Center for Functional Genomics and Tissue Plasticity (ATLAS) invites applications from outstanding postdoctoral candidates who are interested in joining our team to work on computational and experimental aspects single-cell biology. The postdoc will be dually affiliated with leading groups in the field, the Mandrup group, Section for Functional Genomics and Metabolism, Department of Biochemistry and Molecular Biology and the Madsen group, Section for Data Science and Statistics, Department of Mathematics and Computer Science. The position is available from 15 May 2022, or as soon as possible thereafter. Application deadline: 11 May 2022.

Research projects and roles
Droplet-based single-cell and single-nucleus RNA-seq has revolutionized the way we are analysing and interrogating human biology and disease. One of the major analytical challenges is controlling for ambient RNA contamination. Ambient RNA is free floating RNA, which is released during cell lysis, and which can get (co-)encapsulated during droplet-formation, barcoded, and sequenced. This makes it difficult to distinguish between bona fide cell- or nucleus-containing droplets, and droplets loaded with ambient RNA. Furthermore, it introduces noise into the observed transcriptomes of cells or nuclei.

You are expected to spearhead a project generating the necessary experimental data in the Mandrup group and computational methods in the Madsen group to better distinguish between bona fide cell- or nucleus-containing droplets, and droplets loaded with ambient RNA, as well as methods to denoise the transcriptomes of cells or nuclei.

Research environment
The Functional Genomics & Metabolism Research Unit
The Mandrup Group is located in the Functional Genomics & Metabolism Research Unit, at Department of Biochemistry and Molecular Biology, SDU. The research unit currently 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 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).

The Section for Data Science and Statistics
The Madsen Group is located at the Section for Data Science and Statistics (DSS) at the Department of Mathematics and Computer Science, SDU. The DSS currently hosts sixteen independent research groups focusing on various aspects of data science, including three groups working with bioinformatics and computational biology. The Section constitutes an international, ambitious, highly dynamic, and well-equipped working environment having access to state-of-the-art computing facilities, including high performance computing systems. The successful candidate works at the DSS and have opportunities to (net)work with other research groups in the DSS.

The Center for Functional Genomics and Tissue Plasticity (ATLAS)
The Center for Functional Genomics and Tissue Plasticity (ATLAS) is a Centre of Excellence funded by the Danish National Research Foundation hosted by the Functional Genomics & Metabolism Research Unit (FGM) at the Department of Biochemistry and Molecular Biology (BMB), SDU. The overarching aim of ATLAS is to obtain systems-level, mechanistic and cell type-resolved understanding of adipose and hepatic tissue plasticity in response to severe obesity and weight loss. The centre applies a combination of functional genomics approaches, including single cell sequencing technologies, proteomics, in vivo targeting, and computational biology to study tissue plasticity in both mouse models and human biopsies.

Requirements:
We are looking for highly motivated, dedicated, and ambitious candidates with:
• A PhD degree in Life Science, preferably Molecular Biology, Biomedicine, or Computational Biology.
• Documented experience with machine learning and/or single-cell RNA-seq analysis.
• Proficiency in R, Python, or both.
• Documented experience in leading a research project.
• Strong communication and collaborative skills and a desire to work in an interdisciplinary environment.
• Proficiency in spoken and written English.

We offer:
• Two two-year postdoc positions in stimulating and supportive, international research environments with possibility for extension.
• 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]) or Professor Susanne Mandrup ([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:
• Letter of motivation (max. one page).
• A brief summary of the applicant's most important research results.
• CV incl. education, previous and current work/research experience, and skills relevant for the position.
• A full list of publications, stating the scientific publications on which the applicant wishes to be evaluated.
• Copy of PhD Diploma.
• At least one signed reference letter (with referee contact details and relationship). Should your referees wish to send their letters directly to us, please have them directed to the Faculty of Science administration (e-mail: [email protected]) mentioning your name and title of the position in the subject line. Please note that the letters need to reach us before the application deadline.

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 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.

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