PhD in computational science with focus on chemistry; dynamic imaging data - Befattningen är under tillsättning eller redan tillsatt, och det är inte längre möjligt att lämna in en ansökan

The Department of Chemistry, Umeå University, Umeå, Sweden is seeking a PhD-student in computational science with focus on chemistry. The position is for 4 years of research including courses on graduate level. Application deadline is 10th August 2020.

Project description
Biological drugs have over last 15-20 years revolutionized treatment of life threatening and chronic diseases. Development of new biologics is very expensive and time consuming, with approximately 20 % of the cost spent in early R&D and preclinical studies. Key to accelerating these phases is to rapidly evaluate thousands of candidate drugs, for their potential clinical effect.

Modern microscopy has created completely new ways to quickly and efficiently study and evaluate new drug candidates in living cells or in multicellular organoids. The actual data analysis of these images is critical and at the same time challenging due to very large amounts of data and their high complexity.

Image analysis has over last 10 years been revolutionized by AI and so-called deep learning. Deep learning has been successfully used to detect and segment cells, track cell movement over time, and predict cell differentiation. To date, image data analysis has been limited to analyzing single images rather than to capturing over time dynamic biological processes.

This project aims to use Deep Learning-based algorithms and multivariate data analysis tools to develop novel workflow for data analysis of dynamic image data. This aim will be achieved by 1) segmenting out individual cells and track them over time, 2) use deep learning and multivariate data analysis to model the behavior over time, 3) use the models to extract information of cell behavior over time and 4) applying steps 1-3 to study complex biological samples. Data will be provided among others by BICU (Biochemical Imaging Centre Umeå) which recently has received a Sartorius IncuCyte®-system for live cell imaging. The developed algorithms will enable insight into biology that has not previously occurred for high-capacity imaging systems.

Qualifications
To be admitted for studies at third-cycle level the applicant is required to have completed a second-cycle level degree, or completed course requirements of at least 240 ECTS credits, of which at least 60 ECTS credits are at second-cycle level or have an equivalent education from abroad, or equivalent qualifications.

To fulfil the specific entry requirements to be admitted for studies at third-cycle level in computational science and engineering, the applicant is required to have completed at least 90 ECTS credits in computational science and engineering courses, of which at least 30 ECTS credits shall have been acquired at second-cycle level. Computational science and engineering courses refers to courses with major quantitative, statistical or computing science elements, such as courses in computing science, mathematics and mathematical statistics, and relevant courses in biology, ecology, physics and chemistry. Applicants who in some other system either within Sweden or abroad have acquired largely equivalent skills are also eligible.

Good knowledge in English, both written and spoken, is required. The candidate must be structured, have a solution-oriented approach and an interest to learn new things, especially in Advanced Data Analytics. Very good communication skills and the ability to work in a team are also requirements.

Experience with data science tools and machine learning methods, including scripting, mainly in Python and other languages (MATLAB, C, JavaScript, etc.) is a merit as well as experience in experimental planning and data analytics.

Terms of employment
The appointment aims at a PhD degree and the main task of the PhD student is to pursue their doctoral studies, which includes participation in research projects as well as postgraduate courses. In the assignments, teaching and other departmental work (up to a maximum of 20%) can be included. The employment is limited to four years full-time or up to five years when part-time teaching. The salary placement takes place according to the established salary level for doctoral employment.

Application
A complete application should contain the following documents:

• A cover letter including a description of your research interests and motivation for applying
• A Curriculum Vitae
• Certified copies of degree certificates or equivalent, including documentation of completed academic courses, obtained grades and other relevant certificates
• Name and contact information of at least two reference persons

Applications must be submitted via our e-recruitment system. The last day to apply is 10th August 2020.

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

About us
The Department of Chemistry is one of the largest departments within the Faculty of Science and Technology with approximately 200 employees, of which approximately 40 doctoral students, and a strong and expanding research. The Department has three major research areas: Biological Chemistry, Environmental and Biogeochemistry, and Technical Chemistry. We are also a strong partner in the KBC, Chemical-Biological Center. Information about the postgraduate education can be found on the Faculty of Science and Technology website: www.umu.se/en/faculty-of-science-and-technology/education/doctoral-studies/chemistry/. For more information about working at Umeå University: https://www.umu.se/en/work-with-us/.