PhD Bioinformatics student - sloppiness in mRNA

Updated: about 1 month ago
Deadline: 31 May 2024

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.



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