Careers And Study

Postdoc Bioinformatics - mRNA translation in cancer

Function description

The Netherlands Cancer Institute (NKI) in Amsterdam is a Comprehensive Cancer Centre combining a hospital and research laboratories in a single independent organization. The research group of Reuven Agami at the division of Oncogenomics is interested in identifying novel cellular vulnerabilities that can be exploited for cancer therapies. For this purpose, they develop innovative genomic and functional genetic tools and use biochemical and bioinformatics tools to understand the underlying mechanisms. 
In recent years the Agami lab studied amino acid shortages and its impact on mRNA translation in cancer mainly using Ribosome Profiling (Ribo-seq) and CRISPR-screens (Loayza-Puch et al., Nature 2016; Slobodin et al., Cell 2017; Sun et al., EMBO 2020). This research line has led them to uncover a surprising impact of amino acid shortages on proteins' quality. They showed that prolonged amino acid deprivation induces cancer cells to produce defective proteins by ribosomal frameshifting (Bartok et al., Nature 2020). Following up, the lab demonstrated that such ribosomal frameshifting is under regulation of oncogenic signalling pathways (Champagne et al, Mol. Cell 2021). These defective proteins can be processed and presented at the cell surface of cancer cells and be recognized by immune cells. Currently, the lab is active in expanding the outreach of these vulnerabilities to be tested in clinical setting. These projects, apart from inviting computational challenges, compel to ask novel research questions and provide possibility of directing them to success. In terms of computational resources, the lab has recently acquired 5X independent computational servers and obtained NWO computational time grant for using Dutch National Server (Snellius).

Responsibilities:
The successful candidate will continue an ongoing research line in the lab to establish the link between defective protein production and cancer. In this context, the applicant will be responsible for the analysis and further development of bioinformatics pipelines to examine various large datasets of Ribo-seq, DNAseq, RNAseq, and mass spectrometry. In addition, the applicant will analyse functional genetic screenings and biochemical experiments. Apart from this, the applicant can incorporate in-house and external resources to develop predictive models of defective protein production. We expect the successful applicant to have direct interactions with other computational and experimental researchers, to supervise PhD and undergraduate students, and finally to be involved in writing of scientific papers, project reports and grant applications. 

Job requirements

The Agami lab seeks to recruit an ambitious Postdoc with a strong publication background in large-scale data analysis and a strong commitment to science.
In particular, we seek a person with the following computational skills;
  1. Experience with the analysis of proteomics datasets (protein expression, phosphoproteomics etc) is a big advantage.
  2. Experience with the analysis of genomics (RNA-seq, Ribo-seq, CRISPR-screening) datasets.
  3. Proficient in R, and at least one the following programming language; PERL and Python.
  4. Experience with high performance computing and proficient in UNIX and BASH scripting.
  5. Experience with cancer datasets (TCGA, CPTAC etc.), will be beneficial.
  6. Experience with proteogenomics pipelines is a big plus.
  7. Experience with machine-learning and statistical modelling is a big plus.

Furthermore, general knowledge in cancer biology and functional genetics tools is an advantage. We expect the candidate to be highly self-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, to have a problem-solving attitude and have strong analytical and technical abilities in addition to excellent communication and presentation skills. 

Compensation

You will join an international research team in a stimulating and interactive research environment. You will be employed for a period of at least 2 years. The gross salary for a fulltime appointment will range from
€ 3.447,- to € 4.077,- per month, depending on previous experience. The terms of employment will be in accordance with FWG 55 of the CAO Ziekenhuizen (Collective Labour Agreement for 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. For more information in regard to the secondary conditions please visit our website: https://www.nki.nl/careers-study/how-to-apply/ 
 
Interested?
For further information and addresses visit our websites (http://research.nki.nl/agamilab/; https://www.nki.nl/divisions/oncogenomics/agami-r-group/) or contact Reuven Agami, r.agami@nki.nl.

Applications can be submitted via the portal (http://www.nki.nl/working-at-the-nki/) and should include your CV, a motivation letter and the contact information of your references. 

The NKI values diversity and is committed to creating an inclusive work environment that stimulates the best in each individual. Applications of all individuals are welcomed regardless of age, ancestry, religion, disability, distance from the labor market, sexual orientation or gender identity.

Acquisition in regards to this vacancy is not appreciated.
 

Details

  • Hours per week: 36
  • Salary level: FWG 55
Carly  DeSantis

Carly DeSantis

Recruiter
Reuven  Agami

Reuven Agami

Group leader

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