Doctoral (PhD) student position in computational network-based cancer precision medicine

Updated: about 1 month ago

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.

One Ph.D. position is available in cancer precision medicine using advanced machine learning methods and AI methods on large-scale data. The position is part of the SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS).

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: Data-Driven Life Science (DDLS) - SciLifeLab  

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


The research group

The doctoral studies will be conducted in the Cancer Proteomics Mass spectrometry research group headed by professor Janne Lehtiö . The research group  is placed at SciLifeLab in Solna, Stockholm. The Lehtiö research group is a translational team of scientists dedicated to advancing human proteome analysis. We develop innovative methods to enhance personalized cancer treatments.  

Proteomics is the large-scale study of proteomes - entire sets of proteins in a biological system. This field of science focuses on understanding the proteins in biological processes. By analysing the proteome, we can gain insights into cellular behaviour, disease mechanisms, and potential therapeutic targets. Proteomics involves various technologies and methods, such as mass spectrometry and bioinformatics.

Our aim is to connect cancer proteome knowledge to genome and clinical data to improve personalized cancer treatment by increasing the understanding of cancer biology. We believe that this is important development in precision medicine in selecting most effective treatment for each patients.

For this translational project, we have formed a supervisor team with Professor Chacholski leading the Topological Data Analysis (TDA) group at KTH's mathematics department with an aim to reveal structures of biomedical datasets using algebra, topology, and geometry,and Assistant professor Nilsson who recently joined from the Massachusetts Institute of Technology (MIT), and is establishing a research group at KI as a DDLS fellow, with a research focus on explainable artificial intelligence using extensive bio-datasets.


The doctoral student project and the duties of the doctoral student

At Karolinska Institutet/SciLifeLab, we are looking to fill the position as PhD Student in Data-driven precision medicine and diagnostics.

Data-driven precision medicine and diagnostics covers data integration, analysis, visualization, and data interpretation for patient stratification, discovery of biomarkers for disease risks, diagnosis, drug response and monitoring of health. The precision medicine research is expected to make use of existing strong assets in Sweden and abroad, such as molecular data (e.g. omics), imaging, electronic health care records, longitudinal patient and population registries and biobanks.

This doctoral research project aims to develop new methods to improve analysis and data interpretation of future diagnostics data on cancer precision medicine using large-scale omics data. Beyond chemotherapy, modern drug treatments now focus on targeted therapies. This approach uses genomic analysis of individual tumour samples to identify specific DNA alterations, guiding treatment choices. Despite advancements by targeted treatments, the continued occurrence of patient relapses highlights the urgent need for further developments. We have worked successfully on broadening the diagnostics toolkit to understand cancer and match effective treatments to patients based on this knowledge.

We are now looking for a doctoral student with an interest in computational biology, bioinformatics, cancer precision medicine, proteogenomics and network analysis to develop methods that transition analysis from cohort-level to patient-specific protein-protein interaction networks, using in-house generated and publicly available data. Specifically, the doctoral student will construct cell type- and patient-specific protein networks as well as develop geometry-based classifiers to discover new cancer biology and predict patient subgroups that could benefit from targeted therapy. The student will be involved in developing machine learning models using neural networks and topological data analysis on proteogenomics data. Explainable models will be prioritized to support transparency in clinical decision support systems. Overall, the candidate is expected to acquire expertise in data analysis techniques for proteogenomics in cancer precision medicine.


What do we offer?

A creative and inspiring environment full of expertise and curiosity at LehtioLab as well as with co-supervisor teams. Our multinational team of co-workers have diverse background both on education and expertise embedded at SciLifeLab and Karolinska Institutet, which 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. In this position, also the DDLS PhD program offers great opportunities for peer interaction and cutting-edge education. Karolinska Institutet and SciLifeLab 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.


Eligibility requirements for doctoral education

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:

  • have been awarded a second-cycle/advanced/master qualification (i.e. master degree), or
  • have satisfied the requirements for courses comprising at least 240 credits of which at least 60 credits were awarded in the advanced/second-cycle/master level, or
  • have acquired substantially equivalent knowledge in some other way in Sweden or abroad.*
  • 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 .


    Skills and personal qualities

    We are looking for an enthusiastic and highly motivated candidate to join our team. Applicants should hold a masters' degree (or equivalent) in computer science, bioinformatics, biostatistics, mathematics, systems biology or another relevant life science or related fields. Knowledge of R and/or Python programming language as well as experience with machine learning is required. Familiarity with some large-scale data analysis is desired. Experience with deep learning frameworks (TensorFlow, PyTorch, Keras, Scikit-learn) and topological data analysis is also considered a plus. Proficiency in oral and written English is necessary. As the PhD student will be part of a multi-disciplinary team of experts in cancer biology, proteomics, bioinformatics and mathematics, ability to work with other scientists and good communication skills are important.


    Terms and conditions

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


    Application process

    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)


    Selection

    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.


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