Department of Biology invites applicants for a PhD fellowship in computational modeling of gene regulation in single cells.
Start date is (expected to be) 1st of May 2025 or as soon as possible thereafter.

THE PROJECT

Large-scale genetic association studies (GWAS) have succeeded in identifying hundreds of thousands of associations between genetic loci and diseases and traits in humans. The next grand challenge — linking disease genetics to disease biology — has yet to be solved. Most GWAS associations involve non-coding variants that lie within gene regulatory elements — enhancers or promoters. However, a lack of precise tools for the accurate assessment of regulatory activities, especially for heterogeneous cell populations, has prevented progress in connecting genetic variants to their impacted gene regulatory processes. To address this challenge, we are 1) developing new assays and 2) computational frameworks to resolve gene regulatory activities in single cells and 3) apply these to map regulatory activities across cell types to investigate the mechanisms and cell-type specific effects of genetic variants. We are seeking a PhD student to join this effort, focusing on developing computational and statistical methods to model enhancer activity, enhancer-gene regulation, and cellular heterogeneity based on single cell data. Specific focus will be to integrate transcription initiation data into modeling of gene regulation and develop frameworks for enhancer-guided variant-to-function analysis.

WHO ARE WE LOOKING FOR?

We are seeking a genuinely motivated individual with a MSc in Bioinformatics or Computational Biology, or a comparable field with extensive experience in the analyses of high-throughput sequencing data. Theoretical understanding in statistical modelling and practical experiences in the analyses of single-cell sequencing data are expected from the applicant. Importantly, the applicant should have a strong interest in gene regulation and variant-to-function analysis, and a desire to work on an interdisciplinary and highly collaborative project bridging single-cell genomics and genetics. Continuous scientific discussions and a strong dedication for ongoing research questions within the group also require proactive participation and enthusiasm for problem solving.

In particular, we are looking for candidates with:

• A MSc in Bioinformatics, Computational Biology, or a related discipline with extensive experience in the analyses of high-throughput sequencing data
• Strong programming and data analytical skills
• Experience in genomics analyses and computational analyses of high-throughput sequencing data
• Strong programming and data analytical skills
• A high proficiency in spoken and written English

QUALIFICATIONS NEEDED FOR THE PHD PROGRAMME

To be eligible for the regular PhD programme, 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. Computer Science, Bioinformatics, Computational Biology. For information of eligibility of completed programmes, see General assessments for specific countries and Assessment database .

• 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 projec