atthe Department of Biochemistry and Biophysics. Closing date: 21 September 2022 .
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: "Deep Learning for Protein-Protein interactions”.
Protein structure is essential for understanding their function as well as for developing drugs targeting proteins. Recently, a deep learning method that can predict the structure of most proteins was made freely available, and a database with predicted structure was released. However, proteins do not act alone - they act together with other proteins. Therefore, the next major challenge is to use these types of methods for predicting protein-protein interactions. Initial studies from us have shown that it is possible to predict accurate structures of a large part of dimeric proteins using either a modified version of AlphaFold2 or AlphaFold-multimer. However, there are still many proteins that cannot be built accurately, nor are we able always to distinguish interacting from non-interacting protein pairs and to build larger complexes accurately is still an unsolved problem. In this project, we are recruiting 1-2 PhD students which will work together with two recently recruited postdocs to leverage recent advances in the field of machine learning to build better deep-learning models for predicting protein-protein interactions and to apply these methods to biologically relevant problems.
The Elofsson group is located at the Science for Life Laboratory. Elofsson has worked on protein structure predictions for more than two decades. He has worked on various techniques, both using machine learning and other computational techniques. His most important contributions for this work are the methods he has developed to identify the quality of protein models, Pcons and various versions of ProQ. The group consists currently of five PhD students and one senior researcher.
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; 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 Arne Elofsson, email@example.com.
General information about the PhD programs can be given by the Director of Doctoral Studies, Pia Ädelroth, firstname.lastname@example.org or the Head of the Department, Martin Högbom, email@example.com.
Union representatives Ingrid Lander (Saco-S), telephone: +46 708 16 26 64, firstname.lastname@example.org, Alejandra Pizarro Carrasco (Fackförbundet ST/Lärarförbundet), telephone: +46 8 16 34 89, email@example.com, firstname.lastname@example.org (SEKO), and PhD student representative, email@example.com.
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
and, in addition, please include the following documents
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)
The instructions for applicants are available at: How to apply for a position.
You are welcome to apply!
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