Umeå University (UmU)

Postdoctoral fellowship (2 years) – deep learning for automatic processing and analysis of LC-MS metabolomics data

Department of Chemistry, Umeå University

Umeå, Sweden

Department of Chemistry, Umeå University, is now offering a postdoctoral fellowship within a project where we will develop new AI approach for improvement of ’omics’ data processing. Apply no later than April 30, 2020.

Project description
Being so far mainly a basic research field, metabolomic reserarch (global analysis of low mass molecules in biological samples) is now slowly entering a wide range of industrial applications. For example, biopharmaceutical process development, monitoring and quality assurance are more and more focused on collecting omics data for understanding the dynamic biochemical states of the cell-based systems for efficient optimization of gene, cell and immunotherapies, serving patients worldwide. Metabolomic research starts also to be crucial in food and beverage industry where in-depth understanding of the process (for example fermentation) can improve its efficiency, reduce product cost and eliminate unnecessary food waste.

Metabolomics data from combined liquid chromatography / mass spectrometry analysis (LC-MS) are extremely complex and hence extraction of relevant information from them, even before any data analysis is done, is a challenging task. So far, processing of metabolomics data is done partly manually, and is a time-consuming process, requiring high level of technical expertise.

The presented project is aiming at overcoming this bottle neck by application of modern Artificial Intelligence (AI) tools for fast, possible to automate and reliable processing of complex ‘omics’ data. More specifically, this project will be focused on development of deep-learning based automated data-processing methods that will support and enhance extraction of information from the LC-MS metabolomics data. Results of this project will be implemented in the data analysis protocols of Swedish Metabolomics Centre, a national platform supporting researchers in Sweden and abroad. By providing open-access to tools developed in this project we will support ‘omics’ community worldwide. The presented project will also contribute and strengthen the rapidly developing AI research in Umeå.

The fellowship, funded by the Kempe Foundations, is for two years starting April 1, 2020 or according to agreement. The stipend is 300 000 SEK per year.

Qualifications
The required qualification is a doctoral degree or a foreign degree that is deemed equivalent in chemistry, applied physics, computer science, statistics, applied mathematics, or equivalent. To be eligible the degree must have been completed a maximum of three years before the end of the application period unless certain circumstances exist.

A solid understanding of mass spectrometry methodology, as well as experience with data science tools including scripting, preferably in Python is required. Good skills in English, both spoken and written, are required. A structured and solution-oriented approach and good communication skills and ability to cooperate in a team are also requirements. Experience in Design-of-Experiments and data analytics are desirable.

Application
The application, written in Swedish or English, must contain the following documents:

- A cover letter that describes qualifications, research interests, and motivation for application (maximum 2 pages)
- A curriculum vitae, including a publication list
- A copy of PhD thesis and relevant publications
- A copy of doctoral degree certificate or equivalent and other relevant degree certificates and grades,
- Name and contact information of at least two reference persons
- Other relevant documents

Your complete application, marked with reference number FS 2.1.6-142-20 should be sent in PDF format to medel@diarie.umu.se (with reference number on the subject line) no later than April 30, 2020.

Additional information
For more information please contact Professor Johan Trygg, email: johan.trygg@umu.se

About us
Department of Chemistry (www.umu.se/en/department-of-chemistry) is the largest department in the Faculty of Science and Technology, with approximately 200 employees, including about 50 doctoral students, and with a strong and expanding research. Three major areas of research; Biological Chemistry, Environmental and Biogeochemistry and Technical Chemistry, represents the research and chemistry education of our department.

We are also a strong partner in KBC, the Chemical-Biological Centre, an interdisciplinary research centre for the life/natural sciences and medicine at Umeå University and the Swedish University of Agricultural Sciences. The centre is unique in its collaborative structure and offers an excellent scientific infrastructure with several core facilities and technical platforms. Our goal is to promote a positive, creative, and interdisciplinary environment for research combined with an excellent graduate and undergraduate education. You can find more information here: www.umu.se/en/kbc.

Umeå University is dedicated to providing creative environments for learning and work. We offer a wide variety of courses and programs, world leading research, and excellent innovation and collaboration opportunities. More than 4 300 employees and 31 500 students have already chosen Umeå University.

We welcome your application!

Apply with CV and Cover Letter

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Position

Postdoctoral fellowship (2 years) – deep learning for automatic processing and analysis of LC-MS metabolomics data