Master's thesis in data science

We are looking for a Master's thesis student with a strong background in data science and motivation to contribute to cutting-edge research on hematological malignancies. The task is to apply machine learning to identify malignant and healthy cells from bone marrow samples of patients with acute myeloid leukemia (AML) based on single-cell RNA-seq data. Random Forest could be a good model to start with. Deep learning approaches might also work here, although our current GPU resources are limited (we'll probably find a solution if the student is highly motivated to explore deep learning). The data have been partially produced in our lab and we would also utilize publicly available data from van Galen et al. 2019 (DOI: 10.1016/j.cell.2019.01.031).
Helsinki University Research Unit in Hematology (HRUH) focuses on translational research, merging basic cancer research with clinical trials. We apply high-throughput methods such as WES, scRNA-seq, and CROP-seq to understand the mechanisms of autoimmunity or immune evasion in hematologic diseases, such as aplastic anemia and leukemia. We are located in Biomedicum 1 in Meilahti, Helsinki. Please find more information about us in https://www.helsinki.fi/en/researchgroups/hematology-research-unit-helsinki
An eligible student should be machine learning literate, fluent in at least one programming language, preferably R or Python, comfortable with a unix environment, familiar with basic concepts in transcriptomics and genomics, and fluent in English. To apply for the job, please send an application with a CV and a transcript of records by e-mail to essi.laajala@helsinki.fi and satu.mustjoki@helsinki.fi by April 21st 2024. Harri Lähdesmäki has promised to be the supervisor from Aalto (Department of Computer Science). We prioritize candidates who are able to start before summer, but August or September might also be possible starting times.

Essi Laajala
Postdoctoral bioinformatician
Translational Immunology Research Program (TRIMM)
Hematology Research Unit Helsinki, University of Helsinki
and Helsinki University Hospital Comprehensive Cancer Center

Satu Mustjoki
Professor of Translational Hematology
Director of Translational Immunology Research Program (TRIMM)
Hematology Research Unit Helsinki, University of Helsinkiand Helsinki University Hospital Comprehensive Cancer Center