Research Assistant/PhD student in stem cell biology at NNF Center for Stem Cell Medicine, reNEW

Copenhagen University
April 03, 2023
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The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) at University of Copenhagen is looking for a PhD fellow to join the Kirkeby Lab group led by PI Agnete Kirkeby. The position is scheduled to commence on the 21st of August 2023 or on a nearby alternative date upon agreement with the chosen candidate. The position as Research Assistant is for 1 year and the subsequent position as PhD fellow is for 3 years.

Research group The Kirkeby Lab research team is located at the The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) at the Faculty of Health and Medical Sciences of University of Copenhagen. Our group works to develop stem cell transplantation therapies for neurodegenerative disorders by producing high- purity cultures of subtype-specific human neural cells in the lab and testing these in animal models of disease. We further apply advanced stem cell technologies to study normally inaccessible stages of human brain development as well as to produce models of human brain diseases in the dish (i.e. Parkinson's Disease, Schizophrenia, dementia and hypothalamic disorders).

We offer creative and stimulating working conditions in a dynamic and highly international research environment. Our team currently consists of 18 team members at University of Copenhagen + 2 team members in our sister group at Lund University, representing a total of 12 different nationalities. Our labs at University of Copenhagen are located in a new and modern research facilities and include state-of-the-art laboratories, pleasant office facilities and access to high-quality core facilities in transcriptomics, imaging, flow cytometry and proteomics.

To read more about the team: https: // renew.ku.dk/research/reseach-groups/kirkeby-group/ https: // www. stemcellcenter.lu.se/research-groups/kirkeby

Job description We are seeking a highly motivated and ambitious pre-doctoral candidate with a strong educational background in the field of data science or bioinformatics. The candidate will be responsible for bioinformatic single cell RNAseq (scRNAseq) analysis of differentiating human neural cells, harvested both in vitro as well as from long-term matured grafts in rats and to integrate these with published datasets from human and mouse tissue. The aim is to apply such analysis to uncover human neural lieage trajectories and the compositions of human neural stem cell transplants. The main tasks of the position will be bioinformatic analyses, but combination with wet lab experiments will be possible, depending on the skills and wishes of the candidate. You will be working on projects together with other team members and we therefore expect experience in working in teams.

The technologies you will apply are:

  • Analysis of single cell and single nuclear RNA sequencing datasets from raw sequence reads to clustering and annotation
  • Application of publicly available trajectory and pseudotime algorithms (e.g. SCENIC, SPRING, Pseudotime, RNA velocity and deconvolution of barcodes) towards studying cell/tissue subtype specification, lineage trajectories, cell differentiation/maturation.
  • Spatial transcriptomics on human neural grafts to assess graft composition
  • In vitro and in vivo barcoding studies
  • The following requirements for the candidate will be assessed as key criteria for the recruitment.

    Mandatory requirements:

  • Masters degree in bioinformatics, computer science, data science or equivalent fields
  • Prior experience from working on biology/life science projects
  • Prior experience in working with single cell RNA sequencing data, including application of algorithms for clustering, integration and lineage trajectories
  • Extensive programming skills in R and Python
  • Fluency in English, written and spoken.
  • Positively assessed criteria:

  • Prior experience in working with neural/brain or stem cell datasets
  • Prior experience from working in collaboration with biologists
  • Prior experience in analysing datasets with cellular barcodes
  • Terms of salary, work, and employment The successful candidate will be offered a full-time position for a total of 4 years – the first year as research assistant and the following 3 years as PhD fellow. The transfer to employment as a PhD student after the first year is conditioned upon a positive assessment of the candidate ́s research performance during the first year as well as acceptance of enrolment in the Graduate School at the Faculty of Health and Medical Sciences. The transfer from Research assistant to PhD student may take place at an earlier time point than 1 year, if agreed upon between the PI and candidate, and conditioned by a positive assessment.

    Salary, pension and terms of employment are in accordance with the agree­ment between the Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. Depending on seniority, the monthly salary starts at approximately 27,800 DKK/Roughly 3,700 EUR (October 2021 level) plus pension.

    The PhD study must be completed in accordance with the ministerial orders from the Ministry of Education on the PhD degree and the University ́s rules on achieving the degree. General information about PhD study at the Faculty of Health and Medical Sciences is available at the Graduate School's website: https: // healthsciences.ku.dk/phd/guidelines/

    Application procedure Your application must be submitted electronically by clicking ‘Apply now' below. The application must include the following documents in PDF format:

    1. Motivated letter of application (max. one page)

    2. CV incl. education, experience, language skills and other skills relevant for the position

    3. Certified copy of original Master of Science diploma and transcript of records in the original language, including an authorized English translation if issued in other language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted. As a prerequisite for a PhD fellowship employment, your master's degree must be equivalent to a Danish master's degree. We encourage you to read more in the assessment database: https: // ufm.dk/en/education/recognition-and-transparency/find- assessments/assessment-database. Please note that we might ask you to obtain an assessment of your education performed by the Ministry of Higher Education and Science

    4. Publication list (if possible)

    Contact information: For questions about the project and group, please contact the principal supervisor:

    Associate Professor Agnete Kirkeby, NNF Center for Stem Cell Medicine, reNEW

    e-mail: [email protected] phone: +45 5168 5353

    Application deadline: 3 April 2023, 23.59pm CET We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

    Assessment procedure After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor.

    The assessor makes a non-prioritized assessment of the academic qualifications and experience with respect to the above-mentioned area of research, techniques, skills and other requirements listed in the advertisement.

    Once the assessment work has been completed each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself.

    The applicant will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities. You can read about the recruitment process at https: // employment.ku.dk/faculty/recruitment-process/

    The Faculty of Health and Medical Sciences comprises approximately 7500 students, 1500 PhD students and 3200 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 . www. ku.dk

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