The Department of Biosciences and Nutrition performs research and education in several areas of medical science including bioorganic chemistry, molecular endocrinology, cancer biology, functional genomics, systems biology, epigenetics, structural biochemistry, cellular virology, and nutrition. It offers an excellent international research and working environment, including around 300 scientists, students, administrative and technical personnel. The Department resides in the new biomedical research building Neo, aimed at being a creative and open environment that enables meetings, synergies, and exploration of areas of mutual interest across disciplines.

A doctoral position is an available doctoral education project to which a PhD student is to be recruited. After the selection process the process for admission to doctoral education will commence. An admission decision will not be taken until an individual study plan has been approved by the departmental admission board.

For more information regarding doctoral (PhD) education, see:

Description of research group and project
The research group of Carsten Daub at the Department of Biosciences and Nutrition aims at understanding the changes of transcriptional regulation connected to diseases, either as consequence or as cause for the disease. For this, we are working together with several research groups in the medical and clinical field at Karolinska Institutet and Karolinska Hospital as well as with other research groups and consortia around the world. We profile the expression of coding and non-coding transcripts using RNASeq, Cap Analysis Gene CAGE) and small RNA-Seq. Employing state-of-the-art computational methods we infer likely underlying gene regulatory events. By intensively discussing with our collaborators we take full advantage of the usually rich body of knowledge available for the studied disease or process together with complementary phenotypic sample characteristics. Through this, and together with our collaborators, we are as a team able to identify a core set of targets for in-depth functional validation. The Daub lab is co-affiliated with the Science for Life Laboratory (SciLifeLab), Sweden’s largest high-throughput sequencing and proteomics facility.

The position offered here is part of a European Union Marie Sklodowska Curie Initial Training Network named “ZENCODE-ITN” ( The scientific focus of the consortium is to understand genome regulation through combined experimental and computational approaches in the model vertebrate zebrafish. The consortium aims at training young scientists in both computational biology and experimental wet lab biology. The consortium comprehensively annotates functional epigenetic and transcribed elements, decipher genomic codes of transcription, as well as coding and noncoding gene function during vertebrate development and enhance zebrafish as an attractive developmental, comparative genomic and disease model. The appointed fellow will immensely benefit from other training network participants, which include major zebrafish genomics laboratories, eminent computational biologists and world-class genomics technology experts.

The consortium will produce a variety of complementary genome-wide data including ChIP-Seq, CAGE, miniCAGE, and RNA-Seq. The PhD student will first develop data structures that are the basis for sharing heterogeneous data across the consortium as well as for data dissemination with the publication. The student will consolidate consortium data and develop annotation strategies together with the consortium members. Importantly, the student will creatively develop and implement data visualization methods for the consortium data including primary data and analysis results. The student will also be involved in data analysis of consortium data related to specific biological questions.

The PhD program at Karolinska Institutet corresponds to 4 years full time studies. We are seeking a highly motivated and talented PhD student who creatively plans, thoroughly executes and interprets data structures, annotation and visualization of heterogeneous high-throughput sequencing data. As successful candidate you have a masters degree in Bioinformatics, computer science, computational biology or a related field. Systematic thinking and excellent programming skills are essential. Experience with analysis of high-throughput data and experience with sequencing data is a strong plus. Excellent communication skills, a proactive and constructive personality as well as fluent English speaking and writing abilities are expected.

The position is funded by a European Union Marie Sklodowska Curie Initial Training Network (ITN). Therefore, potential candidates must not have resided or carried out their main activity (work, studies, etc.) in Sweden for more than 12 months in the 3 years immediately prior to the recruitment, and have no more than 4 years of research experience since the degree that would qualify for admission onto the PhD programme, e.g. Masters degree.

Entry requirements for doctoral education at KI
To be eligible for doctoral education following requirements has to be met:

General entry requirements
A person meets the general entry requirements for doctoral/third-cycle/PhD education (according to Higher Education Ordinance Chapt 7, section 39) if he/she:

  1. has been awarded advanced/second-cycle/master qualification (i.e. master degree) or
  2. has satisfied the requirements for courses comprising at least 240 credits of which at least 60 credits were awarded in the second-cycle/master level, or
  3. has acquired substantially equivalent knowledge in some other way in Sweden or abroad.

Specific entry requirements
Proficiency in English equivalent to the course English B/English 6 at Swedish upper secondary school:
Proficiency in the English language can be documented by an internationally recognized test such as TOEFL or IELTS, see web-link below for more information.
Applicants who meet the general entry requirements (1 or 2 above) from a university in one of the Nordic countries fulfill the requirements in English.

For more information regarding general and specific entry requirements:

Assessment criteria
A selection will be made among qualified applicants on the basis of the ability to benefit from doctoral education. Karolinska Institutet uses the following bases of assessment:
- Documented subject knowledge of relevance to the area of research
- Analytical skill
- Other documented knowledge or experience that may be relevant to doctoral studies in the subject

The qualifications of the applicants will be evaluated on an overall basis.

Terms and conditions
The most common way of financial support for doctoral students at KI is doctoral grant the first year and a doctoral studentship (doctoral employment) for year 2, 3 and 4. During the time between recruitment and admission a short-term employment can be offered for up to 6 months.

Application process
An application must contain the following documents in English:

  • A personal letter and curriculum vitae
  • A copy of degree certificates and associated certificates
  • A copy of degree projects and any previous publications

The application is to be submitted through the MyNetwork recruitment system.

Type of employment PhD placement
Contract type Full time
Reference number 2-1637/2015
  • Carsten Daub
  • Thomas Tinglöv, Head of Administration, +46- 8-524 835 49
Union representative
  • Joseph Rafter, SACO, +46-8-524 83 545
  • Gunnar Stenberg, SEKO, +46- 8-524 880 75
  • Birgitta Lindqvist, OFR, +46-8-524
Published 20.Apr.2015
Last application date 18.May.2015 11:59 PM CEST

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