Postdoc Bioinformatics - Aberrant Proteins in Cancer

The Dark Proteome consists of a collection of unannotated open reading frames. In recent years, we have studied the impact of various amino acid shortages on mRNA translation and identified a novel layer of the Dark Proteome never imagined before. We discovered that amino acid shortages stimulate cancer cells to produce aberrant proteins by ribosomal frameshifting and codon reassignments (Bartok et al., Nature 2021; Champagne et al., Mol. Cel. 2022; Pataskar et al., Nature 2022). 

Potentially, aberrant proteins are processed to neo-epitopes presented at the surface of cancer cells to the immune system (Champagne et al., Immunity 2025). We recently received the ERC-AdG award (pepTalks) to study the impact of such aberrant protein products on cell phenotype, their regulation, and how to utilize them for cancer therapies. 

Responsibilities
We seek a bioinformatics postdoc candidate to continue our research line studying the impact of amino acid shortages in cancer. The applicant will be responsible for the analysis and further development of bioinformatics pipelines to examine proteomics and immunopeptidomics datasets, as well as Ribo-seq, DNA-seq, tRNA-seq, and various other genome-wide technologies. We expect the successful applicant to have direct interactions with other computational and experimental researchers, supervise PhD and undergraduate bioinformatics students, and finally, to be involved in the writing of scientific papers, project reports, and grant applications. 

The Agami lab seeks to recruit an ambitious bioinformatics Postdoc with a strong background in large-scale data analysis and a strong commitment to science.

In particular, we seek candidates with the following computational skills; 
1. Strong experience in analysing proteomics datasets from raw files. 
2. Strong background in analysing genomics (RNA-seq, Ribo-seq, CRISPR-screening) datasets. 
3. Proficient in R and at least one of the following programming languages: PERL and Python. 
4. Experience with high-performance computing and proficiency in UNIX and BASH scripting. 

Furthermore, general knowledge of cancer biology and functional genetics tools is advantageous. We expect the candidate to be highly motivated, creative, and able to work in a team. Apart from being a true team player, we expect the candidate to exhibit a high degree of independence, a problem-solving attitude, strong analytical and technical abilities, and excellent communication and presentation skills. 

• The position is full-time (36 hrs./week), part-time 32 hrs. can be discussed;
• The vacancy is available starting May 1^st;
• You will be employed for a period of four years, one plus three year contract; 
• You will work in a cutting-edge research environment;
• You will collaborate with scientists with expertise in different disciplines; 
• The gross salary per month can range from € 3.606,- to € 5.084,- (salary scale 55), depending on your experience; the terms of employment will be in accordance with the Collective Labor Agreement for Hospitals (CAO Hospitals); 
• In addition, you will receive a fixed end-of-year bonus in December (8,33%) and in May you will receive 8,33% holiday pay;
• You will have access to state-of-the-art lab equipment; 
• Your travel expenses will be reimbursed at € 0,23 per km. Free parking at the Antoni van Leeuwenhoek is also part of the package; 
• Personnel is stimulated to use public transport and bicycle and therefore we offer an interesting arrangement for bikers and/or discount on the NS-business card;
• Amsterdam is a stunning city with many cultural amenities. The institute is located within a 20-minute tram or bicycle ride from the center of Amsterdam and within 20 minutes from Schiphol airport by car, bus or bicycle.

Contact information 
For further information about this position visit our website:
www.nki.nl/divisions/oncogenomics/agami-r-group/ or contact Reuven Agami at r.agami@nki.nl

Please attach your application letter, CV, and contact information for two references to the application form (link) on our website.
Ensure that the reference information is included along with your cover letter, as there is no option to submit them separately.
Apply by the 'Apply now'  button at the bottom of the page.
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