and PacBio long-read transcriptome data, as well as the evolution of isoforms in insects. This work will be carried out in collaboration with Prof. Gregor Bucher (University of Göttingen) within the framework of the project “Alternative Splicing and the Evolution of Holometaboly,” which is part of the DFG Priority Programme “Genomic Basis of Evolutionary Innovations (GEvol).”

Job tasks:

• Design, training and benchmarking of deep learning sequence-to-sequence architectures
• Implementation of new machine learning layers and model components
• Application of tools for genome analysis and molecular evolution
• The position offers the opportunity to pursue a doctorate on a topic in the aforementioned research area.

Hiring requirements:

• Master’s degree in bioinformatics, biomathematics, computer science, biology or a related field
• Solid programming skills in Python
• Mastery of the mathematical foundations of machine learning (linear algebra, analysis)
• English language skills at B2 level or higher (the working language is English)

Desired are:

• Experience with Unix shell, Git, PyTorch, TensorFlow, SLURM
• Experience in handling genome or transcriptome data
• Knowledge of sequence-to-sequence models (Hidden Markov Models, Attention Mechanisms, Recurrent Neural Networks)
• Motivation to work in an interdisciplinary team with biologists and computer scientists

This job posting is open to all persons regardless of gender. Applicants with disabilities will be given preference if equally qualified.

According to § 68 para. 3 PersVG MV, the participation of the staff council in personnel matters of the scientific/artistic staff only takes place upon request. 

Unfortunately, the state of Mecklenburg-Vorpommern cannot reimburse any costs you incur as part of the application process.

Please note that submitting your application constitutes your consent under data protection law to the processing of your application data by us. Further details regarding the legal basis and data usage can be found  here .

Applications with the usual documents (especially CV, cover letter, copies of certificates, and, if applicable, a list of publications) should preferably be sent by email (one PDF file) quoting job posting number 26/Sa19  by June 30, 2026 to:

University of Greifswald,
Institute of Mathematics and Computer Science,
Prof. Dr. Mario Stanke,
Walther-Rathenau-Str. 47,
17489 Greifswald

mario.stanke@uni-greifswald.de