PhD Student in Precision Medicine in Pediatric Cancer

PhD Student in Multi-Omics Integration and Machine Learning for Precision Medicine in Pediatric Cancer

Are you interested in working with cutting-edge research, with the support of competent and friendly colleagues in an international environment? Are you looking for an employer that invests in sustainable employeeship and offers safe, favourable working conditions? We welcome you to apply for a PhD student position at Uppsala University.

The Department of Medical Sciences is a large clinical institution with more than 250 employees and over 900 additional coworkers connected via the Uppsala University Hospital. The Department of Medical Sciences has a broad research profile with strong research groups in a number of different areas. The research carried out at the department is performed in close connection with the clinical activities at the Uppsala University Hospital, which includes both basic studies on the causes of a variety of illnesses and the development and evaluation of improved diagnostics and new treatment methods. More information about the Department of Medical Sciences can be found at https://www.uu.se/en/department/medical-sciences

We are recruiting a driven PhD student to join the Molecular Precision Medicine research group at the Department of Medical Sciences, located at the Uppsala Biomedical Center (BMC). The research group focuses on various diseases using large-scale genetic methods, bridging advanced wet-lab and computational approaches (current projects can be found on our website: https://www.uu.se/en/department/medical-sciences/research/research-groups/molecular-precision-medicine). Through close collaboration with clinical researchers at Uppsala University Hospital, our research group has access to unique sample collections and clinical patient information. A close collaboration with the National Genomics Infrastructure (NGI) at the Science for Life Laboratory (SciLifeLab), gives the research group access to cutting-edge sequencing technologies (https://ngisweden.scilifelab.se/).

The project focuses on analyzing samples from children with leukemia or lymphoma, healthy controls, and in vitro cell models using various -omics techniques. The PhD student is expected to pre-process the generated data and perform downstream analyses, including multi-omics integration and machine learning. To achieve the overarching goal of advancing precision medicine in pediatric leukemia/lymphoma, we aim to identify biomarkers that can differentiate high-risk patients from low-risk patients. This study seeks to shorten chemotherapy treatment for low-risk patients, while specifically targeting the high-risk group. We will also conduct drug screenings for targeted therapies, testing promising new drugs currently in early clinical trials. The PhD student may participate in selecting drug candidates through bioinformatics approaches.

This PhD project will be carried out in close collaboration with leading research groups in pediatric hematology from the Nordic Society of Pediatric Hematology and Oncology (NOPHO) and ALLTogether (A2G) consortiums. As a PhD student in this project, you will play a key role in integrating and analyzing multi-omics data within the consortium to deepen the understanding of pediatric leukemia and lymphoma at the molecular level and contribute to the development of new treatment strategies.

Duties

• - Analyze multi-omics data from pediatric leukemia samples and in vitro models, including genomic (WGS), transcriptomic (bulk and scRNA-seq), epigenomic (DNA methylation arrays), and proteomic (Olink Explore PEA) data.
• - Develop and apply machine learning models to identify disease subtypes and predict treatment responses.
• - Develop reproducible frameworks and/or user-friendly applications to promote high quality research and accelerate scientific discovery.
• - Collaborate with pediatric oncologists, molecular biologists, bioinformaticians, and computational biologists, both within the research group and with our international partners.
• - Write scientific articles and present the project’s results at scientific meetings and conferences.

Requirements
To meet the entry requirements for doctoral studies, you must

• - hold a Master’s (second-cycle) degree in bioinformatics, computational biology, molecular biology, or a related field.
• - have completed at least 240 credits in higher education, with at least 60 credits at Master’s level including an independent project worth at least 15 credits, or
• - have acquired substantially equivalent knowledge in some other way.

Additional requirements for this position include:

• - documented experience in large-scale data analysis and programming in relevant languages, such as Python and R.
• - proficiency in handling large datasets in a LINUX/UNIX environment.
• - excellent communication and collaboration skills.
• - excellent verbal and written English.

Additional qualifications

• - Experience with DNA methylation analysis.
• - Experience with proteomics data (e.g. Olink PEA).
• - Experience with multi-omics data integration.
• - Experience with single-cell sequencing analysis.
• - Competence in machine learning for biomedical applications.
• - Experience working with workflows (e.g. Snakemake, Nextflow).
• - Experience working with interactive web apps (e.g. Shiny).

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

About the employment
The employment is a temporary position according to the Higher Education Ordinance chapter 5 § 7. Scope of employment 100 %. Starting date February 1st 2026 or as agreed. Placement: Uppsala

For further information about the position, please contact: Jessica Nordlund, jessica.nordlund@medsci.uu.se, +46704250806

Please submit your application by January 2nd 2026, UFV-PA 2025/3795.

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