PhD student in Bioinformatics

The Department of Biochemistry and Biophysics. 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. 

More information about us, please visit: the Department of Biochemistry and Biophysics.

Project description

Project title: Biology-informed Robust AI Methods for Inferring Complex Gene Regulatory Networks.

The project encompasses several challenges in the gene regulatory network (GRN) field, from simulating realistic networks and data to accurate inference of GRNs from noisy gene expression data.

The student will work in a group addressing all these challenges, developing new AI-based methods to improve biological realism in simulations which will lead to more accurately inferred GRNs from real data. The project will develop fundamental theory and tools that will be key for understanding biological mechanisms causing diseases that are due to gene dysregulation, such as cancer. 

The core of the project is a digital biological system for generating labeled data using biology-informed DNNs and GenAI. The objectives will be achieved by combining methods and techniques from separate research fields - (a) biological knowledge about GRNs from bioinformatics and system biology, (b) graph theory and topological data analysis for network modeling from mathematics, and (c) robust machine learning (ML) and GenAI from AI / ML.

The unique inter-disciplinary combination will enable: (i) a-priori biological knowledge infusion for GRN modeling and developing GenAI methods for generating GRNs; (ii) generating simulated gene expression data using biology-informed GenAI; and (iii) robust learning of DNN-based GRN inference methods using the combined data - real and simulated gene expression data - in a semi-supervised learning approach.

Qualification requirements

In order to be admitted to postgraduate education, the applicant must have the general and specific entry requirements. The qualification requirements must be met by the deadline for applications.

You meet general entry requirements if you have completed a second-cycle degree, or 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).

Selection

The selection amongst 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.

Extensive experience with Python, Matlab, and R, and good UNIX knowledge are essential skills, as well as familiarity with biological omics data analysis techniques.

Admission Regulations for Doctoral Studies at Stockholm University.

About the employment

We offer a fixed-term employment as a doctoral student according to Chapter 5 of the Higher Education Ordinance (1993:100). The period of employment may not be longer than what corresponds to full-time doctoral education for four years. As a doctoral student, you should 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 employment as a doctoral student is for a maximum of one year, the employment is then renewed for a maximum of two years at a time.

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

Contact

For more information, please contact Professor Erik Sonnhammer, erik.sonnhammer@scilifelab.se.

General information about the PhD programs can be given by the Professor and Director of Doctoral Studies, Andreas Barth, andreas.barth@dbb.su.se.

Application

Apply for the PhD student position at Stockholm University's recruitment system. Attach a personal letter and CV as well as the attachments requested in the application form. It is the responsibility of the applicant to ensure that the application is complete in accordance with the instructions in the job advertisement, and that it is submitted before the deadline.

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