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.

About the DDLS PhD student program

Data-driven life science (DDLS) uses data, computational methods and artificial intelligence to study biological systems and processes at all levels, from molecular structures and cellular processes to human health and global ecosystems. The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) aims to recruit and train the next generation of data-driven life scientists and to create globally leading computational and data science capabilities in Sweden. The program is funded with a total of 3.3 billion SEK over 12 years from the Knut and Alice Wallenberg (KAW) Foundation.

In 2025 the DDLS Research School will be expanded with the recruitment of 19 academic and 7 industrial PhD students. During the course of the DDLS program more than 260 PhD students and 200 postdocs will be part of the Research School. The DDLS program has four strategic research areas: cell and molecular biology, evolution and biodiversity, precision medicine and diagnostics, epidemiology and biology of infection. For more information, please see www.scilifelab.se/data-driven/ddls-research-school/.

The future of life science is data-driven. Will you be part of that change? Then join us in this unique program!

Project description

At the Department of Biochemistry and Biophysics at Stockholm University, we are announcing a position as DDLS PhD student in Data driven cell and molecular biology. Data driven cell and molecular biology covers research that fundamentally transforms our knowledge about how cells function by peering into their molecular components in time and space, from single molecules to native tissue environments.

Your studies in Bioinformatics will be in the project "Quantitative predictions of protein – DNA interactions from high-throughput biophysical binding data".

Sequence specific binding and recognition between transcription factors and DNA control gene expression at the molecular level. While structural predictions using deep learning methods like AlphaFold have revolutionized our understanding of sequence dependent molecular structure, we currently have much more limited understanding of how the genetic code specifies binding rates and affinities for interacting molecules. Despite the significance of these interactions, quantitatively predicting binding from nucleotide or protein sequences still remains a challenge. The research group of Emil Marklund investigates how sequence information in biological macromolecules governs recognition, binding, and dynamical structure. This project aims to build predictive and physical binding models of protein – DNA interactions using high-throughput and quantitative biochemical binding data across hundreds of thousands of sequence variants.

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.

We are seeking a PhD candidate with strong and documented background in machine learning, deep learning, data analysis and programming. Previous experience in research and knowledge in bioinformatics, biophysics, biochemistry, molecular biology, or other related topics in the molecular life sciences is advantageous. Priority will be given to candidates with the overall highest experience in these fields, however prior experience with all the listed topics is not a requirement, and we encourage applicants of different backgrounds to apply. We are looking for motivated candidates who work well in a team and contribute to a positive work environment. The selected PhD candidate will be joining a dynamic and interdisciplinary lab that do ambitious science, based in SciLifeLab in Stockholm, a vibrant hub for scientific research.

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 project leader Emil Marklund, emil.marklund@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.