Staff Scientist in Spatial Genomics

Deutsches Krebsforschungszentrum
February 03, 2023
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Position: Staff Scientist in Spatial Genomics

Department: AI in Oncology

Code number: 2022-0472

The German Cancer Research Center is the largest biomedical research institution in Germany. With more than 3,000 employees, we operate an extensive scientific program in the field of cancer research.

The laboratory of Dr. Moritz Gerstung (Division of Artificial Intelligence in Oncoclogy) at the German Cancer Research Center DKFZ is looking for a senior staff scientist / postdoc to head their experimental spatial genomics team.

The group uses a combination of spatial genomics, transcriptomics, and proteomics to understand how interactions between tumour and normal cells control cancer evolution 1. These efforts build on commercially available technologies such as 10x Xenium for single-cell resolved spatial transcriptomics, but also involves bespoke protocols for detecting mutations in tissue sections 2. These approaches generate signals from 100,000s of cells in a tissue, which are assembled into maps of cell types and subclonal growth patterns using machine learning and AI algorithms 3. The protocols also allow for measuring the histopathological and transcriptomic changes acquired during tumour progression.

Job description:

We are looking for a senior staff scientist to oversee our experimental spatial genomics efforts carried out by a team of multiple technicians and graduate students. These wet lab experiments are key to the lab's mission to chart tumour growth patterns in hundreds of tumours of various types to unlock secrets of tumour evolution, progression and therapy resistance 4. The work will be carried out in collaboration with the DKFZ Single-cell Open Lab 5 and interfaces with a broad range of inter-institutional activities involving the Department of Neuropathology, the National Center for Tumour Diseases (NCT) and international collaborators.

Being part of an international interdisciplinary group working both experimentally and computationally we will offer you a comprehensive training and opportunities to broaden your horizon in many ways. Furthermore, you will have the opportunity to take full advantage of all the training and social activities the DKFZ International Postdoc Program has to offer 6.

Your responsibilities:

  • Oversee the spatial genomics lab work
  • Implement and run BaSISS 2
  • Run commercially available spatial transcriptomics assays such as 10x Xenium of Visium on arrays on fresh and fixed tissues
  • Implement other standard in situ hybridisation assays (e.g. RNAscope, Nanostring GeoMx) widely utilized in the field
  • Requirements:

    Key skills:

  • PhD in biological sciences or related field, with a focus on histology
  • Advanced experience with tissue preservation (e.g. fixation, cryo- preservation) and sectioning including both paraffin embedded and frozen tissue material
  • Experience in fluorescence microscopy of cells or tissues
  • A proven track record of delivering ambitious biomedical research projects
  • Excellent communication skills in English and ability to work effectively within a team
  • Desirable skills:

  • Experience with immunohistochemistry and in situ hybridization
  • Knowledge of image data pre-processing
  • Ability to test, implement and troubleshoot new techniques and protocols
  • Attention to detail and record keeping for sample and experimental tracking
  • Further information:

  • Seferbekova, Z., Lomakin, A., Yates, L. R. & Gerstung, M. Spatial biology of cancer evolution. Nat. Rev. Genet. (2022).
  • Lomakin, A., et al. Spatial genomics maps the structure, nature and evolution of cancer clones. Nature (2022).
  • Fu, Y., et al. Pan-cancer computational histopathology reveals mutations, tumor composition and prognosis. Nature Cancer 800–810 (2020).
  • Gerstung, M. et al. The evolutionary history of 2,658 cancers. Nature 578, 122–128 (2020)
  • https: // www. dkfz.de/en/single-cell-sequencing/open-lab.html
  • https: // www. dkfz.de/en/kuenstliche-intelligenz-in-der-onkologie/index.php
  • https: // www. dkfz.de/en/postdoc-program/index.html
  • We offer:

  • Interesting, versatile workplace
  • International, attractive working environment
  • Campus with modern state-of-the-art infrastructure
  • Salary according to TV-L including social benefits
  • Possibility to work part-time
  • Flexible working hours
  • Comprehensive further training program
  • Access to the DKFZ International Postdoc Program
  • Important notice:

    The DKFZ is subject to the regulations of the Infection Protection Act (IfSG). As a consequence, only persons who present proof of immunity against measles may work at the DKFZ.

    Earliest possible start date: as soon as possible

    Duration: The position is initially limited to 2 years with the possibility of prolongation. ​

    The position can in principle be part-time.

    Application deadline: 03.02.2023

    Contact:

    Dr. Moritz Gerstung Phone +49 (0)6221/42-4522

    Please note that we do not accept applications submitted via email.

    The DKFZ is committed to increase the proportion of women in all areas and positions in which women are underrepresented. Qualified female applicants are therefore particularly encouraged to apply.

    Among candidates of equal aptitude and qualifications, a person with disabilities will be given preference.

    To apply for a position please use our online application portal (https: // www. dkfz.de/en/stellenangebote/index.php).

    We ask for your understanding that we cannot return application documents that are sent to us by post (Deutsches Krebsforschungszentrum, Personalabteilung, Im Neuenheimer Feld 280, 69120 Heidelberg) and that we do not accept applications submitted via email. We apologize for any inconvenience this may cause.

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