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Computational scientist for new optical pooled screening infrastructure at the Danish Cancer Institute

Copenhagen

November 12, 2024

Computational scientist for new optical pooled screening infrastructure at the Danish Cancer Institute
Do you want to be part of a state-of-the-art core facility helping researchers understand the genetic underpinnings of complex biological phenomena? The Danish Cancer Institute (DCI) is seeking a highly motivated and experienced computational scientist to support a new open-access infrastructure for microscopy-based pooled CRISPR screening using in situ sequencing. The ideal candidate will have a scientific background in and experience with managing workflows for analyzing biological imaging and CRISPR screening data. The responsibility of the computational scientist is to establish and maintain the computational framework for the infrastructure and provide computational support for users of the infrastructure.
About us
DCI is committed to leading the way in cancer research, focusing on innovative excellence in technology innovation and application. As an integral part of the Danish Cancer Society, we are working to reduce cancer risks, advance early diagnostics, develop novel therapeutic solutions, and improve patients’ lives. We function as a cross-collaborative international cancer research institute with an interdisciplinary and translational agenda, based on excellent research within basic biology and epidemiology. DCI features 23 research groups and a range of core facilities.
About the position
DCI will establish a new open access infrastructure for optical pooled screening (OPS), a state-of-the-art technology for coupling genetic perturbations using CRISPR technologies with visual microscopy-based readouts. The infrastructure will enable researchers across Denmark to perform OPS screens by supporting both the experimental and computational parts of the pipeline. The computational scientist will engage with researchers on their specific projects and provide dedicated support in developing computational analysis tools and pipelines required for performing and analyzing individual OPS screens. Furthermore, the computational scientist will be responsible for establishing the computational infrastructure including data storage and handling.
Start: April 1st, 2025, or after agreement
About you
We are looking for a highly motivated and open-minded candidate that can work independently and as part of a team and has excellent communication skills in English. The candidate is expected to have the following qualifications, competencies and experience:
Required experience:

Proficient in executing and scripting Python frameworks
Building custom image analysis pipelines using Python
Workflow management using Snakemake and/or Nextflow
User experience with high-performance computing (cloud or cluster)
(Bio)-informatic analysis of big data
Working with Unix/Linux environment

Preferred experience:

Sequencing or screen data analysis
Training and executing deep learning models for image analysis
Statistics analysis, particularly bootstrapping and model fitting
Data storage and organization with the FAIR principles

We offer

A stimulating and rewarding position within a renowned research institution.
An inspiring interdisciplinary and international environment
A collaborative and inspiring working environment
Opportunities for professional development and training

We offer several benefits for the personnel, such as an excellent canteen, a daily selection of free fruit, and a sports and art association.
Terms of salary and employment
We offer a 2-year position with the possibility of extension
Working hours are 37 hours/week including lunch.
You will receive salary and pension in accordance with the current agreement between the Danish Cancer Society and the relevant trade union.
Additional information
More information can be obtained by contacting group leader Jakob Nilsson; Jakob.nilsson@cpr.ku.dk
Application and closing date for applications
The deadline for application is January 17th, 2025.
The application should be written in English and must be submitted by clicking on the button “Apply for position”. Do not submit application by email.
The application should contain:

A motivation letter (max 1 page)
A short CV
A copy of relevant documents
Contact information of at least two references.

Application due

1/17/2025

Start date

4/1/2025

Workplace

Copenhagen

Homepage

cancer.dk

Contact

Jakob Nilsson

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