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Postdoctoral Researcher in mucosal immunology with focus in single-cell RNA-seq and spatial transcriptomics analysis and data visualization.

A postdoctoral position to study the transcriptomic landscape of intestinal tissue regeneration, with clear implications for intestinal diseases such as inflammatory bowel diseases (IBD) and colorectal cancer (CRC). The position is available in the laboratory of Dr. Eduardo Villablanca, who is a renowned leader in mucosal immunology (twitter @ejvillablanca). The candidate will be part of a research program that integrate experimental models, patient material and cutting-edge technologies (spatial and single cell transcriptomics) to understand how intestinal homeostasis is maintained and how breakdown in these processes might lead to IBD or CRC.

Division
Immunology and Allergy Division

Research group

The Immunology and Allergy Unit at the Department of Medicine, Solna performs research on different aspect of allergy and autoimmune diseases. Our research group (PI: Eduardo Villablanca) will investigates the molecular and cellular mechanisms underlying the establishment of intestinal homeostasis and how breakdown of these mechanisms might lead to inflammatory bowel diseases (IBD). Our group works in an inspiring and interactive research environment at the Karolinska University, Solna and has ongoing collaborative projects with national and international colleagues.

To tackle these questions, Eduardo’s team are using Single Cell RNA-Sequencing and spatial transcriptomics to generate a comprehensive transcriptomic landscape of the intestinal tissue during the reestablishment of intestinal homeostasis upon damage. We are closely collaborating with the clinics to translate our findings from experimental models.

Duties
We are seeking a Computational Biologist at post-doctoral level for a 24-48 months project. The main duties include bioinformatics analysis with particular focus in RNA-seq, single cell RNA-seq and spatial transcriptomics analysis. An interest in data visualization and big data analysis is a plus. The applicant is expected to have a strong interest in mucosal immunology. The applicant will work in close collaboration with other PhD students, postdocs and researchers. The applicant is expected to actively participate in other lab projects and present results to general and specialized audiences. An interest in the application of machine learning approaches is also desirable.

The duties also include: 

  •  Data QC, data management and archival storage
  • Analysis of large datasets, preparation of codes, development of new methods/tools for advanced analysis of datasets
  • Support the ongoing research in the group, help write papers, grants and scientific meeting presentations
  • Shape, develop and maintain the current computing resources of the group 

Entry requirements

The successful candidate has a solid background in bioinformatics, statistics and computational biology, good expertise in statistical and bioinformatics software, and an ability to work in a multidisciplinary research environment. The individual should be highly motivated and be able to work independently, while being able to communicate effectively with other members of the team.

Preferably, the candidate should hold a PhD degree (or complete one within the next 2 months) or have a track record of performing independent research over the past 4 years. A proven publication record in well-regarded journals is also advantageous. Outstanding programming skills in at least R, Matlab, Python, Perl or other mathematical software/programming languages is required.

Requirements: Qualified candidates should have:

  • A Ph.D. or M.D./Ph.D. in immunology or computational biology.
  • Outstanding creative thinking, problem solving, motivation, persistence as well as personal initiative and communication skills
  • Independent work at the laboratory as well as extensive collaboration with clinicians and other experimental groups.
  • Excellent molecular and cell biology as well as microbiology skills and strong background in mucosal immunology
  • Strong publication record in peer-reviewed journals
  • Fluency in both oral and written English is necessary

Scholarships for postdoctoral qualification can be established for foreign researchers who place their qualifications in Sweden. The purpose of scholarships for postdoctoral qualification is to promote internationalization and contribute to research qualification after a doctorate or equivalent. A scholarship for carrying out postdoctoral research can be granted for a maximum of two years within a four-year period following the receipt of a doctoral degree or equivalent.

To be eligible for a postdoctoral scholarship, the person must have obtained a doctorate or a foreign degree deemed to be equivalent to a doctorate. The head of the department determines whether their previous training and scholarly qualifications correspond to a Swedish doctorate or higher.

Location

The position is located within the Department of Medicine, Solna. The department consists of twelve divisions and each division consists of several research groups. The position is located within the research group lead by Associate Professor Eduardo Villablanca at the Immunology and Allergy division. Our research group investigates the molecular and cellular mechanisms underlying the establishment of intestinal homeostasis and how breakdown of these mechanisms might lead to inflammatory bowel diseases (IBD). To tackle these questions, Eduardo’s team are using single cell RNA-sequencing and spatial transcriptomics to generate a comprehensive transcriptomic landscape of the intestinal tissue during the reestablishment of intestinal homeostasis upon damage. We are closely collaborating with the clinics to translate our findings from experimental models. Dr. Villablanca serves as co-director of the single cell RNAseq core at the Center of Molecular Medicine (CMM) and leads the bioinformatics group within the mucosal immunology lab.

For more information please visit:

https://ki.se/en/meds/eduardo-villablanca-group

https://villablancalab.com/

Type of scholarship

The amount is tax free and it is set for twelve months at a time, paid out on a six months basis. In exceptional cases, shorter periods may be acceptable.

Application process

An application must contain the following documents in English or Swedish:

  • A complete curriculum vitae, including date of the thesis defence, title of the thesis, previous academic positions, academic title, current position, academic distinctions, and committee work
  • A complete list of publications
  • A summary of current work (no more than one page)

The application is to be submitted on the Varbi recruitment system.

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Reference number STÖD 2-2075/2022
Contact
  • Eduardo J. Villablanca, eduardo.villablanca@ki.se
Union representative
  • Afsar Rahbar OFR, Afsar.Rahbar@ki.se
  • Bruna Gigante, SACO, bruna.gigante@ki.se
  • Louisa Cheung, SACO, Louisa.Cheung@ki.se
Published 10.May.2022
Last application date 08.Jun.2022 11:59 PM CEST
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