Researcher in Genomics

University of Copenhagen

Bioinformatics Specialist - Genomics Platform

The role of the bioinformatics specialists is to ensure daily operations at the Genomics Platform and to support researchers from our centres working on fundamental biological mechanisms - the Novo Nordisk Centres for Protein Research (CPR) and Stem Cell Biology (DanStem) - with expertise in functional genomics and single-cell sequencing data processing and analysis. The advertised job is an exciting opportunity for strong candidates with a background in bioinformatics to establish themselves in the field of genomics services. The genomics platform represents a joint venture that bridges the vibrant scientific environment that spans DanStem and the CPR and is central to scientific activities in both centres.

Background

DanStem addresses fundamental research questions in stem cell and developmental biology and has activities focused on the translation of promising basic research results into new therapeutic strategies for cancer and chronic diseases. DanStem is a vibrant, internationally diverse and ambitious research centre with state-of-the-art facilities. The setting is ideally suited for seamless collaboration and exchange with other centres and departments of the Faculty and Copenhagen science community.

Learn more about DanStem at https://danstem.ku.dk.

CPR promotes basic and applied research on human proteins of medical relevance. CPR spans broad areas of protein research, ranging from structural and mechanistic understanding of proteins and their cellular functions in chromatin biology and genome maintenance, to development of clinical applications of proteomics and systems biology. The vision of CPR is to combine the power of integrative protein technologies and their application to accelerate understanding of the biological processes underlying health and disease.

For more information about CPR, please visit http://www.cpr.ku.dk.

The genomics platform was established in 2017 by DanStem and CPR and has been run by a sequencing specialist and a bioinformatics specialist. We are seeking a highly motivated and ambitious candidate to join the platform as an additional bioinformatics specialist with a focus on user support, method development and training. The genomics platform has access to its own NextSeq500, Chromium 10X and other necessary genomics equipment, as well as the national High-Performance Computing infrastructure (Computerome) and its newly acquired server (including 4 GPUs) hosted by KU-IT. Groups at CPR and DanStem are seeing a steady increase in genomics-based experiments and assays which massively benefit from input and advice by the combined expertise of the genomics platform.

Job description

The role of the bioinformatics specialist is to ensure daily operations of the dry lab part of the Genomics Platform. The tasks include:

  • Support of experimental design and analysis strategy for genomics-based assays and method development
  • Mapping and curation of sequencing data coming from the CPR/DanStem sequencing pipeline (potentially curating data coming from collaborations on 3rd GenSeq platforms)
  • Teaching and supporting researchers with genomics analysis tools and methodologies.

Your profile

  • A degree in computer science, bioinformatics, computational biology, or appropriate computational and data science with either PhD or MSc
  • Strong experience in Python or R and in Linux/UNIX computing environment
  • Broad experience with analysing functional genomics data (e.g. RNA-seq, ATAC-seq, ChIP-seq, HiC, scRNA-seq, Cut&Run/Tag, etc.)
  • Strong interest in user support and training
  • Other aspects that will be considered a plusTeam-oriented communication style and ability to manage experiment associated cost transparently and efficiently            
    • Previous experience with single-cell data processing and analysis
    • Interest in modern visualization tools (e.g. shiny, plotly, dash, tableau)
    • Experience/interest with workflow tools (e.g. snakemake, NextFlow)
    • Experience with system administration, Computerome 2, modules
  • Good English communication skills, both oral and written, are required
  • Ability to connect and actively participate in an exchange with other genomics platforms nationally and internationally.

We offer

  • A stimulating, challenging and multifaceted research environment
  • A combination of active scientific service platforms to interact and to develop ideas together and expand available methodology at CPR and DanStem
  • Possibility for continued education and training
  • Attractive employment conditions
  • Centrally located workplace.      

Employment conditions

The employment is a permanent position and is scheduled to start 15 April 2021 or upon agreement with the chosen candidate. The place of work is at DanStem, University of Copenhagen, Blegdamsvej 3B, Copenhagen. Salary, pension and terms of employment are in accordance with the provisions of the collective agreement between the Danish Government and AC (the Danish Confederation of Professional Associations).

In addition to the basic salary, a monthly contribution to a pension fund is added by the employer (17.1% of the salary).

The employment will be as Research consultant (Specialkonsulent) depending on the selected candidate’s experiences and qualifications and the working time is full time (37 hours per week on average).

Application

Your application must be submitted in English by clicking “Apply now” below and must include:

  1. Motivation letter
  2. Curriculum vitae incl. education, experience, previous employments, language skills and other relevant skills
  3. Copy of diplomas/degree certificate(s).

Only applications received in time and consisting of the above-listed documents will be considered. Applications and/or any material received after the deadline will not be taken into consideration.

Deadline for applications: 1 March 2021.

Questions

For further information about the position, please contact Dr Malte Paulsen malte.paulsen@sund.ku.dk or Professor Anja Groth anja.groth@cpr.ku.dk.

The Faculty of Health and Medical Sciences comprises approximately 7,850 students, 1,700 PhD students and 4,800 employees. The Faculty advances the field of health sciences through its core activities: research, teaching, knowledge sharing and communication. With basic research fields ranging from molecular studies to studies of society, the Faculty contributes to a healthy future through its graduates, research findings and inventions benefitting patients and the community. The University of Copenhagen wishes to reflect the surrounding community and invites all regardless of personal background to apply for the position.

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Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.

Contact

Anja Groth
E-mail: anja.groth@cpr.ku.dk

Contact

Malte Sören Paulsen
E-mail: malte.paulsen@sund.ku.dk

Info

Application deadline: 01-03-2021
Department/Location: DanStem
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