PhD fellowship in single-cell gene regulatory networks of heat and drought responses in crops

The Department of Plant and Environmental Sciences (PLEN) invites applicants for a PhD fellowship in plant stress physiology and single-cell biology. The project is financed by the Novo Nordisk Foundation through the Ascending Investigator grant “Accelerating crop resilience with AI-enabled gene function prediction and stress regulatory networks” (NNF26OC0113093).

Start date is expected to be 1 May 2027 or as soon as possible thereafter.

The project Stress responses are usually measured in whole organs, which averages away the fact that different cell types respond differently, and sometimes in opposite directions. This project will resolve heat and drought responses at single-cell resolution in four major Nordic crops – the dicots rapeseed and potato and the monocots wheat and barley – and ask which regulatory programmes are conserved across them.

You will design and carry out the stress experiments yourself: heat, drought and the two combined, sampled at early (3 h), middle (6 h) and late (2 days) stages, in leaves, roots and floral meristems. Single-cell RNA-seq and chromatin accessibility (ATAC-seq) libraries are generated on the group’s 10x Genomics platform and sequenced by an external provider. You will then analyse the data yourself – we will train you in data science, so no prior programming experience is required. What we need from you at the start is the experimentalist’s judgment: how to grow, stress and sample plants so that the data can answer the question.

Depending on your interests, the work may include:

• Designing and running the stress experiments: growth conditions, stress intensities, time points, physiological read-outs and replication, so that the resulting data can actually answer the question
• Phenotyping and physiological characterisation of the stressed plants, and nuclei/cell isolation for single-cell sequencing
• Quality control, integration and cell-type annotation of single-cell atlases across stresses, organs and species
• Extending the group’s TEA-GCN method to single-cell data to infer cell-type- and stress-specific transcription factor–target relationships
• Linking transcription factors to cis-regulatory elements using ATAC-seq, known motifs and sequence-based deep learning
• Ranking regulatory edges by conservation across the four crops to obtain high-confidence networks, and comparing them with the group’s cross-species stress atlases

You will not be alone with the data: the grant also funds a computational postdoc who develops the multimodal integration methods alongside you, and the work draws on a collaboration with Prof. Ryan Lister (University of Western Australia) on multimodal single-cell methods and on stress-physiology expertise at PLEN Taastrup.

Who are we looking for? We are looking for an experimentalist: a candidate within the field(s) of plant physiology, plant molecular biology, agronomy or crop science, preferably with hands-on experience of growing plants and running stress or phenotyping experiments. Applicants can have a background from biology, plant sciences, agricultural sciences, biotechnology or a related discipline. Experience with RNA-seq, single-cell methods or programming is an advantage but not expected – we provide structured training in data analysis and will pair you with the group’s computational members. What is required is the willingness to become fluent in analysing your own data.

What we value Programming experience is not required at entry – we teach it, and the training in data science is part of the position. What we cannot teach quickly, and therefore select for, is scientific judgment:

• questioning data rather than accepting it – asking what was measured, how, and against which expectation
• noticing anomalies in a growth chamber or a dataset and treating them as information rather than noise
• organising several lines of investigation in parallel and knowing when to stop or redirect one
• connecting a measurement to a concrete biological question
• changing your mind when the evidence changes

We are looking for a plant experimentalist who wants to own the analysis of their own data, not hand it to someone else.

Our group and research – and what do we offer? The Mutwil group at PLEN works at the interface of comparative and evolutionary plant biology and AI-driven biological discovery. We build large cross-species gene expression atlases, comparative co-expression networks and knowledge graphs, and we use machine learning and large language models to turn the plant literature and omics archives into testable hypotheses. The group comprises several PhD students, postdocs and master’s students, and maintains a portfolio of widely used community resources under the .plant.tools domain, including PlantConnectome, CoNekt, diurnal.plant.tools and evorepro.plant.tools.

The group is part of the Department of Plant and Environmental Sciences (PLEN), Faculty of Science, University of Copenhagen. We are located on the Frederiksberg Campus in Copenhagen.

We offer creative and stimulating working conditions in a dynamic and international research environment. Our research facilities include modern molecular biology laboratories, plant growth facilities and dedicated high-performance computing and GPU resources.

Principal supervisor is Associate Professor Marek Mutwil, Department of Plant and Environmental Sciences (PLEN), University of Copenhagen. E-mail: mutwil@plen.ku.dk.

The PhD programme A three year full-time study within the framework of the regular PhD programme (5+3 scheme), if you already have an education equivalent to a relevant Danish master’s degree.

Qualifications needed

To be eligible, you must have completed a degree programme equivalent to a Danish master’s degree (180 ECTS/3 FTE BSc + 120 ECTS/2 FTE MSc) related to the subject area of the project, e.g. plant sciences, biology, agricultural sciences, biotechnology, molecular biology or a related field. For information on the eligibility of completed programmes, see General assessments for specific countries and the Assessment database.

Terms of employment

Employment as a PhD fellow is full time and for a maximum of 3 years. Employment is conditional upon your successful enrolment as a PhD student at the PhD School at the Faculty of Science, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

Terms of appointment and payment accord to the agreement between the Danish Ministry of Taxation and the Danish Confederation of Professional Associations on Academics in the State. The position is covered by the Protocol on Job Structure.

You can read more about salary levels in the state sector www.loenoverblik.dk (in Danish).

Responsibilities and tasks

• Carry through an independent research project under supervision
• Complete PhD courses corresponding to approx. 30 ECTS / ½ FTE
• Participate in active research environments, including a stay at another research institution, preferably abroad
• Teaching and knowledge dissemination activities
• Write scientific papers aimed at high-impact journals
• Write and defend a PhD thesis on the basis of your project

We are looking for the following qualifications

• Professional qualifications relevant to the PhD project
• Relevant publications
• Hands-on experience with plant growth, abiotic stress experiments or physiological phenotyping is a strong advantage
• Relevant work experience, e.g. with molecular biology, RNA-seq or single-cell methods
• Programming experience is not required – training in data science is provided
• Other relevant professional activities
• A curious mind-set with a strong interest in how crops cope with heat and drought
• Good written and spoken English

Application and assessment procedure Your application including all attachments must be in English and submitted electronically by clicking APPLY NOW below.

Please include:

• Motivated letter of application (max. one page), stating your motivation for applying for this specific PhD project
• Written answers to the four questions below (max. 250 words each). You may use AI tools to help draft your answers; please say so if you do. The written answers are a starting point for the interview, where we will explore your reasoning in conversation.
• Curriculum vitae including information about your education, experience, language skills and other skills relevant for the position
• Original diplomas for Bachelor and Master and transcript of records in the original language, including an authorised English translation if issued in another language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted.
• Publication list (if possible)
• Reference letters (if available)

Application questions

1. Research interest. Which biological question would you like to work on in this project, and what evidence would you need to answer it?
2. Reading data. A gene has an expression value of 100 under control conditions, 200 under heat stress, 200 under drought, and 400 under heat and drought combined. What do you conclude, and what would you want to know before concluding it?
3. Working in parallel. You have two weeks, a set of publicly available expression data, and a literature you do not yet know. How would you organise the two weeks, and what would you deliver at the end of each?
4. Changing your mind. Describe a case where you believed something about a project or dataset and evidence made you revise it. What was the evidence?

Application deadline: The deadline for applications is 31 January 2027, 23:59 GMT +1.

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 deadline, a number of applicants will be selected for academic assessment by an unbiased expert assessor. You are notified whether you will be passed for assessment. The assessor will assess the qualifications and experience of the shortlisted applicants with respect to the above-mentioned research area, techniques, skills and other requirements. The assessed applicants will have the opportunity to comment on their assessment. You can read about the recruitment process at http://employment.ku.dk/faculty/recruitment-process/.

Interviews with selected candidates are expected to be held in March 2027.

Questions For specific information about the PhD fellowship, please contact the principal supervisor, Associate Professor Marek Mutwil (mutwil@plen.ku.dk).

General information about PhD study at the Faculty of Science is available at the PhD School’s website: https://www.science.ku.dk/phd/.

The University of Copenhagen wishes to reflect the surrounding community and invites all regardless of personal background to apply for the position.