PhD Scholarships to Study Plasticity of Liver and Adipose Tissues at Single Cell Resolution

Application deadline: 28 July 2024 at 23:59 hours local Danish time.
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 PhD fellows. We have three positions available from September 1, 2024, or as soon as possible thereafter.

Application deadline: 28 July 2024 at 23:59 hours local Danish time.
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 stipends
We offer three new PhD stipends in the center - one for each of the following projects. All PhD students will be part of our highly ambitious and interdisciplinary research environment in ATLAS as well as the Functional Genomics and Metabolism Research Unit.

Project 1: Transcriptional regulation of adipose tissue plasticity at single cell resolution (Mandrup Group)
In this project, we are investigating the cellular and molecular mechanisms of adipose tissue plasticity in human adipose tissue and mouse models in response to obesity and weight loss. We are particularly interested in the molecular mechanisms driving the differentiation of progenitor cells to adipocytes as well as the plasticity of mature adipocytes in vivo. To investigate this, we apply a wide range of functional genomics, and cell and molecular biology technologies, including single cell technologies and bioimaging.

As a PhD student on this project, you will work in close collaboration with other PhD students and postdocs in the Mandrup Group and ATLAS to uncover transcriptional networks that drive adipogenesis of progenitor cells as well as how crosstalk between cell types may stimulate these networks in in adipose tissue of mouse models and human subjects. Furthermore, you will work with clinicians to link molecular features of adipose tissue to clinical phenotypes.

For this project, documented hands-on experience with NGS data analysis, adipocyte biology, mouse physiology, and/or transcriptional regulation is considered an advantage.

Prof. Susanne Mandrup is Director of ATLAS, and leader of Work Package 1 on “Molecular and cellular mechanisms of adipose tissue plasticity in the context of obesity”. You can read more about the Mandrup Group here.

Project 2: Single-cell and spatially resolved analyses of hepatic tissue plasticity (Ravnskjaer Group)
For this project, we seek a computational biologist with experience in single-cell and spatial transcriptomics data analysis and interest in liver disease biology. In close collaboration with our ATLAS partners, other PhD students and postdocs we will spatially map cellular interactions and liver tissue plasticity during development and regression of steatohepatitis. The successful candidate will combine data from single-cell and spatial omics technologies recently developed in our group and translate results into biological insights.

For this project, documented working experience with similar analyses using R and Python is considered an advantage.

Assoc. Prof. Kim Ravnskjaer is leader of Work Package 2 on “Molecular and cellular mechanisms of hepatic tissue plasticity in the context of obesity”. You can read more about the Ravnskjaer Group here.

Project 3: Functional genomics and hepatic tissue plasticity (Grøntved Group)
The candidate will work primarily in the Grøntved Group and will be responsible for in vivo investigation of dynamic transcription and chromatin remodeling in hepatic tissue in response to metabolic challenges and development and regression of hepatosteatosis. The studies will primarily focus on the hepatocyte population in liver tissue and crosstalk with other hepatic cell types such as stellate cells, endothelium and Kupffer cells. Experiences with mouse models, genome-wide studies of transcriptional regulation, next generation sequencing and bioinformatics are an advantage.

Assoc. Prof. Lars Grøntved is core co-Principal Investigator in ATLAS, focusing on transcriptional regulation of liver function. You can read more about the Grøntved Group here.

We offer:

• Three three-year PhD positions (or four-year for Master students) in a highly stimulating, supportive, international, and interdisciplinary research environment
• Enrollment in PhD school of Biochemistry and Molecular Biology, 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 the Mandrup, Ravnskjaer, and Grøntved Groups 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 highly motivated, dedicated, and ambitious candidates with:

• A Master’s degree in Life Science, preferable Molecular Biology, Biomedicine, or Computational Systems Biology.
  • If you have not yet completed your master program, you can apply to be enrolled in our 4+4 PhD program, which is a way to commence the PhD study whilst concurrently completing the master program
    Read more about the PhD programme at the Faculty of Science.
• Strong communication and collaborative skills and an interest in working in an interdisciplinary environment
• Proficiency in spoken and written English
• Documented hands-on experience with NGS data analysis, adipocyte biology, mouse physiology, or transcriptional regulation is considered an advantage.

For further information please contact the relevant PI:

• Project 1: Center Director Professor Susanne Mandrup ([email protected])
• Project 2: Associate Professor Kim Ravnskjaer ([email protected])
• Project 3: Associate Professor Lars Grøntved ([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).

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

Application must be in English and made in the form of a Declaration of Interest including the following:

• A letter stating your specific interest, motivation, and qualifications for the project in question – remember to clearly indicate which project(s) you wish to be considered for (max. one pages) (please attach this under box "Application form")
• A project description including how you see your research interests match the overall aim of the project in question (max one page excluding references)
• Detailed CV, including personal contact information.
• Copies of diplomas, Bachelor as well as Master’s degree, including transcript of notes/grades. If awaiting master’s diploma, provide a written statement from the supervisor.
• 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.
Incomplete applications and applications received after the deadline will neither be considered nor evaluated. This also applies to reference letters.

Applications will be assessed by an expert assessor/committee. Applicants will be informed of their assessment by the university.

Applications should be sent electronically via the link "Apply now". The faculty expects applicants to read the information "How to apply" before applying. Please note that the application documents should be in pdf-format and attached as three documents: motivation letter, CV and the remaining documents.

We recommend that as an international applicant you take the time to visit Work in Denmark where you will find information and facts about moving to, working and living in Denmark, as well as the International Staff Office at SDU.

Placering: Odense, Denmark