Postdoc in Agentic Systems Biology for Biomanufacturing

Do you want to shape the future of biomanufacturing by combining computational biology with cutting-edge AI methods? We are seeking a postdoctoral researcher at the Division of Systems and Synthetic Biology, Department of Life Sciences, to develop intelligent systems that integrate metabolic modeling, omics analysis, and automated literature mining.

The Department of Life Sciences  conducts research, innovation, and education to enable a biobased society and improve human health. We explore how biological systems, and innovative technologies can be used to convert biomass into valuable products. We use advanced computational technologies to discover how biomolecules and organisms function and interact. We pioneer new methods for prediction, prevention, diagnostics and treatment of diseases. 

At the Division of Systems and Synthetic Biology  biologists, chemists, mathematicians, and engineers work together with the goal of understanding and quantitatively describing the complex functioning of living organisms. We develop technologies that contribute to human health and biosustainability. 

Industrial biotechnology generates large multi-omics datasets and relies on computational models of metabolism to guide the engineering of microbial cell factories. Extracting actionable insight from these data and models requires reasoning across multiple layers of biological organization and synthesizing findings with prior knowledge from the scientific literature, a process that today depends heavily on manual expert interpretation. Recent advances in large language models, agentic systems, and retrieval-augmented generation open fundamentally new possibilities for automating and scaling this process.

In this project, you will develop intelligent computational systems that combine constraint-based genome-scale modeling and resource allocation modeling with agentic methods. Your work will span three connected directions:

• extending and applying mechanistic models of metabolism to interpret experimental data,
• building agentic pipelines that autonomously analyze omics data,
• developing systems that mine the scientific literature to ground hypotheses in established knowledge.

The position offers a rare opportunity to extend your modeling expertise with groundbreaking AI methods, working on high-impact problems in biotechnology.

• A doctoral degree in computational biology, bioinformatics, systems biology, computer science or an equivalent foreign degree. This eligibility requirement must be met no later than the time the employment decision is made.
• Demonstrated experience with constraint-based genome-scale modeling, resource allocation modeling, or other computational models of metabolism, including hands-on use of established tools (e.g., COBRApy, COBRA Toolbox, RAVEN).
• Demonstrated experience with machine learning methods and their application to biological or scientific data.
• Strong programming skills in Python, with experience in building software systems beyond scripting (e.g., API design, modular architectures, version control).
• Familiarity with omics data analysis (transcriptomics, proteomics, or related), including standard bioinformatics workflows.
• Strong written and verbal communication skills in English.
• Personal competences including the ability to work both independently and collaboratively in an interdisciplinary research environment.

The following experience will strengthen your application: 

• Experience with enzyme-constrained or proteome-constrained metabolic models, and integration of proteomics or other omics data with such models.
• Experience with machine learning methods applied to biological data.
• Familiarity with large language model APIs and frameworks (e.g., Claude/Anthropic API, OpenAI API, LangChain, LangGraph).
• Experience building agentic LLM systems with tool-calling, multi-step reasoning, or autonomous workflow orchestration.
• Experience with retrieval-augmented generation (RAG), vector databases, or knowledge graph construction.
• Familiarity with gene regulatory network inference or multi-omics data integration.
• Background in metabolic engineering, microbial physiology, or industrial biotechnology.
• Experience developing open-source research software (documentation, testing, community engagement).
• It is highly meritorious if the doctoral degree has been obtained within the last three years prior to the application deadline.

• Apply and extend computational models of metabolism (constraint-based genome-scale models, resource allocation models) to interpret multi-omics datasets in the context of cell factory engineering.
• Develop software tools that enable programmatic interaction between large language model agents and metabolic models, enabling automated simulation, interpretation, and hypothesis generation.
• Design and implement agentic systems that autonomously analyze omics data, query biological databases, and generate structured scientific reasoning.
• Build retrieval-augmented generation (RAG) pipelines over the scientific literature and curated knowledge bases, allowing agents to perform automated literature studies and ground their outputs in established knowledge.
• Design systematic benchmarking frameworks to evaluate the accuracy and reliability of computational predictions and agent-generated hypotheses.
• Publish methods and results in high-impact journals and present at international conferences.
• Supervise master's and/or PhD students to a certain extent.
• Possibility to engage in teaching at undergraduate/master's level.

The position is a temporary full-time employment for two years with the possibility of a one-year extension. 

The position requires physical presence throughout the entire employment. A valid residence permit must be presented by the start date, otherwise the offer may be withdrawn. 

• As a postdoc at Chalmers, you are an employee and enjoy all employee benefits. Read more about  working at Chalmers   and our benefits   for employees. 

• A dynamic and inspiring working environment in the coastal city of Gothenburg . 

• Read more about Sweden’s generous parental leave, subsidized day care, free schools, healthcare etc at Move To Gothenburg.  

Chalmers is dedicated to improving gender balance and actively works with equality projects, such as the GENIE Initiative for gender equality and excellence . We celebrate diversity and consider equality and inclusion as fundamental aspects of all our activities. 

If Swedish is not your native language, Chalmers offers Swedish courses to help you settle in. 

The application should be written in English be attached as PDF-files, as below. Maximum size for each file is 40 MB. Please note that the system does not support Zip files. 

• A comprehensive CV, including a complete list of publications. 
• Details of previous teaching and pedagogical experience. 

• A brief introduction about yourself. 
• A summary of your previous research fields and key research outcomes. 
• An outline of your future goals and research focus. 

Use the button at the foot of the page to reach the application form.  

A background check may be conducted as part of the application process.

Please note: The applicant is responsible for ensuring that the application is complete. Incomplete applications and applications sent by email will not be considered. Contact details to references will be requested after the interview. 

We welcome your application no later than May 16, 2026.

Eduard Kerkhoven
Group Leader in Computational Metabolic Engineering
eduardk@chalmers.se 

*** Chalmers declines to consider all offers of further announcement publishing or other types of support for the recruiting process in connection with this position. ***  

Chalmers University of Technology in Gothenburg conducts research and education in technology and natural sciences at a high international level. The university has 3100 employees and 10,000 students, and offers education in engineering, science, shipping and architecture. With scientific excellence as a basis, Chalmers promotes knowledge and technical solutions for a sustainable world. Through global commitment and entrepreneurship, we foster an innovative spirit, in close collaboration with wider society.
Chalmers was founded in 1829 and has the same motto today as it did then: Avancez – forward. 

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