# Three PhD positions starting in 2027 **Computational plant biology & AI · Mutwil Lab · University of Copenhagen** We have **three PhD positions starting in 2027** for curious scientists who want to understand how plants adapt, make remarkable molecules, and evolve. Opportunities include projects supported by the **Novo Nordisk Foundation** and the **Marie Skłodowska-Curie Actions programme**. You will develop a focused research question within our connected research directions, with the project shaped around its scientific aims and your developing interests. - **Location:** Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark. - **Supervisor:** Associate Professor Marek Mutwil. - **Start:** 2027; exact dates will be announced. - **Coding experience:** optional at entry. A willingness to learn computational and quantitative approaches is essential. **[Email your CV and answers →](mailto:[email protected]?subject=PhD%202027%20application&body=Hello%20Marek%2C%0D%0A%0D%0AI%20would%20like%20to%20express%20interest%20in%20one%20of%20the%202027%20PhD%20positions.%0D%0A%0D%0AFull%20name%3A%0D%0AAcademic%20background%3A%0D%0AResearch%20direction%28s%29%20of%20interest%3A%0D%0A%0D%0APlease%20find%20my%20CV%20attached.%20My%20answers%20are%20below%20%28up%20to%20150%20words%20each%29.%0D%0A%0D%0A1.%20What%20would%20you%20like%20to%20investigate%3F%0D%0A%0D%0A%0D%0A2.%20What%20can%20this%20result%20tell%20us%3F%0D%0A%0D%0A%0D%0A3.%20How%20would%20you%20organise%20the%20next%20two%20weeks%3F%0D%0A%0D%0A%0D%0A4.%20When%20did%20evidence%20change%20your%20mind%3F%0D%0A%0D%0A%0D%0ABest%20wishes%2C)** An initial expression of interest by email. No Google account needed. Read the four questions below before sending. *Grow a question into a discovery.* ## What could you investigate? Our research connects biological questions, molecular data, AI and experiments. The directions below are possible starting points—not a checklist that every PhD student is expected to complete. ### Knowledge graphs and gene function How can we connect what has already been discovered to predict what an uncharacterised gene does? Build on PlantConnectome to connect evidence from the plant literature with molecular data. Use knowledge graphs and language models to generate biological hypotheses, while tracing predictions back to their supporting evidence and identifying where that evidence is incomplete or contradictory. ### Stress responses and Boolean networks How do plants integrate competing environmental signals—and which stress response takes priority? Extend our work on stress-response hierarchies in *Marchantia polymorpha* with regulatory and Boolean-network models. Investigate how plants respond to combined stresses such as heat and drought, and which regulatory principles are conserved across species. Related directions include single-cell data and testing predictions in crops. Boolean-network modelling is a proposed extension of this work, not a result already established by the published study. ### Specialised metabolism and plant pigments Can connected evidence reveal the genes behind a remarkable plant molecule? Investigate the enzymes, regulators and pathways underlying plant pigments and other specialised metabolites. Combine literature-derived knowledge, gene-expression networks and multi-omics data with experimental evidence, in the scientific direction of Stripes & Stars. ### Comparative and evolutionary biology Which biological mechanisms are shared across plants, and which have been reinvented? Use comparative transcriptomics and regulatory networks to investigate gene function, development, reproduction and the evolution of new traits. Connect patterns across species to specific biological questions that can be tested. ## Who are we looking for? We value scientific judgment and learning potential. You do not need to arrive knowing every method, and prior coding experience is not a prerequisite. We are particularly interested in people who: - **Notice what does not fit:** question unexpected results, spot anomalies and consider competing explanations. - **Question the evidence:** ask how data were generated, what assumptions an analysis makes and what could change a conclusion. - **Connect detail to the bigger picture:** explain why a result matters and what an informative next experiment would be. - **Organise parallel investigations thoughtfully:** identify what can proceed independently, what depends on earlier results and how to bring the findings together. - **Learn and update:** seek help, build understanding, change their mind when warranted and follow through on difficult questions. Biology, biochemistry, bioinformatics, mathematics, computer science and related backgrounds can all bring useful perspectives. Formal qualification requirements will be specified in the individual vacancy announcements. **AI is part of the toolkit.** We welcome its thoughtful use, but a convincing answer is not necessarily a correct one. You should want to understand, question and eventually audit the computational analyses you use. ## Send your CV and short answers Email **[email protected]** with the subject **PhD 2027 application**. Please keep this subject unchanged so your message can be identified easily. **[Start your email with the answer template →](mailto:[email protected]?subject=PhD%202027%20application&body=Hello%20Marek%2C%0D%0A%0D%0AI%20would%20like%20to%20express%20interest%20in%20one%20of%20the%202027%20PhD%20positions.%0D%0A%0D%0AFull%20name%3A%0D%0AAcademic%20background%3A%0D%0AResearch%20direction%28s%29%20of%20interest%3A%0D%0A%0D%0APlease%20find%20my%20CV%20attached.%20My%20answers%20are%20below%20%28up%20to%20150%20words%20each%29.%0D%0A%0D%0A1.%20What%20would%20you%20like%20to%20investigate%3F%0D%0A%0D%0A%0D%0A2.%20What%20can%20this%20result%20tell%20us%3F%0D%0A%0D%0A%0D%0A3.%20How%20would%20you%20organise%20the%20next%20two%20weeks%3F%0D%0A%0D%0A%0D%0A4.%20When%20did%20evidence%20change%20your%20mind%3F%0D%0A%0D%0A%0D%0ABest%20wishes%2C)** The link opens a draft in your email app with the recipient, subject and answer headings filled in. **Attach your CV yourself before sending**—the webpage does not upload files or send the message for you. If the link does not open an email app, use the address and subject above. Include the following in one email: - Your full name and academic background, including whether your current degree is completed or in progress. - The research direction or directions that interest you. - Your CV as a **PDF or DOCX attachment, no larger than 5 MB**. - Your answers to the four questions below, **pasted into the email body**, with the same numbered headings. Use up to 150 words per answer; shorter answers are welcome. No separate cover letter is needed for this initial enquiry. Please avoid unnecessary personal information such as national ID numbers. > [!info] Initial interest, not a formal KU application > This email is an initial expression of interest to the research group. It does not replace an application through the official University of Copenhagen recruitment system. Formal vacancy links, deadlines, eligibility requirements and exact start dates will be announced separately. Allow around 20–30 minutes. You may use AI to help with your application. Your examples must reflect your own experience, and you should be ready to discuss your reasoning. ### 1. What would you like to investigate? Choose one research direction above. Describe a biological question that interests you, why it matters, and a useful first step. ### 2. What can this result tell us? Imagine these average expression values for a plant gene: | Control | Heat | Drought | Both | | --- | --- | --- | --- | | 100 | 200 | 200 | 400 | An AI assistant concludes: “Heat and drought act synergistically because expression is highest when they occur together.” How would you assess that conclusion? State any assumptions and the first information or check you would request. No particular statistical method is required. ### 3. How would you organise the next two weeks? You have a candidate gene that might affect stress resilience. Propose two useful lines of investigation, explain what could run in parallel and what depends on earlier results, and say how you would bring the evidence together. You may use AI, experiments, literature or existing data. ### 4. When did evidence change your mind? Describe something you investigated or found difficult to understand. What did you initially think, what did you try or learn, and what changed? An honest unresolved outcome is welcome. Examples from study, work or independent projects are all suitable. ## Requirements: M.Sc. degree is a must. Duration is 3 years for 2 year M.Sc. or 1+3 years for 1 year M.Sc. holders. ## What happens next? The proposed selection process combines a structured review of your application with a conversation about how you work. Shortlisted candidates would explore a small research problem with AI, examine new evidence and discuss their reasoning. There will also be time to discuss training, supervision and your questions about the group. ## Explore our work - [Stress-response hierarchies in Marchantia — Nature Communications, 2023](https://pubmed.ncbi.nlm.nih.gov/36813788/) - [PlantConnectome — The Plant Cell, 2025](https://doi.org/10.1093/plcell/koaf169) - [Plant Expression Omnibus — The Plant Journal](https://doi.org/10.1111/tpj.16566) - [Marek Mutwil’s University of Copenhagen research profile](https://researchprofiles.ku.dk/en/persons/marek-mutwil/)