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Karolinska Institute - Department of Microbiology, Tumor and Cell Biology (MTC) conducts research and teaching in immunology, infection biology, cell biology and cancer. Key words are multidisciplinary, bridging, translational, national and international collaborations


Division
The research group of Dr Claudia Kutter seeks applications for a postdoctoral position (either computational or computational/experimental) in the field of functional and/or comparative genomics, transposon biology, chromatin and RNA biology. The Kutter lab has a track record in deciphering molecular mechanism by which noncoding RNAs (i.e. long noncoding, transfer and small RNA) regulate genes and genome structure in mammalian somatic tissue and in the germline (Sondergaard et al. CommsBio, 2020, Kutter et al, Mobile DNA, 2018; Ernst et al, NatComm, 2017; Rudolph et al, PLoS Genetics, 2016; Schmitt et al, Genome Research, 2014; Kutter et al, PLoS Genetics, 2012; Kutter et al, Nature Genetics 2011).

The research project for this position focuses on gene regulation during cell differentiation and disease progression in mouse and human. In particular, this project focusses on the roles of regulatory RNAs. The group interrogates genome- and transcriptome-wide regulation and functionality by employing a combination of next generation sequencing technologies (both bulk and single-cell) and high-throughput genetic screening approaches, develops computational methods, along with applying experimental techniques. The group uses an integrative and collaborative approach, works closely with computational and experimental groups at KI, Science for Life Laboratory (SciLifeLab), and other local and international research groups. Frequent courses are provided on campus (in person or virtually). Additional professional training is available through summer schools and recurrent workshops.

The laboratory is located at SciLifeLab on the Karolinska Institute campus in Stockholm. SciLifeLab offers an attractive research environment, provides state-of-the-art instrumentation and core facilities, and is home to the second largest sequencing cluster in Europe. SciLifeLab is a joint effort between Karolinska Institute, the Swedish Royal Institute of Technology, and Stockholm University. It hosts research groups with diverse backgrounds and expertise, creating a unique interface between basic biology, genomics, bioengineering, drug discovery, and translational medicine.

Duties
The successful applicant will develop and integrate novel transcriptome- and genome-wide computational methods (based on RNA- and ChIP-sequencing data) to study genomic sequence and epigenetic signatures (enhancer, promoters and polymerase activity) as well as the regulatory mechanisms of regulatory RNAs mouse and human. The unique dataset has been generated in the Kutter group. The work implies original research in computational biology, designing computational methods and implementing existing analytical pipelines to infer underlying molecular mechanisms. The post holder will take a strong lead in the project design and management, data generation and interpretation, and collaborate with other team members. The ideal candidate is expected to report the scientific results by writing scientific papers, attending scientific meetings, and effectively communicate with peers. The ability to work in a highly interdisciplinary and international environment, and to engage in continuous professional development is a must.

Key responsibilities:

  • Original research contributions as part of the group’s core program
  • Project leadership
  • Use and further development of research methodologies
  • Analysis, management, communication and publishing of research findings and software tools
  • Active participations in academic research activities (group meetings, journal clubs, seminar participation, continuous training in form of workshops, supervision of junior staff)
  • Presenting at national and international scientific meetings

Entry requirements
A strong background in genomics, computational biology, and/or statistics as well as experience in high-throughput sequence and gene expression data analysis techniques is essential. Excellent skills in programming (primarily Python, R/Bioconductor, UNIX), knowledge of biological databases and data integration as well as data visualization is required. The candidate should be comfortable with version control systems like Git, Conda, Snakemake, R Markdown, Jupiter notebooks or Docker. Candidates wishing to combine computational and experimental approaches should be proficient in methodologies related to functional genomics (e.g ChIP-seq, Hi-ChIPseq, RNA-seq, ATAC-seq, GRO-seq, HiC or equivalent). Prior knowledge in eukaryotic RNA biology, gene regulation, and transcriptome-wide studies is an asset.

The ideal candidate should be collaborative, scientifically adventurous, curiosity-driven, and should bring independent and original ideas into the project. Any previous records of independent research as well as productive interactions within a multi-disciplinary team environment (e.g. first- and/or co-author publications in high profile journals) are advantageous. The applicant should be eager to learn new concepts and acquire new skills. Given that the work is a group effort and conducted in an international setting with other researchers from the field, the applicant should have good communication skills, be proficient in spoken and written English.

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. Applicants who have not completed a doctorate at the end of the application period may also apply, provided that all requirements for a completed degree are met before the (intended) start date of the post doctoral education.

The head of the department determines whether their previous training and scholarly qualifications correspond to a Swedish doctorate or higher.

For more information on the work of the laboratory, please visit https://www.scilifelab.se/researchers/claudia-kutter/ or http://ki.se/en/mtc/claudia-kutter-group

To make informal enquiries about the post, please contact Dr Claudia Kutter at claudia.kutter@ki.se

Location: Solna

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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First day of employment According to agreement
Salary Stipend
Reference number STÖD 2-4383/2020
Contact
  • Dr Claudia Kutter , claudia.kutter@ki.se
Union representative
  • Taher Darreh-Shori, SACO, taher.darreh-shori@ki.se
  • Henry Wölling SEKO, henry.wolling@ki.se
  • Gunnel Brolin, gunnel.brolin@ki.se
Published 14.Oct.2020
Last application date 15.Nov.2020 11:59 PM CET

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