Doctoral (PhD) student position in computational proteomics and AI for cancer precision medicine Full-time

Doctoral (PhD) Student Position in Computational Proteomics and AI for Cancer Precision Medicine

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 Research Group

The doctoral studies will be conducted in the Cancer Proteomics Mass Spectrometry (MS) research group headed by Professor Janne Lehtiö. The research group is part of the Department of Oncology-Pathology at Karolinska Institutet (KI) and is based at Science for Life Laboratory (SciLifeLab) in Stockholm. The Lehtiö research group is a translational team of scientists dedicated to advancing human proteome analysis and enhancing personalized cancer treatments.

The Lehtiö group is a translational and multidisciplinary research environment dedicated to advancing proteome analysis and its application to cancer precision medicine. The group develops and applies experimental and computational methods in proteomics and proteogenomics to better understand how genomic alterations combined with tumor environment shape the molecular phenotype of cancer. Current research focuses on leukemia as well as solid tumors, including lung and breast cancer, with the aim of identifying clinically relevant disease mechanisms, therapeutic vulnerabilities, and immune escape pathways. Our overall aim is to improve individualized cancer treatments to achieve major improvements on patient survival and quality of life.

To complement the proteome data, we have access to a wide range of state-of-the-art omics and high throughput methods by our close proximity to SciLifeLab facilities. In close affiliation to the research group we also provide access to MS-based proteomics for external users through our core facilities at KI and SciLifeLab.

The Doctoral Student Project and the Duties of the Doctoral Student

We are seeking a highly motivated doctoral student for a position within the sub-group led by Yanbo Pan. This project lies at the interface of cancer biology, computational proteomics, and AI-driven bioinformatics. The doctoral student will analyze and integrate diverse proteomics data generated in the laboratory, including bulk proteomics, single-cell proteomics, proteogenomics, and spatial proteomics across different cancer types. A major focus of the project will be to reconstruct signaling networks at single-cell resolution, taking into account proteoform variation, protein subcellular localization and immune interactions.

The project will also explore advanced machine learning and AI methods, including large language models (LLMs) for functional annotation, information retrieval and integration from biological databases, literature, and omics datasets, as well as AI-assisted hypothesis generation. These approaches will be used to help interpret complex cancer proteomics data, identify mechanisms underlying cancer progression and immune evasion, and prioritize candidate therapeutic targets. The long-term goal is to generate biologically grounded insights that may support future combination therapy and immunotherapy strategies in precision medicine.

The PhD student will be part of a multi-disciplinary team with expertise in cancer biology, proteomics, bioinformatics and oncology. Within this framework, the student will be expected to work through collaboration, as well as individually and with increasing independence during the PhD studies that corresponds to 4 years of full-time studies. Apart from research work, the PhD position includes general and project related research courses, active participation in seminars, participation in writing scientific papers and presenting results at seminars and meetings.

What Do We Offer?

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.

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:

1. have been awarded a second-cycle/advanced/master qualification (i.e. master degree), or
2. 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
3. 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.

(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 with a strong interest in computational biology and cancer research. Applicants should hold a masters' degree (or equivalent) in computer science, bioinformatics, biostatistics, mathematics, systems biology or another relevant life science or related fields. Strong programming skills in Python and/or R, as well as experience with machine learning, deep learning, or AI methods, are required. Familiarity with omics data analysis is desired.

Experience with deep learning frameworks (e.g., PyTorch, TensorFlow) and large language model frameworks (e.g., Hugging Face Transformers, LangChain, or similar), as well as knowledge of prompt engineering, evaluation, and benchmarking of LLM-based models, and retrieval-based or retrieval-augmented generation (RAG) methods, is 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)

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.

Apply at the latest 7th May.

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