PhD student in Bioinformatics  

at the Department of Biochemistry and Biophysics. Closing date: 21 February 2024.

SciLifeLab (SciLifeLab) is a national center for molecular biosciences with a focus on health and environmental research. The center combines frontline technical expertise with advanced knowledge of translational medicine and molecular bioscience. SciLifeLab is a national resource hosted by Karolinska Institutet, KTH Royal Institute of Technology, Stockholm University and Uppsala University. The center also collaborates with several other universities.

The employment will be placed at the Department of biochemistry and biophysics, at Stockholm university.

Project description

Your studies in Bioinformatics will be in the project: “Gene Regulatory Network Inference and Systems Biology”.

The goal of this project is to develop computational algorithms and methods that use omics data to infer gene regulatory networks (GRNs), and apply these to understand regulatory mechanisms that lead to cancer formation. Cancer cells are subjected to scRNA-seq to measure the transcriptomic response of gene knockdown perturbations via CRISPR interference on a large scale. The Sonnhammer group has recently shown that such data data offers a significant improvement in GRN quality compared to non-perturbed data. The project involves developing and applying computational methods that can work optimally with this new type of data, either by adapting and optimizing existing methods, or designing new methods based on deep learning neural networks and variational autoencoders. Also new methods for quality assessment need to be developed.  The resulting predicted regulatory mechanisms will be forwarded for evaluating their clinical relevance.

Qualification requirements

In order to meet the general entry requirements, the applicant must have completed a second-cycle degree, completed courses equivalent to at least 240 higher education credits, of which 60 credits must be in the second cycle, or have otherwise acquired equivalent knowledge in Sweden or elsewhere.

In order to meet the specific entry requirements, for acceptance in the Biochemistry, especially Bioinformatics, program the applicant must have passed courses within the first and second cycles of at least 90 credits in either, a) Chemistry/Molecular Biology/Biotechnology, or b) Computer Science/Mathematics/Physics and at the second cycle level, 60 credits in Life Science, Computer Science Mathematics, Physics or Bioinformatics including a 30 credit Degree Project (thesis).

The qualification requirements must be met by the deadline for applications.

Selection

The selection among the eligible candidates will be based on their capacity to successfully complete the program. Important criteria when assessing this capacity are; the candidate must be highly motivated and have an M.Sc. in bioinformatics or related field, and knowledge of molecular biology. Alternatively, an M.Sc. in molecular biology or related field and at least 1 year of documented practical experience in bioinformatics research and programming. Demonstrable familiarity with sequence and molecular data analysis techniques is essential. Extensive experience with Python, Matlab, and R, and good UNIX knowledge are necessary skills. Documented knowledge and skill in the field of the thesis project, written and oral proficiency in English, the capacity for analytical thinking, the ability to collaborate, as well as creativity, initiative, and independence.

The assessment will be based on previous experience and grades, the quality of the degree project, references, relevant experience, interviews and the candidate’s written motivation for seeking the position.

Admission Regulations for Doctoral Studies at Stockholm University are available at: www.su.se/rules and regulations.

Terms of employment

Only a person who will be or has already been admitted to a third-cycle programme may be appointed to a doctoral studentship.
The term of the initial contract may not exceed one year. The employment may be extended for a maximum of two years at a time. However, the total period of employment may not exceed the equivalent of four years of full-time study.

Doctoral students should primarily devote themselves to their own education, but may engage in teaching, research, and administration corresponding to a maximum of 20 % of a full-time position.

Please note that admission decisions cannot be appealed.

Stockholm University strives to be a workplace free from discrimination and with equal opportunities for all.

Contact

For more information, please contact the project leader, Professor Erik Sonnhammer, erik.sonnhammer@dbb.su.se.

General information about the PhD programs can be given by the Director of Doctoral Studies, Pia Ädelroth, pia.adelroth@dbb.su.se or the Head of the Department, Martin Högbom, martin.hogbom@dbb.su.se.

Union representatives

Ingrid Lander (Saco-S), telephone: +46 708 16 26 64, saco@saco.su.se, Alejandra Pizarro Carrasco (Fackförbundet ST/Lärarförbundet), telephone: +46 8 16 34 89, alejandra@st.su.se, seko@seko.su.se (SEKO), and PhD student representative, doktorandombud@sus.su.se.

Application

Apply for the PhD student position at Stockholm University’s recruitment system. It is the responsibility of the applicant to ensure that the application is complete in accordance with the instructions in the advertisement, and that it is submitted before the deadline.

Please include the following information with your application

• Your contact details and personal data
• Your highest degree
• Your language skills
• Contact details for 2–3 references

and, in addition, please include the following documents

• Cover letter
• CV – degrees and other completed courses, work experience and a list of degree projects/theses
• Research proposal (no more than 3 pages) describing: 
  – why you are interested in the field/project described in the advertisement 
  – why and how you wish to complete the project 
  – what makes you suitable for the project in question
• Degree certificates and grades confirming that you meet the general and specific entry requirements (no more than 6 files)
• Letters of recommendation (no more than 6 files)
• Degree projects/theses (no more than 6 files).

The instructions for applicants are available at: How to apply for a position.

You are welcome to apply!

Stockholm University contributes to the development of sustainable democratic society through knowledge, enlightenment and the pursuit of truth.

Closing date: 21/02/2024