Postdoc Position in Computational Transcriptomics

Application deadline: 29 May 2024 at 23:59 hours local Danish time
The Madsen group at the Section for Functional Genomics and Metabolism, Department of Biochemistry and Molecular Biology, University of Southern Denmark, invites applications from outstanding Postdoc candidates who are interested in joining the team and the Islet Cartography-project in a two-year Postdoc position. The position is available from September 1, 2024, or as soon as possible thereafter.

Application deadline: 29 May 2024 at 23:59 hours local Danish time

The Section for Functional Genomics and Metabolism
The Madsen group is a part of the Functional Genomics & Metabolism Research Unit (FGM) at the Department of Biochemistry and Molecular Biology, University of Southern Denmark. The research unit hosts seven independent research groups focusing on various aspects of gene regulatory mechanisms controlling cellular identity, differentiation, and metabolism. 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 computation, including access to interactive HPC resources. Strategic research alliances exist with Odense University Hospital (OUH).

In addition to FGM, the Madsen group is a partner in ambitious national and international research centers, in which the successful candidates can actively participate and (net)work:

The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease (NNFC)
The Madsen group is a partner in the Human Gene Regulation Map (HGRM), a part of the new Novo Nordisk Foundation Center for Genomic Mechanisms of Disease (NNFC). The HGRM is an international joint research center between four research groups at the Broad Institute of MIT and Harvard and four Danish research groups. The aim of HGRM is to build comprehensive maps of gene regulation in the human genome as a resource for uncovering biological mechanisms on common genetic diseases, with an initial focus on cell types relevant to cardiometabolic diseases including type 2 diabetes. We aim to combine recent advances in genomics, molecular biology, single-cell analysis, and stem cell models with approaches in computational biology and machine learning to identify fundamental rules of gene regulation.

The Center for Functional Genomics and Tissue Plasticity (ATLAS)
The Madsen group is a partner in the Center for Functional Genomics and Tissue Plasticity (ATLAS) at University of Southern Denmark is supported by the Danish National Research Foundation. ATLAS is a national joint research center between five research groups at the University of Southern Denmark and three research groups at the Odense University Hospital (OUH). The aim of 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 in mouse models; and to translate this for in-depth understanding of the functional changes in human adipose and hepatic tissues in response to severe obesity and reversal. The center applies a combination of functional genomics approaches including single cell sequencing, mouse models, proteomics, in vivo targeting, computational biology, and clinical studies.

Research Projects and Roles
As a Postdoc in the Madsen group, you will be engaged in a highly ambitious project aimed at shedding new light on the regulatory and functional architecture of the human pancreatic Islets of Langerhans with the aim of furthering the understanding of how it contributes to health and disease. You will interact and collaborate closely with other researchers in the Madsen group as well as with members of the other research groups within the FGM, the department and the research centers.

The successful candidate will be responsible for collecting, curating, and integrating large-scale single-cell RNA-sequencing datasets derived from human islets of Langerhans and combining the resulting atlas with other data modalities. Hands-on experience with applied bioinformatics, and statistical programming (R or Python) is required, and experience with applied machine learning and islet biology is considered an advantage.

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

• A PhD degree within Bioinformatics, Computational Biology, Molecular Biology, or a closely related topic.
• Documented experience with statistical programming (e.g., R, Python, or both).
• Documented experience with -omics data analysis (e.g., single-cell RNA-seq).
• Experience with type 2 diabetes biology is considered an advantage.
• Strong communication and collaborative skills and an interest in working in an interdisciplinary environment.
• Proficiency in spoken and written English.

We offer:

• A two-year Postdoc position in a stimulating and supportive, international research environment.
• 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.

For further information please contact Associate Professor Jesper Grud Skat Madsen ([email protected]).

Application, salary etc.
The successful applicant will be employed in accordance with the agreement between the Ministry of Finance and AC (the Danish Confederation of Professional Associations). Please check links for more information on salary and taxation.

The application must include the following:

• A curriculum vitae including information on previous employment
• A full list of publications stating the scientific publications on which the applicant wishes to rely
• Copy of PhD diploma - if PhD diploma has not yet been received, please include statement from your supervisor

Shortlisting may be used in the assessment process.
Incomplete applications and applications received after the deadline will neither be considered nor evaluated.

To qualify you must have passed a PhD or equivalent. Applications will be assessed by an expert assessor/committee. Applicants will be informed of their assessment by the university.

The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.

Applications must be submitted electronically using the link "Apply now". Attached files must be in Adobe PDF format. We strongly recommend that you read How to apply for a position at SDU before you apply.

Further information for international applicants about entering and working in Denmark.

Placering: Odense, Denmark