PhD Bioinformatics student - sloppiness in mRNA

The research group of Reuven Agami at the division of Oncogenomics at the Netherlands Cancer Institute in Amsterdam has recently uncovered a novel phenomenon in cancer termed “Sloppiness”. They showed that the tumor microenvironment enforces the production of aberrant proteins in cancer cells (Bartok et al., Nature 2021; Champagne et al., Molecular Cell 2022; Pataskar et al., Nature 2022; Yang., Molecular Cell 2024). In a project awarded by ERC-AdG-2024 for five years, the Agami group will characterize Sloppiness in cancer, investigate how it is regulated, study the impact of the resulting defective protein products on cell phenotype, and generate novel tools for cancer (immune)therapies. These research lines comprise the usage and development of several computational approaches in the field of genomics and proteomics. The lab is well-equipped with computational resources, including five powerful high-performance servers.

Responsibilities

We seek a highly motivated and enthusiastic PhD student who will develop an independent research line studying the impact of amino acid shortages in cancer. In this context, the applicant will be responsible for analyzing and further developing bioinformatics pipelines to examine datasets of DNAseq, RNAseq, Ribosome profiling, CRISPR screens, and mass spectrometry. We expect the successful applicant to team up with other computational and experimental researchers in the lab and be involved in the writing of scientific papers, project reports, and grant applications.

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

In particular, we seek candidates with the following computational skills;

1. Experience with analyzing genomic datasets.
2. Knowledge of analyzing proteomics datasets is a plus.
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.

Finally, 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. In addition to being a true team player, the candidate should have a problem-solving attitude, strong analytical and technical abilities, and excellent communication skills.

Compensation

The gross salary per month for our PhD will range from €3.523,- to a maximum of €4.277,- according to the standard PhD scales. The terms of employment will be in accordance with the Collective Labor Agreement for Hospitals. In addition you will receive a fixed end-of-year bonus (8,33%) and you will receive 8,33% holiday pay.

Your travel expenses will be reimbursed at € 0,19 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.