PhD position – Co-regulation structures for large-scale single-cell transcriptomics – within the HDS-LEE graduate school

Shaping change: this is what drives us at Forschungszentrum Jülich. As a member of the Helmholtz Association with some 7,600 employees, we conduct interdisciplinary research into a digitalized society, a climate-friendly energy system, and a sustainable economy. We focus on the natural, life, and engineering sciences in the fields of information, energy, and bioeconomy. We combine this with expertise in high-performance computing and artificial intelligence using unique scientific infrastructures. The Bioinformatics Division of the Institute of Biological and Geosciences (IBG-4) processes and develops methods and algorithms to achieve a fundamental understanding of high-dimensional data and processes in the bioeconomy in particular. Bioinformatics at Forschungszentrum Jülich plays a leading role at the international level, for example in the field of plant and microbial data management, in the evaluation of new methods of genome analysis, in the integration, interpretation, and visualization of high-dimensional omics data from the field of bioeconomics, and in the modeling, simulation, and engineering of biomolecular systems, including enzymes. Apply your data science skills to real-world challenges! At the Helmholtz School for Data Science in Life, Earth and Energy (HDS-LEE), we train the next generation of data scientists to tackle key global issues in domain sciences such as life, earth or energy. Learn more at www.hds-lee.de. Institute specific promise here. We are looking to recruit a PhD position – Co-regulation structures for large-scale single-cell transcriptomics – within the HDS-LEE graduate school

Develop methods and workflows to construct robust co-regulation networks from large single-cell and spatial transcriptomics datasets

Integrate ontologies and metadata (e.g., tissue, cell type, developmental stage, treatment) to build tissue- and context-specific co-regulation networks

Design and implementation clustering and integration approaches (e.g., network-based and subspace clustering)

Use co-regulation networks for gene function and protein functional relationship prediction (guilt-by-association), and benchmark them against existing bulk co-expression resources

Compare and optimise the developed methods on real biological datasets; work close with experimental partners for interpretation and validation of results

Contribute to the integration of the developed methods into open-source software tools and data portals of the institutes Collaborate with internal and external, as well as national and international, project partners

Present your results at national and international conferences

Prepare scientific publications and project reports

Genuine interest in data science and one or more of its application domains: life and medical sciences, earth sciences, energy systems, or material sciences

A master's degree with a strong academic background in mathematics, science, material science, earth science, engineering, or a related field

Proficiency in at least one programming language (Python, R, C++, Julia, ...)

Good analytical skills with a sound understanding of data evaluation

Prior experience with single-cell data analysis, network analysis, or machine learning is a plus

Good organizational skills and ability to work both independently and collaboratively

Effective communication skills and an interest in contributing to a highly international and interdisciplinary team

Motivation for academic development, supported by bachelor's and master's transcripts and two reference letters

Working proficiency in English for daily communication and professional contexts (TOEFL or equivalent or exemption required)

Knowledge of German is beneficial

We work on the very latest issues that impact our society and are offering you the chance to help in shaping the change! This HDS-LEE PhD position will be located at Forschungszentrum Jülich, HHU Düsseldorf and Aarhus. We offer ideal conditions for you to complete your doctoral degree:

Outstanding scientific and technical infrastructure

Cutting edge data is available for analysis

Highly motivated groups as well as an international and interdisciplinary working environment at one of Europe's largest research establishment

Continuous scientific mentoring by your scientific advisors

Chance of participating in (international) conferences

Unique HDS-LEE graduate school program (including data science courses, soft skill courses and annual retreats) https://www.hds-lee.de/about/

Qualification that is highly welcome in industry

Further development of your personal strengths, e.g. via a comprehensive further training program; a structured program of continuing education and networking opportunities specifically for doctoral researchers via JuDocS, the Jülich Center for Doctoral Researchers and Supervisors: https://www.fz-juelich.de/judocs

30 days of annual leave and flexible working arrangements, including partial remote work

Targeted services for international employees, e.g. through our International Advisory Service The position is initially limited to three years, with a planned one-year extension. Pay in line with 75% of pay group 13 of the Collective Agreement for the Public Service (TVöD Bund) and additionally 60% of a monthly salary as special payment (''Christmas bonus''). Further information on doctoral degrees at Forschungszentrum Jülich including our other locations is available at: www.fz-juelich.de/gp/Careers_Docs Further information on doctoral degrees at Forschungszentrum Jülich (including its various branch offices) is available at https://www.fz-juelich.de/en/careers/phd We welcome applications from people with diverse backgrounds, e.g. in terms of age, gender, disability, sexual orientation/ identity, and social, ethnic and religious origin. A diverse and inclusive working environment with equal opportunities in which everyone can realize their potential is important to us. The following links provide further information on diversity and equal opportunities: https://go.fzj.de/equality and on specific support options for women: https://go.fzj.de/womens-job-journey