PhD fellowship in AI for Cancer Genomics

Faculty of Health and Medical Sciences
University of Copenhagen

We are offering a PhD fellowship in AI for Cancer Genomics commencing 1 March 2025, or soon thereafter (flexible start date).

The PhD project will be linked to the Danish Cancer Society project “AI-DRIVERS” awarded to Prof. Fran Supek to study cancer driver mutations in non-coding DNA, by developing and applying AI tools for decoding tumor genome evolution.

Our group and research
The Supek group is an interdisciplinary team, working at the intersection of genomics, molecular biology, and artificial intelligence. The lab performs statistical analysis of large-scale datasets (cancer genomics, population genomics) using cutting-edge techniques including artificial intelligence (e.g. DNA and protein language models). We further generate our own genomics data by DNA/RNA sequencing (particularly by Oxford Nanopore), and gene editing to generate models of cancer evolution (e.g. CRISPR/Cas12a system for combinatorial gene disruption).

In our research, we focus in frontier research projects e.g. recently finished ERC project “HYPER-INSIGHT”, and ongoing ERC “STRUCTOMATIC: Mutational processes and impact of structural variants in somatic cells”. Furthermore, we are embedded in a broad network of international collaborators (see e.g. EU Horizon consortia “DECIDER” and “LUCIA”, where we study ovarian cancer and lung cancer genomics, respectively).

The Supek group fosters a dynamic and inclusive atmosphere, where excitement about science is valued. We are highly committed to mentoring and career development of PhD students, postdoctoral fellows, and other team members. We are looking for enthusiastic, driven lab members to join us in our mission in pushing the boundaries of human knowledge, and fighting cancer with genomics.

The lab is at the Biotech Research & Innovation Centre, a flagship Danish biomedical research institute, and a part of the University of Copenhagen, the top-3 ranked university in continental Europe in the latest Shanghai Rankings. More information about the group is given on the lab website https://www.genomedatalab.org/

Project description

We invite brilliant minds in computational biology to join us at the cutting-edge of cancer genomics research, harnessing the power of artificial intelligence and evolutionary modeling. As part of our innovative team, you'll be at the forefront of identifying non-coding driver mutations in cancer genomes, a challenge that has long puzzled traditional analysis methods.

Our AI-DRIVERS project aims to understand of cancer evolution by developing and applying state-of-the-art AI models to predict the functional impact of non-coding mutations. Your work will innovate by combining these AI predictions with novel evolutionary frameworks, allowing us to infer selection on regulatory elements and identify new cancer drivers hidden in the 'dark matter' of the genome.

You'll work with extensive whole-genome sequencing datasets from various cancer types, applying and refining AI models to predict changes in gene regulation. Your research will involve developing new methodologies to account for heterogeneous mutation rates across the genome, a critical step in accurately detecting selection in non-coding regions.

This project offers a unique opportunity to bridge computational genomics, artificial intelligence, and cancer biology. You'll be applying cutting-edge deep learning architectures, including convolutional networks and transformers, to genomic data. Additionally, you'll have the chance to collaborate with experimental biologists to validate your computational predictions using CRISPR-based approaches.

Your PhD work will employ a powerful combination of AI, evolutionary modeling, and large-scale genomic analysis. The results of your studies will be pivotal in uncovering new diagnostic markers, potential therapeutic targets, and fundamental insights into cancer genome evolution. Join us in this exciting endeavor to unlock the secrets of non-coding cancer drivers and pave the way for new approaches in personalized cancer medicine.

Questions

For informal inquiries about the project and the PhD student position, please contact Prof. Fran Supek; [email protected]

Foreign applicants may find this link useful: www.ism.ku.dk (International Staff Mobility office).

Principal supervisor is Prof. Fran Supek, BRIC, [email protected], +45 3533 3008

Start: 1 March 2025, or soon thereafter (with flexibility)

Duration: 3 years as a PhD student, with possible extension

Job description
Your key tasks as a PhD student at SUND are:

• Carrying through an independent research project under supervision.
• Completing PhD courses or other equivalent education corresponding to approximately 30 ECTS points.
• Participating in active research environments including a stay at another research team.
• Obtaining experience with teaching or other types of dissemination related to your PhD project
• Teaching and disseminating your knowledge.
• Writing a PhD thesis on the grounds of your project

Key criteria for the assessment of applicants
Applicants must have qualifications corresponding to a master’s degree related to the subject area of the project, e.g. bioinformatics/genomics, mathematics, physics, computer science or molecular biology. Please note that your master’s degree must be equivalent to a Danish master’s degree (two years).

Other important criteria are:

• The grade point average achieved
• Professional qualifications relevant to the PhD project
• Previous publications
• Relevant work experience
• Other professional activities
• A curiosity driven mind-set, with a strong interest in genomics and/or AI
• Language skills

Place of employment

The place of employment is at the BRIC, Faculty of Health and Medical Sciences, University of Copenhagen. We offer creative and stimulating working conditions in dynamic and international research environment. Our research facilities include modern laboratories and high-performance computing facilities.

Terms of employment
The average weekly working hours are 37 hours per week.

The position is a fixed-term position limited to a period of 3 years. The start date is 1 March 2025, or later thereafter, as agreed.

The employment is conditioned upon the applicant’s success­ful enrolment as a PhD student at the Graduate School at the Faculty of Health and Medical Sciences, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

The PhD study must be completed in accordance with The Ministerial Order on the PhD programme (2013) and the Faculty’s rules on achieving the degree.

Salary, pension and terms of employment are in accordance with the agree­ment between the Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. Depending on seniority, the monthly salary starts at approximately 30,716 DKK/Roughly 4,090 EUR (April 2024 level) plus pension.

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

General information about PhD studies at the Faculty of Health and Medical Sciences is available at the Graduate School’s website: https://healthsciences.ku.dk/phd/guidelines/

Application procedure
Your application must be submitted electronically by clicking ‘Apply now’ below. The application must include the following documents in PDF format:

1. Motivated letter of application (max. one page)

2. CV incl. education, experience, language skills and other skills relevant for the position

3. Certified copy of original Master of Science diploma and transcript of records in the original language, including an authorized English translation if issued in other 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. As a prerequisite for a PhD fellowship employment, your master’s degree must be equivalent to a Danish master’s degree. We encourage you to read more in the assessment database: https://ufm.dk/en/education/recognition-and-transparency/find-assessments/assessment-database . Please note that we might ask you to obtain an assessment of your education performed by the Ministry of Higher Education and Science

4. Publication list (if possible), including also preprints, with brief summaries of selected publications, describing the main impact and specifying your contributions to each particular study.

Application deadline: 14 November 2024, 23.59pm CET

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 expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the hiring committee. All applicants are then immediately notified whether their application has been passed for assessment by an unbiased assessor.

The assessor makes a non-prioritized assessment of the academic qualifications and experience with respect to the above-mentioned area of research, techniques, skills and other requirements listed in the advertisement.

Once the assessment work has been completed each applicant has the opportunity to comment on the part of the assessment that relates to the applicant him/herself.

You find information about the recruitment process at: http://employment.ku.dk/faculty/recruitment-process/

The applicants will be assessed according to the Ministerial Order no. 242 of 13 March 2012 on the Appointment of Academic Staff at Universities.

Interviews are expected to be held during December 2024.

The University of Copenhagen wish to reflect the diversity of society and encourage all qualified candidates to apply regardless of personal background.

Kilde: Jobnet.dk