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.

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-Stiftung Center for Synthetic Genomics and the Center for Molecular Biology Zentrum für Molekulare Biologie Heidelberg, ZMBH 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.

We are looking for three highly motivated PhD candidates holding a Master's 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.

Our Junior research group develops Deep Genomic Sequence-to-Function (S2F) models to explore how genomic sequences influence gene regulatory functions ( More about projects here). These highly scalable models integrate various data modalities that measure different aspects of gene regulation in a high-throughput manner. Our research is at the forefront of advancing these models' foundational understanding of gene regulation. We are pursuing three exciting directions: 1) Scaling up current models with single-cell data across diverse species and data types, 2) Incorporating readily available cell type-specific data to train the next generation of cell type-agnostic models, capable of predicting for unseen cell types and conditions, and 3) Developing new generative models to leverage S2F's foundational knowledge for creating synthetic regulatory elements with tailored properties for biotechnology.

The junior research group is part of the newly founded CZS Center SynGen and the Center for Molecular Biology Zentrum für Molekulare Biologie Heidelberg, ZMBH 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 ZMBH has a long tradition of conducting cutting-edge research in molecular and cell biology, as well as biomedicine. In the years to come, we anticipate rapid advancements and new technologies in the fields of synthetic DNA, artificial intelligence, and all natural sciences. These advancements will collectively drive progress in synthetic and molecular biology, presenting entirely new possibilities for biomedicine, bioengineering, and biomanufacturing. With the CZS Center SynGen Initiative the ZMBH is on a mission to contribute to these developments with fundamental, theoretical or applied research towards programmable biology. Heidelberg University is a comprehensive university with a strong focus on research and international standards. With around 30,000 students and 8,400 employees, including numerous top researchers, it is a globally recognised institution that is also of outstanding economic importance for the Rhine-Neckar metropolitan region. The University has recently established a new Faculty of Engineering Sciences at the interface of material science, molecular biotechnology and computational science.

Joining our junior research group 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 and genomics, essential for a successful research career. You'll have the freedom to explore and develop your own research ideas, fostering innovative thinking and enhancing problem-solving skills in a supportive setting that builds your confidence as an independent researcher. The positions come with flexible working hours, company pension scheme, annual special payments, 30 days of vacation, and a subsidised job ticket for public transit. The PhD students will be members of the Heidelberg Biosciences International Graduate School (HBIGS) or the Heidelberg Graduate School of Mathematical and Computational Methods for the Sciences (HGS MathComp).

The salary of these positions will be based on the German public TV-L E13 standard table and PhD students will be paid an equivalent of 25.675 hours/week (65% work). 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 contacts of 2-3 references. Please understand that application documents received by post will not be returned. Closing date for applications: October 31, 2024.

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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