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Department of Biochemistry and Biophysics. SciLifeLab (SciLifeLab) is a national center for molecular biosciences with a focus on research in health and the environment. The center combines leading technical expertise with advanced knowledge in translational medicine and molecular biosciences. SciLifelab is a national resource run by Karolinska Institutet, KTH, Stockholm University and Uppsala University. The center collaborates with several other universities.
Administratively, the position will be placed at the Department of Biochemistry and Biophysics, Stockholm University.
More information about us can be found at: Department of Biochemistry and Biophysics.
Project description
Project title: “Perturbation-based Multi-omics Inference of Gene Regulatory Networks”.
The goal of this project is to develop gene regulatory network (GRN) inference from multiomics data by developing novel AI techniques that exploit the knowledge of perturbations (experimental design). It has been previously shown that the use of perturbation design significantly improves the quality of GRN inference with bulk data. The goal is to exploit this principle and develop novel techniques for perturbation-based GRN inference for single cell and spatial multiomics data, to increase GRN quality and add cell type and heterogeneity dimensions to causal regulatory analysis. A deep learning framework will be developed with a specialized architecture to efficiently link data to specific perturbations. A system to infer the perturbation design based on gene expression and chromatin accessibility data will also be developed. The framework will be adapted and applied to spatial data to link the GRN models to specific phenotypes and to gain a better understanding of e.g. cancer development.
Eligibility requirements
To be admitted to doctoral studies, the applicant must have basic and specific eligibility requirements. The eligibility requirements must be met at the time the applicant is admitted to the doctoral studies at the Department of Biochemistry and Biophysics.
You have basic eligibility if you have completed a degree at advanced level, or have completed course requirements of at least 240 higher education credits (ECs), of which at least 60 ECTS credits are at advanced level, or have otherwise acquired essentially equivalent knowledge within or outside the country.
Special eligibility for admission to doctoral education in bioinformatics requires that the applicant in undergraduate education has passed courses of at least 90 credits, either a) chemistry/molecular biology/biotechnology, or b) computer science/mathematics/physics, and an independent project of at least 30 credits, as well as courses at advanced level in molecular life sciences, computer science, mathematics, physics and/or bioinformatics so that a total of 60 credits at advanced level are achieved. Special eligibility also applies to those who have acquired essentially equivalent knowledge in another order within or outside the country, as assessed by the examiner and/or director of studies for doctoral education.
Selection
Selection of eligible applicants shall be made with regard to their ability to benefit from the education. Important assessment criteria are the following: familiarity with theory, proficiency in the subject area of the dissertation work, ability to express oneself orally and in writing in English and/or Swedish, analytical ability, creativity, initiative, independence and ability to collaborate.
The basis for assessing how the applicant meets these requirements is the relevance of previous studies to the subject, grades on completed university courses (especially those at advanced level), quality and scope of the independent work, references to people who can describe the applicant’s skills and interviews.
Extensive experience with Python, Matlab and R, as well as good UNIX skills are essential skills, as is knowledge of biological omics data analysis. Experience with PyTorch or TensorFlow is highly valuable.
Admission procedure for doctoral education at Stockholm University.
About the employment
We offer a fixed-term employment as a doctoral student in accordance with Chapter 5 of the Higher Education Ordinance (1993:100). The employment period may not be longer than the equivalent of four years of full-time doctoral education. As a doctoral student, you will primarily devote yourself to your own doctoral education, but the employment may include work with education, research and administration to a limited extent (maximum 20%).
A new appointment as a doctoral student is valid for a maximum of one year, and the appointment is then renewed for a maximum of two years at a time.
Stockholm University strives to be a workplace that is free from discrimination and provides equal rights and opportunities for everyone.
Contact
Further information is provided by Professor Erik Sonnhammer, erik.sonnhammer@scilifelab.se.
General information regarding the doctoral program can be obtained from Professor and Director of Studies Andreas Barth, andreas.barth@dbb.su.se.
Application
You apply for the doctoral position via Stockholm University’s recruitment system. Attach a cover letter and CV as well as the attachments requested in the application form. As an applicant, you are responsible for ensuring that the application is complete in accordance with the advertisement and that it reaches the university by the application deadline.
Instructions for applicants can be found on the website: applying for a job.
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