Postdoctoral Fellow in Spatial Single-Cell Multi-Omics

Stockholm University

Sweden

September 5, 2021

Description

atthe Department of biochemistry and biophysics. Closing date: 5 September 2021.

SciLifeLab is a national center for molecular biosciences with focus on health and environmental research. The center combines frontline technical expertise with advanced knowledge of translational medicine and molecular bioscience. SciLifeLab is a national resource hosted by Karolinska Institutet, KTH Royal Institute of Technology, Stockholm University and Uppsala University. The center also collaborates with several other universities.

Mats Nilsson's research group at the Department of Biochemistry and Biophysics (DBB) is located at SciLifeLab in Solna, and is now seeking a postdoctoral fellow to perform and optimize spatial single-cell multi-omics technology.

Project description The field of spatially resolved omics is emerging to provide new insights into the spatial organization of tissues and organs at the molecular level. The Targeted Spatial Omics (TSO) units within the SciLifeLab Spatial and Single Cell Biology platform has been launched this year with the mission to provide in situ sequencing (ISS, PI: Mats Nilsson/Chika Yokota), single- molecule fluorescence in situ hybridization (smFISH, PI: Magda Bienko/Xiaoze Li Wang) and multiplexed immunofluorescence (CODEX, PI: Emma Lundberg/Charlotte Stadler) service to scientists across the country. The platform has also a mission to develop new capabilities, and that is the main objective of the postdoc. The position is closely linked to the platform units and to the research groups at SciLifeLab, pioneering these spatial omics methods.

With the support of a dedicated grant from Vetenskapsrådet, there is an opening for a postdoctoral fellow at the Mats Nilsson's group in spatial single-cell multi-omics. The aim of the project is to establish integrated protocols of TSO technologies, in order to make these state-of-the-art technologies to be effectively deployed by a wide research community, particularly in biotech/pharma and hospitals. The project will focus on developing useful analysis pipelines for clinical oncology research. Currently, there is no protocol for integrating ISS/FISH/CODEX on the same sample. However, multi-modal data collection from the same tissue section is desirable especially in the case of precious samples, such as small biopsies. A particular focus will be, therefore, on identifying optimal conditions that allow performing different types of sequential assays on the same sample.

Main responsibilities The postdoc will participate in the project and contribute to general reseach group activities and responsibilities. The postdoc will be responsible for establishing the protocols for sequential assays, such as (i) DNA/RNA FISH followed by CODEX; (ii) ISS followed by CODEX; (iii) mutation detection by ISS followed by CODEX. As such, the successful candidate will operate closely with the TSO research groups and the platform to jointly develop laboratory research protocols, including handling tissue, performing TSO technologies, handling sensitive instruments such as fluorescence microscopes and liquid handling robots, and storing, sharing and tracking samples and data. The role also includes setting up pipe lines for integrated analysis of the data, mainly in collaboration with bioinformaticians from the Bioinformatics platform at SciLifeLab.

Qualification requirements Postdoctoral positions are appointed primarily for purposes of research. Applicants are expected to hold a Swedish doctoral degree or an equivalent degree from another country.

Assessment criteria The degree should have been completed no more than three years before the deadline for applications. An older degree may be acceptable under special circumstances, which may involve sick leave, parental leave, clinical attachment, elected positions in trade unions, or similar.

In the appointment process, special attention will be given to research skills. Doctoral degree should be from a relevant field e.g. Cell Biology, Molecular Biology, Biochemistry, Biomedical Science, Biotechnology or similar discipline and the applicant should have experience with standard molecular and cellular biological techniques. The applicant should also have previous experience with microscopy. The applicant should be fluent enough in Python and/or R to be an advanced user of different open-source analysis packages.

Experience in in situ hybridization, immunohistochemistry or similar techniques is highly desirable. Good knowledge and experience in bioimage analysis will be highly valued. The successful candidate should enjoy learning new methods, and should be able to demonstrate an ability to complete projects within a defined time frame. Previous work in the field of cancer research is an advantage. Excellent interpersonal, organizational skills, communication skills and good knowledge of English are essential. Emphasis will be placed on qualities of responsibility, flexibility, teamwork and ability to solve problems.

Terms of employment The position involves full-time employment for a maximum of two years, with the possibility of extension under special circumstances. Start date as per agreement.

Stockholm University strives to be a workplace free from discrimination and with equal opportunities for all.

Contact Further information about the position can be obtained from Professor Mats Nilsson, telephone: +46 73 053 78 76, mats.nilsson@scilifelab.se.

Union representatives Ingrid Lander (Saco-S), telephone: +46 708 16 26 64, saco@saco.su.se, Alejandra Pizarro Carrasco (Fackförbundet ST/Lärarförbundet), telephone: +46 8 16 34 89, alejandra@st.su.se, and seko@seko.su.se (SEKO).

Application Apply for the position at Stockholm University's recruitment system. It is the responsibility of the applicant to ensure that the application is complete in accordance with the instructions in the job advertisement, and that it is submitted before the deadline.

Please include the following information with your application

  • Your contact details and personal data
  • Your highest degree
  • Your language skills
  • Contact details for 2–3 references
  • and, in addition, please include the following documents

  • Cover letter that also describes (max 2 pages): – why you are interested in the field/project described in the advertisement – why and how you wish to complete the project – what makes you suitable for the project in question

  • CV – degrees and other completed courses, work experience and a list of publications

  • Copy of PhD diploma
  • Letters of recommendation (no more than 3 files)
  • Publications in support of your application (no more than 3 files).
  • The instructions for applicants are available at: How to apply for a position.

    You are welcome to apply!

    Stockholm University contributes to the development of sustainable democratic society through knowledge, enlightenment and the pursuit of truth.

    Closing date: 05/09/2021

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