Computational PhD Scholarship to Develop Novel Methods for Disentangling Transcriptional Regulation Using Advanced Fu...

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. The PhD fellow will be affiliated with the Madsen group. The position is available from 1 September 2021 or as soon as possible thereafter. Application deadline: 1 July 2021.

ATLAS
Center for Functional Genomics and Tissue Plasticity (ATLAS) at University of Southern Denmark is supported by the Danish National Research Foundation. 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 centre applies a combination of functional genomics approaches including single cell sequencing, mouse models, proteomics, in vivo targeting, computational biology, and clinical studies.

The centre involves the following PIs:

Susanne Mandrup, Professor, Department of Biochemistry and Molecular Biology (Director)
Søren Kragh Moestrup, Professor, Department of Molecular Medicine
Blagoy Blagoev, Professor, Department of Biochemistry and Molecular Biology
Aleksander Krag, Professor, Institute of Clinical Medicine & Odense University Hospital
Lars Grøntved, Associate Professor, Department of Biochemistry and Molecular Biology
Jonas Graversen, Associate Professor, Department of Molecular Medicine
Kim Ravnskjær, Associate Professor, Department of Biochemistry and Molecular Biology
Jesper Grud Skat Madsen, Assistant Professor, Department of Biochemistry and Molecular Biology

The Functional Genomics & Metabolism Research Unit
The Mandrup and Madsen groups as well as the centre administration of ATLAS are located in the Functional Genomics & Metabolism Research Unit at Department of Biochemistry and Molecular Biology, SDU. The research unit currently hosts eight independent research groups focusing on various aspects of functional genomics with focus on 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 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).

Research Project and Role
As a PhD fellow in ATLAS you will be engaged in a highly ambitious and interdisciplinary project covering gene regulatory mechanisms involved in liver and adipose tissue plasticity. You will interact and collaborate closely with other researchers in the Madsen group and the Mandrup group as well as with members of the other research groups within ATLAS and at the Department of Biochemistry and Molecular Biology.

The successful candidate will be responsible for developing new computational methods to obtain deeper insight into transcriptional regulation from both bulk and single cell -omics data. The project will use both public and internal data and there are rich possibilities to collaborate with wet-lab ATLAS scientists to use the computational models to push the boundaries of adipocyte and liver biology. Hands-on experience with bioinformatics, statistical programming (R or python) and machine learning is considered an advantage.

Qualifications/requirements
We are looking for a highly motivated, dedicated, and ambitious candidate with:
• A Master’s degree in either Life, Data or Computer Science (e.g. Bioinformatics, Molecular Biology, Biomedicine, or Computational Systems Biology.
• Documented experience with statistical programming (e.g. R or Python).
• Documented experience with -omics data analysis (e.g. single-cell RNA-seq).
• Strong communication and collaborative skills and an interest in working in an interdisciplinary environment.
• Proficiency in spoken and written English.

We offer
• A three-year PhD 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 Assistant Professor Jesper Grud Skat Madsen ([email protected]).

Application, salary etc.
Appointment as a PhD Research Fellow is for three years. Employment stops automatically at the end of the period. The holder of the scholarship is not allowed to have other paid employment during the three-year period.

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

The successful candidate will be enrolled at this university in accordance with faculty regulations and the Danish Ministerial Order on the PhD Programme at the Universities (PhD order).

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

Application must be made in the form of a Declaration of Interest including the following:
• A research proposal/description of your approach to the above project (max one page excluding references)
• A letter stating your specific interest, motivation and qualifications for the project in question (max. two pages) (please attach this under box "Application form")
• Detailed CV, including personal contact information
• Copies of diplomas, Bachelor as well as Master’s degree, including transcript of notes/grades
• At least two signed reference letters. Should your referees wish to send their letters directly to us, please have them use e-mail: [email protected] mentioning your name and the title of the position in the subject line. And please note that these also need to reach us before deadline.

Shortlisting may be used in the assessment process.

Further information about the PhD-study can be found at the homepage of the University.

Applications must be submitted electronically using the link "Apply online". Attached files must be in Adobe PDF or Word format. Each box can only contain a single file of max. 10 Mb. We strongly recommend that you read How to apply before you apply.

Incomplete applications and applications received after the deadline will neither be considered nor evaluated. This also applies to reference letters.

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