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Postdoc position in Bioinformatics, Cancer biology, Functional genetics – NKI, Netherlands

The Netherlands, The Netherlands Cancer Institute, NKI

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The Netherlands Cancer Institute (NKI) in Amsterdam invites applications for a Postdoc position in Bioinformatics – mRNA translation in cancer, at the division of Oncogenomics, in the Netherlands – Dec 2021

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General Info

Position: Postdoc position
No. of Positions: 1
Research Field: , ,
Deadline to Apply:
Joining Date: ASAP
Contract Period: 2 Years
Salary: 3.447 to 4.077 Euro/Month

Workplace:
Division of Oncogenomics
The Netherlands Cancer Institute (NKI)
The Netherlands Cancer Institute, NKI
Amsterdam , ,

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Qualification Details

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.

Responsibilities/Job Description

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.

How to Apply?

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Reference Number: -
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Documents Required

CV, a motivation letter and the contact information of your references.

About the Project

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).

About the Employer: The Netherlands Cancer Institute, NKI

Note or Other details

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/

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Contact details

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.

Advertisement Details: Postdoc Bioinformatics - mRNA translation in cancer

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