PhD fellowship in Bioinformatics

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

Our group and research
The lab of Robin Andersson focuses on modeling gene regulation with the ultimate aim to gain insights into molecular mechanisms by which enhancer or promoter dysregulation contributes to disease risk. We take an interdisciplinary approach and combine machine learning, statistical learning, genetics, and molecular biology to: 1) Determine which noncoding sequences act as enhancers, which genes they regulate, and in which cell types they are active; 2) Learn how the human genome encodes regulatory activity; and 3) Predict the impact of regulatory genetic variants. For more information, see https://anderssonlab.org/.

The Andersson lab is a part of Department of Biology, Faculty of SCIENCE, University of Copenhagen. The group is based in a highly collaborative environment in the Section for Computational and RNA Biology, which is currently composed of 13 strong research groups. We are also affiliated with the Novo Nordisk Foundation Center for Genomics Mechanisms of Disease (https://www.broadinstitute.org/nnfc) at the Broad Institute of MIT and Harvard.

We are located at the Biocenter in central Copenhagen, Denmark. Due to its close proximity to the Biotech Research & Innovation Centre (BRIC) as well as the Faculty of Health and Medical Science, collaborations across disciplines, groups and institutes are a natural part of the efforts in the lab. We offer creative and stimulating working conditions in a dynamic and international research environment. Our research facilities include modern laboratories and computational infrastructures.

Principal supervisor is Associate Professor Robin Andersson, Department of Biology, [email protected].

The PhD programme

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.

Terms of employment in the regular programme
Employment as PhD fellow is full time and for maximum 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.

The terms of employment and salary are in accordance to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State (AC). The position is covered by the Protocol on Job Structure.

Responsibilities and tasks in the PhD programme

• 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

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

Please include: 

1. Motivated letter of application (max. one page)
2. Curriculum vitae including information about your education, experience, language skills and other skills relevant for the position
3. Original diplomas for Bachelor of Science or Master of Science and transcript of records in the original language, including an authorized 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.
4. A list of publications (if any)
5. Reference letters or contact information for 2-3 references

Application deadline:
The deadline for applications is 6 March 2025, 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 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 assessor will conclude whether each applicant is qualified. 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/.

Questions
For specific information about the PhD fellowship, please contact the principal supervisor.

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.