Postdoctoral Scholarship (2 years) within computational modeling of human cell signaling and metabolism
The Department of Medical Biosciences is offering a postdoctoral scholarship within the project “Unified computational modeling of human cell signaling and metabolism to advance precision oncology”. The scholarship is full-time for 2 years, with access starting in September 2026 or by agreement.
Departmental specific information
The research will be carried out in the laboratory of Cemal Erdem at the Department of Medical Biosciences, which offers an international, collaborative, and open-minded research environment. Please visit the lab’s webpage for more information: https://erdemlab.github.io.
The Erdem research group is part of the SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS), which 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. 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.
Project description
A key missing capability in current cancer research is the ability to predict how a particular cancer cell will respond to a perturbation (e.g., drug inhibition or gene knockdown). However, building computational models of complex, large-scale, and incompletely understood systems remains extremely challenging. To address this issue, we recently developed the SPARCED pipeline to convert structured lists of species, parameters, and reaction types into an SBML (Systems Biology Markup Language) model file, and we created a model based on one of the largest pan-cancer signaling models in the literature. SPARCED is compatible with high-performance and cloud computing, can simulate thousands to millions of single-cell trajectories, is easily expandable with new pathways, and is retrainable with new omics data for new cellular contexts.
SPARCED currently has two interlinked modules, where the first part simulates protein signaling cascades and the second part simulates mRNA levels using stochastic methods. Doing so enables SPARCED to realistically represent mRNA numbers (or bursts), which are slightly different for each simulation, and thus a single-cell like behavior. However, SPARCED currently does not contain one key aspect: cellular metabolism. Recently, a metabolic atlas of human cells has been released, making it now possible to merge protein signaling models with metabolic network information.
In this project, the postdoctoral fellow will have the opportunity to:
Curate the human metabolic atlas information into SPARCED format and incorporate them to generate SPARCED-Metabolome (SPARCED-Me) model.
Curate other databases to incorporate required crosstalk interactions to construct a complete model.
Help collect multi-omics (transcriptomic, proteomic, and metabolomic) data from different cancer cell lines to parametrize the SPARCED-Me model in various contexts.
In our lab, we are committed to fostering a collaborative and inclusive environment that promotes reproducible and rigorous research practices. As a postdoctoral fellow in our team, you will benefit from a safe and respectful research environment, receive dedicated mentorship, and have the freedom to pursue innovative ideas. This scholarship is ideal for researchers eager to develop and use computational tools to study in silico cellular processes and who would like to grow in a supportive environment.
This postdoctoral scholarship is financed by the Kempe Foundation and administered by Umeå University.
Qualifications
To qualify as a postdoctoral scholarship holder, the postdoctoral fellow is required to have completed a doctoral degree or a foreign degree deemed equivalent to a doctoral degree. This qualification requirement must be fulfilled no later than at the time of the decision about scholarship recipient.
Priority should be given to candidates who completed their doctoral degree, according to what is stipulated in the paragraph above, no later than three years prior. If there are special reasons, candidates who completed their doctoral degree before that may also be eligible. Special reasons include absence due to illness, parental leave, appointments of trust in trade union organisations, military service, or similar circumstances, as well as clinical practice or other forms of appointment/assignment relevant to the subject area.
The doctoral degree should be in computational/systems biology, computer science, bioinformatics, biostatistics, molecular biology/medicine, or a related field.
Additional requirements
A strong track record in a relevant field of research, documented by first authorships in peer-reviewed original publications Comprehensive skills in data analysis and bioinformatics Proficiency in programming with Python Proficiency in version control (Git, GitHub)
Meriting criteria are:
Experience in metabolic network modeling
Experience in metabolomic data analysis and research
Experience in ODE-based computational modeling
Experience in SBML file handling
Experience in Docker or other container-based platforms
Basic understanding of wet-lab work and cell culture
We are looking for candidates with a strong interest in large-scale computational modeling and cancer research. Candidates should be team players, engaging in scientific discussions and exchanging ideas.
Application
The application must include:
A brief description of your research interests and a statement describing why you are interested in the postdoctoral scholarship (max two A4 pages)
CV (max six A4 pages)
List of publications (max two A4 pages)
Degree certificate from doctoral studies and other relevant degrees
Contact details of two reference persons (email address and phone number with country code)
The application should be written in English or Swedish, and the attached documents should be in Word or PDF format. The application should be registered via Umeå University’s e-recruitment system Varbi and submitted by the deadline 2026-06-15.
Further information
For further information about this project, please contact Cemal Erdem at cemal.erdem@umu.se.
