Bioinformatics Staff Scientist at the Center for Adipocyte Signaling (ADIPOSIGN) (Academic Employee)

Updated: 17 days ago
Deadline: 27 May 2021



center was established in 2019 through a major grant from the Novo Nordisk Foundation and runs for period of six years. We combine experimental and computational systems approaches to obtain unprecedented insights into how fat cells receive and respond to signals at the level of the (epi)-genome and the cell membrane. Our goal is to understand how the signaling states of adipocytes depend on depot, gender, and genetic variation, and how changes in these signaling states during development of obesity contribute to the pathophysiological consequences of obesity. 

Job Description and Role in Research Center 
As a computational staff scientist in ADIPOSIGN you will play a major role in bridging experimental and computational analyses in this highly ambitious and interdisciplinary project. You will interact and collaborate closely with other researchers in the Mandrup group as well as with members of the groups of Jan-Wilhelm Kornfeld (Odense), Zach Gerhart-Hines (Copenhagen), and M. Madan Babu (Memphis). You will investigate the primary data generated from the experimental interrogation of adipocyte signaling states in isolated murine and human adipocytes using an array of functional genomics, proteomics and computational approaches. You will design user-friendly databases, develop semantics for metadata describing the various experiments, develop web interface and computational pipelines for data archiving, sharing, and exploratory data analysis by the various research groups. You will train PhD students and post-docs to analyze large-scale datasets and with interpreting their results. Some of these findings will be translated into functional studies in transgenic mouse models so you will help with identifying key candidates for such experiments. You are expected to provide substantial general input to projects in our groups and help with generating high-quality representation of complex data. You will also have the opportunity to develop your own ideas within our research frame. 

We are looking for highly motivated and dedicated candidates with:

• Documented expertise in computational biology, NGS data analysis, processing of experimental datasets, network analysis and investigation of multi-omics datasets
• Research experience within the fields of Computational Biology, Systems Biology, or Bioinformatics
• Hands-on experience with NGS-related laboratory (wet lab) procedures is considered a plus
• Proficiency in at least two of the following programming languages: Python, R, C++, Java.
• Strong background in database development: SQL, graph databases, etc.
• Experience in designing web interfaces for exploratory data analysis and data sharing
• Experience in Machine Learning would be desirable
• Passion for complex data visualization and representing data into interpretable figures.
• Ideally at least one major first author publication in a relevant journal in the field
• Strong communication and collaborative skills and an interest in working in an interdisciplinary environment
• Proficiency in spoken and written English

We offer
• An up to four-year staff scientist position in a stimulating and supportive, international research environment at SDU with the possibility of extension and career development for the high-performing candidate.
• Exchange program to travel and work with the Babu Group at St Jude Children’s Research Hospital in the USA
• Access to state-of-the-art equipment, computational 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 center involves the following PIs:
Susanne Mandrup, Professor, Department of Biochemistry and Molecular Biology, University of Southern Denmark (Director)
M. Madan Babu, Member & Endowed Chair in Biomedical Data Science, Department of Structural Biology, St Jude Children's Research Hospital, Memphis, TN, USA
Jan-Wilhelm Kornfeld, Professor, Department of Biochemistry and Molecular Biology, University of Southern Denmark
Zach Gerhart-Hines, Associate Professor, Center for Basic Metabolic Research, University of Copenhagen

The primary affiliation of the staff scientist will be with the Mandrup Group ; however the staff scientist will be working closely with  Prof. Madan Babu and other partners in the center.

The Mandrup Group
The Mandrup Group has a long-standing interest in understanding the molecular cross-talk between transcriptional regulation and metabolism in adipocytes and pancreatic β-cells and to understand the molecular basis for the plasticity of cells in the adipose tissue and endocrine pancreas. We also have a long-time interest in the transcriptional network regulating lineage determination and differentiation of adipocyte progenitors.  Our laboratory combines genome-wide studies of factor binding, epigenetic marks and chromatin structure with detailed molecular analyses of the crosstalk between transcriptional regulators. We run an inhouse sequencing platform including single cell sequencing and bioinformatic pipeline.

Susanne Mandrup is Director of ADIPOSIGN as well as the Center of Excellence in Functional Genomics and Tissue Plasticity (ATLAS ) funded by the Danish National Research Foundation, and she heads the Functional Genomics and Metabolism Research Unit . 

The Babu Group
The Babu Group is interested in data science approaches to make biological discoveries and reveal fundamental principles of biological systems. We employ and develop computational and experimental methods to study biological systems at all scales of complexity – from systems at the atomic level (e.g., structures) to the network of interactions between molecules (e.g., signaling and regulatory networks) and those pertaining to the level of an entire population (e.g., variation in the human population). By integrating these data, we are working to understand G protein-coupled receptor (GPCR) signaling in human physiology and diseases and using that knowledge to develop novel therapeutic strategies. 

Madan Babu is a Member and Endowed Chair in Biomedical Data Science in the Department of Structural Biology & Director of the Center of Excellence for Data Driven Discovery at St Jude Children's Research Hospital. 

The Functional Genomics & Metabolism Research Unit 
The Mandrup group as well as the center administration of ATLAS and ADIPOSIGN 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 as it pertains to the regulation of cellular 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 the Odense University Hospital (OUH). This means that you will be in a highly stimulating research environment with numerous opportunities for learning and developing new ideas.

For further information please contact Center Director prof. Susanne Mandrup, .

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).

The application must be in English and include the following:

• Motivation letter (max. one page)
• CV incl. education, work/research experience and skills relevant for the position
• Copy of certificates relevant for the position
• List of publications
• At least two letters of reference (with referee contact details and relationship). Should your referees wish to send their letters directly to us, please direct them to: . Please note that letters of reference also need to reach us before the deadline.

Incomplete applications and applications received after the deadline will neither be considered nor evaluated.

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 recommend that you read how to apply before you apply.

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

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