Postdoc (Bioinformatics/Data Science) in data-driven protein-protein interaction research at Department of Drug Design and Pharmacology, University of Copenhagen

We are seeking a talented and motivated postdoctoral researcher with experience in large-scale data processing and resource development to join a cutting-edge project decoding protein-protein interactions. This two-year position involves designing and implementing computational pipelines, managing complex biological data, and building web-based tools for data access and interpretation.

Principal supervisor
Associate Professor Albert J. Kooistra, Department of Drug Design and Pharmacology
E-mail (preferred): albert.kooistra@sund.ku.dk, phone: +45 35 32 83 05

Start: 1 November 2025
Duration: 2 years as a postdoctoral researcher

Our group and research
The “Data Science for Drug Design” (DSDD) research group is dedicated to the development and application of cutting-edge and data-driven technologies to advance network medicine. The DSDD group has a broad expertise encompassing structural bioinformatics, cheminformatics, computer-aided drug discovery & design, research tool/database development and applying machine learning/AI approaches. The research conducted within our research groups revolves around three primary pillars:

1. Data: this pillar involves the systematic curation and annotation of publicly available data encompassing protein structures, protein sequences, protein-protein interactions, cellular compositions, natural variations, drug effects, expression levels, and more. A prime illustration of our work in this realm is the publicly accessible KLIFS resource revolving around the protein kinase family catering to >1600 unique users per month.
2. Protein signaling networks: our second pillar delves into the analysis, simulation, modeling, and prediction of protein signaling networks. This endeavor aims to enhance our comprehension of protein-protein interactions, with a specific emphasis on ultimately understanding the regulation and deregulation of these processes.
3. Drug design: in the third pillar, we harness knowledge-driven and machine learning techniques to design molecules capable of modulating protein-protein signaling within cells. This research is geared towards developing innovative approaches to influence cellular signaling behavior, i.e. network medicine.

Our department
Department of Drug Design and Pharmacology is committed to research-based teaching and interdisciplinary research that supports the development and understanding of chemical and pharmacological properties of drugs and drug targets. We work as part of a dynamic academic community of research, education and innovation within the Pharmaceutical Sciences bridging Health Sciences and Life Sciences.

Information about the Department can be found at https://drug.ku.dk/

Project description
This position is part of a research project generously supported by the Carlsberg Foundation, titled:

"Look who’s talking: decoding protein-protein dialogue."

WHAT? Inside every cell, hundreds to thousands of proteins engage in constant interactions, orchestrating nearly every cellular process. Understanding this intricate "dialogue" among proteins is crucial to unraveling cellular function and behavior.

WHY? Despite their fundamental importance, the mechanisms behind protein-protein interactions remain poorly understood. Key questions persist:

• Which proteins interact with each other?
• How do they select their interaction partners?
• What are the precise mechanisms at an atomic level?
• What are the functional purposes of these interactions?

HOW? Recent advances in protein modeling, such as AlphaFold and ESM-Fold, have revolutionized our ability to understand molecular structures. In this project, you will:

• Build high-performance (HPC) and distributed computing pipelines
• Automate data collection and analysis workflows
• Design and manage databases
• Develop user-friendly web interfaces and APIs. All with adherence to FAIR data principles, enabling reproducible, accessible, and efficient PPI research.

Profile
We are looking for a true computational allrounder who enjoys working across the stack, from raw data to APIs and web frontends. Someone who is comfortable switching between building robust data pipelines, designing scalable databases, and developing clean, user-friendly web interfaces. You should be excited about tackling technical challenges, creating reliable and maintainable data workflows, handling large and dynamic datasets, and making this data accessible through well-documented APIs and intuitive web platforms.

Essential experience and skills:

• An MSc and PhD related to bioinformatics, computational biology, computer science, pharmaceutical sciences, data science, or related fields.
• Proficient programming skills in Python
• Experience designing databases, software architecture, and setting up computational pipelines
• Hands-on experience with large-scale data processing, parsing, and analysis
• Code versioning with GitHub
• Strong communication skills and ability to work in teams
• Excellent in written and spoken English

Desirable experience and skills:

• Background in protein structures and protein-protein interactions (e.g. structural bioinformatics)
• Knowledge of cell biology, signaling pathways, protein dynamics, and evolution
• Well-organized, reliable, and able to work both independently and flexibly
• Comfortable in a collaborative international team environment

The person will be required to relocate to Copenhagen and key responsibilities will include: establishing research ideas together with the principal investigator, leading the research project on a day-to-day basis, presenting research in internal meetings and international conferences, taking an active part in manuscript writing, and translating new knowledge in the subject area into research activities. There will be the opportunity to supervise more junior group members and contribute to teaching and dissemination activities.

Place of employment
The place of employment is at the of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen as well as the newly founded Center for Pharmaceutical Data Science Education (CPDSE). We offer creative and stimulating working conditions in a dynamic and international research environment. Our research facilities include a competitive computational core facility and modern environment. Moreover, we are part of the cluster for Integrated Structural Biology (ISBUC), and the pharmaceutical informatics research section (link).

Terms of employment
The average weekly working hours are 37 hours per week.

The position is a fixed-term position limited to a period of 2 years. The starting date is the 1st of November 2025 (little room for changes).

Salary, pension and other conditions of employment are set in accordance with the Agreement between the Ministry of Taxation and AC (Danish Confederation of Professional Associations) or other relevant organisation. Currently, the monthly salary starts at 38,700 DKK/approx. 5,185 EUR (April 2025 level). Depending on qualifications, a supplement may be negotiated. The employer will pay an additional 18.07 % Cto your pension fund.

Foreign and Danish applicants may be eligible for tax reductions, if they hold a PhD degree and have not lived in Denmark the last 10 years.

The position is covered by the Job Structure for Academic Staff at Universities 2020.

Questions
For further information, applicants may contact the principal supervisor, Associate Professor Albert J. Kooistra, e-mail: albert.kooistra@sund.ku.dk, phone: +45 35 32 83 05.

For more information on working and living in Denmark visit http://ism.ku.dk (International staff mobility) and https://www.workindenmark.dk

Application procedure
Your online application must be submitted in English by clicking ‘Apply now’ below. Furthermore, your application must include the following documents/attachments – all in PDF format:

1. Motivated letter of application (max. one page). Your motivation letter is an essential part of your application. It must clearly explain why you are applying for this specific position and why this project is the right fit for you. Highlight how your background, skills, and interests align with the research goals.
   ⚠️ Only applications with a clear, specific, and well-reasoned motivation will be considered.
2. CV incl. education, work/research experience, language skills and other skills relevant for the position.
3. A certified/signed copy of a) PhD certificate and b) Master of Science certificate. If the PhD is not completed, a written statement from the supervisor will do.
4. List of publications.
5. References and recommendations
6. Link to your GitHub account

Application deadline: 10 August 2025, 23.59pm CET
We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process
After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor. Once the assessment work has been completed each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself.

You can read about the recruitment process at http://employment.ku.dk/faculty/recruitment-process/

The applicant will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities.

Interviews are expected to be held in the first half of September.

The University of Copenhagen wish to reflect the diversity of society and encourage all qualified candidates to apply regardless of personal background.