Doctoral Student In Medical Science - Stem Cell Development Single Cell Analysis

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Doctoral position in Medical Science

Project title: Cell fate benchmarking of in vitro models of human development and disease

The Department of Microbiology and Immunology is located at the Institute of Biomedicine at the Faculty of Medicine at Sahlgrenska Academy, University of Gothenburg.

General information about being a doctoral student at the University of Gothenburg can be found on the university's doctoral student pages https: // www. gu.se/en/doctoral-studies

Doctoral education in Medical Science comprises carrying out a scientific project and completing at least 30 credits of courses at third-cycle level. The doctoral student must also write a scientific compilation thesis or monograph corresponding to at least 120 credits. For more information about third-cycle studies at Sahlgrenska Academy, see https: // www. gu.se/en/sahlgrenska-akademin/doctoral-studies

Project: Half of all childhood cancers have a suspected prenatal origin, limiting access to the cancer-initiating developmental progenitor. Human pluripotent stem cells (hPSCs) can be differentiated in vitro, mimicking defined processes of embryonic development, and thus represent a promising tool to dissect the molecular mechanisms of malignant transformation taking place in prenatal cell populations. It has however been challenging to establish a direct equivalence between cell types arising in vitro from hPSCs and their in vivo counterparts. This becomes ever more apparent in functional assays, when hPSC-derived progenitors fail to perform upon transplantation in animal models.

The goal of this project is to harness single-cell profiling data, both from already published datasets and from our newly obtained data using a novel hPSC differentiation protocol, to establish a new set of benchmarks for the evaluation of in vitro systems as models of human development and disease. We will employ a data-driven approach to 1) define the early cell-fate decision processes driving in vitro human embryonic development and 2) identify cell populations susceptible to prenatal transformation events leading to childhood leukemia.

Single-cell transcriptional datasets will be analysed in Python and R, using national computing resources (command line), through clustering and annotation using signature genes. Identification of developmental trajectories will draw from the evolving set of published statistical and bioinformatics tools. These include visualization methods such as uniform manifold approximation and projection dimensionality reduction and force-directed graphs, partition-based graph abstraction, and Waddington optimal transport. Systematic comparison of developmental trajectories identified in human cultures and those in published datasets of human fetal tissue and mammalian model systems will be tested using several published methods.

Doctoral studies comprises four years of full-time study, and leads to a doctoral degree. As part of your employment as a doctoral student, you may have departmental duties corresponding to up to 20 % of full-time employment, distributed throughout your study period, and result in a corresponding extension of the studies. Departmental duties usually consist of teaching at first- and second-cycle levels, but may also include research and administration.

Doctoral education requires general eligibility and, where appropriate, specific eligibility as set out in the general syllabus for the subject.

The general eligibility requirements for doctoral studies are:

1. having completed a degree at second-cycle level, or 2. the fulfilment of course requirements totalling at least 240 credits, of which at least 60 credits must be at second-cycle level, or 3. the acquisition of equivalent knowledge in some other way, either in Sweden or abroad.

Specific entry requirements for this subject, according to the general syllabus, are:

having successfully completed the English B/6 course or is considered to have acquired equivalent knowledge through previous studies.

The selection of applicants who meet the basic and specific eligibility requirements will be based on the ability to assimilate the doctoral studies. The assessment shall attach particular importance to documented qualifications for:

- specific knowledge and skills within the subject area and related research fields - experience of scientific theory and relevant research methodology - scientific analysis and presentation verified through an academic paper, degree project, scientific journals or the like.

Documented experience in coding, and in computational analysis of single-cell profiling is a merit. Furthermore, a background on stem cell biology, developmental biology and/or hematopoiesis is desirable.

Once you have been admitted to doctoral studies, you will be employed as a doctoral student at the University of Gothenburg. The provisions for employment as a doctoral student can be found in ordinance SFS 1993:100. Initial employment as a doctoral student may apply for a maximum of one year, and may be renewed by a maximum of two years at a time. A doctoral student may be employed as a doctoral student for a maximum of eight years, but the total period of employment may not be longer than the equivalent of full-time education at doctoral level for four years.

Location: Sahlgrenska Academy, Institute of Biomedicine, Department of Microbiology and Immunology. Extent: 100%. First day of employment: as agreed.

The University applies a local agreement on salaries for doctoral students.

Please note, doctoral studies at the Institute of Biomedicine requires physical presence to conduct the studies. If the admitted applicant needs a residence permit for higher education to pursue studies in Sweden, the Institute of Biomedicine has the right to revoke the admission decision if the applicant cannot present a valid residence permit no later than at the start of the studies.

For more information about the project please contact principal supervisor, Carolina Guibentif, Institute of Biomedicine, e-mail: [email protected]

Union representatives at the University of Gothenburg can be found here: https: // www. gu.se/om-universitetet/jobba-hos-oss/hjalp-for-sokande

You can apply to be admitted to doctoral education via the University of Gothenburg's recruitment portal. It is your responsibility to ensure that the application is complete as per this notice, and that the University receives it by the final application deadline.

You must include the following, in pdf format

If your degree is from a university outside of Sweden, make sure that you attach a diploma and full transcripts that makes assessing your degree easier .

If your degree has not been verified by a Swedish authority you need to provide contact details to the issuing university, registrar or similar, that can verify the degree at our request.

For information on what you need to submit in order to fulfill the English language requirement see https: // www. universityadmissions.se/en/entry- requirements/english-language-requirements/

Applications must be received by: 2025-02-27

The University works actively to achieve a working environment with equal conditions, and values the qualities that diversity brings to its operations.

Salaries are set individually at the University.

In accordance with the National Archives of Sweden's regulations, the University must archive application documents for two years after the appointment is filled. If you request that your documents are returned, they will be returned to you once the two years have passed. Otherwise, they will be destroyed.

In connection to this recruitment, we have already decided which recruitment channels we should use. We therefore decline further contact with vendors, recruitment and staffing companies.