PhD or postdoc position (bioinformatics):
Deep learning models and the evolution of mammalian gene regulation
Center for Molecular Biology (ZMBH), Heidelberg University, Germany
We are looking for a highly motivated PhD candidate or postdoctoral fellow, holding a Master’s or a PhD degree in computer science, computational biology, bioinformatics, or similar. A strong background in computational biology, machine Learning with pytorch or similar deep learning libraries is required.
The candidate will be co-supervised between the labs of Henrik Kaessmann (evo-devo single-cell genomic analyses) and Alexander Sasse (S2F models for synthetic genomics). The Kaessmann lab generates and analyzes single-cell data covering different aspects of gene regulation across mammals and other vertebrates to improve our understanding of their evolution and development. Dr. Sasse’s junior research group develops Deep Genomic Sequence-to-Function (S2F) models to explore how genomic sequences encode gene regulatory functions (Sasse lab).
This project aims at understanding the evolution of the cis-regulatory grammar across the development of humans and other primates/mammals. The candidate will develop and apply new S2F models on single-cell (or cell type specific) genomic data from different species to learn the cis-regulatory sequence elements that orchestrate development. Through multi-species training, the candidate will use these models to perform functional and evolutionary analyses across species and cell types to uncover regulatory changes that underlie phenotypic innovations.
The junior research group is part of the newly founded Carl-Zeiss Center for Synthetic Genomics (CZS Center SynGen, https://www.syn-gen.de/) and the Center for Molecular Biology (Zentrum für Molekulare Biologie Heidelberg, ZMBH, https://www.zmbh.uni-heidelberg.de/) at the renowned Heidelberg University. The CZS Center SynGen is supported by the Carl-Zeiss-Stiftung to promote research and development at the participating Universities in Heidelberg, Karlsruhe and Mainz to develop an internationally visible research focus on synthetic genomics. The Kaessmann lab is part of the ZMBH, which has a long tradition of conducting cutting-edge research in molecular and cell biology, as well as biomedicine.
Heidelberg is a picturesque international city next to the large Odenwald forest and Neckar river. It offers a very stimulating, diverse and collaborative research environment, with the European Molecular Biology Laboratory (EMBL), German Cancer Research Center (DKFZ), Heidelberg Institute of Theoretical Studies (HITS), and the Max Planck Institute for Medical Research located in close proximity to the University.
Joining the two groups offers a collaborative and international work environment where you can gain hands-on experience and develop crucial research skills. The roles provide invaluable opportunities for professional growth, equipping you with technical expertise at the intersection of AI/ML, genomics, and evolution. The positions come with flexible working hours, company pension scheme, annual special payments, 30 days of vacation, and a subsidized job ticket for public transport.
The salary of these positions will be based on the German public standard table TV-L E13. Applications should be sent to Dr. Alexander Sasse (office-sasse@zmbh.uni-heidelberg.de). The application should contain a short letter of motivation, a CV with a short description of prior research experience, copy of transcripts, and contact information for 2-3 references. Closing date for applications: January 10th, 2025.
Heidelberg University stands for equal opportunities and diversity. Qualified female candidates are especially invited to apply. Disabled persons will be given preference if they are equally qualified. Information on the application process and the collection of personal data is available at www.uni-heidelberg.de/stellenmarkt.
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