Cell2Sample: PhD position for multi-omics computational framework

Cell2Sample: PhD position for multi-omics computational framework

Join Cell2Sample as a PhD student and help build cutting-edge tools to integrate multi-omics data, unravel cellular complexity, and advance precision medicine through innovative computational research.

The project

Achieving precise patient care requires an accurate understanding of the mechanisms underlying disease development and drug resistance, but these processes are often heavily dependent on complex interplays between cells within their microenvironment. Cellular heterogeneity can be attributed to cell type composition in the microenvironment, activation states, and their function in terms of interactions with other cell types (e.g., immune cells and tumour cells; immune cells and microglia). While advanced single-cell molecular and imaging data can address some aspects of this complexity, their availability is limited due to high costs and cannot be expanded to large series of patient samples, which is necessary for biomarker discovery. Furthermore, these techniques individually cannot cover all modalities (e.g., proteome) as efficiently as others (e.g., transcriptome), which makes it challenging to provide a complete picture.

The Cell2Sample project aims to overcome these limitations by establishing a comprehensive computational framework that integrates diverse omics data types — ...

About your role

We are looking for a PhD student who will focus on bulk multi-omics data integration, working in close collaboration with another PhD student appointed for spatial transcriptome analysis in the Bioinformatics Lab of the Department of Epidemiology and Data Science.

The core objective of this project is to enhance Statescope — a Bayesian framework developed by our team for cell state profiling using bulk RNA-seq data. This enhancement will focus on integrating additional omics layers, such as proteomics and phospho-proteomics, to characterize individual cell types based on their multi-omics profiles and pathway activation states. Expanding Statescope to incorporate diverse omics modalities aims to improve deconvolution accuracy, especially for datasets lacking single-cell data for certain modalities. This expansion will require the development of tailored statistical models for each data type.

About you

We are looking for a PhD student with the following profile:

• MSc in Bayesian statistics, biomedical informatics, bioinformatics, computer science or a closely related discipline;
• Experience with computer programming (R/Python/C/C++ or etc) and work-flow management (e.g., Snakemake);
• Basic understanding of or strong interest in genomics / transcriptomics / proteomics data analysis;
• Excellent communication skills and fluency in English, both written and spoken.

Our offer

• A flying start to your career in scientific research.
• Plenty of room for your drive to shape tomorrow's healthcare.
• Working on large-scale and in-house research, with motivated colleagues from all over the world.
• You will be employed by Amsterdam UMC Research BV.
• A contract for 12 months, with the intention to extend for a total of 4 years. The Guideline PhD contract applies to this vacancy.
• Salary scale OIO: € 3.017 to € 3.824 gross based on full-time employment (depending on education and experience) and a year-end bonus of 8.3%. From July 1st, 2025, there will be a salary increase of 3%.
• Holiday hours: 190,4 per year for fulltime and a possibility to save additional hours.
• Pension accrual with BeFrank, a modern, comprehensible and fairly priced pension.
• For >7 km each way, 100% reimbursement for public transport travel costs and, for private transport, €0.18 per km up to a maximum of 40 km each way.
• Do you prefer walking or cycling? Take advantage of our good bike scheme. Moreover, you will receive a reimbursement of €0.18 per km.

About your workplace

You will join the Tumor Genome Analysis Core (TGAC) laboratory at the Department of Pathology of Amsterdam UMC, location VUmc. Our team focuses on understanding and optimizing treatment care primarily for cancer patients, based on the research using next-generation sequencing (NGS) data. Our team hosts multiple bioinformatic researchers in the domain of oncology and tumor microenvironment research using advanced NGS techniques such as DNA-seq / RNA-seq / single-cell RNA-seq as well as imaging techniques such as Xenium. Therefore, there will be ample opportunity to interact and learn from fellow researchers.

You will also be part of the ADORE Biocomputational Focus group, which unites Amsterdam UMC biocomputational researchers who develop and apply computational methods relevant to onco- and neurological applications.

Amsterdam UMC Research BV supports non-profit scientific research. In doing so, we provide researchers with everything they need to excel. Our principal investigators (PIs) and project leaders offer support in the field of project management, finance and human resources. In medical scientific research projects, legal support is also provided.

Amsterdam UMC has an open culture. This means that we hope that everyone feels welcome in our organization and that we strive to offer equal opportunities to everyone. We therefore cordially invite all interested parties to respond to this vacancy.

Let’s meet!

We have two PhD positions available within the Cell2Sample project. Please apply for the position you are most interested in, but feel free to apply to both positions if you wish. Suitable candidates may be considered for both roles.

If you are interested, please contact Dr. Yongsoo Kim, Assistant professor in oncogenomics via yo.kim@amsterdamumc.nl.

For more information about the application procedure, please contact Chey Edwards, Recruitment advisor, via c.i.edwards@amsterdamumc.nl.

A reference check, screening and hiring test may be part of the procedure. If you join us, we ask you for a VOG (Certificate of Good Conduct).

Internal candidates will be given priority over external candidates in case of equal suitability.