PhD bioinformatics | department of Hematology

Acute myeloid leukemia (AML) is a devastating disease with dismal five-year overall survival rates. Despite the introduction of novel treatments, therapy resistance remains a major problem in achieving cures for patients with AML. This PhD project aims to unravel how cellular heterogeneity and non-genetic adaptation drive therapy resistance in AML by leveraging cutting-edge single-cell multi-omics technologies in combination with a novel genotyping strategy developed in our group.

We are looking for a PhD student who is able to analyze single-cell multi-omics datasets (RNA+ATAC or RNA+ protein) from AML samples. In addition, we generate single-cell long-read sequencing data to genotype individual cells. The ideal candidate enjoys exploring complex datasets in depth, developing new analytical strategies, and working both collaboratively and independently. A strong sense of scientific curiosity and a willingness to learn and apply new computational methods are essential.

As a PhD student, the following responsibilities are part of your role:

• analysis of single-cell RNA-seq datasets from AML samples;
• analysis of single-cell long-read datasets;
• integration of single-cell multi-omics datasets (RNA-seq, ATAC-seq, proteomics, etc);
• collaboration with experimental biologists to interpret results;
• presentation of the project and results at national and international scientific meetings;
• writing scientific papers.

We are looking for an enthusiastic, skilled, highly motivated and ambitious PhD student who can work independently as well as in a team and is creative in seeking solutions to scientific questions demonstrating capability for independent thinking. You have:

• a MSc degree in bioinformatics, computational biology or a related study;
• experience with single-cell RNA-seq analysis (Seurat, Scanpy, or similar tools);
• experience with high-performance computing (HPC);
• strong programming skills in R and/or Python.

Moreover, you have a curious, problem-solving mindset and an interest in new methods. Since you will be working in an international environment you are expected to have excellent command of written and spoken English and be able to communicate scientific ideas effectively.

• 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: € 3.108 to € 3.939 gross based on full-time employment (depending on education and experience) and a year-end bonus of 8.3%. Calculate your net salary here.
• 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.

Watch this video with more information about joining Amsterdam UMC Research BV.

The department of Hematology of Amsterdam University Medical Centers, location VUmc, is one of the largest Hematological Centers in the Netherlands. As part of the Cancer Center Amsterdam (CCA), one of the five Amsterdam UMC research institutes, the department is known for its high-quality translational research aimed at the improving survival outcomes for patients with hematological malignancies.

The Thijssen group consists of wet and dry lab scientists and we have our own single-cell lab to generate the datasets. You will be working in a collaborative environment consisting of hematologists, experienced postdocs, PhD students and experienced technicians.

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.

Watch the video to find out more.

During the publication period, applications will be handled continuously. If the vacancy is filled, it will be closed prematurely.

Note: you can apply by hitting the ‘Apply now’ button and uploading:

1. your CV, including the name and contact information of at least one referee;
2. a cover letter describing your research experience and addressing the key selection criteria, current research interests and career goals.

If you have any questions about this position, please feel free to contact dr. Rachel Thijssen via r.thijssen@amsterdamumc.nl, or dr. Perry Moerland via p.d.moerland@amsterdamumc.nl.

For more information about the application procedure, please contact Rhiannon Sandfort, recruitment advisor, at r.e.sandfort@amsterdamumc.nl.

A reference check, screening and hiring assessment may be part of the procedure. Read here whether that applies to you. 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.

Acquisition in response to this vacancy will not be considered.