PhD student in data-driven life science – Chemistry (DDLS Research School)

Uppsala University, Department of Chemistry – BMC

Department of Chemistry – BMC conducts research and education in analytical chemistry, biochemistry and organic chemistry. More than 100 people, including around 45 PhD students, work at the department. New employees and students are recruited from all over the world and English is the main working language. The department is located at the Biomedical Centre in Uppsala, which facilitates collaborations with research groups in biology, pharmacy, medicine and SciLifeLab and gives access to advanced infrastructure for experimental and theoretical studies. The international environment and good opportunities for interdisciplinary collaborations enables PhD students at the department to participate in relevant research projects and prepare for an international research career.

Read more about the research at The Department of Chemistry – BMC at our website .

Data-driven life science (DDLS) uses data, computational methods and artificial intelligence to study biological systems and processes at all levels, from molecular structures and cellular processes to human health and global ecosystems. The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) aims to recruit and train the next-generation of data-driven life scientists and to create globally leading computational and data science capabilities in Sweden. The program is funded with a total of 3.1 billion SEK (about 290 MUSD) over 12 years from the Knut and Alice Wallenberg (KAW) Foundation.

During 2024 the DDLS Research School will be launched with the recruitment of 20 academic and 7 industrial PhD students. During the course of the DDLS program more than 260 PhD students and 200 postdocs will be part of the Research School. The DDLS program has four strategic areas: cell and molecular biology, evolution and biodiversity, precision medicine and diagnostics, epidemiology and biology of infection. For more information, please see https://www.scilifelab.se/datadriven/ddls-research-school/  

Data driven cell and molecular biology covers research that fundamentally transforms our knowledge about how cells function by peering into their molecular components in time and space, from single molecules to native tissue environments.

The future of life science is data-driven. Will you be part of that change? Then join us in this unique program!

Your goal will to leverage cutting-edge machine learning methodologies to extract conformational ensembles from single-particle cryo-EM data. The project builds on our recently established (not yet published) software, which machine-learns protein structures from cryo EM images and which therefore refines structural heterogeneity directly against single-particle cryo EM data.

Your tasks will be to translate the algorithm from the test-bed to the application stage, to integrate it with chemical force-fields and structure prediction of proteins, and to resolve the structure dynamics of dynamic protein complexes relevant to bacterial and plant photoreception and human circadian timekeeping. You will be involved in all steps of the project, i.e. to design and program the software, to perform computational experiments, to analyze data, and to present and publish the results. The choice of sub-projects will be adjusted to your interests and previous knowledge and experiences.  

You will be given extensive creative space to develop the project, significant resources to produce cutting edge results, and you will profit from being part of our highly collaborative team.

This position is part of the nationwide DDLS graduate school by SciLifeLab. The PhD studentship is shared between the Westenhoff  group in biochemistry at the University of Uppsala and the  Lindsten  group in computational science at the University of Linköping, ensuring expert supervision in both fields. You are expected to be placed in the Lindsten group for extended stay(s).

The main duties of PhD students are to devote themselves to their research studies, which includes participating in research projects and third cycle courses. The work duties can also include teaching and other departmental duties (not more than 20 % of full time). 

• To be eligible for doctoral education, a basic higher education equivalent to at least 240 ECTS credits, including at least 60 ECTS credits at second-cycle level, or essentially equivalent competences acquired in some other way, is required. More information about the general requirements can be found here .
• A student has special eligibility for doctoral studies in chemistry if s/he has passed courses of at least 90 higher education credits (or equivalent), of which at least 40 higher education credits are from courses at advanced level (second cycle). More information about the subject specific requirements can be found here . 
• Very good English proficiency in speech and writing.

Great emphasis will be placed on personal qualities such as good collaborative skills, motivation and independence, as well as how the applicant through his/her experience and competence is judged to have the abilities necessary to develop within and acquire the doctoral education.

Additional qualifications

We are looking for a highly driven person, who shows clear signs to perform research work independently and can work effectively in a team. Primarily, we are looking for a chemist, structural biologist, biophysicist, or other backgrounds if your curriculum contains a strong chemistry component. You must have a strong interest in scientific programming and demonstrated experience in scientific programming, in particular in Python, PyTorch or similar, is a clear plus.  

PhD students at the department are typically engaged in teaching at BSc and MSc level. Prior experience from teaching/mentoring, also from non-academic contexts, and outreach can therefore be considered a merit.

Rules governing PhD students are set out in the Higher Education Ordinance chapter 5, §§ 1-7 and in Uppsala University’s rules and guidelines .

The employment is a temporary position according to the Higher Education Ordinance chapter 5 § 7. Scope of employment 100 %. Starting date as agreed. Placement: Uppsala

For further information about the position, please contact
Prof Sebastian Westenhoff [email protected], +46 73 469 72 67.

Please submit your application by 14 June 2024, UFV-PA 2024/1687.

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Uppsala University is a broad research university with a strong international position. The ultimate goal is to conduct education and research of the highest quality and relevance to make a difference in society. Our most important asset is all of our 7,600 employees and 53,000 students who, with curiosity and commitment, make Uppsala University one of Sweden’s most exciting workplaces.

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