Computational PhD Stipend in Integrative Multi-omics in Metabolic Dysfunction–associated Steatotic Liver Disease

The Center for Functional Genomics and Tissue Plasticity (ATLAS) at the Functional Genomics & Metabolism Research Unit, Department of Biochemistry and Molecular Biology, University of Southern Denmark, invites applications from outstanding candidates who are interested in joining our team as a PhD fellow. We have one position available from March 1, 2025, or as soon as possible thereafter.

ATLAS
The overall aim of Center for Functional Genomics and Tissue Plasticity ( ATLAS ) is to obtain systems-level, mechanistic and cell type-resolved understanding of adipose and hepatic tissue plasticity in response to diet-induced obesity and regression. We apply a combination of functional genomics approaches, including single cell-sequencing, proteomics, in vivo targeting, and computational biology to obtain in depth mechanistic understanding of the plasticity of these tissues in mouse models as well as in humans undergoing weight-reducing surgery. ATLAS is supported by the  Danish National Research Foundation . 

The PhD stipend
We offer one PhD stipend in the center within the project described below. The PhD fellow will become part of the  MadLab  research group led by Assoc. Professor Jesper G. S. Madsen, and at the same time part of our highly ambitious and interdisciplinary research environment in ATLAS, particularly  Work Package 4  on “Disease trajectories and biomarkers”, as well as the  Functional Genomics and Metabolism Research Unit .

Multimodal Predictive Models for Metabolic Liver Disease
In this project, we aim to shed new light on the etiology of metabolic dysfunction–associated steatotic liver disease (MASLD). We are particularly interested in developing predictive algorithms for diagnosis and prognosis of MASLD. To develop such algorithms, we analyze a wide range of data modalities, ranging from clinical parameters to functional genomics readouts.

As a PhD student on this project, you will work in close collaboration with other PhD students and postdocs in MadLab and ATLAS to collect, curate, integrate, and analyze large-scale proteomics, as well as bulk and single-cell RNA-sequencing datasets derived from human liver, adipose tissue, and blood. To that end, you will build, train, and evaluate deep learning-based approaches, such as variational autoencoders.
For this project, hands-on experience with applied bioinformatics, and statistical programming (R or Python) is required, and experience with applied machine learning and/or liver, adipose tissue biology is considered an advantage.

We offer:

• One three-year PhD position in a highly stimulating, supportive, international, and interdisciplinary research environment
• Enrollment in the  PhD school at the Faculty of Science  and in the  Research training programme in Bioinformatics , which allows the candidate to tailor a flexible individualized course program 
• Training in a wide range of skills including research management, communication, networking, presentations, writing of manuscripts etc.
• Mentoring and career development
• Research exchange to collaborating institution, depending on the interest of the PhD student
• Access to state-of-the-art equipment, facilities and infrastructure
• Opportunity to interact with an extensive network of national and international collaborators
• A competitive salary and social benefits (e.g. health coverage, parental leave, social security etc.)
• Dedicated assistance and support with various practical, social, and legal aspects (housing, visa, administration, tax etc.), especially for international candidates through our international staff office ( ISO ) and department

The research environment
ATLAS and MadLab are based in the  Functional Genomics & Metabolism Research Unit , Department of Biochemistry and Molecular Biology, University of Southern Denmark. The research unit constitutes an international, ambitious, highly dynamic, and well-equipped working environment. The unit and the department have state-of-the-art facilities for next generation sequencing, single-cell transcriptomics, flow cytometry, mass spectrometry, metabolomics, bioimaging and transgenic mouse work. Strategic research alliances exist with Odense University Hospital (OUH).

Qualifications/requirements
We are looking for a highly motivated, dedicated, and ambitious candidate with:

• A Master’s degree in Applied Mathematics, Data Science, Bioinformatics, Computational Biology, Biomedicine, Molecular biology, or a closely related field.
• Strong communication and collaborative skills and an interest in working in an interdisciplinary environment
• Documented experience with statistical programming (e.g., R or Python).
• Documented experience with (single-cell) -omics data analysis.
• Experience with applied machine learning, as well as adipose tissue and liver biology is considered an advantage.
• Proficiency in spoken and written English.

Application deadline: 2 January 2025 at 23:59 hours local Danish time.
Please see the full call, including how to apply, on  www.sdu.dk