Doctoral (PhD) student position in probabilistic models of proteins

Do you want to contribute to top quality medical research?

To be a doctoral student means to devote oneself to a research project under supervision of experienced researchers and following an individual study plan. For a doctoral degree, the equivalent of four years of full-time doctoral education is required.

The Department of Microbiology, Tumor and Cell Biology (MTC) at Karolinska Institutet conducts research and teaching within immunology, infection biology, cell biology and cancer. MTC has about 40 research groups and our key words are multidisciplinary, bridging, national and international collaborations.

The position is in Ben Murrell’s group in MTC, based in the Biomedicum, in Karolinska’s Solna campus. The lab has worked across the experimental/computational interdisciplinary spectrum, in topics in virology and immunology, and currently specializes in computational biology focusing on developing methods and applications of deep learning for protein sequence and structure, as well as topics in phylogenetics. This project will involve working closely with experimentalists, and will be co-supervised by Prof Gerald McInerney and Dr Daniel Sheward, who have expertise in virology and immunology.

For a recent list of topics that the Murrell lab works on, please see: https://scholar.google.com/citations?hl=en&user=I80vy5cAAAAJ&sortby=pubdate  and https://staff.ki.se/people/benjamin-murrell

This Data Driven Life Sciences (DDLS) PhD project focuses on probabilistic models of protein structure, which can be used primarily for computational protein design, but also for an array of other applications related to modeling and understanding proteins and their behavior. The heart of the project will be the development and refinement of novel computational methods and models, including extending methods already under development in the lab, with a particular focus on ways of exerting more precise control for protein design.

In collaboration with the co-supervisors and their labs, the project will also involve the use of these methods (and methods developed by others) for applications in infection biology, chiefly for designing immunogens for new vaccines, but also exploring other applications. Another aim is to use the properties specific to some of the methods we are developing to try and improve secondary model use cases, such as evaluating designed backbones and predicting the functional effects of protein variants.

In addition, the doctoral student will be part of the DDLS initiative, and participate in the DDLS Research School.

The data-driven life science initiative

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 3.3 billion SEK (about 330M USD) over 12 years from the Knut and Alice Wallenberg (KAW) Foundation.

In 2025 the DDLS Research School will be expanded with the recruitment of 19 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 research 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/data-driven/ddls-research-school/

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

At Karolinska Institutet, we are announcing the position as DDLS PhD student in Data driven epidemiology and biology of infection.

Data driven epidemiology and biology of infection covers research that will transform our understanding of pathogens, their interactions with hosts and the environment, and how they are transmitted through populations. Research will have a strong focus on computational analysis or predictive modelling of pathogen biology or host-microbe systems for which multidimensional, genome-scale experimental data are now available or it may use population-scale genetic, clinical, or public health data from pathogen surveillance efforts and biobanks.

A creative and inspiring environment full of expertise and curiosity. Karolinska Institutet is one of the world’s leading medical universities. Our vision is to pursue the development of knowledge about life and to promote a better health for all. At Karolinska Institutet, we conduct successful medical research and hold the largest range of medical education in Sweden. As a doctoral student you are offered an individual research project, a well-educated supervisor, a vast range of elective courses and the opportunity to work in a leading research group. Karolinska Institutet collaborates with prominent universities from all around the world, which ensures opportunities for international exchanges. You will be employed on a doctoral studentship which means that you receive a contractual salary. Employees also have access to our modern gym for free and receive reimbursements for medical care.

In order to participate in the selection for a doctoral position, you must meet the following general (A) and specific (B) eligibility requirements at latest by the application deadline.

It is your responsibility to certify eligibility by following the instructions on the web page Entry requirements (eligibility) for doctoral education.

A) General eligibility requirement

You meet the general eligibility requirement for doctoral/third-cycle/PhD education if you:

Follow the instructions on the web page Entry requirements (eligibility) for doctoral education.

*If you claim equivalent knowledge, follow the instructions on the web page Assessing equivalent knowledge for general eligibility for doctoral education.

B) Specific eligibility requirement

You meet the specific eligibility requirement for doctoral/third-cycle/PhD education if you:

• Show proficiency in English equivalent to the course English B/English 6 at Swedish upper secondary school.

Follow the instructions on the web page English language requirements for doctoral education.

Verification of your documents: Karolinska Institutet checks the authenticity of your documents. Karolinska Institutet reserves the right to revoke admission if supporting documents are discovered to be fraudulent. Submission of false documents is a violation of Swedish law and is considered grounds for legal action.

(A) and (B) can only be certified by the documentation requirement for doctoral education .

In addition to the aforementioned requirements for the position:

• A demonstrable computational competence, comfortable with using and developing algorithms, data structures, etc to solve challenging problems is required (there will be a practical coding assessment during recruitment)
• A solid mathematical foundation is required (multivariable calculus, linear algebra, probability theory, etc)
• A competence in quantitative topics equivalent to a mathematics, statistics, physics, computer science, or engineering degree is required (if your degree was not in one of these domains, you will need to demonstrate that you have nevertheless acquired this level of competence)
• A strong motivation to develop new computational methods, interrogate their behavior in detail, and apply them to biological challenges, is required.
• Some degree of experience and understanding of probabilistic modeling and/or deep learning is required, as is a desire to deepen this understanding.
• The candidate must demonstrate a willingness to work independently and strong communication abilities to work in collaboration within a team.

Meritorious for the position:

• Experience with deep learning model development and/or implementation is advantageous (especially if in the context of protein structure)
• Experience with structural biology and/or molecular dynamics is advantageous
• Publicly available code is advantageous
• Experience with the Julia programming language is advantageous

The doctoral student will be employed on a doctoral studentship maximum 4 years full-time.

Submit your application and supporting documents through the Varbi recruitment system. Use the button in the top right corner and follow the instructions. We prefer that your application is written in English, but you can also apply in Swedish.

Your application must contain the following documents:

• A personal letter and a curriculum vitae
• Degree projects and previous publications, if any
• Any other documentation showing the desirable skills and personal qualities described above
• Documents certifying your general eligibility (see A above)
• Documents certifying your specific eligibility (see B above)

A selection will be made among eligible applicants on the basis of the ability to benefit from doctoral education. The qualifications of the applicants will be evaluated on an overall basis.

Karolinska Institutet uses the following bases of assessment:

• Documented subject knowledge of relevance to the area of research
• Analytical skill
• Other documented knowledge or experience that may be relevant to doctoral studies in the subject.

All applicants will be informed when the recruitment is completed.

Want to make a difference? Join us and contribute to better health for all